CBM SMART Teams Archive

The SMART Team Program began in 2001 and has grown dramatically over the years, both in the number of Local SMART Teams as well as expansion to National SMART Teams outside the Milwaukee area (Note that National SMART Teams are not archived on this page).

In 2019, the SMART Team program was converted into the MAPS Teams (Modeling a Protein Story) program, where it continues to expand and can be accessed by students and educators online from any location.

2018-2019 SMART Teams

Twelve schools participated in the local SMART Team program during the 2018-2019 school year. The remote SMART Teams, HHMI SMART Teams and MAPS Teams also expanded. Completed local projects are described below.

Download the full 2018-2019 SMART Team Abstract Booklet.

• Brown Deer High School
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Brown Deer High School

Increased Hexokinase Interactions with Mitochondria Protect Against Cell Damage


Brown Deer High School SMART
Team model based on 1BG3.pdb

Students:

• D. Collison
• A. Hoppe
• B. Kaur
• B. Keebler
• E. Kolb
• K. Noll
• E. Walker
• L. Wilson
• L. Yang

Teacher:

• Dave Sampe

Mentor:

• Dr. Amadou KS Camara, PhD, Professor, Department of Anesthesiology, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Death due to cancer and ischemic heart disease are the most common; dysfunction of mitochondrial energy (ATP) metabolism is key in these pathologies. Therefore, therapeutic strategies, which remain elusive, have focused on energetic metabolism. Cells use glucose and oxygen in glycolysis and oxidative phosphorylation to generate ATP. The cytosolic protein hexokinase (HK) plays a crucial role in glycolysis by catalyzing the breakdown of glucose to produce most of the ATP generated from mitochondria. For efficient glycolysis, HK must access the mitochondrial ATP, which flows out via the voltage dependent anion channel (VDAC), a 30-kDa protein in the outer mitochondrial membrane (OMM). Cancer cells grow and proliferate by increasing access to ATP via increased HK-VDAC associations. This strategy has potential implications for protection against cardiac ischemic injury. Ischemia promotes dissociation of HK from VDAC leading to cardiac damage, but cardio-protective interventions can increase HK-VDAC association, preserving function. The overall objective is to determine the biophysical and biochemical features that lead to HK-VDAC association or dissociation. HK, a 100-KDa dimeric protein, has 918 amino acids in two domains: an N-terminus and C-terminus joined by a linker α-helix. HK interactions with mitochondria are not well known but, HK, with its non-polar sequence of 15 amino acids on the N-terminus, may insert in the OMM close to VDAC. Glucose and glucose-6-phospate have distinct binding sites on HK. Glucose binds at K173, D209, and E260 in the N-terminus and at K621, D657, and E708 in the C-terminus. The Brown Deer High School SMART Team designed a model of HK using 3-D printing technology to investigate structure-function relationships. Understanding HK-VDAC binding mechanisms could provide better targeted approaches to manage pathologies, including cancer, cardiac and neurodegenerative diseases.

• Cedarburg High School
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Cedarburg High School

MppP: The Beginning of L-End (Synthesis)


Cedarburg High School SMART
Team model based on 6C8T.pdb

Students:

• Ahmed, A.
• Amundson, J.
• Boeselager, A.
• Bote, K.
• Burgarino, M.
• Burns, R.
• Ertl, E.
• Fairchild, E.
• Fueger, K.
• Garey, S.
• Going, J.
• Ketelhohn, A.
• Khmelevsky, B.
• Kubiak, K.
• Kunz, J.
• Langholz, A.
• Levy, S.
• Novack, M.
• Phelps, K.
• Remington, E.
• Schoenberg, S.
• Tiffany, B.

Teachers:

• Karen Tiffany

Mentor:

• Nicholas Silvaggi, PhD Department of Chemistry and Biochemistry, University of Wisconsin Milwaukee

Project Files:

• Poster
• Model Description Sheet

Abstract:

Infections caused by antibiotic-resistant pathogens like MRSA are serious problems that require the development of new antibiotics. The non-proteinogenic amino acid L-enduracididine (L-End) is looked at as a solution, as it could be used to synthesize new versions of L-End-containing antibiotics and improve drug efficacy of antibiotics not normally containing L-End. However, L-End is difficult to synthesize and is not commercially available. The enzyme MppP, an L-arginine deaminase/hydroxylase from Streptomyces wadayamensis, is involved in L-Arg biosynthesis. MppP is a pyridoxal 5’-phosphate (PLP)-dependent oxidase catalyzing the oxidation of L-Arg to 2-oxo-4-hydroxy-guanidinovaleric acid, which continues along the pathway to produce L-End. Four electrons are transferred to L-Arg from molecular oxygen via the PLP cofactor; water contributes the hydroxyl and ketone oxygen atoms of the product. MppP functions as a homodimer. Each 376-residue protomer contains a large domain, primarily composed of beta sheets, and a smaller domain consisting of a mix of alpha helices and beta sheets. The active site, containing PLP and the catalytic Lys221, is located between these two domains. The N-terminal portion of the protein is not ordered unless substrate or product is bound in the active site, and this region appears to be critical for catalysis. The Cedarburg SMART (Students Modeling A Research Topic) Team has designed a model of MppP using 3D printing technology to investigate MppP structure-function relationships. Studying the structure and function of MppP can elucidate the mechanism of L-End biosynthesis, making possible the commercial production of L-End for use in new MRSA-fighting antibiotics.

• Cudahy High School
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Cudahy High School

Flipping a Light Switch: Halorhodopsin’s Role as a Light-Sensitive Ion Channel


Cudahy High School SMART
Team model based on 5G36.pdb

Students:

• Acherman, M.
• Asselin, E.
• Brzezinski, K.
• Burki, Z.
• Fricke, N.
• Hall, M.
• Kressin, S.
• Miliacca, G.
• Michalski, M.
• Romfoe M.
• Thomas, A.
• Stehling, B.
• Zager, L.

Teachers:

• Billo, D.
• Koslakiewicz, D.

Mentor:

• Herbst, M. - Marquette University
• Kramer, K. - Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

The brain is a complex organ still being decoded. Having the ability to control precise brain regions would positively impact research, influencing treatment of various neurological conditions. Optogenetics can help lead to treatments of Parkinson's disease allowing for the selective stimulation of axons. Parkinson’s disease is a disabling neurological condition, characterized by tremors, inability to maintain balance, and slow movements. One way to alleviate patients of these symptoms might be through the use of halorhodopsin, a light-sensitive chloride channel found in bacteria. Once expressed in the nervous tissue, it opens precise chloride channels, making specific cells less likely to reach an action potential. This is a major advantage over other research techniques due to the high level of control and sub-second precision. Halorhodopsin is comprised of 261 residues arranged in three subunits of seven transmembrane helices, creating the chloride channel. Channel residues Tyr77, Arg108, Thr111, Trp112, Ser115, and Thr126 hydrogen-bond with chloride ions, assisting passage through the channel. Activation also involves the use of a ligand: retinal. Retinal, when activated by light, will cause a conformational change, opening the channel and allowing chloride ions to pass through. This reduces cellular activity due to hyperpolarization. The Cudahy SMART (Students Modeling A Research Topic) Team designed a model of halorhodopsin using 3D printing technology to analyze its structure-function relationship. Activating halorhodopsin with light through optogenetics may make it possible to manipulate cells to treat Parkinson’s disease, alleviate symptoms of other neurodegenerative diseases, and other medical conditions.

• Divine Savior Holy Angels High School
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Divine Savior Holy Angels High School

The Three Blind Men: How Adhesion Protein Binding Affects the Retinas of People with Retinoschisis


Divine Savior Holy Angels High School SMART
Team model based on 3JD6.pdb

Students:

• E. Bauer
• E. Cobb
• C. DebBaruah
• E. Fricker
• A. Griffith-Topps
• M. Jessick
• C. Kuehn
• T. Kulju
• C. Lois
• L. Thota
• C. Sargent
• L. Schraufnagel
• S. Strandberg
• C. Strother
• S. Urban

Teachers:

• Mr. Fleischmann
• Mrs. Strandberg

Mentor:

• Alison Huckenpahler, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

X-linked retinoschisis, an early-onset macular degenerative disease occurring primarily in young boys, can result in blindness. As many as two hundred different mutations on the X chromosome can lead to a malformation of retinoschisin, a structural protein which normally holds the photoreceptors and bipolar cells together. The photoreceptors detect wavelengths of light, and bipolar cells transmit these stimuli to the brain for interpretation. An improperly folded retinoschisin prevents the photoreceptors and bipolar cells from interacting. Retinoschisin is composed of sixteen subunits arranged in a double octomer. Because retinoschisin relies on extensive interactions between subunits, many different mutations can lead to a dysfunctional protein. The C110 and C142 bonds stabilize the spikes protruding from the discoid fold- the part of the protein that allows the retinoschisin to bind to the retinal cells. Mutations in these residues lead to the inability of the protein binding to retinal cells. Since the retinoschisin cannot attach to the retina, the cells comprising the retina begin to split and cause eventual blindness. In order to further understand the structure and function of this protein, the Divine Savior Holy Angels SMART (Students Modeling a Research Topic) team modeled retinoschisin using 3D printing technology. Although no cure exists, current research is focusing on the structure of retinoschisin, and how mutations prevent adhesion between retinal cells with an ultimate goal of developing a gene therapy. By correcting the mutated X chromosome segment, retinoschisis could be prevented.

• Grafton High School
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Grafton High School

Modeling the Influence of eIF6 in the Starvation Response to Develop Treatments for Metabolic Disorders


Grafton High School SMART
Team model based on 1G62.pdb

Students:

• Jaden Autey
• Hannah Belanger
• Noah Ellison
• Selena Esparza
• Hannah Hacker
• Olivia Konzen
• Chloe Kultgen
• Payton Riddle
• Kate Senczyszyn
• Laura Stockhausen
• Emma Wagner
• Cailyn Yang

Teachers:

• Frances Grant, M.S.

Mentor:

• Dr. Sofia Origanti, Department of Biology, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

In 2017, diabetes mellitus affected 30.3 million individuals in the United States (CDC, 2017). Learning how cells adapt to starvation may provide a more effective therapeutic target for treatment of diabetes and other metabolic disorders. Human eukaryotic initiation factor 6 (eIF6) is a 245 amino acid translation factor that aids in both ribosome biogenesis and protein synthesis. eIF6 is crucial for protein synthesis as it prevents the association between 40S and 60S ribosomal subunits and is important for the synthesis of the 60S subunits. Current research shows that during starvation, the C-terminus of eIF6 is phosphorylated by the kinase GSK3. Phosphorylation of T231, S235, S239, S243 residues on eIF6 by GSK3 restricts its localization to the cytoplasm, which may disrupt its function in synthesizing 60S subunits in the nucleolus during starvation. The phosphorylation of Ser235 on the C-terminus prevents eIF6 association with the 60S subunits which may cause the 60S and 40S subunits to randomly associate even without mRNA and give rise to inactive 80S complexes that inhibits protein synthesis during starvation. The Grafton High School SMART (Students Modeling a Research Topic) Team has designed a model of eIF6 using 3D printing technology to model the structure-function relationship and to display the specific sites of phosphorylation. This new mode of regulation of eIF6 helps to better understand its role in translation control based on nutrient availability. Understanding these mechanisms may help develop new drug targets for metabolic disorders like diabetes.

• Hartford Union High School
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Hartford Union High School

Shocking! The Effect of TSST-1 in Toxic Shock Syndrome


Hartford Union High School SMART
Team model based on 2QIL.pdb

Students:

• E. Anderson
• C. Benson
• J. Brown
• M. Colwell
• T. Colwell
• M. Flanagan
• L. Hautala
• D. Hennes
• G. Hoffmann
• C. Kennedy
• L. Lisowski
• T. Stoeckmann
• E. Witt
• R. Zuern

Teachers:

• Mark Arnholt

Mentor:

• Alex Gardner, Medical College of Wisconsin
• Joseph Barbieri, Ph.D., Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Almost 20% of children who die of Sudden Infant Death Syndrome have a protein called Toxic Shock Syndrome Toxin-1 (TSST-1), produced by Staphylococcus aureus. This protein is also responsible for toxic shock and food poisoning. S. aureus produces this superantigen TSST-1 to divert the immune system and multiply rapidly inside the body. TSST-1 contains 194 amino acids and three domains. Identical domains A, B, and C consist of a larger alpha-helix, residues 152-168, along with two beta-sheets, and three shorter alpha helices. The long alpha helix defines the protein as a superantigen. Antigen-presenting cells, such as macrophages, contain Major Histocompatibility Complex class II. These domains are bound to T-cell receptor beta sheets by TSST-1, bypassing the normal interface, and activating up to 24% more than the average immune response. Despite TSST-1 having no disulfide bridges, therefore lack of thermal denaturation resistance, TSST-1 thrives in the human body due to an immune system distraction. TSST-1 can move through mucous membranes, allowing S. aureus to disrupt the immune response without being inside the body. In the wild form of TSST-1, His-135 located adjacent to the long alpha-helix is mutated to Alanine, creating mutant TSST-1, making the superantigen inactive for reasons unknown. The HUHS SMART Team (Students Modeling A Research Topic) Team has designed a model of the wild form of TSST-1 with 3D printing technology to investigate structure‐function relationships. By studying how TSST-1 interacts with the immune system, advances can be made to control the spread of these pyrogenic toxin superantigens.

• Kettle Moraine High School
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Kettle Moraine High School

Fis1 and Diabetes – Might-ochondria be the Answer?


Kettle Moraine High School SMART
Team model based on 1NZN.pdb

Students:

• James Dowd
• Logan Elkin
• Mark Ibrahim
• Lindsey Knuth
• Ava Lirette
• Jack Mulcahy
• Liam Mulcahy
• Habiba Odogba
• Richard Perschon
• Divyank Sharma
• Aaron Smet
• Emily Stuart

Teachers:

• Melissa Kirby

Mentor:

• John Egner – Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

1.5 million U.S citizens are annually diagnosed with diabetes (American Diabetes Association, 2018). Excess mitochondrial fission has been implicated in type 2 diabetic endothelial dysfunction. Mitochondrial fission is necessary for mitosis and apoptosis. Human mitochondrial Fission Protein 1 (Fis1) is a mitochondrial outer membrane (MOM) protein involved in the assembly and function of mitochondrial fission machinery. Structurally, Fis1 is a 152-residue protein with six helices: two flanking helices (Helices 1 and 6), two divergent tetratricopeptide repeats (TPR), motif 1 (Helices 2 and 3), motif 2 (Helices 4 and 5), and a C-terminal transmembrane domain. The TPR helices create an amphipathic, concave surface to potentially bind small peptide(s), which we predict may also bind small molecules. Naproxen is a compound commonly found in analgesic drugs, which was observed to decrease mitochondrial function. If Fis1 could be inhibited by compounds like naproxen, it could help inhibit excess mitochondrial fission, allowing cells to process energy more efficiently and potentially improve endothelial function in type 2 diabetic patients. Using Nuclear Magnetic Resonance (NMR), we determined structural models and binding constants of small molecules targeting Fis1. We hypothesize that Glu109, Leu110, Tyr76, and Val79 are important for naproxen-binding. The Kettle Moraine High School SMART (Students Modeling A Research Topic) Team designed a model of Fis1 with bound naproxen using 3D printing to understand its structure and role in cellular energy production. Continued research on Fis1 and its interactions with naproxen could elucidate methods to reduce excess mitochondrial fragmentation, providing new therapies for type 2 diabetes.

• Laconia High School
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Laconia High School

Recent Research Reveals Possible Dimer Structure of Human MiD51


Laconia High School SMART
Team model based on 4NXU.pdb

Students:

Teachers:

Mentor:

Project Files:

• Poster
• Model Description Sheet

Abstract:

• Saint Joan Antida High School
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Saint Joan Antida High School

Is It Possible to Find a Cure for Cancer?


Saint Joan Antida High School SMART
Team model based on 4JX5.pdb

Students:

Teachers:

Mentor:

Project Files:

• Poster
• Model Description Sheet

Abstract:

• St. Dominic Middle School
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St. Dominic Middle School

Amyloid Beta and Alzheimer Disease


St. Dominic Middle School SMART
Team model based on 5OQV.pdb

Students:

Teachers:

Mentor:

Project Files:

• Poster
• Model Description Sheet

Abstract:

• Westosha Central High School
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Westosha Central High School

Blood in the Eye, Diabetes; You Give VEGF a Bad Name


Westosha Central High School SMART
Team model based on 5T89.pdb

Students:

Teachers:

Mentor:

Project Files:

• Poster
• Model Description Sheet

Abstract:

• Whitefish Bay High School
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Whitefish Bay High School

The Ricin Fall of Select Agents


Whitefish Bay High School SMART
Team model based on 2AAI.pdb

Students:

Teachers:

Mentor:

Project Files:

• Poster
• Model Description Sheet

Abstract:

2017-2018 SMART Teams

Thirteen schools participated in the local SMART Team program during the 2017-2018 school year. The remote SMART Teams, HHMI SMART Teams and MAPS Teams also expanded. Completed local projects are described below.

Download the full 2017-2018 SMART Team Abstract Booklet.

• Brown Deer High School
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Brown Deer High School

CB₁: The Misunderstood Marijuana Receptor


Brown Deer High School SMART
Team model based on 5TGZ.pdb

Students:

• Kyle Higgins
• Izzy Hughes
• Braden Keebler
• Jailyn Mays
• Mitchell Mietkowski
• Kalli Noll
• Toni Jo Rowney
• Noel Stoehr
• Ehlona Walker

Teachers:

• David Sampe

Mentor:

• Christopher Cunningham, PhD, Concordia University of Wisconsin, Pharmaceutical Sciences

Project Files:

• Poster
• Model Description Sheet

Abstract:

As of September 2017, seven states have legalized the recreational use of marijuana, while 22 states have legalized its medical use. Regardless of attitudes toward recreational use, constituents of marijuana (Cannabis sativa, C. indica) known as cannabinoids are potentially useful in treating pain and inflammation, stress and anxiety disorders, and possibly seizure disorders. Diseases such as obesity and substance abuse disorders may be treated by agents that block the actions of cannabinoids. The main receptor in the brain activated by cannabinoids is the cannabinoid receptor 1 (CB1). CB1 is a transmembrane protein found on presynaptic neurons throughout the brain. Seven alpha helices span the cell membrane. Various ligands bind to these alpha helices throughout the protein. Agonists such as tetrahydrocannabinol (THC) and other cannabinoids bind with CB1 in the area of alpha helices 3, 6, and 7, at Phe268 and Phe379. Antagonists such as AM6538 or rimonabant bind with CB1 in the area of alpha helix 2 at Phe170 and Phe174. Antagonist binding brings helices 3 and 6 close together, causing an “ionic lock” to form between Arg214 and Asp338 that prevents G protein signaling. The Brown Deer SMART Team (Students Modeling a Research Topic) has designed a model of CB1 using 3D printing technology to investigate structure-function relationships. Research on the agonists and antagonists of the CB1 receptor is important because it is not completely understood how much therapeutic potential they possess. Perhaps when the therapeutic potential of the CB1 receptor is developed, quality healthcare can be given to patients using cannabinoid receptor-based therapeutics.

• Cedarburg High School
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Cedarburg High School

In with the Good and out with the Bad: The Role of SR-BI in Lowering Blood Cholesterol


Cedarburg High School SMART
Team model based on 4F7B.pdb

Students:

• D. Arzumanyan
• L. Arzumanyan
• E. Esser
• A. Kuborn
• B.Tiffany
• A. Woods

Teachers:

• Karen Tiffany

Mentor:

• Daisy Sahoo, PhD, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the CDC, 1 in 3 adults in the US has high cholesterol, which is linked to cardiovascular disease. Cholesterol, a hydrophobic molecule, is transported in the blood by binding a lipoprotein. Scavenger receptor class B type 1 (SR-B1), a transmembrane protein that binds high density lipoprotein (HDL) carrying cholesterol, helps transfer cholesterol from HDL into liver cells where it can be excreted in bile. This is important for lowering blood cholesterol levels and reducing the risk of heart disease and stroke. SR-B1 belongs to a larger family of scavenger receptor proteins that includes lysosome membrane protein 2 (LIMP-2), and SR-B1 and LIMP-2 share structural homology. The structure of the C-terminal transmembrane domain of SR-B1, determined through NMR, is composed of three helices with a leucine zipper motif. Mutagenesis studies implicate this leucine zipper motif in dimerization of SR-B1 and proper receptor function. A crystal structure of LIMP-2 revealed the existence of a large, primarily hydrophobic cavity that runs the entire length of the protein that suggests a role in the selective transfer of cholesterol into the liver cell. Using 3D printing technology, the Cedarburg SMART (Students Modeling A Research Topic) Team utilized the known structure of LIMP-2 to investigate structure-function relationships in SR-B1. Determining important HDL/SR-B1 interactions will increase knowledge of how SR-B1 functions in transferring cholesterol from plasma HDL to the liver for excretion and can lead to the development of medical treatments to increase cholesterol excretion by the liver and prevent heart disease and stroke.

• Cudahy High School
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Cudahy High School

eIF We Could Cure Cancer: eIF6 and the Connection to Cancer


Cudahy High School SMART
Team model based on 4V8P.pdb

Students:

• M. Acherman
• S. Borck
• C. Broeckel
• K. Brzezinski
• Z. Burki
• S. Kressin
• E. Paine
• K. Pomianek
• R. Rivas
• M. Romfoe
• A. Thomas
• B. Stehling
• J. Vaughn
• M. Vesey
• L. Zager

Teachers:

• D. Billo
• D. Koslakiewicz

Mentor:

• Dr. S. Origanti

Project Files:

• Poster
• Model Description Sheet

Abstract:

The World Health Organization (2017) lists cancer as a leading cause of death. Eukaryotic Initiation Factor 6 (eIF6) is critical for cancer cell growth/survival. Understanding its mechanism of action will help to develop new drug targets that can slow the cancer epidemic. One of the hallmarks of cancer is increased rate of protein synthesis, supporting the rapid growth and reproduction of cancer cells. eIF6 is crucial to maintaining these enhanced levels of protein production. Data show eIF6 is upregulated in human cancer cells, but its mode of regulation is unknown. eIF6 is essential for the synthesis of the 60S ribosomal subunit and for mediating interactions between the 60S and 40S ribosomal subunits. eIF6 binds to 60S using residues Y151, T150, N106, S102, K100, T75, and D12 to interact with 60S ribosomal protein L23 (RPL23) residues K132, N136, A137, G138, S139, V140, and V141. eIF6 was modeled by the Cudahy SMART (Students Modeling A Research Topic) Team using 3D printing technology to investigate structure and function relationships. eIF6 interactions with 60S must be regulated as the release of eIF6 from the 60S allows the 60S and 40S subunits to bind and initiate protein synthesis. C-terminus sites could functionally regulate eIF6 interaction. One model suggests that when the C-terminal tail is phosphorylated, eIF6 is released from 60S, initiating protein synthesis. Previous research suggests by reducing levels of eIF6 or by preventing its release from the 60S subunit, protein synthesis is attenuated and tumor growth is inhibited. Therefore, determining the exact mechanism of binding between eIF6 and the 60S ribosomal protein-RPL23 in cancer cells is important and could aid in the development of new treatments for cancer patients.

• Divine Savior Holy Angels High School
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Divine Savior Holy Angels High School

Yo GABA_A GABA_A: How the Structure of Human GABA_A Receptor Affects the Action of Anesthetics


Divine Savior Holy Angels High School SMART
Team model based on 2BG9.pdb

Students:

• E. Bauer
• S. Franczak
• E. Fricker
• A. Griffith-Topps
• M. Jessick
• C. Kuehn
• C. Lois
• C. Sargent
• L. Schraufnagel
• S. Strandberg
• C. Strother
• J. Strother
• L. Thota
• S. Urban

Teachers:

• Mr. Fleischmann
• Mrs. Strandberg

Mentor:

• Dr. R. Peoples, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

Propofol, a powerful anesthetic, can be used safely in medical settings, but proves deadly when used recreationally. Propofol binds to the GABA_A receptor, which consists of an integral ion channel protein embedded in the membrane of neurons in the brain that is activated by the neurotransmitter molecule gamma-aminobutyric acid, or GABA. When propofol binds to the GABA_A receptor, a conformational change occurs, holding the neurotransmitter GABA in its binding site and keeping the ion channel open. This allows more chloride ions to diffuse into the cell. Resting potential becomes more negative, so even with the diffusion of Na+ ions during nerve stimulation, the threshold cannot be reached and the action potential is not generated. Since the neurons cannot communicate normally, a person given propofol remains unconscious. The lower part of the GABA_A receptor, located in the cytoplasm of a neuron, has an unidentified molecular structure. Phe 393 variants in the A and D chains prevent propofol from acting on the GABA_A receptor. The DSHA SMART (Students Modeling A Research Topic) Team modeled the similar nicotinic receptor using 3D printing technology to better understand the structure of the GABA_A receptor. A greater understanding of the structure of the GABA_A receptor and the role of the Phe 393 variants in the action of propofol can lead to the development of more effective anesthetics.

• Grafton High School
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Grafton High School

Dynamic Duo: Leptin and PACAP Receptors Fight Obesity


Grafton High School SMART
Team model based on 3V6O.pdb

Students:

• M Anciaux
• S Bangalore
• H Fick
• L Glaza
• J Grandinetti
• A Jobe
• F Kettenhoven
• A Knier
• A Loughlin
• K Mills
• S Schmitt
• T Wilder

Teachers:

• Fran Grant

Mentor:

• SuJean Choi, PhD, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

Obesity is a risk factor for cancer, diabetes, and strokes, causing 300,000 deaths annually in the U.S.1 Facets of obesity, such as adipose-tissue mass, hunger, and energy use are, in part, regulated by leptin, which binds to the leptin receptor (LR) within the hypothalamus, regulating mammalian feeding behaviors and promoting metabolic homeostasis. The LR is a homodimer belonging to the cytokine family. It binds leptin at ten residues between amino acids 433 and 617. Leptin binding activates the JAK-STAT signaling cascade, which promotes gene transcription altering feeding behavior and metabolism. The putative structure of the LR is composed of 206 amino acids, containing two exposed tryptophan residues, four-helical bundle cytokines, and four antiparallel α-helices. Understanding LR activation is crucial for obesity as studies have shown that defects in LR binding may disrupt normal metabolic function and overeating leading to metabolic disorders such as obesity. Overeating also occurs when PACAP (pituitary adenylate cyclase activating polypeptide) which functions similarly to leptin, is blocked. Importantly, leptin is blocked from producing its anorexic effects when PACAP receptors are blocked. Understanding how leptin receptors function with PACAP receptors would advance the understanding of leptin signaling in obesity. The Grafton High School SMART (Students Modeling A Research Topic) Team designed a leptin receptor model using 3D printing technology to specifically explore the structure-function relationship between PACAP and leptin, and their shared common pathway. To date, effective treatments for obesity are lacking, therefore research focused on the relationship between PACAP and LR activation could lead to the development of new therapeutic medications.

• Hartford Union High School
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Hartford Union High School

Serine Rich Splicing Factor 2 (SRSF2) Flips for RNA Binding


Hartford Union High School SMART
Team model based on 2LEB.pdb

Students:

• M. Bohn
• M. Cina
• A. Downing
• M. Flanagan
• L. Hautala
• A. Jaeke
• C. Kennedy
• B. Lane
• A. O’Bryon
• J. Pepin
• E. Rohloff
• F. Rrahmani
• S. Schmitt
• J. Spudich
• S. Staus
• K. Tadlock
• M. Tomashek
• E. Witt

Teachers:

• Mr. M. Arnholt

Mentor:

• M. McNally, Ph.D. Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Mistakes in alternative splicing of RNA cause diseases such as acute myeloid leukemia. Serine Rich Splicing Factor 2 (SRSF2) is a splicing factor that controls alternative splicing by promoting exon inclusion, so it is not surprising that mutations to SRFS2 are linked to cancers. SR proteins harbor an RNA recognition motif (RRM) at the N-terminus that binds to mRNA. SRSF2 has the unusual ability to bind to both pyrimidine and purine rich RNA sequences by flipping two C or G nucleotides in the mRNA into anti or syn orientations. The RRM specifically recognizes only C2, C3, and G5. Arg61 forms a hydrogen bond to C3, Phe59 hydrogen bonds to C2, and Lys17 is involved in flipping C2 or G2 into syn or anti conformations. Tyr92 binds with C2 and forms a hydrogen bond with C3. The mutation Pro95His binds better to UCCAGU and has been linked to cancer. The Hartford Union High School SMART (Students Modeling A Research Topic) Team modeled SRSF2 using 3D printing technology to highlight structural characteristics involved in RNA binding. Additional research on SRSF2 mutations and sequence binding has the potential to find both causes of and treatments for diseases like cancer.

• Kettle Moraine High School
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Kettle Moraine High School

NLRP3 – So Important It Hurts


Kettle Moraine High School SMART
Team model based on 2NAQ.pdb

Students:

• Ellena Hein
• Ethan Helfenstein
• Ava Lirette
• Kelsi Morris
• Jack Mulcahy
• Liam Mulcahy
• Divyank Sharma
• Aaron Smet

Teachers:

• Melissa Kirby

Mentor:

• Ashley Cowie, Sarah Langer, and Francie Moehring of the Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to The Migraine Research Foundation, more than 39 million people in the U.S. suffer from migraines; some using addictive drugs like codeine to relieve them. Understanding the inflammasome NLRP3 (nucleotide-binding domain and leucine-rich repeat containing family pyrin domain containing 3) could lead to the development of more effective pain medications with fewer side-effects. NLRP3 is part of the innate immune system and is a type of inflammasome found in the trigeminal ganglia, a nerve structure that contributes to migraine pain. ATP and other damage-associated molecular patterns released from injured cells start a signaling cascade, causing the activation of TLR4 and P2X7 receptors on the cell membrane of non-damaged cells, like the trigeminal ganglion neurons. This triggers the formation of the NLRP3 inflammasome. NLRP3 initiates production of active IL-1β (which leads to migraine pain) by inducing the activation of caspase-1. NLRP3 contains seven subunits and forms a multiprotein oligomer with ASC (apoptosis-associated speck-like protein containing a carboxy-terminal CARD) and caspase-1. Each subunit of NLRP3 is a small, 91 amino acid peptide composed of 6 alpha helices. Amino acids Lys24, Asp29 and Arg41 of NLRP3 allow the molecule to bind to the ASC. The Kettle Moraine High School SMART (Students Modeling A Research Topic) Team has designed a model of one NLRP3 subunit using 3D printing technology to further understand its structure and role in pain. Further research into this protein could lead to a deeper understanding of NLRP3’s role in inflammation and cell damage, and result in more effective treatments for pain.

• Laconia High School
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Laconia High School

Recent Research Reveals Possible Dimer Structure of Human MiD51


Laconia High School SMART
Team model based on 4NXU.pdb

Students:

• Alexis Coffeen
• Theodore Holdmann
• Alyssa Jodarski
• Sarah Laudolff
• Logan Meyer
• Theresa Oliver
• Chloe Smith
• Bekah Tilstra
• Elizabeth Walters
• Cora Williams

Teachers:

• Joshua Demski

Mentor:

• John Egner and Amber Bakkum, Department of Biochemistry, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Disruption of Mitochondrial Dynamics Protein of 51 kDa (MiD51) has been linked to neurological diseases, such as Parkinson’s, Alzheimer's, and Huntington’s disease. MiD51 recruits Dynamin Related Protein 1 (Drp1) from the cytosol to bring about mitochondrial fission. MiD51 belongs to the nucleotidyltransferase fold superfamily of proteins. MiD51 also interacts with ligands ADP and GDP. MiD51 is a globular protein anchored on the mitochondrial outer membrane, and is organized into three domains; a disordered domain, an N-terminal domain containing a binding pocket for ADP/GDP and a recruitment region for Drp1, and a C-terminal domain. The soluble N- and C-terminal structured domains of MiD51 contain 11 alpha helices, 9 beta sheets, and 335 amino acid residues. Residues 215-251 make up the Drp1 recruitment region (beta 3, beta 4, alpha 4). ADP and GDP ligands are present, but research shows that Drp1 recruitment occurs in humans whether ligands are present or not. Human dimeric MiD51 has never been crystallized, but is believed to exist based on the dimeric crystal structure of the mouse homolog. This is further supported by SAXS data collection and modeling. Modeling suggests that R169, R182, and D183 are important for mediating dimer formation. The Laconia High School SMART (Students Modeling A Research Topic) Team modeled MiD51 using 3D printing technology to investigate structure-function relationships. MiD51 research is important because if the structure of the protein and its function of mitochondrial fission could be understood, it could possibly be used to prevent and treat neurological diseases in the future.

• Ronald Reagan High School
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Ronald Reagan High School

ABCD – The Language of Replication Protein A (RPA)


Ronald Reagan High School SMART
Team model based on 4GNX.pdb

Students:

• C. Anderson
• R. Bhatia
• M. Ehlers
• K. Ledger
• H. Lentz
• S. Marsh
• B. Haralson
• A. Puls
• S. Sheikh
• A. Smith
• M. Spellecy
• M. Sweeney
• A. Ya

Teachers:

• Ms. Schuld
• Mr. Perez

Mentor:

• Edwin Antony, Ph.D. Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

RPA is a ssDNA binding protein whose function is essential to DNA replication, recombination, and repair. RPA coordinates DNA repair processes responsible for maintaining genomic integrity, and hence is an attractive target for oncology. RPA interacts with ssDNA, and recruits other proteins onto ssDNA. RPA binds to ssDNA very tightly. Current research focuses on determining how an ssDNA-RPA complex is removed from the DNA by weaker DNA binding enzymes. Structurally, RPA is a heterotrimer made up of three subunits (RPA70, RPA32 and RPA14). The DNA binding function of RPA is carried out by four distinct DNA binding domains (DBDs), A (residues 182 - 305), B (residues 306 - 424), C (residues 425 - 623) and D (residues 46 - 175), that directly attach to the single stranded DNA (ssDNA). DBDs A, B and C reside in the RPA70 subunit and are connected by flexible linkers. DBD-D resides in the RPA32 subunit. The heterotrimer is held together as a complex through interactions between DBD-C (RPA70), DBD-D (RPA32) and the RPA14 subunit. Scientists use unnatural amino acids and chemical fluorophores to capture how each DBD binds and disconnects from ssDNA. This approach shows that DBD-A binds rapidly to ssDNA, but detaches quickly, while DBD-D binds more slowly to ssDNA, but is stable. Ronald Reagan High School’s SMART (Students Modeling A Research Topic) Team has designed a model of RPA using 3D printing technology to investigate its structure and function. Additional research on RPA structure and mutations may prove helpful in determining cause and risk for cancer and developing potential treatments.

• Saint Joan Antida High School
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Saint Joan Antida High School

Is It Possible to Find a Cure for Cancer?


Saint Joan Antida High School SMART
Team model based on 4JX5.pdb

Students:

• C. Lopez

Teachers:

• Cindy McLinn
• Katie DiFonzo

Mentor:

• Martin St. Maurice Ph.D, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

Inhibiting pyruvate carboxylase could lead to future treatments for cancer by preventing cancer cells from multiplying. Pyruvate carboxylase is an enzyme found in the mitochondria of animal cells and contributes to the mitochondrial tricarboxylic acid (TCA) cycle by converting pyruvate into oxaloacetate that the cycle needs to generate precursors used to make lipids, amino acids, and nucleotides. Cancer cells rely heavily on many of these precursors to divide. Pyruvate carboxylase is a homotetramer with four domains and about 1200 amino acids. A truncated construct of pyruvate carboxylase from Rhizobium etli has 632 amino acids and is primarily comprised of the carboxyltransferase domain. It has 32 helices and 16 beta sheets. Thr882 shuttles a proton between the biotin cofactor and pyruvate, while Arg 548, Gln552 and Arg621 stabilize the enolpyruvate intermediate. Asp590 and Tyr628 form a binding pocket where carboxybiotin cofactor is inserted into the active site. All of these amino acids may react with experimental inhibitors. The active site is centered on the ligand Zinc2+, and while pyruvate does not directly bind to Zn2+, the ion affects the orientation of the pyruvate in the binding site. The Saint Joan Antida High School SMART (Students Modeling A Research Topic) team designed a model of the carboxyltransferase domain of pyruvate carboxylase using 3D printing technology to study structure-function relationships and model novel inhibitors. Ongoing research should continue to seek inhibitors that will shut down pyruvate carboxylase, potentially leading to new cancer treatments.

• St. Dominic Middle School
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St. Dominic Middle School

Amyloid Beta and Alzheimer Disease


St. Dominic Middle School SMART
Team model based on 5OQV.pdb

Students:

• Matthew Conrad
• Bryan Fura
• Jonah Jensen
• Luca Kowalik
• Sofia Miranda
• Isabella Mullen
• Paige Nelson
• Christopher Nicholas
• Michael Nicholas
• Jack Norfolk
• Charles Novak
• Elizabeth Otten
• Elayna Pasqua
• Grace Pasqua
• Nathan Petrucci
• Paige Platz
• Maxwell Rankin
• Molly Roeder
• Isabella Schweitzer
• Lia Simon
• Ryan Sohn
• Peter Warner
• Carter Wells

Teachers:

• Ms. Donna LaFlamme

Mentor:

• Matt Scaglione, PhD, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the U.S. Centers for Disease Control, Alzheimer’s disease (AD) is the sixth leading cause of American deaths, affecting 5.5 million people and striking one in ten people over age 65. The dementia characteristic of AD is associated with the over-production and aggregation of amyloid beta (Aβ), a 40-42 amino acid peptide clipped from the trans-membrane portion of the amyloid precursor protein (APP); a large membrane protein important for neural growth and repair. In a healthy brain, Aβ is recycled; while in AD, Aβ strands form neurotoxic aggregates outside neurons called senile plaques. A major component of plaques, Aβ fibrils are homodimers consisting of two protofilaments. The protofilaments are stacked, parallel, LS-shaped amyloid-β peptides connected to each other in a cross-beta sheet structure. Interactions of three groups of hydrophobic sidechains on neighboring Aβ strands stabilize each protofilament and maintain the N-terminus L-shape and C-terminus C shape. While over 50 mutations in the APP protein are associated with early onset AD, our model of the Aβ fibril highlights the six located on Aβ: Glu22Gln, Ala21Gly, Glu22Lys, Leu34Val, Ala2Thr, Glu22Gly, Asp23Asn, and Ala2Val. The St. Dominic Middle School SMART (Students Modeling A Research Topic) Team designed a model of an Aβ fibril using 3D printing technology to investigate structure-function relationships. Current research investigates peptides that can prevent the aggregation of Aβ. Research on Aβ could lead to the discovery treatments that prevent Aβ plaques from forming and killing neurons, which could greatly impact millions of lives.

• Westosha Central High School
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Westosha Central High School

Blood in the Eye, Diabetes; You Give VEGF a Bad Name


Westosha Central High School SMART
Team model based on 5T89.pdb

Students:

• T. Andrews
• T. Millhouse
• C. Muff
• J. Riphagen
• E. VanKammen
• T. Vassos
• M. Williams

Teachers:

• Jonathan Kao

Mentor:

• Alison Huckenpahler, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

The WHO estimates that in 2014, 422 million adults were living with diabetes, a condition which limits blood flow to the small blood vessels of the eye. To restore blood flow, the body triggers angiogenesis, or the growth of new blood vessels, using vascular endothelial growth factors (VEGF) and the VEGF receptor (VEGF-R). Blood vessels created by VEGF-R signalling are weak and leak blood and fluid into the back of the eye, causing diabetic retinopathy and eventually blindness. The VEGF-R is a dimer and each monomer is composed of seven extracellular domains and an intracelleular kinase domain. Dimerization of the receptor occurs after binding VEGF, causing the correct positioning of the kinase domain to begin a signal cascade that stimulates the growth of endothelial cells into new blood vessels. Domains 1-3 are responsible for binding VEGF, with the amino acids Q263, F292, V278, R224, N259, R261, R280, Q284, and N290 forming the binding pocket for the VEGF. Domains 2-7 are responsible for the dimerization and activation of the VEGF-R. The amino acids R351, K393, A381, K379, E513, K517, T455, S346, A434, K433, and Q429 in domains 4 and 5 form homotypic interactions and control the VEGF-R activation. The Westosha Central High School SMART (Students Modeling A Research Topic) team has designed a model of VEGF-R to study structure-function relationships. Although VEGF-R inhibitors are widely used to treat diabetic retinopathy, they are extremely expensive and not effective in all patients. Elucidation of VEGF-R's targeting and activation could lead to more effective inhibitoin of angiogenesis, thereby preserving vision in diabetic patients.

• Whitefish Bay High School
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Whitefish Bay High School

The Ricin Fall of Select Agents


Whitefish Bay High School SMART
Team model based on 2AAI.pdb

Students:

• D. Coleman
• E. Davis
• L. Dragseth
• A. Gent
• A. Janssen
• S. Koch
• A. Ramirez
• B. Sevart

Teachers:

• Ms. Brown
• Ms. Krukar

Mentor:

• Dr. Joseph T. Barbieri and Madison Zuverink, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Ricin has a long history of use as a weapon of terrorism. Ricin attacks have been planned and thwarted by terrorist groups in the United States and across the globe. Ricin, generated from castor beans, is fatal to humans because it causes cell death. Ricin is a protein composed of two chains, A and B, linked by a disulfide bond. The A chain detaches from the B chain, and in the active site, Glu177 de-adenylates a base on RNA found within the 60S ribosome, thus inhibiting cellular protein synthesis. The A chain is composed of three domains: one characterized by a five-stranded beta sheet, one by five alpha helices, and the final by a disc-like shape. The B chain facilitates entry into the cell by binding to surface receptors. The B chain is composed of two nearly identically-folded domains that share high amino acid similarity. The ligands are Gal264, whose domain is defined by Asn46, Lys40, and Asp22, and Gal267, whose domain is defined by Asn255 and Asp234. The Whitefish Bay High School SMART Team (Students Modeling A Research Topic) modeled ricin using 3D printing technology to better understand its function and structure. Further research is required to develop a vaccine, although two putative formulations exist: RiVax and RiVEc. Unexpectedly, these vaccines are composed of the A chain, rather than the receptor binding B chain. A successful vaccine could be given primarily to military and national security personnel to prevent the deadly effects of biological military action using ricin.

2016-2017 SMART Teams

Thirteen schools participated in the Local SMART Team program during the 2016-2017 school year. The remote SMART Teams, HHMI SMART Teams and MAPS Teams also expanded. Completed local projects are described below.

Download the full 2016-2017 SMART Team Abstract Booklet.

• Audobon High School
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Audobon High School

Calbindin: A Marker for Synaptic Integration Following Spinal Injury


Audobon High School SMART
Team model based on 2G9B.pdb

Students:

• Sumaya Ahmed
• Roberto Arce
• Jehousa Gomez-Mendez
• Rolando Martinez

Teachers:

• Brian Coffey
• Julissa Chavez

Mentor:

• Audra Kramer, MS, Marquette University, Department of Biomedical Sciences

Project Files:

• Poster
• Model Description Sheet

Abstract:

The World Health Organization reports that 250,000 to 500,000 people suffer a spinal cord injury annually. The injury interferes with presynaptic to postsynaptic communication necessary for proper motor function. Neurons do not typically regenerate, rendering damage permanent. To work around this damage, a virus that expresses an axon growth-promoting protein is injected into the motor cortex. This induces regeneration of injured axons and synaptogenesis. However, newly sprouted axon-to-cell connections can be mistargeted. The integration of newly regenerated axons with postsynaptic cells can be seen by studying the expression of postsynaptic cell markers, such as the calcium-binding protein calbindin. Calbindin contains twelve alpha helices, four calcium binding sites, and six EF-hands. Calbindin connects EF-hands by making hydrophobic contacts to amino acids on each arm. Ile19, trp20, and phe23 from the first arm make contact with leu36, leu39, and ala46 on the second hand while an EF-hand loop is made by contacts between asp24 and ala46. The two cystine residues, cys100 and cys219 play an important role in calcium binding in the protein. Calbindin is more heavily expressed in classes of cells found in the ventral portion of the spinal cord, suggesting a role in motor function. The Audubon High School SMART (Students Modeling a Research Topic) Team has designed a model of calbindin using 3-D printing technology to investigate structure-function relationships. Using calbindin as a marker to identify the location of synaptogenesis in regenerating axons can lead to therapies for regaining motor function in individuals suffering from spinal cord injuries.

• Brown Deer High School
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Brown Deer High School

NMDAR Helps You Think, So Please Reconsider That Extra Drink


Brown Deer High School
Team model based on 4PE5.pdb

Students:

• Gavin Block
• T.J. Davis
• Nancy Dong
• Jonah Freuler
• Mitchell Mietkowski
• Tony Jo Rowney
• Noel Stoehr

Teachers:

• David Sampe

Mentor:

• Robert Peoples, PhD, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the U.S. Centers for Disease Control and Prevention, each year 88,000 people die from alcohol-related causes in the United States. Ethanol misuse, a deadly and expensive societal problem, cost the United States $249 billion in 2010 (1). Ethanol targets many proteins in the brain. Specifically, it acts as an inhibitor of the N-Methyl-D-aspartate receptor (NMDAR), which mediates much of the excitatory synaptic transmission in the brain. Normally, the NMDAR is activated when glutamic acid binds to it allowing positive ions to flow through the cell membrane; this facilitates learning and memory in the brain. However, ethanol inhibits the activity of the NMDAR, interfering with synaptic transmission. A type of glutamate ion channel receptor found in neurons, NMDAR, has four domains: the amino terminal domain, the ligand binding domain, the membrane-associated (M) domains, and the carboxyl terminal domain. NMDAR is a heterotetrameric protein with two GluN1 and two GluN2 subunits. Ethanol interacts with NMDAR in the M domains with specific amino acids including Gly638 in the GluN1 subunit as well as Phe637 and Gly826 in the GluN2B subunit (2,3). Researchers are determining the location of the strongest NMDAR-ethanol interactions using amino acid substitutions. The Brown Deer High School SMART (Students Modeling A Research Topic) Team has designed a model of NMDAR using 3D printing technology to visualize the NMDAR-ethanol interactions. If researchers can develop molecules to help minimize the effect of ethanol on the brain, it could reduce the cost of alcoholism to society.

• Cedarburg High School
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Cedarburg High School

Coughing up a Cure for Whooping Cough with Pertussis Toxin


Cedarburg High School
Team model based on 1PRT.pdb

Students:

• A. Arnholt
• S. Arnholt
• D. Arzumanyan
• L. Arzumanyan
• A. Butt
• A Houghtaling
• L. Ketelhohn
• J. Levy
• N. Miller
• N. Minerva
• E. Remington
• B. Tiffany
• J. Wankowski

Teachers:

• Karen Tiffany

Mentor:

• Joseph Barbieri, PhD and MAdison Zuverink, BS, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

The CDC reported 32,971 cases of pertussis, or whooping cough, in 2014. This respiratory infection mainly affects unvaccinated infants and toddlers, and symptoms include paroxysmal coughing with whooping, vomiting, and pulmonary complications which can lead to death. Pertussis toxin (PT), produced by the pathogenic bacteria Bordetella pertussis, causes whooping cough by ADP-ribosylating the Gi protein that inactivates adenylyl cyclase. The inactive ADP-ribosylated Gi protein is unable to interact with G protein-coupled receptors, leading to an increased intracellular concentration of cAMP. Increased concentrations of cAMP can interfere with normal cell signaling, disrupting specific cellular functions. PT is a critical virulence factor for B. pertussis that also has potential to create human immunity against pertussis. The Cedarburg SMART Team (Students Modeling A Research Topic) modeled PT using 3-D printing technology to study structure-function relationships. PT contains a total of six subunits, four individual subunits (S1, S2, S3, and S5) and a pair of identical subunits (S4). The A domain consists of the S1 subunit, the catalytic portion of the toxin. Mutations in Glu129 and His35 can reduce ADP-ribosyltransferase activity. Mutations in Arg9, Asp11, and Arg13 also reduce catalytic activity. Trp26 interacts with NAD+, an important cofactor. The B domain, responsible for binding to cell receptors, contains the remaining subunits. Effective vaccines contain chemically-inactivated PT. However, whole cell pertussis vaccine may cause severe side effects, while acellular pertussis vaccine is not as potent. Non-toxic derivatives of pertussis toxin may be engineered, improving the potency of the acellular vaccine without harmful side effects.

• Whitefish Bay High School
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Whitefish Bay High School

Inhibition of δ-Opioid Receptors


Whitefish Bay High School
Team model based on 4DKL.pdb

Students:

• Katrina Burmeister
• Evan Davis
• Luke Dragseth
• Austin Gent
• Andrew Janssen
• Stephen Koch
• Mohammad Shaheer
• Shadika Panta

Teachers:

• Paula Krikar
• Katie Brown

Mentor:

• Christopher W. Cunningham, PhD, Concordia University of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Opioid addiction and abuse affects between 26 and 36 million people worldwide (Volkhow, 2014), prompting researchers to try to design a drug that both has painkilling effects but does not create a dependency. Most opioid analgesics work through activation of mu opioid receptors (MOR). They naturally bind to opioid peptides, such as endomorphins 1 and 2, in order to regulate pain. Another important target is the delta opioid receptor (DOR). Inhibition of DOR has been shown to slow the development of addiction to MOR agonists in animal models of pain. DOR are proteins that transpermeate the cell membrane with seven alpha helices. Schiller and colleagues first reported an endomorphin analogue, DIPP-NH2, that activates MOR and also inhibits DOR. DIPP-NH2 is structurally similar to the natural endomorphins, so it can bind DOR through similar mechanisms. The DIPP-NH2 interacts with the Met132, Tyr129, Val217, Ile277, and Trp284 on the DOR. Moreover, one of the two methyl groups on DIPP-NH2 engages Val281 and Ile277. Finally, a salt bridge forms between the DIPP-NH2 N-terminus and Asp128, and this salt bridge is crucial for opioid receptor ligand recognition. The Whitefish Bay High School SMART team (Students Modeling a Research Topic) is modeling DOR using 3D printing technology. DIPP-NH2 may be the basis of a non-addictive painkiller, which would be a significant advancement toward alleviating the major societal and financial problem of opioid addiction.

• Cudahy High School
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Cudahy High School

The Ouchless Kind: The Role of P2X4 receptors in Pain Signaling


Cudahy High School
Team model based on 3I5D.pdb

Students:

• Cori Windsor
• Andrew Kressin
• Madeline Romfoe
• Cody Broeckel
• Ramon Rives
• Katelyn Pomianek
• Maddie Acherman
• Stephanie Kressin
• Allie Thomas
• Briana Stehling
• Emily Paine
• McKenzie Vaughn

Teachers:

• Dan Koslakiewicz
• Dean Billo

Mentor:

• Francie Moehring and Ashley Reynolds, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to Apfelbaum et al., (2003), 80% of patients experience acute pain after surgery where opiates are most commonly prescribed to alleviate this pain. Twenty-five percent of these postoperative patients experience adverse side effects related to opiates, including increased pain, addiction, and itching. To prevent these side effects, researchers are looking into localized treatment for pain, targeting peripheral ion channels instead of targeting the whole central nervous system. The ion channel P2X4 in microglia has been shown to be involved in pain perception after spinal nerve injury, aiding in the transmission of pain signals to the brain by initiating the signaling processes in cutaneous sensory neurons indicating nerve and/or tissue damage. P2X4 is a two-domain ATP-gated channel; the transmembrane domain comprising the channel and the extracellular domain containing the potential ATP binding region. ATP binding, potentially occurring in the groove between the three set of subunits A and B, involving Lys70, Lys72, Phe188, Thr189, Asn296, Phe297, Arg298, Lys316, is required for activation. Once bound, ATP causes a conformational change in the transmembrane portion, opening the channel at Gly350 causing movement at Leu340, Gly343, and Ala344, modeled by the Cudahy SMART (Students Modeling A Research Topic) Team using 3D printing technology. The open channel allows an influx of positive ions into the neuron, resulting in depolarization and the transmission of pain. Therefore, it may be more effective to inhibit P2X4 at the site of pain, such as the incision site, with targeted topical analgesics, instead of systemically treating pain.

• Divine Savior Holy Angels High School
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Divine Savior Holy Angels High School

The RNA Exosome: Gene Expression Terminator


Divine Savior Holy Angels High School
Team model based on 41FD.pdb

Students:

• K. Arnold
• J. David
• J Diez
• S. Franczak
• A. Griffith-Topps
• C. Kuehn
• C. Lois
• Stephanie Kressin
• S. Mikhaeel
• M. Pitts
• C. Sargent
• L. Schraufnagel
• T. Siy
• S. Strandberg
• C. Strother
• J Strother
• M. Thew
• S. Urbam

Teachers:

• Scott Fleischmann
• Stacey Strandberg

Mentor:

• Mark T. McNally, PhD, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

The RNA exosome is a multicomponent molecular machine with many functions, including the degradation of mRNA. RNA degradation is a natural process in prokaryotic and eukaryotic organisms and regulates protein abundance. In most organisms, RNA can be degraded in both directions (from 5’ or 3’ ends) and the exosome is an entity that degrades RNA from the 3’ end. The minimal exosome is made up of eleven proteins that form three overall domains. The cap, or top of the structure, pulls in a single strand of RNA and feeds into a six-protein barrel shaped center portion, which directs the strand to the RNase domain at the bottom where the RNA is degraded from the 3’-to-5’ direction. A cap protein, Rrp4, contains an active site consisting of Arg 110, Arg 123, Phe 177, and Asp 179 that unfolds RNA into single strands. The RNase active site on protein Rrp44 consists of Arg 847, Tyr 595, Asn 724, Gln 892, Gly 895, Glu 700 and Tyr 654 along with two magnesium ions and a water molecule which are needed to break down RNA into individual nucleotides. The Divine Savior Holy Angels SMART (Students Modeling A Research Topic) Team modeled the exosome using 3D printing technology. While the exosome is fundamentally important, exosome variants may also predispose people to cancers like multiple myeloma, as exosome mutations are recurrent in these patients. Thus, the understanding of how these mutations influence exosome function and may lead to treatments for these cancers.

• Westosha High School
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Westosha High School

Getting N2 Sustainable Fertilizer Production: Nitrogenase


Westosha High School
Team model based on 2AFI.pdb

Students:

• John Dietz
• Brett Niederer
• Trevor Millhouse
• Connor Muff
• Joyce Riphagen
• Victoria Salerno
• Elizabeth Van Kammen

Teachers:

• Jonathan Kao

Mentor:

• Edwin Antony, PhD. Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

Fertilizer is an essential component of agriculture globally that is artificially produced through the Haber-Bosch process. This process requires energy to generate temperatures of 400-500 oC and pressures of 15-25 MPa to reduce N2 to NH3. The greenhouse gas CO2 is produced as waste in this reaction. In nature, bacteria in plant root nodules reduce N2 into NH3 catalyzed by nitrogenase. Nitrogenase is a complex comprised of two proteins: a heterotetrameric MoFe protein, and two heterodimeric Fe proteins bound on each end. The MoFe proteins consists of two 491 residue ɑ-subunits and two 522 residue β-subunits. The Fe proteins are bound to the exterior of the MoFe protein creating two mirrored functional halves. In an ATP facilitated process, the Fe protein captures an electron using an iron metallocluster, then donates an electron to the molybdenum/iron metallocluster in the MoFe protein. Electrons are moved within the MoFe protein to the active site. The two halves of the protein alternate in a coordinated manner, transferring one electron at a time until eight electrons are transferred. The electrons then reduce the N2 substrate into 2(NH3)+ H2. The Westosha Central SMART (Students Modeling a Research Topic) Team has created a 3D model of nitrogenase highlighting the metalloclusters and how the complex assembles/disassembles. Understanding how this protein functions may allow mass production of ammonia through a biological process reducing the dependency on the Haber-Bosch process therefore reducing CO2 emissions.

• Grafton High School
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Grafton High School

“Buzz Off” Zika


Grafton High School
Team model based on 5KQR.pdb

Students:

• N. Arendt
• K. Ducheny
• M. Norton
• T. Ovsepyan
• M. Ruege
• H. Wildermuth

Teachers:

• Fran Grant

Mentor:

• Dr. Silvaggi, PhD, University of Wisconsin, Milwaukee

Project Files:

• Poster
• Model Description Sheet

Abstract:

Zika virus, or ZIKV, a mosquito-borne pathogen, is a current public health concern due to its link to microcephaly and Guillain-Barré syndrome. A flavivirus, ZIKV contains an RNA genome translated using the host cell’s protein synthesis machinery. The 5’ end of the viral RNA possesses a “cap” of methylated bases that protect it from being destroyed by the host’s immune system. This cap is produced by a virally-encoded methyltransferase enzyme, the NS5 methyltransferase (MTase). Since the 5’-RNA cap is required for viral reproduction, inactivating the NS5 MTase with a small molecule inhibitor should be a viable treatment for ZIKV infections. The NS5 MTase transfers CH3 groups from the ubiquitous methyl donor molecule S-adenosylmethionine (SAM) to specific positions on bases at the 5’ end of the viral RNA. Based on the binding mode of SAM observed in a crystal structure (5KQR), an analog of SAM was developed that could inhibit the enzymatic activity of the MTase. SAM binds in a pocket composed of Ser56, Arg84, Trp87, Thr104, Lys105, His110, Glu111, Asp131, Val132, Phe133, Asp146, and Ile147. The Grafton SMART (Students Modeling A Research Topic) Team has modeled the NS5 MTase with either SAM or the hypothetical inhibitor MO2 bound using 3D printing technology. Models with such compounds bound to the enzyme provide information that might help increase the potency of potential inhibitors and improve their selectivity for the ZIKV MTase.

• Hartford Union High School
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Hartford Union High School

The Role of MeCP2 Mutations in a Reg-Rett-Able Syndrome


Hartford Union High School
Team model based on 5BT2.pdb

Students:

• H. Bertucci
• M. Bertucci
• T. Dorosz
• T. Hart
• A. Heimermann
• M. Lentz
• T. Rusch
• J. Schultz
• N. Weber
• H. Weiss

Teachers:

• M. Arnholt

Mentor:

• G Makky, PhD Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

Rett Syndrome affects about one in every 10,000 to 15,000 births. It is a genetic neurodevelopmental disorder that mainly occurs in females. Affected males die in infancy because the syndrome exhibits an X-linked dominant pattern of inheritance. Rett Syndrome is caused by mutations in the X-linked Methyl CpG binding protein 2 (MeCP2) coding gene. MeCP2 is necessary for epigenetic regulation of gene expression. This protein represses transcription by acting as a molecular bridge between methylated DNA and a complex of co-repressor proteins including histone deacetylases and Sin3A. Mutations of MeCP2 cause overexpression of several genes during brain development. MeCP2 is a 52-kDa protein with two functional domains: the transcriptional repressor domain (TRD) and the methyl-CpG binding domain (MBD). Within the MBD, mutations of Arg106, Arg133, Phe155, and Thr158 result in a decreased binding affinity of MeCP2 to methylated DNA: 2-fold for mutated Thr158 and 100-fold for the remaining mutated amino acids. The MBD has three beta sheets with Thr158 located on the c-terminal end. Here, hydrophilic residues interact specifically with the methylated DNA. The Hartford Union High School SMART (Students Modeling A Research Topic) Team designed a model of MeCP2 using 3D printing technology to represent the MBD-methylated DNA complex. The model highlights the amino acids involved in the interaction between MeCP2 and methylated DNA. Modeling the structure of MeCP2 allows for a more detailed understanding of the interaction between MeCP2 and DNA. This information will be crucial for designing treatments or interventions to improve the quality of life for Rett syndrome patients.

• Kettle Moraine High School
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Kettle Moraine High School

Leptin and PACAP: Possible Co-op?


Kettle Moraine High School
Team model based on 1AX8.pdb

Students:

• Mahi Gokuli
• Ethan Helfenstein
• Kathryn Hallada
• Kelsi Morris
• Liam Mulcahy
• Autumn Saunders
• Divyank Sharma
• Aaron Smet
• Justin Smet

Teachers:

• Melissa Kirby

Mentor:

• SuJean Choi, PhD Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

More than one-third of American adults are obese, and obesity-related conditions including diabetes, hypertension, and stroke are among the leading causes of preventable deaths. Leptin is a hypophagic hormone secreted by fat cells, thought to regulate satiety. The Ile14 residue in leptin is crucial for the interaction between leptin and its receptor. Leptin helices A and C interact with the CRH2 domain of the leptin receptor. Mutations to Ile14 disrupt the docking conformation in a manner that prevents helices A and C on leptin to position parallel with CRH2 thereby, affecting the binding efficiency. Mutation to the Ile14 residue results in excessive feeding and weight gain. The neuropeptide pituitary adenylate cyclase activating polypeptide (PACAP) produces identical hypophagia via the hypothalamic ventromedial nuclei (VMN) to that of leptin. The proximity of leptin and PACAP receptors combined with their functional similarity suggest they could collaborate to induce hypophagia through a shared intracellular signaling cascade. By identifying critical molecular sites necessary for leptin action, we may better understand how PACAP and leptin receptor signaling are linked, whether changes to the residue also alters PACAP signaling and the degree to which it contributes to obesity or eating disorders. The Kettle Moraine High School SMART (Students Modeling A Research Topic) Team has modeled leptin using 3D printing technology to investigate structure function relationships. Inquiry into leptin and PACAP interactions may reveal the nature of interdependency between neural and peripheral energy-regulating systems in the VMN, new applications of hypophagic drugs, and the biological cause of obesity.

• St. Joan Antida High School
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St. Joan Antida High School

Mitochondrial Fis1’s N-Terminal “Arm” Orientations


St. Joan Antida High School
Team model based on 1NZN.pdb

Students:

• J. Allen
• S. Kopaz
• S. Mitchell

Teachers:

• K. DiFonzo
• C. McLinn
• A. Montgomery

Mentor:

• J. Egner, BA and A. Bakkum, BA Medical College of Wisconsin, Department of Biochemistry

Project Files:

• Poster
• Model Description Sheet

Abstract:

Mitochondria provide over 90% of the energy needed to maintain healthy cell function. Mitochondrial fission is essential to mitochondrial health. Mutations in mitochondrial proteins are implicated in diseases such as heart disease and diabetes. Current research is exploring the role of Mitochondrial fission protein 1 (Fis1) and key interactions with Dynamin related protein 1 (Drp1), and Mitochondrial dynamics protein of 51 kDa (MiD51). Preliminary data suggests that Fis1 competitively binds MiD51, relieving MiD51 inhibition and indirectly stimulating Drp1 activity to activate mitochondrial fission. These processes assist in removal of damaged mitochondria and support apoptosis during high cellular stress levels. Potential ligands that interact with Fis1 have been found to be MiD51 and Drp1, which may be regulated by Fis1’s intramolecular interactions. Using 3D printing technology, the St. Joan Antida SMART (Students Modeling a Research Topic) Team modeled cytosolic domain of Fis1 and the twice-repeated tetratricopeptide (TPR) repeat motif which is the predicted binding interface for Fis1-MiD51. TPR1 contains helices 2 & 3 and TPR2 contains helices 4 & 5. Residues 1-8 of the N-terminal arm are modelled in two orientations – “arm open” and “arm closed” – representing potential blocking of the active site within the concave pocket formed by TPR1&2 of Fis1. Current research hypothesizes sidechains of Asn6 and Arg83 to be responsible for “arm” orientation blocking the active site. Elucidating the role of Fis1-MiD51 axis in mitochondrial fission in the context of healthy and diseased models can lead to developing better therapeutics and treatments for heart disease and diabetes.

• St. Dominic Middle School
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St. Dominic Middle School

CHIP is a Neuroprotective Ubiquitin Ligase


St. Dominic Middle School
Team model based on 2C2L.pdb

Students:

• Jacqueline Ausitn
• Elizabeth Cobb
• Rose Gundrum
• Madelyn Jessick
• Will Kahler
• Cecilia Kornburger
• Kathryn Lagore
• Grace Lois
• Liam McQuown
• Alejandro Miranda
• Mary Ratnayake
• Tara Reilly
• Grace Strebe
• Jonah Wormington

Teachers:

• Donna LaFlamme

Mentor:

• Matt Scaglione, PhD Medical College of Wisconsin

Project Files:

• Model Description Sheet

Abstract:

CHIP (C-terminus of HSC interacting protein) is a neuroprotective ubiquitin ligase highly expressed in the brain. CHIP plays a crucial role in the ubiquitin proteasome system (UPS), a process that tags proteins with polyubiquitin chains targeting them for degradation. CHIP helps regulate protein quality control through its E3 ligase activity. As an E3 ligase, CHIP acts as a scaffold binding the E2 (ubiquitin conjugating enzyme) and the molecular chaperone Hsp90. CHIP aids the transfer of ubiquitins from E2 to a target protein bound to its chaperone, Hsp90. The polyubiquitin chain tags proteins for proteasomal degradation. The St. Dominic SMART Team (Students Modeling A Research Topic) modeled the homodimer CHIP using 3D-printing technology. Each monomer contains a tetratricopeptide repeat (TPR), helical hairpin (HH), and a U-Box domain. The N-terminal TPR domain binds the molecular chaperone Hsp90 using the sidechains Phe38, Lys73, Asn66, Leu69, Phe100, Lys96, Phe99, Phe132, and Asp135. The C-terminal U-Box binds E2 ubiquitin conjugates using Asp230, Phe238, Ile236, Val271, and Arg273. The HH domain is a long straight helix in one monomer but bends at a 900 angle in the other. Autosomal recessive mutations in the TPR, HH, and U-Box domains cause neurodegeneration in multiple areas of the brain leading to various combinations of symptoms such as ataxia, dementia, hypogonadism, seizures, and loss of language. Further research of CHIP’s structure and function could also lead to new understanding more common neurodegenerative diseases such as Alzheimer’s and Parkinson’s.

• Marquette University High School
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Marquette University High School

RPE65 – Essential Visual Cycle Protein


Marquette University High School
Team model based on 4RSC.pdb

Students:

• P. Ahn
• K. Arnold
• S. Bartos
• B. Burkle
• M. Chang
• M. Coury
• N. Cowan
• N. Dittrich
• R. Foster
• J. French
• T. Gamblin
• J. Gorski
• M. Hameed
• L. Homberg
• R. Johnson
• S. Khan
• E. Lewis
• J. Otten
• M. Rivera
• A. Sabatino
• T. Sargent
• J. Schimmels
• A. Smith
• R. Stegeman
• D. Strom
• J. Strom
• B. Tsuji
• C. Visaya
• J. Yamat
• N. Yorke

Teachers:

• Carl Kaiser
• Keth Klestinski

Mentor:

• Alison Huckenpahler, Medical College of Wisconsin

Project Files:

• Model Description Sheet

Abstract:

Leber congenital amaurosis (LCA) is a genetic disease associated with blindness that is caused by mutations in retinal pigment epithelium (RPE65), an enzyme involved in the visual cycle. When light hits photosensitive pigments in the retina, it conformationally changes 11-cis-retinol (a form of vitamin A) to 11-trans-retinol. This conversion allows for a series of chemical reactions and the formation of electrical signals that communicate with the brain. RPE65 is essential to the cycle because it changes 11-trans-retinol back into 11-cis-retinol--recycling the enzyme and allowing for sustained vision. The Marquette High SMART (Students Modeling A Research Topic) Team used 3D printing technology to model how mutations in LCA affect RPE65’s structure and function. RPE65 has 533 amino acids folded into sheets that arrange themselves into seven propeller blades, which collectively create a mostly hydrophilic tertiary structure. One face of RPE65 is hydrophobic and is associated with the microsomal membrane. A hydrophobic, tunnel-like structure leads to an iron cofactor that facilitates its enzymatic efficiency. The iron cofactor is held in the active site by the histidine residues H180, H241, H417, and H527 in a coordinated motif. Mutations near the active site cause lowered enzymatic activity and LCA. Other residues that are commonly mutated in LCA include Gly40, Arg91, Glu102, Arg124, His182, and Val473. Ocular imaging data has shown phenotypic changes in the photoreceptors in patients with RPE65 mutations. With novel gene delivery methods and other treatment strategies, these technologies will be useful to understanding how to treat LCA and other retinal diseases.

2015-2016 SMART Teams

Fourteen schools participated in the local SMART Team program during the 2015-2016 school year. The remote SMART Teams, HHMI SMART Teams and MAPS Teams also expanded. Completed local projects are described below.

Download the full 2015-2016 SMART Team Abstract Booklet.

Click Here to watch a recap video of the 2015-2016 SMART/MAPS Team Poster Session at Marquette University in Milwaukee, Wisconsin.

• Audobon High School
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Audobon High School

NMDA Receptors and Ethanol: How Alcohol Consumption Affects Our Memory and Cognitve Functions at the Molecular Level


Audobon High School SMART
Team model based on 4PE5.pdb

Students:

• Roberto Arce
• Victoria Prokop
• Leslie Vela

Teachers:

• Brian Coffey
• Julissa Chavez

Mentor:

• Robert W. Peoples, Ph.D., Marquette University, Department of Biomedical Sciences

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the National Council on Alcoholism and Drug Dependence, 1 in every 12 adults suffers from alcohol abuse and alcoholism. Alcohol abuse is associated with impaired judgment and cognitive functions and can ultimately be lethal, killing almost 75,000 people a year. The N-methyl-D-aspartate receptor (NMDAR) protein is a major target of alcohol action in the brain. The Audubon High School SMART (Students Modeling A Research Topic) Team has designed a model of NMDAR using 3D printing technology to investigate structure-function relationships. NMDARs, responsible for multiple cognitive functions, are composed of several domains including, the amino terminal domain, a ligand binding domain, a transmembrane domain, and an intracellular domain. NMDARs bind glutamate, a major excitatory transmitter, transporting signals from neuron to neuron through the synapse. Glutamate binds to NMDAR on the postsynaptic cell, the cell that receives a signal, which then opens the ion channel allowing sodium and calcium to enter and stimulate the cell. Alcohol passes through the blood brain barrier, a filtering mechanism of capillaries in the brain, and binds to specific amino acid side chains in the NMDAR. When alcohol is present, NMDAR’s function is limited because the ion channel gate is restricted from opening. When alcohol binds to sites in the transmembrane domain, it blocks the entry of sodium and calcium into the neuron and hinders synaptic transmission via the NMDAR. Research has shown possibilities for multiple approaches to medically treat alcohol abuse and alcoholism. Understanding the structure-function relationship between NMDAR and alcohol should help us learn how to better manage alcohol abuse and alcoholism.

• Brookfield Academy High School
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Brookfield Academy High School

Comparison of Structure and Mechanism in BoNT/A1 and BoNT/A2: Implications for Therapeutic Applications


Brookfield Academy High School SMART
Team model based on 3BTA.pdb

Students:

• Elizabeth Cinquegrani
• Mark Morris
• Leah Wang
• Harry Kalsi
• Shalini Gundamraj
• Suneri Kothari
• Lena Ding
• Srimayi Mylavarapu
• Alex Dortzbach
• Juliana Vollmer

Teacher:

• Robbyn Tuinstra, Ph.D.

Mentors:

• Madison Zuverink, Ph.D. Candidate, Medical College of Wisconsin, Department of Microbiology and Molecular Genetics
• Joseph T. Barbieri, Ph.D., Medical College of Wisconsin, Department of Microbiology and Molecular Genetics

Project Files:

• Poster
• Model Description Sheet

Abstract:

Botulinum neurotoxin type A (BoNT/A) is a potent neurotoxin, causing muscle paralysis in the host by blocking the release of the neurotransmitter, acetylcholine, from motor neurons associated with skeletal muscle. Despite this toxicity, BoNT/A is used pharmaceutically as a treatment for numerous neurological diseases, including migraines, dystonias, and as an anti-wrinkle agent in cosmetic surgery. BoNT/A is one of seven serotypes of botulinum (A-G), which, along with tetanus toxin, are produced by several species of Clostridium. All clostridial neurotoxins, such as BoNT/A, are di-chain proteins, consisting of a 50-kDa light chain, the catalytic domain, connected by a disulfide bond to a 100-kDa heavy chain, containing the receptor-binding and translocation domains. BoNT/A intoxication is a multistep process. First, BoNT/A binds to presynaptic nerve endings, through interactions of the receptor-binding domain with the ganglioside, GT1b, and the protein co-receptor, SV2. SV2 is a synaptic vesicle protein that becomes exposed to the neuron cell surface as vesicles fuse with plasma membrane, releasing neurotransmitter into the synapse. BoNT/A then enters the neuron by receptor-mediated endocytosis. Following endocytosis, the synaptic vesicle acidifies, allowing for neurotransmitter uptake, which triggers the translocation domain to insert and transport the catalytic domain into the cytosol. The catalytic domain is a Zn-dependent protease that cleaves SNAP-25, one of three major proteins present in the SNARE complex. The SNARE protein complex is required for the fusion of synaptic vesicles with the neuronal membrane. Cleavage of SNAP-25 inhibits fusion of synaptic vesicles to the plasma membrane to inhibit acetylcholine release and muscle contraction, leading to flaccid paralysis. Brookfield Academy SMART (Students Modeling A Research Topic) Team students modeled BoNT using 3D printing technology, highlighting amino acid residues associated with protease activity in the catalytic domain, and GT1b and SV2 interactions within the receptor binding domain. This model is meant to help understand and communicate structure/function relationships of BoNT/A and promote potentially therapeutic uses of the toxin.

• Brookfield East High School
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Brookfield East High School

C-fos: Got Your Back!


Brookfield East High School SMART
Team model based on 1FOS.pdb

Students:

• J. Allen
• W. Bowers
• D. Horneffer
• A. Jhaveri
• E. Kreger
• S. Lai
• M. Lazar
• M. Liu
• N. Santebennur
• R. Wolff

Teacher:

• Emily Barmantje

Mentors:

• Audra Kramer, M.S., Marquette University, Department of Biomedical Sciences

Project Files:

• Poster
• Model Description Sheet

Abstract:

Climbing the stairs, speed-walking to class, jumping around the room –– all are instinctually effortless. Spinal cord injuries change all of that. When a spinal column injury occurs, severed nerves prevent commands from being sent to parts of the body beyond the injury site, leaving a person with little hope of a full recovery. Our understanding of the mechanisms behind spinal injury rehabilitation is currently very limited. The transcription factor c-fos is an indicator of active neurons, making it possible to assess functional recovery in a rehabilitation program. The increased presence of c-fos within a group of cells’ nuclei can be compared in different animal rehabilitation program groups to determine ideal cells for specific spinal cord injury rehabilitation methods. C-fos works with other transcription factors such as c-jun, binding to DNA specifically on the 5’-TGAGTCA-3’ sequence. For this to occur, c-fos and c-jun dimerize. Studying c-fos can aid in developing more advanced forms of spinal rehabilitation that aim on rewiring neural connections. The Brookfield East SMART (Students Modeling a Research Topic) Team designed a model of c-fos using 3D printing technology. The c-fos model focuses on the coiled-coil at the carboxy-terminal region. Further research of c-fos improves our understanding of tissues with limited regenerative abilities and allows us to utilize c-fos as a tool to assess functional tissue regeneration otherwise thought to be limited.

• Brown Deer High School
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Brown Deer High School

TRPA1 Makes You Feel The PA1N


Brown Deer High School SMART
Team model based on 3J9P.pdb

Students:

• Georgina Foran
• Noah Freuler
• Teylor Harris
• Ashley Higgins
• Justin Johnson
• Isaac Ngui
• Brett Poniewaz
• Gloria Ramos
• Luke Richmond
• Noel Stoehr
• Virginia Tuncel

Teacher:

• David Sampe

Mentors:

• Andy Weyer, Ph.D., DPT, Medical College of Wisconsin, Department of Cell Biology, Neurobiology and Anatomy
• Katherine Zappia, Ph.D. Candidate, Medical College of Wisconsin, Department of Cell Biology, Neurobiology and Anatomy

Project Files:

• Poster
• Model Description Sheet

Abstract:

About 3-4% of people worldwide suffer from chronic pain. The United States spends $60 billion annually treating pain. Current treatments are ineffective; opioids are addictive and lose efficacy while pregabalin, a non-opioid neuropathic pain drug, only works in 30% of patients. Pain receptors (nociceptors) are activated chemically or mechanically. The nociceptor transient receptor potential cation channel, subfamily A, member 1 (TRPA1) is an ion channel located in the membranes of free nerve endings in the skin. TRPA1 is activated by mechanical stretching, and has many active sites where ligands (e.g. tear gas, mustard gas, and wasabi) can bind to open the channel. Once opened, Ca2+ and Na2+ ions pass through, depolarizing the neuron. Structurally, TRPA1 is a tetramer, with each subunit containing several domains. In the pre-S1 domain, ligands bind covalently to the sulfurs at Cys621, Cys641, Cys665, and Lys710. The TRP-like domain opens for ion passage. The ankyrin repeat domain contains 16 recurring sequences of 33 residues, and may be involved with the stretch activation of TRPA1. In domains S1-S6, -helices hold the protein’s shape and contain binding sites for agonists to open the channel and for antagonists, which prevent functioning. One antagonist, A-967079, binds in a pocket around Phe909, forming a wedge to prevent movement and function of TRPA1. Researchers aim to develop a TRPA1 antagonist that will help treat pain sufferers. The Brown Deer SMART (Students Modeling A Research Topic) Team constructed a model of TRPA1 using 3D printing technology to assist researchers in studying its structure and function.

• Cedarburg High School
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Cedarburg High School

Opsin: To See or Not to See


Cedarburg High School SMART
Team model based on 3CAP.pdb

Students:

• Arnholt, Abigail
• Butt, Abigale
• Griffin, Meggie
• Janecek, Ethan
• Kalmer, Isabelle
• Ketelhohn, Lauren
• Levy, Jake
• Minerva, Nicole
• Navarre, Dawson
• Ratayczak, Miranda
• Severe, Micaiah
• Squires, Elizabeth
• Wankowski, Joshua

Teacher:

• Karen Tiffany

Mentors:

• Alison Huckenpahler, Ph.D. Candidate, Medical College of Wisconsin, The Eye Institute

Project Files:

• Poster
• Model Description Sheet

Abstract:

Colorblindness, a genetic disorder affecting millions of people worldwide, is caused by mutations in a retinal protein, opsin. Opsin is a G-protein coupled receptor which binds to light sensitive retinal. When light enters the cell, the retinal isomerizes from the cis form to the trans form, and opsin is activated; nerves then signal the brain. The opsin complex, sensitive to specific wavelengths of light, is identified by the wavelength that activates it; long (L), middle (M), or short (S). Mutations in opsin may lead to visual problems, including the inability to distinguish between red and green. The Cedarburg SMART (Students Modeling A Research Topic) Team has used 3D printing technology to construct a model of opsin which contains two monomers consisting of several helices that are stabilized by interactions between Lys231-Glu247 and Tyr223-Arg135. Two openings in opsin can be found in the retinal-binding pocket; one allows the cis form of retinal to enter and bind opsin, while another between allows the trans form to exit opsin. Common forms of colorblindness are characterized by mutations in amino acid residues. Three specific mutations responsible for the common red-green form of colorblindness, identified by using the single letter amino acid codes LIAVA, LIAVS, and LVAVA, involve the amino acids at positions 153, 171, 174, 178 and 180. These residues are particularly important for differentiating between M cone opsin and L cone opsin. Because the effect of different opsin mutations on the cell is unknown, a major research focus is to determine whether these mutations can be overcome to restore spectral sensitivity in colorblind people.

• Cudahy High School
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Cudahy High School

Whaddya Mean Ending Antibiotic Resistance: S. wadayamensis May Hold Answers


Cudahy High School SMART
Team model based on 3CAP.pdb

Students:

• Andrew Kressin
• Kaylee Day
• Emily Bahling
• Samantha Brzezinski
• Kaycee Valine
• Maddy Acherman
• Lauren Ligocki
• Cori Windsor
• Jason Hauk
• Madeline Romfoe
• Cody Broeckel
• Alyssa Sims
• Katherine MacDonald
• Ramon Rivas
• Idamae Harris
• Nicholas Kueker
• Katelyn Pomianek

Teacher:

• Dan Koslakiewicz
• Dean Billo

Mentors:

• Nicholas R. Silvaggi, Ph.D., University of Milwaukee-Wisconsin, Department of Chemistry and Biochemistry

Project Files:

• Poster
• Model Description Sheet

Abstract:

Antibiotic-resistant bacteria are common and hard to treat. There is potential to create synthetic antibiotics based on natural products like enduracidin and mannopeptimycin to fight drug resistant bacteria like MRSA. MppP, an enzyme from Streptomyces wadayamensis, is required for the biosynthesis of L-enduracididine (L-end), a non-protein forming amino acid building block found in these and other antibiotics. MppP, the first step in the L-end synthesis pathway, functions to add an oxygen atom to the L-arginine substrate, and replace the α-amino group with a ketone to create 4-hydroxy-2-ketoarginine (4HKA). Hydroxylation is accomplished using a pyridoxal-5’-phosphate (PLP) cofactor, covalently bound by Lys221 to the enzyme, also held by Ser91, Asn160, Asp188, and Ser190 in the active site, which is modeled by the Cudahy SMART (Students Modeling A Research Topic) Team using 3D printing technology. During activity, PLP binds an L-arg substrate, held by Arg352, Asp27, and Asp227 as well as Thr12 and Glu15, performing a hydroxylation through which 4-hydroxy-2-ketoarginine is synthesized. The 4HKA product of the MppP-PLP dependent hydroxylation is used in subsequent reactions in the pathway leading to the creation of the amino acid L-end. Thus, MppP is a critical part of a 3-enzyme team that is responsible for making L-end. The L-end will be incorporated into the different antibiotics by other enzymes. The conversion of L-arg to L-end will help researchers in the creation of new synthetic antibiotics to fight superbugs like MRSA.

• Divine Savior Holy Angels High School
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Divine Savior Holy Angels High School

Myobacterium Delirium: Inhibiting Leucine Biosynthesis to Starve M. tuberculosis


Divine Savior Holy Angels High School
SMART Team model based on 4OV4.pdb

Students:

• K Arnold
• M Carrig
• J David
• J Diez
• S Franczak
• E Grogan
• C Halloran
• G Hilbert
• S Michaeel
• C Pfaff
• M Pitts
• T Rose
• L Schauer
• C Scherrer
• T Siy
• S Strandberg
• J Strother

Teacher:

• Stacey Strandberg
• Scott Fleischmann

Mentors:

• Martin St. Maurice, Ph.D., Marquette University, Biological Sciences

Project Files:

• Poster
• Model Description Sheet

Abstract:

The pathogen Mycobacterium tuberculosis represents a deadly threat to the worldwide population, especially poor, developing countries, as it kills approximately 2 million people each year according to the World Health Organization. Because of overuse and increasing resistance to current antibiotics, researchers are working to develop new drugs to more effectively treat tuberculosis. M. tuberculosis alpha-isopropylmalate synthase (IPMS) is a bacterial enzyme that catalyzes the production of leucine, an essential amino acid. When cellular leucine levels are low, the biosynthetic pathway of leucine is initiated by IPMS when three ligands; alpha-ketoisovaleric acid (alpha-KIV), acetyl-CoA which is not included in our model, and Zn2+ interact at IPMS’s active site. IPMS has two distinct structural domains: an N-terminal alpha/beta catalytic domain which includes the active site and a C-terminal regulatory domain that includes the leucine binding site. As leucine levels increase in the organism, its biosynthetic pathway is shut down by leucine binding to an allosteric site in the C-terminal domain of IPMS which inhibits the further production of additional leucine. The protein amino acids tyr554 and ala536 play a role in the interaction with the leucine ligand. The protein amino acids arg80, asp81, his287, his285, and thr254 interact with the alpha KIV. These interactions allow for the production of leucine through the initiation of the biosynthetic pathway of leucine catalyzed by IPMS. Researchers are working to design a competitive inhibitor that would interact at the allosteric leucine binding site and shut down the pathway, thus depriving M. tuberculosis of this essential amino acid. Without the ligands leucine, Zn2+, and KIV the tuberculosis bacteria would die. The Divine Savior Holy Angel High School SMART (Students Modeling A Research Topic) Team modeled IPMS using 3D printing technology to investigate IPMS catalysis and feedback inhibition within the leucine biosynthetic pathway. The development of new drugs specific to M. tuberculosis offers a promising way to overcome the problem of antibiotic resistance and offers new tools to reduce life-threatening tuberculosis infections.

• Greenfield High School
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Greenfield High School

Not-So-Mighty Mitochondria: Neonatal Lethality Due to Drp1 Malfunction


Greenfield High School SMART
Team model based on 4BEJ.pdb

Students:

• Andrew Braatz
• Pratyusha Emkay
• Sarah Goodman
• Cora Libecki
• Melody Ly
• Karen Nakhla
• Zac Osberg
• Zoe Osberg
• Paige Paniagua
• Lorenzo Vasallo

Teacher:

• Julie Fangmann

Mentors:

• Amber Bakkum, Ph.D. Candidate, Medical College of Wisconsin, Department of Biochemistry
• John Egner, Ph.D. Candidate, Medical College of Wisconsin, Department of Biochemistry

Project Files:

• Poster
• Model Description Sheet

Abstract:

Cells require mitochondria to produce cellular energy, allowing work to be done. Defective mitochondrial function can impair proper cell function, even leading to neurodegenerative diseases, such as Parkinson’s and Alzheimer’s disease, and neonatal lethality. The defect stems from imbalances between mitochondrial fission (splitting) and fusion (combining), resulting in abnormal mitochondrial morphology. Dynamin related protein 1 (Drp1) is a GTPase (enzyme that breaks down GTP) that results in fission of mitochondria by forming tubular spirals around the outer mitochondrial membrane in order to split one mitochondrion into two. The Greenfield SMART Team modeled Drp1 using 3D printing technology to investigate its structure. The structure of Drp1 is ordered by the following four components: GTPase Domain (G Domain), Middle Domain, B-Insert, and GTPase effector domain (GED). The G Domain hydrolyzes GTP and interacts with other G Domains on neighboring Drp1s, while the Middle Domain is the primary site of dimerization. The B-Insert regulates Drp1 assembly, and the GED helps activate the G domain. Drp1 in the cytosol is a dimer; when recruited to the outer mitochondrial membrane Drp1 forms an oligomer. The specific amino acids, Met482, Glu490, Asn635, Asp638, Tyr628, and Lys642, help keep the dimer interface together due to salt bridge interactions. A mutation in Drp1, A395D, was identified as important for causing neonatal lethality due to improper assembly of Drp1 on the outer mitochondrial membrane. When Drp1 malfunctions, such as in the A395D mutation, the imbalance of fusion and fission leads to detrimental issues, such as neonatal lethality. Studying Drp1 could prevent unnecessary death and eventually lead to a better understanding of other Drp1-related neurodegenerative diseases.

• Hartford Union High School
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Hartford Union High School

"Bond. . . One Bond": The Biological Blowtorch and Other Reactive Players in CYP17 Catalyzed Production of Androgens


Hartford Union High School SMART
Team model based on 3RUK.pdb

Students:

• Burg, A.
• Diol L.
• Gall, M.
• Kastner, A.
• Kaul, M.
• Kieckhefer, T.
• Schmidt, N.
• Stoellinger, H

Teacher:

• Mark Arnholt

Mentors:

• Piotr Mak, Ph.D., and James Kincaid,Ph.D., Marquette University, Department of Chemistry

Project Files:

• Poster
• Model Description Sheet

Abstract:

Prostate cancer makes up 4.7 percent of all cancer related deaths. The exact cause of prostate cancer is unknown, but researchers have identified the leading risk factors, including excess testosterone in the body. Early treatments to reduce testosterone levels in patients involved surgical procedures. A particular heme-containing enzyme, known as CYP17, converts cholesterol-derived hormones into androgens including testosterone. Fe(III) is a key part as all reactions occur within this heme group. Pharmacological efforts, such as the drug abiraterone, decrease the efficiency of CYP17 catalysis and may present a valid treatment option for prostate cancer patients. Further efforts would be facilitated by gaining a better understanding of the mechanisms of CYP17 in the presence of its natural substrates, 17-OH progesterone and 17-OH pregnenolone. This enzyme generates an androgen precursor by catalyzing two sequential chemical conversions, the second one by an unknown process, which has been difficult to track. Using rapid-freezing, γ-ray exposure and Raman spectroscopy, the key reaction intermediates in this process are trapped and structurally defined. The Hartford Union SMART (Students Modeling A Research Topic) Team modeled the enzyme CYP17A1 with 3-D printing technology. Research efforts involving CYP17 could assist pharmaceutical companies in the development of treatments for prostate cancer.

• Laconia High School
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Laconia High School

Understanding α-Galactosidase A to Improve Fabry Disease Treatment


Laconia High School SMART
Team model based on 3HG5.pdb

Students:

• Allison Opheim
• Alex Wood
• Josie Stahmann
• McKenzie Englund
• Mckayla Johnson
• Carissa Zibolsky
• Ashley Pluim
• Daniel Ihrig

Teacher:

• Josh Demski

Mentors:

• James Miller, M.D. and Ph.D. Candidate, Medical College of Wisconsin, Department of Biochemistry

Project Files:

• Poster
• Model Description Sheet

Abstract:

Fabry disease is a debilitating lysosomal storage disease. Early in life, patients with Fabry disease experience extreme pain, especially in the extremities (acroparesthesias). Patients are eventually at risk of developing kidney disease, heart failure, and strokes, all of which may lead to a premature death. The prevalence of Fabry disease in its severest form is estimated at 1:40,000; however, the prevalence of milder, later-onset forms may be as high as 1:3,600. Fabry disease is caused by mutations in the X chromosomal GLA gene, which encodes the lysosomal enzyme, α-galactosidase A (α-Gal A). When α-Gal A activity is deficient, glycolipid substrates accumulate within lysosomes, leading to cellular, tissue, and organ pathology. To treat Fabry disease, patients are given enzyme replacement therapy (i.e., bi-weekly intravenous infusion of recombinant α-Gal A). Enzyme replacement therapy costs up to $300,000 per patient per year and commonly causes dangerous immune reactions in patients. A more cost-effective and safer treatment is desperately needed. The Laconia SMART (Students Modeling A Research Topic) Team used 3D printing technology to generate a model of ⍺-Gal A. To be trafficked to lysosomes and to optimally degrade glycolipids, ⍺-Gal A must be glycosylated and must dimerize. Therefore, critical residues are highlighted in the model, such as those involved in catalysis (Asp170, Asp231), N-linked glycosylation (Asn139, Asn192, Asn215), and dimerization (Phe273). Disulfide bonds, which stabilize ⍺-Gal A tertiary structure, are also shown. Studying the structure of α-Gal A is critical in the design of a more potent therapy, which has the potential to reduce the cost and immunogenicity of Fabry disease treatment.

• Marquette University High School
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Marquette University High School

Does Hope Lie Between Apoptosis and Necrosis? Effect of Inhibiting NF-κB on Ischemia-Reperfusion-Induced Cell Apoptosis and Necrosis in Cardiomyocytes


Marquette University High School SMART
Team model based on 1VKX.pdb

Students:

• P Ahn
• K Arnhold
• N Cowan
• N Dittrich
• R Foster
• J Gorski
• R Johnson
• H Khalil
• C Kim
• M Malone
• S Mohiuddin
• L Ortega
• J Otten
• M Rivera
• M Rose
• P Rozewicz
• A Sabatino
• T Sargent
• J Smith
• D Strom
• J Strom
• B Tsuji
• J Yamat
• N Yorke

Teacher:

• Carl Kaiser
• Keith Klestinski

Mentors:

• Judy Maloney, Ph.D., Marquette University, Department of Biomedical Sciences

Project Files:

• Poster
• Model Description Sheet

Abstract:

Cardiovascular disease and its complications are the leading cause of morbidity and mortality in the United States. A myocardial infarction (MI) is caused by a blood clot in a coronary artery and results in loss of blood flow to the heart (ischemia). To prevent necrosis or cell death of heart tissue, ischemia is treated with reperfusion therapy, in which blood flow is restored. Reperfusion therapy paradoxically causes damage to the heart muscle cells via the activation of Nuclear Factor Kappa Beta (NFκB) which can trigger apoptosis or programed cell death, or via the generation of reactive oxygen species and subsequently further necrosis. The extent to which the transcription factor NFκB promotes cell death or even promotes survival is unknown. However, it is known to be a key inflammatory mediator that coordinates cell homeostasis under bodily stress, as with an MI or ischemia reperfusion (IR) injury. NFκB is complexed with Inhibitor Kappa Beta (IκB) and exists as a larger IκB/NFκB complex within the cytosol of the cell until inflammatory mediators activate an IκB kinase. Phosphorylation of this larger complex separates IκB from NFκB, at which point NFκB translocates to the nucleus of the cell, binds to DNA, and initiates transcription of genes responsible for apoptosis. The Marquette University High School SMART (Students Modeling A Research Topic) Team modeled NFκB, a heterodimer, which, in the heart, is composed of the subunits, p50 and p65, complexed with DNA. To study the effect of NFκB inhibition on IR-induced apoptosis and necrosis, cultured cardiac myocytes received two hours of ischemia, and were reperfused with or without the NFκB inhibitor, N4-[2-(4-phenoxyphenyl)ethyl]-4,6-quinazolinediamine (QNZ). Caspase 3 activation and annexin V staining, measurements of apoptosis, revealed that inhibiting NF-κB caused a decrease in IR-induced apoptosis. Propidium iodide staining, a measurement of cell necrosis, revealed that inhibiting NF-κB caused an increase in IR-induced necrosis. Further studies into understanding the effect of NFκB inhibition on IR injury may help provide novel therapies.

• Messmer High School
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Messmer High School

PTP1B Inhibitors for Type 2 Diabetes Treatment


Messmer High School SMART
Team model based on 3EB1.pdb

Students:

• Amya Dorsey
• Hanh Nguyen
• Brittany Slater
• Tariq Mckinney
• Melissa Anguiano
• Babatunde Otukoya
• April Carmicheal
• Kelly Birmingham

Teacher:

• Mark Zachar
• Justin Spaeth

Mentors:

• George Wilkinson, Ph.D., Concordia University Wisconsin School of Pharmacy

Project Files:

• Poster
• Model Description Sheet

Abstract:

People with diabetes have difficulty regulating their blood sugar leading to the malfunctions of the heart, kidney, nerves, and brain if their blood sugar is too high. Most diabetics use insulin to control their condition. Insulin binds to its surface receptor in muscle and fat cells to trigger removal of sugar from the blood. Protein tyrosine phosphatase 1B (PTP1B) affects blood sugar regulation by dephosphorylating the insulin receptor and reducing its activity. Studying PTP1B can help us understand how its inhibitors can slow down the removal of phosphate from the insulin receptor, affecting the blood sugar regulation process. PTP1B normally functions to remove the phosphate group from the insulin receptor. Since PTP1B ordinarily reduces insulin receptor activity, blocking PTP1B could increase insulin sensitivity. The PTP1B active site has a highly positive binding pocket which binds to the highly negative phosphates on the phosphorylated insulin receptor. Many of the current inhibitors of PTP1B act by binding to this active site. However, these inhibitors have difficulty penetrating the cell membrane because of their formal charge, and are unable to inhibit PTP1B inside cells. LZP25 avoids this issue by not having a formal negative charge, but instead a polar area of similar size to phosphate. Binding to the PTP1B active site pocket (sites Ser216, Ala217, Ile219, Gln262, Gln266), its bulky side groups then prevent a key loop in the enzyme active site from closing. If PTP1B is inhibited in the insulin pathway by a potential drug based on LZP25, people who have type 2 diabetes as a result of insufficient insulin receptor activity could better regulate their blood sugar. If the insulin receptor would signal appropriately, the body’s normal control of blood sugar would improve, preventing problems with the heart, kidney, nerves, and brain. Messmer Catholic High School SMART (Students Modeling A Research Topic) Team has designed a model of PTP1B with LZP25 using 3D printing technology to investigate their structure/function relationships.

• Saint Dominic School
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Saint Dominic School

Modeling the Catalytic Domain of Activated Factor X Coagulation Protein Bound to Apixaban


Saint Dominic School SMART
Team model based on 2P16.pdb

Students:

• Jennifer Austin
• Mia Bando
• Christopher Brzozowski
• Giovanni Farciano
• Caroline Flyke
• Nicholas Hilbert
• Isabella Huschitt
• Thomas Hyde
• Elizabeth Klingsporn
• Janna Lieungh
• Emily Maslowski
• Kaitlyn O’Hair
• Mary Rose Otten
• Isabelle Phan
• Sophia Pittman
• Ryan Reilly
• Alexander Reinbold
• Catherine Simmons
• Michael Sohn
• Emma Urban
• Rachel Vasan

Teacher:

• Donna LaFlamme

Mentors:

• Xiaoang Xing, Ph.D. Candidate, Concordia University Wisconsin School of Pharmacy
• Michael Pickart, Ph.D., Concordia University Wisconsin School of Pharmacy

Project Files:

• Poster
• Model Description Sheet

Abstract:

An estimated 900,000 people a year develop venous blood clots in the United States and 60,000 to 100,000 die as a result. Anticoagulants are used to prevent and treat thrombosis. New oral anticoagulants (NOAC’s), like apixaban (Eliquis) are designed to specifically inhibit blood clotting Factor X. Made in the liver, Factor X acts at the end of both the intrinsic and extrinsic blood clotting cascade. With the help of Factor V, calcium ions, and phospholipids, Factor X cleaves prothrombin, to make thrombin. Thrombin in turn activates fibrinogen, which then forms a mesh of fibrin strands to complete clot formation. Using 3D printing technology, the St. Dominic SMART (Student Modeling a Research Topic) Team modeled the catalytic domain of activated Factor X to investigate how apixaban blocks the active site. The catalytic triad (His57, Asp102, and Ser195) is necessary for Factor X to cleave prothrombin by hydrolysis of a peptide bond, but does not interact directly with apixaban. Trp215, Phe174, and Tyr99 surround the phenyllactam group of apixaban, while Gln192 interacts with its pyrazole ring. Gly216 and Glu146 interact with a scaffold carboxamide and the carboxamide group of apixaban, respectively. Asp189 and Tyr228 are important in positioning the natural substrate. NOAC’s are superior to traditional anticoagulants because older anticoagulants, such as warfarin, had a need for constant blood tests to ensure patients were getting the correct dosage. However, apixaban like other NOAC’s, has no reversal agent in case of emergency. A better understanding of Factor X’s structure could help scientists develop a life-saving antidote.

• Westosha Central High School
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Westosha Central High School

Regulating Jeans with Genes – A Protein Driven Pathway to Appetite Suppression


Westosha Central High School SMART
Team model based on 1BND.pdb

Students:

• John Dietz
• Jared Holloway
• Trevor Millhouse
• Connor Muff
• Victoria Salerno
• Zach Wermeling
• Lucas Wysiatko

Teacher:

• Jonathan Kao

Mentors:

• SuJean Choi, Ph.D., Marquette University, Department of Biomedical Sciences

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the World Health Organization, over 1.9 billion people in the world are overweight. Many of these people are overweight as a direct result of overeating. Obesity could potentially be treated by inducing an anorexigenic response, or loss of appetite. Several neurotransmitters are involved in signaling for appetite suppressing or stimulating responses. BDNF, the brain-derived neurotrophin factor, works as one of many appetite regulators in the ventromedial nucleus (VMN) in the hypothalamus. Injection of BDNF into rat VMN has been shown to drastically reduce appetite, increase metabolism, and ultimately lead to weight loss. Conversely, knockout of BDNF has been shown to lead to overeating and obesity. BDNF has a high affinity for the receptor Trk-B due to neurotrophins having variable binding domains. The Westosha Central SMART (Students Modeling A Research Topic) Team modeled BDNF as it binds to Trk-B. Once bound, transduction sends a cascading signal that can stop feeding behavior. Various signals have been shown to affect BDNF concentration leading to anorexigenic and orexigenic responses. BDNF concentration correlates with increased leptin, a hormone made by adipose tissue, physical activity, and glutamate. Concentrations of BDNF decrease as the neurotransmitter GABA increases. Understanding BDNF production and signaling provides researchers with a better opportunity to control expression and elicit a specific response in an attempt to treat obesity or eating disorders.

2014-2015 SMART Teams

Twenty six schools participated in the local SMART Team program during the 2014-2015 school year. The remote SMART Teams and HHMI SMART Teams also expanded, for a total of over sixty SMART Teams nationwide. Completed local projects are described below.

Download the full 2014-2015 SMART Team Abstract Booklet.

• Audubon High School
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Audubon

Nitrophorin: Binding and Transporting Nitric Oxide


Audubon SMART Team model
based on 1erx.pdb

Students:

• Cruz, I
• Giroux, M
• Olguin, L
• Reyes, M
• Rojas, M
• Zurheide, Z

Teacher:

• Brian Coffey

Mentor:

• Peter Geissinger, Ph.D. and Department Chair, University of Wisconsin Milwaukee, Department of Chemistry and Biochemistry
• Hannah E. Waggie, Ph. D. Candidate, University of Wisconsin Milwaukee, Department of Chemistry and Biochemistry

Project Files:

• Poster
• Model Description Sheet

Abstract:

Blood sucking animals will often carry parasites that will infect millions of people each year, resulting in deterioration and sometimes death. When a parasite like the Kissing bug probes its host, it releases salivary proteins that may initiate a variety of allergic reactions in humans. These reactions can be moderate-to-severe, however they can also be life threatening if you don’t realize you have been bitten. Some blood sucking insects have salivary nitrovasodilators called nitrophorin that are unique heme proteins that serve as storage and delivery systems for nitric oxide (NO). Upon a bite from the parasite, the NO is transported to the bloodstream where it is released to bind with soluble guanylate synthase (sGC) which results in vasodilation and blocks blood coagulation. An additional function of nitrophorin, is the uptake of histimine to prevent the immune system from attacking the area. These two mechanisms of nitrophorin allow the insect to suck larger volumes of blood than it could otherwise. The NO is carried in the insect's saliva, where it is at a pH of 5.0 until it is released in the host at the pH level of 7. Nitrophorin binds and transports NO, binding leads to changes in the protein, which prevent binding with other diatomic molecules such as O2 and ensures delivery of NO at the appropriate time and location. NO binds in a linear geometry with iron at the center. Upon binding the distal pocket is buried, residues shifted toward the distal pocket allow Leucine 130 to pack against the NO molecule. The distal pocket leucines also wrinkle the heme found in nitrophorin's center. The NO is then trapped by AB/GH loops. To further bury the bound NO, Val36 packs against Leu130 and Leu133. The new positions are stabilized through a hydrogen bonding network that involves Asp30, Glu32, Asp35, Asp129, and the N-terminus.

• Brookfield Academy Upper School
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Brookfield Academy Upper School

Modeling the N-Terminal Domain of Cystathionine β-Synthase to Identify Mutations Correlated with Homocystinuria


Brookfield Academy Upper School
SMART Team model based on 1JBQ.pdb

Students:

• Ding, L
• Gundamraj, S
• Kaur, T
• Kothari, S
• Lenz, E
• Lo, C
• Morris, M
• Morris, M
• Mylavarapu, S
• Wang, L

Teacher:

• Robbyn Tuinstra

Mentor:

• Noah Leigh
• Ramani Ramchandran, Ph.D

Project Files:

• Poster
• Model Description Sheet

Abstract:

Nitrogen and oxygen are two components of the air we breathe. Bonded together as nitric oxide, they are an important signaling molecule that is involved in numerous physiological processes including the protein S-nitrosylation. The human body cannot function without this effective process, but if the regulation of this process breaks down, it can lead to common diseases such as Parkinson's and Alzheimer's. Irregular nitroslyase and denitrolayse activities may be involved in these diseases, so they are important therapeutic targets. This important process also allows blood vessels to expand, so they can transport more blood and retain more oxygen. The key component, nitric oxide (NO), attaches to glutathione to give the S-nitrosoglutathione molecule (GSNO). The NO from the GSNO then travels to a specific cysteine in a protein, which can affect the properties of that protein. Using 3D printing technology, the Whitefish Bay SMART (Students Modeling A Research Topic) Team is aiding its mentors as they research to figure out why the NO attaches to one cysteine specifically and what exactly this process does. Dr. Timerghazin and Mr. Khomyakov hypothesize that a positive amino acid, such as arginine, catalyzes the NO transfer and causes it to jump to the specific cysteine. Discovering what S-nitrolysation's physiological role as well as why one cysteine is chosen over others could lead to developments in our understanding of certain diseases that are linked to the erratic regulations of S-nitrolysation in the human body.

• Brookfield Central High School
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Brookfield Central High School

ACEing Radiation Protection: The Role of ACE Inhibitors in Mitigation of Radiation Damage


Brookfield Central High School
SMART Team model based on 1O86.pdb

Students:

• Czechowski, M
• El-Meanawy, A
• Gao, J
• Hubler, J
• Iqbal, T
• Jella, T
• Kim, E
• Komandur, R
• Li, C
• Nicoll, S
• Shereen, H
• Yan, Z
• Zheng, A

Teacher:

• Ms. Louise Thompson

Mentor:

• Meetha Medhora, Ph.D, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

In 2001, the United States suffered a major terrorist attack that took the lives of thousands. There is a small, but real, risk of radiological attack or nuclear accident in the future. In addition, exposure of normal tissue to radiation poses a risk to cancer patients undergoing radiotherapy, as radiation induces the production of collagen. Grants were provided to our mentor to research ways to mitigate the harmful effects of radiation. Studies on radiation effects on rats have found that increased collagen is found in the interstitial space of the lungs, which limits free exchange of oxygen and carbon dioxide. Angiotensin Converting Enzyme (ACE) converts angiotensin I into angiotensin II, which binds to fibroblast receptors to produce collagen. By inhibiting the ability of ACE to convert angiotensin I into angiotensin II, the fibroblasts cannot produce the same levels of collagen. As a result, oxygen and carbon dioxide are more easily exchanged in the lung after damages from radiation. The beneficial effects of ACE inhibitors on the collagen buildup in the lungs have been observed in rats 7 months after exposure to radiation (Kma et al 2012). Understanding the collagen synthesis pathway by studying ACE and its inhibitors such as the commonly used drug lisinopril, may lead to the production of an efficacious treatment for radiation-induced fibrosis. The Brookfield Central High School SMART (Students Modeling a Research Topic) Team used the PDB file 1O86 to create a 3D model of the protein ACE and investigate the interaction between ACE and the inhibitor lisinopril to better understand its molecular functions.

• Brookfield East High School
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Brookfield East High School

Myosin: The Cause or Solution for Coarctation of the Aorta?


Brookfield East High School SMART
Team model based on 1l84.pdb

Students:

• Davidsoni, B
• Eddinger, J
• Gray-Hoehn, C
• Horneffer, D
• Jhaveri, A
• Kreger, E
• Lazar, M
• Mani, S
• Novak, R
• Selvaraj, A
• Wolff, R
• Zaidat, B

Teacher:

• Emily Barmantje

Mentor:

• Dr. Thomas Eddinger, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

While more than 1 out of every 2,500 babies are born with a coarctation of their dorsal aorta (CoA), very little is actually known about the cause of this disease. It is hypothesized that the motor protein myosin may be one of the main determining factors of this birth defect. Decreased blood flow and high blood pressure above the coarctation are characteristics of CoA which causes the walls of the aorta to thicken. The cells in the thickened wall of the aorta express more nonmuscle (NM) myosin molecules and are less susceptible to relaxation. During normal development, the NM myosin is down regulated and smooth muscle (SM) myosin becomes the prevalent myosin isoform; however, in a person with CoA, this does not occur. The Brookfield East SMART (Students Modeling a Research Topic) Team has designed a model of SM myosin using 3D printing technology. The model focuses on the structure of dephosphorylated (unregulated) SM myosin S1 and S2 regions which interact with actin and generate contraction. The active sites for actin binding and ATP hydrolysis are on the S1 heads. Phosphorylation of myosin light chain 20 that associates with the S1 head regulates its function. When dephosphorylated, the two myosin heads bind to each other, blocking the actin binding sites, thereby preventing acto-myosin interaction and muscle contraction. While hypothesized to be involved in CoA, increased understanding of SM myosin may also help advance knowledge in other areas of SM research, possibly leading to cures for many other diseases including asthma and various digestive disorders.

• Brown Deer High School
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Brown Deer High School

Human Argonaute-2: For All Your RNA Slicing Needs


Brown Deer High School SMART
Team model based on 4F3T.pdb

Students:

• Bruss, E
• Davis, T.J.
• Hermsen, J
• Johnson, J
• Laughlin, R
• Lucré, M
• Marable, C
• Poniewaz, B
• Tuncel, V
• Wade, G
• Weeden, M

Teacher:

• David Sampe

Mentor:

• Mark McNally, Ph.D., Medical College of Wisconsin, Microbiology and Molecular Genetics

Project Files:

• Poster
• Model Description Sheet

Abstract:

Human cells have the remarkable capability to regulate protein production by degrading target mRNA by two pathways: RNA interference (RNAi) and micro RNA (miRNA). Central to these pathways is the protein Argonaute-2 (Ago-2). In the RNAi pathway, small RNAs derived from viruses are used by Ago-2 to slice virus mRNA, protecting the cells from infection. In the miRNA pathway, Ago-2 utilizes naturally occurring miRNA to slice cellular mRNAs to control protein production. Ago-2 works by binding small (~22 nucleotide) regulatory RNAs (siRNA and miRNA) to target mRNA by base pairing. Ago-2 attaches to the phosphate backbone of the regulatory RNA, that guides Ago-2 to the target RNA. The RNase domain of Ago-2 (containing His807, Asp669, Asp597, and Glu637 in its active site) then “slices” the target to initiate degradation. Scientists can reduce the level of disease-causing proteins (for example, in breast cancer) using the siRNA pathway. Determining the structure of Ago-2 allowed researchers to understand how this enzyme functions in the siRNA/miRNA pathways. The Brown Deer High School SMART (Students Modeling A Research Topic) Team has designed a model of Ago-2 using 3D printing technology to investigate its structure-function relationship. SMART Team programs are supported by a grant from NIH-CTSA.

• Cedarburg High School
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Cedarburg High School

The Protein: Vertebrae Fit to a T


Cedarburg High School SMART
Team model based on 1XBR.pdb

Students:

• Anderson, N
• Arnholt, A
• Baumgartner, I
• Butt, A
• DeBuhr, O
• Dyke, S
• Griffin, M
• Hu, J
• Janecek, E
• Kalmer, I
• Ketelhohn, L
• Lawniczak, J
• Minerva, N
• Naas, A
• Roddy, M
• Satchie, A
• Squires, E
• Tiffany, K
• Wandsnider, M
• Wankowski, J
• Wilde, A
• Zietlow, E

Teacher:

• Karen Tiffany

Mentor:

• Michael A. Pickart, Ph.D. Concordia University Wisconsin, School of Pharmacy

Project Files:

• Poster
• Model Description Sheet

Abstract:

Congenital vertebral malformations (CVMs) comprise a group of spinal abnormalities that include alterations in vertebral shape or number. Evidence suggests CVMs have a genetic link, possibly resulting from mutations in multiple genes. One candidate gene is T. T protein, a transcription factor found in a variety of animals including humans, is essential for correct embryonic development and guides the development of bone and cartilage from embryonic mesodermal tissue. T protein accumulates in the nuclei of notochord cells, interacts with DNA at specific genes, and acts as a genetic switch to activate the genes. T protein binds to the major and minor grooves of DNA as a dimer. Mutations in T (turning “off” the T protein switch) are hypothesized to result in defects in spinal development. The Cedarburg SMART (Students Modeling A Research Topic) Team has designed a partial model of T protein using 3D printing technology to investigate its structure-function relationship, focusing primarily on the residues important for dimerization of T (Pro125, Asp126, and Pro128) and for binding DNA (Arg67). A 3D model could indicate how the location of the mutations may impact the function of T. T could consequently be a potential target for the development of treatment or prevention options. Program supported by a grant from NIH-CTSA.

• Cudahy High School
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Cudahy High School

Think Pink: The Role of Cytochrome Aromatase in Estrogen Production and Breast Cancer Risk P45


Cudahy High School SMART Team
model based on 4KQ8.pdb

Students:

• Bahling, E
• Broeckel, C
• Broeckel, P
• Brzezinski, S
• Bueno, J
• Day, K
• Hauk, J
• Ligocki, L
• MacDonald, K
• Rivas, R
• Tolbert, K
• Valine, K
• Windsor, C

Teacher:

• Dan Koslakiewicz
• Dean Billo

Mentor:

• Piotr Mak, Ph.D., James Kincaid, Ph.D.,Marquette University, Department of Chemistry

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the American Cancer Society (2012), postmenopausal women with high levels of endogenous hormones have about twice the risk of developing cancer compared to women with the lowest levels. A key protein for estrogen biosynthesis from androstenedione (AD), and possibly linked to development of breast cancer, is cytochrome P450 aromatase (CYP19A1) found in adipose breast tissue. CYP19A1 converts AD to an aromatic C18 estrone through two consecutive hydroxylations at the C19 methyl group and catalyzing a third lyase step, culminating in cleavage of the C10−C19 bond of the C19-aldehyde, with concurrent aromatization of the A ring of the steroid framework. AD is attracted to the active site by Arg192, Asp309, and Glu483. A heme group, bound in the CYP19A1 active site by Cys437, is responsible for these 3 oxidation steps. The key residues were modeled by the Cudahy SMART (Students Modeling A Research Topic) Team using 3D printing technology. The heme group binds molecular oxygen and then forms strong oxidizing intermediates that achieve these difficult oxidation reactions. The resonance Raman technique provides detailed structural insight into these important but unstable heme intermediates. Gaining an understanding of the reaction mechanism of CYP19A1 is important. If it can be learned how CYP19A1 functions, a suppression treatment to disable local estrogen production in breast adipose tissue by CYP19A1 could be developed by scientists to control estrogen levels, possibly reducing tumor growth or diminishing the risk of development of breast cancer.

• Divine Savior Holy Angels High School
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Divine Savior Holy Angels High School

Modeling TRPV1, a Detector of Thermal and Chemical Stimuli, Producing Pain: No Capsaicin Sensation


Divine Savior Holy Angels High School
SMART Team model based on 3J5R.pdb

Students:

• Ahmad, A
• Ahmad, Y
• Barrett, E
• Carrig, M
• David,J
• Dzwierzynski, J
• Feller, C
• Gottfried, S
• Hairston, A
• Rooney, C
• Ryan, R
• Scherrer, C
• Schauer, E
• Siy, T
• Soczka, S
• Thew, M
• Zagloul, M

Teacher:

• Stacey Strandberg
• Scott Fleischmann

Mentor:

• Andy Weyer, DPT, Ph.D. Candidate Medical College of Wisconsin, Department of Cell Biology, Neurobiology and Anatomy
• Katherine Zappia, Ph.D. Candidate, Medical College of Wisconsin, Department of Cell Biology, Neurobiology and Anatomy

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the Institute of Medicine, 100 million Americans suffer from chronic pain every year and the US spends over $500 billion trying to treat them. Pain begins as a stimulus that is detected by nociceptors, which are nerve fibers responsible for the detection of noxious mechanical, thermal, or chemical stimuli that give rise to pain sensations. These nociceptors transmit pain signals from the periphery to neurons in the spinal cord and brain. The Transient Receptor Potential Vanilloid 1 (TRPV1) is a nociceptive ion channel activated by capsaicin (the spicy component of hot peppers), heat, and endogenous pain molecules. Therefore, creating an inhibitor that partially blocks TRPV1 could treat chronic pain. The amino acids in the active site of TRPV1 are Y511, S512, M547, and T550. In addition, E600 controls the selectivity filter at the top gate of the channel and the hydrophobic seal mediated through I679 controls the lower gate. When capsaicin binds to the channel, a conformational change occurs that pulls the I679s on each subunit away from each other, opening up the lower gate. Understanding how activation of TRPV1 occurs may lead to the discovery of novel inhibitors of TRPV1 to help treat those suffering from chronic pain and reduce healthcare spending. The Divine Savior Holy Angels SMART (Students Modeling A Research Topic) Team modeled TRPV1 in a partially activated state using 3D printing technology. Program supported by a grant from NIH-CTSA.

• Grafton High School
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Grafton High School

CI-MPR: The Lysosomal Enzyme Receiving Superstar


Grafton High School SMART Team
model based on 2KVA.pdb

Students:

• Ahrenhoerster, R
• Amenda, A
• Bolker, E
• Cassel, B
• Lichosik, C
• Milliken, R
• Mosin, A
• Pavelic, N
• Perry, A
• Weber, H
• Zimmerman, S

Teacher:

• Dan Goetz
• Fran Grant

Mentor:

• James Miller, MD/PhD Candidate Medical College of Wisconsin, Department of Biochemistry

Project Files:

• Poster
• Model Description Sheet

Abstract:

Fabry disease is X-linked and occurs from a deficiency of α-galactosidase A, a lysosomal enzyme that normally degrades the ganglioside globotriaosylceramide (Gb3). Lysosomal accumulation of Gb3 results in cardiovascular, renal, and neurological pathologies, and hemizygous males with Fabry disease tend to have the most severe presentations. The cation-independent mannose 6-phosphate receptor (CI-MPR) recognizes lysosomal enzymes bearing a mannose 6-phosphate (M6P) tag via the amino acids Gln644, Arg687, Glu709, and Tyr714 in its fifth domain, and transports these enzymes from the trans-Golgi network to the lysosome. Four out of CI-MPR’s 15 domains are able to bind M6P or M6P conjugated to N-acetylglucosamine. CI-MPR is also present at the cell surface, and this localization can be exploited to deliver exogenous M6P-tagged biomolecules (i.e., α-galactosidase A) to the lysosome. Intravenous enzyme replacement therapy (ERT) for Fabry disease is extremely expensive, inefficient, and immunogenic. Determining the 3-D structure of CI-MPR is crucial in improving the efficiency of Fabry ERT because this knowledge will allow for the rational design of recombinant α-galactosidase A with optimally placed M6P moieties. The Grafton SMART (Students Modeling A Research Topic) Team will create a physical model of CI-MPR domain 5 using 3-D printing technology, which is made possible by a grant from NIH-CTSA. Further structural studies of CI-MPR will not only lead to a reduction in ERT cost, but will also improve the lives of those suffering from Fabry disease.

• Greenfield High School
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Greenfield High School

Hungry Like PACAP Man- Role of PACAP and PACAP-36 in Eating Behaviors


Greenfield High School SMART Team
model based on 1GEA.pdb and 2JOD.pdb.

Students:

• Alphin, D
• Braatz, A
• Cavins, K
• Deleon-Camacho, F
• Emkay, P
• Granlund, L
• Groth, E
• Kelly, K
• Piotrowski, J
• Shaik, T
• Wallner, J

Teacher:

• Julie Fangmann
• Drew Rochont

Mentor:

• SuJean Choi, PhD, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the CDC, 34.9% of United States adults are obese, which is linked to premature death, heart disease, cancer, respiratory disorders, fertility problems, Type 2 diabetes, and stroke. Over- and under-eating are related to brain chemistry. A 38 amino acid peptide hormone in the hypothalamus, called pituitary adenylate cyclase-activating peptide (PACAP), may be linked to eating disorders. PACAP binds to PACAP type 1 receptor (PAC1R), a G-protein coupled receptor. Seven hydrophobic transmembrane (TM) domains hold PAC1R in hypothalamic cell membranes. PAC1R’s extracellular domain (ECD) contains a ligand binding site. PAC1R’s many negative residues attract PACAP’s many positive ECD residues. PACAP’s V19, K20, and L27 affect PACAP binding to PAC1R. K20 forms a possible salt bridge with PAC1R’s G104, allowing PACAP to align parallel to PAC1R so PACAP’s N-terminus interacts with PAC1R’s TM domains. This activates PAC1R, sending a signal inside the cell. Too much PACAP may cause a person to stop eating and lead to eating disorders. PACAP6-38 is an antagonist formed when a protease removes the first five PACAP residues. When PACAP6-38 binds to PAC1R, eating increases, possibly leading to obesity. SuJean Choi, PhD wants to determine how ratios of PACAP and PACA6-38 are regulated. The Greenfield SMART (Students Modeling A Research Topic) Team modeled PAC1R’s ECD and its two ligands, PACAP and PACAP6-38, using 3D printing technology to investigate their relationships. Studying PACAP and PACAP6-38 regulation and brain chemistry involved in eating behaviors could improve people’s lives and decrease obesity-related US medical costs. Program supported by a grant from NIH-CTSA.

• Hartford Union High School
X

Hartford Union High School

Not So Hot Rods: Mutations in Rhodopsin Kinase in Regards to Oguchi Disease


Hartford Union High School SMART
Team model based on 3C51.pdb.

Students:

• Czerniak, C
• Daley, S
• Bade, J
• Kellicut, A
• Semler, L
• Krupski, L
• Killoren, J
• Wilkins, C

Teacher:

• Mr. Mark Arnholt

Mentor:

• Melissa Wilk, Advanced Ocular Imaging Program at the Eye Institute, Department of Ophthalmology at the Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

The average person’s eyes adapt to darkness within minutes. For those with Oguchi’s disease, adaptation can be slowed to several hours. Oguchi disease is an autosomal recessive disorder that results in greatly slowed phototransduction. Phototransduction is a cascade reaction beginning with a photon activating rhodopsin in the rod and leading to hyperpolarization of the cell. Oguchi disease is caused by mutations in rhodopsin kinase which prevent the phosphorylation of rhodopsin, lowering rhodopsin’s affinity for arrestin. This reduced ability to bind arrestin decreases the speed in which rhodopsin is deactivated and prepped to reactivate. After a long period in a dark environment, the rhodopsin is eventually deactivated by arrestin, allowing it to be recycled. The Hartford Union High School SMART (Students Modelling a Research Topic) Team has designed a model of rhodopsin kinase to investigate its structure-function relationship. Oguchi disease can be caused by two different mutations in rhodopsin kinase: large deletion or point mutation. In our 3D model, we will highlight the complete deletion of exon five, the partial deletion at the C-terminus, and point mutations in the catalytic domain (Val380Asp and Pro391His) that cause Oguchi disease. Understanding the structure-function relationships of rhodopsin kinase could shed more light on night blindness. This program is supported by a grant from NIH and CTSA.

• Kettle Moraine High School
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Kettle Moraine High School

N-methyl-D-aspartate (NMDA) Receptor


Kettle Moraine High School SMART
Team model based on 4PE5.pdb.

Students:

• Czerniak, C
• Daley, S
• Bade, J
• Kellicut, A
• Semler, L
• Krupski, L
• Killoren, J
• Wilkins, C

Teacher:

• Melissa Kirby

Mentor:

• Robert W. Peoples, Ph.D., Marquette University, Department of Biomedical Sciences

Project Files:

• Poster
• Model Description Sheet

Abstract:

Alcohol affects our world more than any other drug. As the third leading preventable cause of death, it is adolescents’ drug of choice, and parental alcoholism impacts the lives of one in four children. Alcohol consumption interferes with communication between neurons in the central nervous system, causing symptoms such as motor incoordination and memory impairment. The NMDA receptor, an ion channel located within neuronal membranes, is a major target upon which alcohol acts. When activated by the signaling molecule glutamate, a gate in its membrane-associated (M) domains opens; allowing calcium and sodium cations to enter the neuron through its ion channel. Alcohol, however, interferes with this process by binding to the M domains, preventing cations from entering the neuron and causing many of the known effects of alcohol consumption. Mutations at positions in the M domains, such as M823 in the GluN2A M4 domain and F636 in the GluN2A M3 domain, have been found to significantly alter alcohol sensitivity; making it less susceptible. The Kettle Moraine High School’s SMART (Students Modeling A Research Topic) Team has designed a model of the NMDA receptor using 3D printing technology to investigate structure-function relationships. Further research on the interactions between alcohol and the NMDA receptor could aid in finding a solution to the abuse of this historically documented and often detrimental drug.

• Laconia High School
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Laconia High School

N-methyl-D-aspartate (NMDA) Receptor


Laconia High School SMART Team
model based on 3XL4.pdb.

Students:

• Garb, A
• Henke, N
• Opheim, A
• Wood, A
• Zibolsky, C

Teacher:

• Jodie Garb

Mentor:

• Jier Huang, Ph. D., Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

The development of clean and renewable energy is critical to partially address the energy crisis and climate issues. Inspired by nature, artificial photosynthesis through water splitting by solar energy conversion is the most attractive approach for the development. The overall water splitting includes two half-catalytic reactions, i. e. hydrogen (HER) and oxygen (OER) evolution reactions. An efficient catalyst is required to perform each of these catalytic reactions. Molecular catalysts that mimic the function of [FeFe] hydrogenase are among the most effective synthetic transition metal complexes known for HER. The Laconia SMART (Students Modeling A Research Topic) Team used 3D printing technology to model the active site of [FeFe] hydrogenase and understand its catalytic function for HER. [FeFe] hydrogenase is an enzyme that catalyzes proton reduction to bind hydrogen together. Arg265, Lys288, and Lys409 are positively charged residues that line the channel entrance. Lys 188 is at the end of the channel and may help to orient the 2Fe subcluster during hydrogen insertion. The fundamental understanding of the catalytic function of the [FeFe] hydrogenase active site in HER will provide insight into the rational design of efficient catalysts for solar fuel generation. The SMART Team program is supported by a grant from NIH-CTSA.

• Madison West High School
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Madison West High School

N-methyl-D-aspartate (NMDA) Receptor


Madison West High School SMART
Team model based on 4DKL.pdb.

Students:

• Cai, Y
• May, J
• Deng, H
• Luo, T
• Hua, C

Teacher:

• Tricia Windgassen
• Christine Petzold

Mentor:

• Chris Cunningham, Ph.D, School of Pharmacy, Concordia University, Wisconsin

Project Files:

• Poster Not Available
• Model Description Sheet

Abstract:

Opium and its derivatives have been used for centuries to treat severe acute or chronic pain by binding to opioid receptors in the body, causing beneficial effects of analgesic and harmful effects. Their addictiveness has led to several opiates becoming recreational drugs such as opium, morphine, and oxycodone. In addition, people build up tolerance to opiates decreasing their effectiveness over time. The main opioid receptors, µ-opioid receptors (µ-OR), are G-protein coupled receptors (GPCRs) that undergo conformational changes when a ligand such as opium or morphine binds to it, initiating a downstream effect that ultimately relieves pain. If scientists can understand the molecular interactions when drugs bind these receptors, they can begin to develop a drug that binds these receptors to relieve pain without signaling these negative side-effects. The crystal structure of the µ-opioid receptor bound to a morphinan antagonist reveals an unusually large binding pocket, allowing quick binding and many different molecules to bind with it. Residues around the binding site contact the bound molecule differently depending on the molecule. It is believed the triggering of these residues is what affects the person. The Madison West High School SMART (Students Modeling a Research Topic) Team modeled this bound G-protein coupled µ-OR by using Jmol protein modeling software and 3D printing technology to investigate the structure and function relationships of receptor interactions. An understanding of the binding site interactions of µ-OR, along with other structures that capture the active form of this bound receptor, will help researchers start to develop more useful drugs.

• Marquette University High School
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Marquette University High School

Nicotinamide Phosphoribosyltransferase (NAMPT) Inhibition Yields Promising Future Implications


Marquette University High School
SMART Team model based on 4N9D.pdb.

Students:

• Ahn, P
• Arnhold, K
• Cephus, K
• Dittlof, A
• Dittrich, N
• Foster, H
• Hernandez, M
• Johnson, R
• Ortega, L
• Otten, J
• Rivera, M
• Sabatino, T
• Strom, D
• Strom, J
• Tsuji, J
• Yang, N
• Yorke, N

Teacher:

• Mr. Carl Kaiser
• Mr. Keith Klestinski

Mentor:

• Mr. Matthew Waas, Ph.D. Candidate, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Human embryonic stems cells (hESC) and induced pluripotent stem cells (hiPSC), collectively termed human pluripotent stem cells (hPSC), differentiate into any cell type. The creation of hPSC free from potentially tumorigenic pluripotent stems is advantageous for research strategies and necessary for future hPSC-based clinical therapies. The STF-31 molecule inhibits an important metabolic enzyme, NAMPT, providing selective toxicity of hPSC in diverse cell culture conditions. This strategy effectively eliminates potentially tumorigenic cells but spares differentiated progeny. The MUHS SMART (Students Modeling A Research Topic) Team has designed a model of NAMPT bound with STF-31 using 3D printing technology. What makes STF-31 unique as a NAMPT inhibitor is its ability to occupy the protein’s active site and act as a substrate for the enzyme. The pyridine ring of STF-31 is situated between the F193 and Y188 sidechains of NAMPT. The central phenyl ring of STF-31 occupies the tunnel region of NAMPT. Other binding sites between STF-31 and NAMPT include H191, R196, S241, V242, A244, S275, I309, and R311. NAMPT inhibition research will lead towards the development of clinically safe hPSC progeny for human stem cell based therapies, drug development, and toxicity testing. This is supported by a grant from NIH-CTSA.

• Messmer Catholic High School
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Messmer Catholic High School

Allosteric Modulation of CB1 by Pregnenolone


Messmer Catholic High School
SMART Team model.

Students:

• Camacho, A
• Rios, B
• McKinney, T

Teacher:

• Justin Spaeth

Mentor:

• Aaron Miller, Ph.D. Assistant Professor of Physiology at Concordia University

Project Files:

• Poster
• Model Description Sheet

Abstract:

The endocannabinoid system plays a role in diverse conditions such as anxiety, addiction, eating and memory disorders. Endocannabinoids are produced by postsynaptic neurons and activate receptors on presynaptic neurons in order to decrease neurotransmitter release. In the brain, the most important receptor activated by endocannabinoids is cannabinoid receptor type 1 (CB1). Tetrahydrocannabinol (THC), the active ingredient in marijuana, also activates this receptor. THC and similar drugs have therapeutic potential in the treatment of pain, Alzheimer’s disease, anxiety, arthritis, and cancer. A downside to the medicinal use of THC is that it also induces psychotropic effects. Recently, it was discovered that pregnenolone binds to CB1, where it acts as an allosteric modulator that decreases the effects of THC. An allosteric modulator is a molecule that modifies receptor function by binding somewhere other than the active site. Discovery of allosteric modulators is significant because it means that there may be additional ways to target CB1 that have a reduced rate of psychotropic effects. The Messmer SMART (Students Modeling a Research Topic) Team has created a model of CB1 bound to pregnenolone using 3D printing technology. Our model highlights the amino acids E133 and R409, which form hydrogen bonds with pregnenolone and are required for its binding to the allosteric site of CB1. Studying the interaction between CB1 and pregnenolone will allow for a greater understanding of the interaction between synaptic function and pregnenolone levels as well as the design of additional allosteric modulators for testing as therapeutics. This program is supported by a grant from NIH-CTSA.

• Milwaukee Academy of Science
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Milwaukee Academy of Science

Allosteric Modulation of CB1 by Pregnenolone


Milwaukee Academy of Science
SMART Team model based on 1PTO.pdb.

Students:

• Barnes, L
• Duadon, B
• Johnson, S
• McCotry, V
• Nash, T
• Roby, J
• Taylor, R
• Tyra, Q
• Washington, D
• Washington, J

Teacher:

• Kevin Paprocki
• Tyler Reed

Mentor:

• Joseph Barbieri, Ph.D. Medical College of Wisconsin, Department of Microbiology and Molecular Genetics
• Faith Blum, Ph.D. Medical College of Wisconsin, Department of Microbiology and Molecular Genetics

Project Files:

• Poster
• Model Description Sheet

Abstract:

AIDS and Ebola are seen as some of the most frightening diseases on the planet; however, a more infectious disease is on the rise. Pertussis, known as whooping cough, has over a 90% transmission rate between members of the same household. More frightening than its virulence and preventability is its role in infant mortality. Pertussis is a respiratory disease that causes a violently uncontrollable cough and breathing difficulty. Even with immunization, over 48.5 million infections occurred in 2012, with infants accounting for 83% of deaths. Pertussis is caused by a species of bacteria called Bordetella pertussis (Bp), which is an airborne, aerobic coccobacillus pathogenic only to humans. Bp infects humans by colonizing respiratory epithelium and producing tracheal cytotoxin, which prevents the cilia from clearing debris from the respiratory tract. Bp then produces pertussis toxin (PT), which binds to a cell-membrane receptor. The Milwaukee Academy of Science SMART (Students Modeling A Research Topic) Team modeled the pertussis toxin using 3D printing technology. PT is an AB5 toxin, and exhibits ADP-ribosyltransferase activity. The toxin is endocytosed into respiratory epithelia and traffics through the endocytic pathway through the Golgi complex into the endoplasmic reticulum. The S1 subunit translocates into the cytosol, where the S1 subunit ADP-ribosylates a Gɑi protein. This prevents normal migration of leukocytes to the site of infection. This leukocyte immobility contributes to the longevity of symptoms and overall lethality. A greater understanding of this toxin will inevitably result in a more effective and enduring vaccination protocol than currently implemented.

• Monona Grove High School
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Monona Grove High School

RecQ DNA Helicases in Human Disease


Monona Grove High School SMART
Team model based on CsRecQ.pdb.

Students:

• Hanson, B

Teacher:

• Sarah Wright

Mentor:

• James Keck, PhD, Department of BioMolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI

Project Files:

• Poster not avaliable
• Model Description Sheet

Abstract:

Many cellular processes are regulated and maintained through genetic recombination. RecQ DNA helicases form , a very important family of enzymes that drives this activity in cells. Recombination is initiated by RecQ unwinding paired double-stranded DNA using ATP hydrolysis as the chemical fuel during this process. In addition to recombination, RecQ helicases also have ties to cellular aging, gene silencing, and DNA repair, and organisms that lack RecQ due to mutations are plagued by genomic instability and a predisposition to cancer. Three heritable human diseases have been linked to mutations in genes that encode RecQ helicases. Mutations in these genes, WRN gene in Werner Syndrome, BLM gene in Bloom's Syndrome, and RECQ4 in Rothmund-Thomson Syndrome, can give the rise to diseases of premature aging, cancer, type 2 diabetes, osteoporosis and atherosclerosis. Over the past decade, a considerable amount of research has focused on the cellular functions, genomic regulation, and maintenance of RecQ helicases. Our study has focused on high-resolution X-ray crystal structures of the core region shared among RecQ helicases and on how mutations within this domain could be linked to human diseases. We also discuss how researchers think that RecQ helicases cooperate with another enzyme, topoisomerase, to function in genomic maintenance.

• Saint Dominic School
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Saint Dominic School

Hepcidin: The Key Regulator of Iron in the Blood


Saint Dominic School SMART
Team model based on 2KEF.pdb.

Students:

• Jessup, E
• Kowalik, D
• Lois, C
• Larcheid, A
• Larcheid, L
• Maslowski, S
• Pittman, E
• Platz, J
• Puccetti, M
• Shecterle, T
• Simson, N
• Wenger, E

Teacher:

• Donna LaFlamme

Mentor:

• Matthew S. Karafin M.D, Medical College of Wisconsin, Blood Center of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Hepcidin, a peptide hormone, is the key regulator of plasma iron levels in humans, and is known to play an important role in various human diseases, such as hemochromatosis. Hepcidin inhibits the entry of iron into circulation by binding to ferroportin, a trans-membrane iron export channel found primarily on enterocytes, hepatocytes and macrophages where iron is sequestered. When hepcidin binds to ferroportin, both are drawn into the cell by endocytosis and degraded in a lysosome. When hepcidin levels increase, ferroportin levels on cells decrease and iron cannot be released from cells into the blood. Hepcidin production by the liver is affected by erythropoiesis in bone marrow, blood oxygenation, certain inflammatory cytokines, intracellular iron storage, and plasma transferrin. The St. Dominic SMART Team (Students Modeling A Research Topic) has modeled hepcidin using 3D printing technology. Hepcidin is a 25 amino acid, β hairpin containing one beta sheet, and four disulfide bonds (Cys1-Cys8, Cys3-Cys6, Cys2-Cys4, and Cys5-Cys7). Removal of the first five amino acids of hepcidin strongly decreases its ability to bind ferroportin and trigger endocytosis. Tests are currently commercially available for measuring both urine and plasma hepcidin concentrations, and research into their clinical applications is underway. Hepcidin is not currently being used to treat iron disorders, but hepcidin agonists and antagonists are being developed and investigated for possible future therapeutic use.

• Saint Joan Antida High School
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Saint Joan Antida High School

Thrombin: Nature’s Band Aid


Saint Joan Antida High School
SMART Team model based on 1PPB.pdb.

Students:

• Allen, J. D
• Allen, J.T
• Alvarez, A
• Garcia, F
• Kopacz, S
• Ray, A

Teacher:

• Emily Harrington Vruwink

Mentor:

• Dr. Anja Blecking, Ph.D. Candidate University of Wisconsin-Milwaukee, Department of Chemistry & Biochemistry
• Megan Josephine Corby, Ph.D. Candidate University of Wisconsin-Milwaukee, Department of Chemistry & Biochemistry

Project Files:

• Poster
• Model Description Sheet

Abstract:

Normal blood flow plays an essential role in many life processes. If an abrasion to the blood vessels disrupts normal blood flow. A protein called thrombin acts as a signaling cascade that forms a clot and fixes the abrasion. Thrombin is the central molecule in hemostasis, which is the process of stopping blood flow. When blood vessels are cut open, Factor VII – a protein that helps the process of blood clotting – is released and comes into contact with tissue factor found on cells. When this happens, factors V, IX, and X are activate. Collectively, these factors trigger the signaling cascade that results in the activation of thrombin. Thrombin is circulated in plasma as prothrombin, which is the inactive state of thrombin. Thrombin catalyzes the conversion of fibrinogen into fibrin, which then constructs an insoluble network of fibers that eventually dries to form a scab. The Saint Joan Antida SMART (Students Modeling a Research Topic) Team has modeled thrombin using 3D printing technology. Thrombin is a serine protease composed of two chains. The active site amino acids involved in cleaving the peptide bonds in fibrinogen are His-57, Asp-102, and Ser-195. Defective thrombin can either lead to too few or too many blood clots. Too little clotting could result in a disorder called hemophilia; too much could result in deep vein thrombosis (DVT) – a blood clot in major leg veins. DVT could lead to less blood flow to the heart, causing a stroke or heart attack. Research continues on the role thrombin plans in the progression of hemostasis and restoring the balance of homeostasis.

• Valders High School
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Valders High School

Gonads Go Mad and the Effects of Neonatal Stress on Hypothalmic-Pituitary-Gonadal Function in Rats


Valders High School SMART
Team model based on 1GOT.pdb.

Students:

• Bratz, V
• Christianson, A
• De Bruijin, S
• Evans, E
• Green, M
• Howard, P
• Leitner, S
• Schneider, K
• Ulness, M
• Wenzel, J

Teacher:

• Joe Kinscher

Mentor:

• Karin Bondensteiner, Ph.D., University of Wisconsin Stevens Point, Professor of Biology

Project Files:

• Poster
• Model Description Sheet

Abstract:

Neonatal stress may permanently alter hypothalamic-pituitary-gonadal function and accelerate the onset of puberty in female rats. Heterotrimeric G proteins, found coupled to membrane-bound receptors on the inside of cell membranes, form a central link in cell signaling. Inactive G proteins bind guanosine diphosphate (GDP). When a signaling molecule, such as gonadotropin releasing hormone (GnRH), binds to membrane receptors of cells in the anterior pituitary gland, GDP is displaced by GTP (guanosine triphosphate), and the alpha subunit separates from the beta and gamma subunits. The alpha-GTP subunit then triggers a cell signaling cascade. In pituitary gonadotroph cells, this cascade results in the release of follicle stimulating hormone (FSH) and luteinizing hormone (LH). These hormones will cause female gonads (ovaries) to release estrogen and progesterone and, if hypothalamic-pituitary-gonadal function is altered, may trigger early onset of puberty in female rats. The Valders SMART Team modeled a G Protein using 3D printing technology to study structure-function relationships in cell signaling. Hydrophobic amino acids form the switch interface between the alpha subunit and the beta-gamma subunits stabilizing the heterotrimeric G protein. When the alpha subunit binds GTP, Gly199 interacts with the terminal (gamma) phosphate of GTP, and the activated alpha subunit separates from the beta-gamma subunits resulting in cell signal propagation. Understanding how the hypothalamic-pituitary-gonadal axis is influenced by neonatal stress in rats may help scientists to better understand puberty onset in humans.

• Wauwatosa West High School
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Wauwatosa West High School

Opioid Oppression Mu-Opioid Receptor (µOR)- a G Protein- Coupled Receptor (GPCR)


Wauwatosa West High School SMART
Team model based on 4DKL.pdb.

Students:

• Bonner, P
• Fendos, A
• Hassan, Z
• Ho, A
• Ho, M
• Kaine, J
• Ng, S
• Monty, C
• Sear, R
• Zielonka, A

Teacher:

• Mary A. Haasch

Mentor:

• Christopher Cunningham, Ph.D. Concordia University Wisconsin - School of Pharmacy

Project Files:

• Poster
• Model Description Sheet

Abstract:

Opioid abuse is now a leading cause of accidental death in North America; yet, opioids remain the most prescribed drugs in the United States. Opioid drugs are powerful painkillers, but their adverse side effects — addiction, tolerance, and extreme constipation — severely limit their medical use. The mu-opioid receptor (μOR), is one of the G protein-coupled receptors (GPCR) traversing the cell membranes of primarily neuronal cells in the brain and spinal cord. μOR is embedded in the membrane of presynaptic cells in the brain. Normally, endorphins (such as beta-endorphins, which are classed as opiates) bind to the receptor, which results in a release of ions and a cascade to effector proteins (such as ion channels), ultimately leading to various reward circuit oriented behaviors and analgesic effects. Other opiates (natural derivatives, e.g. morphine), opioids (synthetic derivatives), and similar compounds instead bind to μOR, which prevents normal endorphin-binding activity. μOR is a single chain protein with 8 helices. Its active site is on the inside of the protein; binding involves 14 residues. Interactions between the other helices, disulfide bond (Cys140-Cys217), and salt bridge (Arg165-Asp164) stabilize the protein structure. Polar bonding between Thr279-Ile256 maintains the protein in the inactive state. Lys233 covalently binds to both morphine (agonist) and beta-FNA-funaltrexamine hydrochloride (antagonist). The Wauwatosa West SMART (Students Modeling a Research Topic) Team used 3D printing technology to study the structure/function relationship of the mu-opioid receptor. Currently, naltrindole partially excites the μ-active site without the loss of effectiveness overtime. Other chemicals need to be investigated that will provide an effective analgesic while eliminating all side effects.

• West Bend High School
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West Bend High School

Botulinum Neurotoxin Serotype A


West Bend High School SMART Team
model based on 2lMA.pdb and 2lMB.pdb

Students:

• Dommisse, L
• Fisher, R
• Kassin, S
• Miller, L
• Monday, R
• Richards, E
• Vachuska, K

Teacher:

• Judy Birschbach

Mentor:

• Nicholas Silvaggi, Ph.D. University of Wisconsin-Milwaukee, Department of Chemistry and Biochemistry

Project Files:

• Poster
• Model Description Sheet

Abstract:

USATODAY reports that the most toxic biological compound is used by 5.6 million people annually. The bacterium, Clostridium botulinum makes a toxin called botulinum neurotoxin (BoNT) (or BotoxA). Signs say BoNT may remedy ailments, but excess Botox can cause nerve damage and death. It is key to create a drug that can block BoNT’s effects if misused. BoNT enters motor neurons and interrupts nerve impulses, causing paralysis. The toxin consists of a heavy chain that is the targeting infiltration system, and a light chain is the warhead. When the light chain enters a motor neuron, it cleaves SNAP-25 at a Gln-Arg peptide bond, ending the nerve’s ability to release neurotransmitters. Vital for the toxin’s catalysis, key amino acids include His223, His227, and Glu262, which bind the Zn(II) ion. The Glu224 side chain joins in the BoNT catalytic machinery. Asp370 is essential for interacting with the Arg residue in the substrate’s scissile peptide bond. The BoNT/A active site can alter its structure to bind to unlike molecules: arginine and a hydrophobic cinnamic acid derivative. The West Bend SMART (Students Modeling A Research Topic) Team made a model showing how BoNT houses polar and hydrophobic molecules using 3D printing.

• Westosha Central High School
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Westosha Central High School

An Exciting ERα in Breast Cancer Treatment


Westosha Central High School SMART
Team model based on 3ERT.pdb.

Students:

• Alberth, J
• Bielski, N
• Holloway, J
• Katzer, J
• Kirsch, M
• Lawrence, B
• Murphy, M
• Patel, S
• Quist, S
• Reeves, A.J
• Wermeling, Z
• Williams, J
• Wysiatko, L

Teacher:

• Jonathan Kao

Mentor:

• Oleg Brodsky BSc. MBA – Pfizer Inc

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the American Cancer Society, one in eight U.S. women will develop breast cancer in their lifetime. Strikingly, many of these women share a significant genetic commonality. It has been shown that many breast cancer patients test positive for high levels of Estrogen Receptor (ERα), a protein that regulates the differentiation and maintenance of neural, skeletal, cardiovascular, and reproductive tissues in their cells. ERα aids in the process of DNA transcription as a transcription factor. The activation of ERα occurs when a ligand, estradiol, diffuses through the lipid membrane and binds to the active site at the Ligand Binding Domain (LBD) while ERα is in the cytoplasm. Initially the LBD is inhibited by a chaperone protein, which immediately disjoins from ERa to allow estradiol to bind. The LBD is located at amino acid residues 303 to 552 highlighted in the model designed by the Westosha Central High School SMART Team using 3D printing technology. Afterwards, the complex is transported into the nucleus where the DNA Binding Domain (DBD) of the ERa protein binds to DNA and commences gene transcription. An overabundance of ERα leads to excessive transcription which may cause breast cancer. Therefore, in the treatment of breast cancer, inhibiting or degrading ERa is of immediate interest as a therapy.

• Whitefish Bay High School
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Whitefish Bay High School

Modeling the Binding Site of α-bungarotoxin to Nicotinic Acetylcholine Receptors


Whitefish Bay High School SMART
Team model based on 2QC1.pdb.

Students:

• Heo, J
• Joshi, R
• Potter, M
• Shin, M

Teacher:

• Katie Brown
• Paula Krukar

Mentor:

• George Wilkinson, Ph. D., Concordia University Department of Pharmaceutical Sciences

Project Files:

• Poster
• Model Description Sheet

Abstract:

Myasthenia gravis, a disease characterized by muscle fatigue and weakness, affects thirty million people a year. The venom of certain snakes generates a similar phenomenon in its prey, causing paralysis. In both cases, symptoms result from interference with neuromuscular transmission. In normal neuromuscular function, binding to acetylcholine creates changes in nicotinic acetylcholine receptors (nAChRs) that catalyze ion-selective transmembrane pore openings. The resultant ion flux enters the muscle cell via the neuromuscular junction, ultimately inducing movement. The Whitefish Bay High School SMART (Students Modeling A Research Topic) Team used 3D print technology to model the site where snake venom α-bungarotoxin (α-Btx) binds to nAChRs, located in a muscle’s plasma membrane at neuromuscular junction. Binding primarily takes place between the tips of nAChR fingers I and II, which form a mobile region essential for proper binding; and the C-terminal loop of α-Btx, loops A, B, and C; and the carbohydrate chain in the nAchR. The α-Btx residues Y93, Y190, Y198, and R149 are inserted into the aromatic cage of the receptor by R36 and F32 in fing er II of α-Btx. This binding blocks the agonists’ access to the activation site. Thus, α-Btx prevents the opening of ion channels that allow the passage of electrical signals that induce movement. Further study of these ion channels and nAChRs as pharmaceutical targets could lead to medical breakthroughs in diseases such as myasthenia gravis, Parkinson’s, Alzheimer’s, and epilepsy.

• Wisconsin Virtual Learning
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Wisconsin Virtual Learning

Modeling P2X4


Wisconsin Virtual Learning SMART
Team model based on 4DW1.pdb.

Students:

• Wicklund, A
• Minter, C
• Gad, C
• Merkel, E
• Mangiulli, R

Teacher:

• Karen O’Donnell

Mentor:

• Andrew Karls, Ph.D. M.S. Marquette University
• Audra Kramer, M.S. Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

To someone who has excessive P2X4 receptors, simple gestures like hugs could cause unbearable pain. P2X4, a protein receptor located on the membrane of neurons, plays a large role in neuronal communication and pain perception. Ion channels on dendrites, located on one end of a neuron, allow ions to enter, causing an electrical current that continues through the cell. Once a current reaches the axon terminals, neurotransmitters are released to the next neuron, opening more ion channels and allowing transmission of the signal. This relay between neurons causes the perception of pain. In its resting position, P2X4 is closed inhibiting ions to enter the neuron, signaling no pain. In order for the receptor to open, ATP acts as the neurotransmitter attaching to the binding site of P2X4. In some, repeated sensory injury can lead to a need for extra receptors to be produced leading to chronic pain. Current studies are finding ways to block ATP from binding to receptors, keeping the receptor closed. P2X4 consists of 3 units forming the quaternary structure of the protein and 3 binding sites allowing for ATP to attach, opening the structure. Wisconsin Virtual Learning’s SMART (Students Modeling A Research Topic) Team, using 3D printing technology, has modeled an open structure of P2X4, highlighting amino acids Leu 217, Leu 191, Lys 193, Lys 70, Thr 189, and Ile 232 from PDB file 4DW1. With more knowledge of P2X4, scientists can unravel the mystery of chronic pain. This program is supported by a grant from NIH-CTSA.

2013-2014 SMART Teams

Twenty-five schools participated in the local SMART Team program during the 2013-2014 school year. The remote SMART Teams and HHMI SMART Teams also expanded, for a total of over sixty SMART Teams nationwide. Completed local projects are described below.

Download the full 2013-2014 SMART Team Abstract Booklet.

• Audubon High School
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Audubon

Cholera Catastrophe


Audubon SMART Team model based on 1lta.pdb

Students:

• N. Loeffler
• Z. Zurheide
• C. De Leon
• E. Tovar

Teacher:

• Brian Coffey

Mentor:

• Joseph Barbieri, Ph.D., Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the Centers for Disease Control, there are 3-5 million reported cases and 100,000 deaths each year from a diarrheal illness known as cholera. Cholera is caused by an infection of the intestine with the bacterium Vibrio cholerae. The toxin causes rapid and deadly dehydration and electrolyte imbalance in the infected person. Cholera is common in undeveloped countries, but has caused epidemics in all parts of the world. The bacterium spreads through the intake of contaminated food and water and is extremely unlikely to be spread directly from person to person. Vibrio cholerae produces a toxin that is heterodimeric, consisting of A and B subunits. The B subunit consists of five identical protein chains. These five chains are what binds to the surface of the cell and allows the catalytic part of the molecule to enter the cell. Once inside the cell, the catalytic A subunit seeks out the G protein, and attacks. With the G protein now corrupt, the cell becomes confused and sends mass amounts of sodium and water out of the cell. This action causes the flooding of the intestine and ultimately the diarrhea that can lead to deadly dehydration. Although this illness can be fatal, it is surprisingly easily cured. A person can be treated simply by getting rehydrated with clean uncontaminated water to replace the lost electrolytes. Currently there are two oral Cholera vaccines available, but they are only temporary protection. Researchers are working to find more efficient and permanent solutions, but currently the best way to combat cholera is good hygiene.

• Brookfield Academy High School
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Brookfield Academy

Modeling the Alcohol Binding Site of the NMDA Receptor Using the GluA2-receptor Structure


Brookfield Academy SMART Team model based on 3kg2.pdb

Students:

• M. Ali
• S. Gundamraj
• T. Kaur
• S. Morris
• S. Puri
• R. Singh
• V. Singh
• L. Smith-Feinburg
• L. Wang

Teacher:

• Robbyn Tuinstra, Ph.D.

Mentor:

• Robert Peoples, Ph.D., Department of Biomedical Sciences, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the National Institute of Alcohol Abuse and Alcoholism, about 18 million people have an alcohol abuse disorder. Alcohol binds to the N-Methyl-D-aspartate Receptor (NMDA) receptor, inhibiting cognition, short-term memory formation, motor coordination, and overall regular CNS function. The Brookfield Academy SMART (Students Modeling A Research Topic) Team used 3D printing technology to model the alcohol binding site on the NMDA receptor. This receptor is an ion channel in CNS neurons. Binding of the neurotransmitter, glutamate, allows the passage of calcium and sodium ions through the channel, thus controlling multiple intracellular signaling pathways. Alcohol inhibits the gating of the receptor, preventing the flow of ions, leading to the symptoms of intoxication. The NMDA receptor is a heterotetramer, containing two GluN1 and two GluN2A subunits. Alcohol binds to the transmembrane domain of the receptor, interacting with the amino acids Gly638, Phe639, Phe639, Leu819, and Met818 (of subunit GluN1) and Met 823, Phe636, Leu824 and Phe637 (on GluN2A). Site-directed mutagenesis studies have identified the importance of these residues. Mutations in the same position on different subunits can drastically modulate the inhibition of the receptor by alcohol. Further understanding of the NMDA receptor mechanisms could lead to treatment for long-term alcohol abuse.

• Brookfield Central High School
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Brookfield Central

Now You See It: The Role of Ocular Albinishm 1 in Foveal Development


Brookfield Central SMART Team model based on oa1.pdb

Students:

• E. Afreen
• D. Ajjampore
• M. Czechowski
• A. El-Meanawy
• A. Fung, K. Gopal
• J. Hubler
• T. Iqbal
• T. Jella
• R. Karanam
• E. Kim
• R. Komandur
• H. Mogallapalli
• A. Morgan
• E. Nesler
• R. Sachdev
• H. Shereen
• N. Sood
• A. Zheng

Teacher:

• Louise Thompson

Mentor:

• Joseph Carroll, Ph.D., Department of Ophthalmology, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

One in every 60,000 children is born with ocular albinism type 1. Ocular albinism is a genetic disease in which pigmentation is lost in the eye, in the retinal pigment epithelium (RPE) located just below the photoreceptors in the retina. This reduced pigmentation affects the development of the fovea (an area of the retina responsible for 99% of vision) and leads to poor visual acuity (the capacity to see fine detail). The mutation causing ocular albinism occurs in the gene Oa1, which encodes a G-protein coupled receptor called Ocular albinism type 1 (OA1). OA1 is found in RPE cells, which normally absorb scattered light with melanin, allowing the eye to generate a high-contrast image. While its exact function is unknown, OA1 is known to be central to melanin biosynthesis and foveal development in the retina. Under normal conditions, the highly-selective ligand L-DOPA binds to OA1, which triggers tyrosinase to increase melanin synthesis. Simultaneously, tyrosinase also triggers L-DOPA to further bind with OA1, which activates a positive feedback loop. However, in many cases of albinism, this pathway is disrupted and tyrosinase is not fully efficient. To counter this, scientists are researching the possibility of bypassing the enzyme and flooding the cells with L-DOPA. Further understanding of OA1 and its function could lead to more effective treatments for albinism. The Brookfield Central High School SMART (Students Modeling A Research Topic) Team created a physical model of OA1 using 3-D modeling printing technology to better understand its structure-function relationship.

• Brown Deer High School
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Brown Deer

Myoglobin: O2 or Not O2... That is the Question


Brown Deer SMART Team model based on 2mgk.pdb

Students:

• E. Bord
• R. Laughlin
• A. LeMense
• C. Marable
• S. Mielke
• B. Poniewaz
• V. Tuncel
• G. Wade
• M. Weeden
• R. Wisth

Teacher:

• David Sampe

Mentor:

• Hannah Wagie, Ph.D. Candidate, Chemistry and Biochemistry Department, University of Wisconsin-Milwaukee
• Peter Geissinger, Ph.D., Chemistry and Biochemistry Department, University of Wisconsin-Milwaukee

Project Files:

• Poster
• Model Description Sheet

Abstract:

Free divers can't hold their breath as long as whales, but they train their bodies to maximize their oxygen (O2) storing potential using the protein myoglobin. Myoglobin's structure has been known for decades, but researchers are still trying to determine just how myoglobin functions. Found in muscle tissue, myoglobin stores O2, a molecule needed to produce chemical energy. Toxic ligands, such as carbon monoxide (CO) and cyanide, also bind to myoglobin. When CO binds to a free heme group, the heme's binding affinity for CO is 20,000 times that for O2. When heme is surrounded by myoglobin, that binding affinity ratio drops to only 25. The decrease was thought to be due to steric interactions which prevented CO from occupying the same space as His64. Recent evidence suggests that electrostatic interactions and hydrogen bonds play a more important role. The O2 is stabilized as opposed to the CO being pushed out. Several amino acids (His64, Val68, Phe43, Phe46, and Leu29,) seem to stabilize the ligand. With 3D printing technology, the Brown Deer SMART (Students Modeling a Research Topic) Team, funded by a grant from NIH-CTSA, created a model of myoglobin. If researchers can fully understand ligand discrimination by heme proteins, not only will divers be able to hold their breath longer, but we may be able to cure diseases like anemia where there is a lack of O2 in the blood.

• Cedarburg High School
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Cedarburg

Getting "Rit-R" Iron in the Cell: The Role of RitR in Reducing Iron Transport into Streptococcus pneumonia


Cedarburg SMART Team model based on a hypothetical PDB

Students:

• B. Allbee
• N. Anderson
• D. Blank
• J. Bolgert
• A. Bothe
• N. Britt
• A. Butt
• S. Dyke
• E. Geiser
• T. Hammer
• E. Janecek
• I. Kalmer
• J. Lawniczak
• M. Lesiecki
• J. Levy
• M. Marshall
• N. Meaux
• M. Ruzicka
• J. Temmer
• K. Tiffany
• B. Vandenberg
• J. Wankowski
• E. Zeitlow

Teacher:

• Karen Tiffany

Mentor:

• Nicholas Silvaggi, Ph.D., Chemistry and Biochemistry Department, University of Wisconsin-Milwaukee

Project Files:

• Poster
• Model Description Sheet 1
• Model Description Sheet 2

Abstract:

According to the World Health Organization, pneumonia is the leading cause of death in children worldwide, and infection of lung tissue by Streptococcus pneumonia causes the bulk of bacterial pneumonia cases in children. The atypical response regulator, RitR (Repressor of iron transport Regulator), helps S. pneumoniae survive in the hostile oxidizing conditions in the lungs. RitR has two domains, a DNA-binding domain (DBD) and an aspartate-less receiver domain (REC). In its "inactive" form, these domains are docked (i.e., close together) and the DBD is unable to bind DNA. In its "active" form, the domains are undocked; the DBD is freed from the REC. The "active" form dimerizes and can bind to DNA to turn off the iron transport genes. To study the changes that occur when RitR is activated, the Cedarburg High School SMART (Students Modeling A Research Topic) Team used 3D printing technology to model inactive RitR and a hypothetical active RitR dimer. RitR helps the bacterium survive in the oxygen-rich environment in lungs by stopping iron transport into the bacterial cell. If iron is transported into the cell, oxygen forms reactive oxygen species that damage and kill cells. S. pneumonia cells without RitR are unable to infect lung tissue, so RitR is a potential target for drug design.

• Cudahy High School
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Cudahy

Myosin: Mighty Morphing Movement Molecule


Cudahy SMART Team model based on 1br1.pdb

Students:

• G. Ademi
• S. Munoz
• R. Dombrowski
• S. Brzezinski
• K. Tolbert
• K. McDonald
• P. Broekel
• C. Schoemann
• J. Hauk

Teacher:

• Dan Koslakiewicz
• Dean Billo

Mentor:

• Thomas Eddinger, Ph.D., Department of Biological Sciences, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

Muscle contraction is caused by the contractile protein myosin, which exists in various isoforms in different muscle types such as smooth, cardiac, and skeletal. Current data suggests smooth muscle myosin is in a non-functional conformation until light chain 20, which is associated with the myosin head, is phosphorylated. This allows either head to freely bind to actin, a protein also involved in contraction. The contractile process is initiated when ATP is hydrolyzed in the ATP binding region. The release of the products from ATP hydrolysis causes the "lever arm" portion of each myosin head to bend relative to the "motor domain," pulling the actin fibers closer together, shortening the muscle cells for movement. If the contractile process is disrupted, bodily function is impaired. These key areas were modeled by the Cudahy SMART (Students Modeling A Research Topic) Team using 3D printing technology. Aortic coarctation, a developmental problem, involves a constriction of proximal aorta which increases blood pressure by narrowing the aorta, changing vascular smooth muscle in this region of vessel. While surgery can correct this anatomical constriction and prolong life, there remain long-term consequences that reduce life span. Drug treatments for a specific smooth muscle problem can be complicated by also altering function of other smooth muscles, causing undesired side effects such as incontinence. The question researchers face is targeting of a drug to a specific smooth muscle. Further understanding of smooth muscle function and regulation helps to better treat, prevent, and/or cure this and other smooth muscle diseases.

• Divine Savior Holy Angels High School
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Divine Savior Holy Angels

"I Wanna New Drug" Manipulating Kappa Opioid Receptor Ligands to Induce a Pain Relieving Response


Divine Savior Holy Angels SMART Team model based on 4djh.pdb

Students:

• C. Assana
• C. Feller
• M. Fogel
• A. Frelka
• S. Gottfried
• R. Jaber
• M. Keyes
• M. Koehler
• K. Kujawa
• N. Lautz
• S. Olson
• J. Pena
• L. Ries
• L. Schauer
• C. Scherrer
• C. Strandberg

Teacher:

• Stacey Strandberg

Mentor:

• Christopher Cunningham, Ph.D., Concordia University Wisconsin School of Pharmacy

Project Files:

• Poster
• Model Description Sheet

Abstract:

Dangerous painkillers may cause serious problems for those who fall into drugs' addictive trap, such as former NFL quarterback Brett Favre. The addictiveness of painkillers such as OxyContin and Vicodin is largely attributed to the response they trigger in proteins such as mu opioid receptors (MORs). This receptor activates cellular signaling pathways responsible for dulling pain; however, the protein also has the ability to stimulate cellular signaling pathways that makes MOP-based painkillers rewarding. An alternate target that alleviates pain but does not produce reward is the kappa opioid receptor (KOP). Unfortunately, many KOP agonists also activate intracellular signaling pathways that produce hallucinogenic effects. To investigate the changes that occur when KOP binds to different ligands, the Divine Savior Holy Angels SMART (Students Modeling A Research Topic) Team has used 3D printing technology to model the active site of the KOP with the neoclerodane diterpene, salvinorin A, to see how the induced fit changes the signal transduction pathways in a neuron of post-synaptic cells. KOP acts as a target for agonists, which are chemicals that bind to a receptor of a cell to trigger a response that activates chemical signaling pathways in cells. Manipulating receptor proteins such as the KOP to inhibit pain pathways without the addictive effect of MOP-targeting painkillers would represent a significant breakthrough in chronic pain management. Computer-aided drug design is being used to streamline the development of KOP ligands that activate this receptor in ways that result in less hallucinogenic effects.

• Grafton High School
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Grafton

Growths in Your Colon Aren't Fun, Get Yourself Some LKB1! The Role of LKB1 in Cancerous Growth


Grafton SMART Team model based on 2wtk.pdb

Students:

• S. Haider
• B. Konon
• A. Mosin
• D. Potter
• Y. Sueoka
• H. Weber

Teacher:

• Dan Goetz
• Fran Grant
• Lisa Neeb

Mentor:

• Stephanie Cossette, Ph.D., Department of Developmental Vascular Biology, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

The National Cancer Institute alone spends $4.9 billion every year on cancer research. Liver Kinase B1 (LKB1) stands out as one important protein that regulates cell metabolism, cell division, and therefore, cancerous growth. LKB1 is a key regulator of cell metabolism and cell division acting as a tumor suppressor by turning on other proteins that suppress tumor growth. Human mutations in LKB1 cause the disease Peutz-Jeghers syndrome, resulting in benign tumor-like growth called polyps in the intestine and a 50% chance of developing cancer by the age of 50. When cell energy, ATP, is low LKB1 will be activated. Active LKB1 regulates the activity of adenosine monophosphate-activated protein kinase (AMPK). LKB1 directly activates AMPK by adding a phosphate group to Thr-172. AMPK activity increases the production of ATP by activating glycolysis and fatty acid oxidation. AMPK can also decrease the amount of energy needed by the cell by inhibiting protein synthesis and cell growth. Both of these processes play a role in cancer development. Drugs like metformin, a successful diabetic drug, are thought to activate LKB1 by phosphorylating Thr-336, which in turn causes LKB1 to activate AMPK to cease cancerous growth by shutting down anabolic pathways. The Grafton SMART (Students Modeling a Research Topic) Team modeled LKB1 using 3D printing technology.

• Greenfield High School
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Greenfield

The Great Escape: How Urea Amidolyase Allows a Pathogenic Fungus to Excape the Immune System


Greenfield SMART Team models based on 4iss.pdb and 3va7.pdb

Students:

• D. Alphin
• A. Braatz
• K. Cavins
• F. Deleon-Camacho
• S. Emkay
• H. Flees
• A. Franitza
• A. Gerwig
• E. Groth
• L. Gangland
• A. Idell
• L. Klug
• V. Nakhla
• Z. Osberg
• P. Paniagua
• J. Wallner

Teacher:

• Julie Fangmann
• Drew Rochon

Mentor:

• Martin St. Maurice, Ph.D., Marquette University, Department of Biological Sciences

Project Files:

• Poster
• Model Description Sheet 1
• Model Description Sheet 2

Abstract:

According to Rice University, 70% of people are affected by the infectious fungus Candida albicans. The immune system uses T and B cells to stop pathogens. People with suppressed immune systems, such as children with transplants, AIDS or cancer patients, lack functional T and B cells, so they rely on macrophages to destroy Candida. Candida can kill and exit macrophages due to an enzyme: urea amidolyase (UAL). While in the macrophage, Candida goes through a morphological switch from a sphere to a structure with hyphae due to an environment change. UAL converts urea to ammonia and CO2, creating an environment for hyphae to form, bursting the macrophage. The Greenfield SMART (Students Modeling A Research Topic) Team used 3D printing technology to model the four domains of UAL. The biotin carboxylase (BC) domain uses energy from ATP cleavage to attach CO2 to the swinging arm portion, or biotin carboxyl carrier protein (BCCP) domain. The BCCP domain swings across UAL, attaching CO2 to urea forming allophanate in the carboxyl transferase (CT) domain. Allophanate moves to the allophanate hydrolase (AH) domain, which hydrolyzes the allophanate into CO2 and ammonia. Increases in CO2 and ammonia cause hyphae to form, destroying macrophages and allowing Candida to spread. Since humans lack UAL, researchers could block UAL's active sites to prevent Candida's macrophage-killing shape change, thus preventing systemic candidiasis without damaging human cells.

• Hartford Union High School
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Hartford Union

Correct Splicing: The Desolation of SMA Interactions Between Gemin-2 and SMN


Hartford Union SMART Team model based on 3s6n.pdb

Students:

• M. Daley
• K. Erickson
• J. Griesmer
• M. Heimermann
• B. Lewandowski
• J. Loosen
• O. Hoffman
• G. Rigden

Teacher:

• Mark Arnholt

Mentor:

• Mark McNally, Ph.D., Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Spinal muscular atrophy (SMA) is a genetic disorder usually leading to death before age two. This is caused by the degeneration of motor neurons in the spine and affects one in six thousand babies yearly (Families of SMA, 2013). It is unknown why a point mutation or deletion of the SMN1 gene, which produces survival motor neuron (SMN) protein, causes this degeneration. The SMN complex, found in the cytoplasm, is made of SMN and smaller units called Gemin proteins. In a normally functioning system, the SMN1 gene codes for SMN proteins that are part of the SMN complex that forms small nuclear ribonucleoproteins (snRNPs) from SM proteins and sRNA. The SMN protein binds to Gemin-2 which holds five of the seven SM proteins, the smaller units in snRNPs, in place until the target snRNA sequence is located. The final SM proteins are added when the N-terminus of Gemin-2 is moved. The snRNPs have many functions in cells, and five of them are involved in RNA splicing. The knowledge that is available on normal interactions of SMN and Gemin-2 allow modeling of these proteins to be completed through 3D printing by the Hartford Union SMART (Students Modeling a Research Topic) Team. In children with SMA, the SMN protein cannot to bind to Gemin-2 because Asp44 is replaced by valine, causing a break in the ionic bond holding the helices together. While this situation still produces normally operating snRNPs, there are too few to correctly splice the pre-mRNA, leading to SMA.

• Kettle Moraine High School
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Kettle Moraine

GABA_B Thera_P


Kettle Moraine SMART Team model based on 4f12.pdb

Students:

• J. Doenier
• J. Grewe
• M. Griesbach
• M. Gokuli
• E. Hinds
• L. Kim
• M. King
• A. Schwarzkopf
• A. Smith

Teacher:

• Melissa Kirby

Mentor:

• Michelle Mynleiff, Ph.D., Deparment of Biological Sciences, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

In the mammalian central nervous system, gamma-aminobutyric acid (GABA) is the primary inhibitory signaling molecule. One receptor for this molecule, GABAB, has been linked to feelings of calmness, as well as mental disorders such as alcoholism and depression. Pharmaceutical compounds that bind the GABAB receptor are currently used to treat muscle spasticity and various types of addiction. However, excessive activation of this receptor can hinder muscle function. Activation of the metabotropic GABAB receptor by GABA influences neuronal activity by coupling with G proteins to activate a signaling cascade that leads to downstream effects including the modulation of various ion channels. The GABAB receptor is a dimer composed of two different subunits (GBR1 and GBR2), each with 7 helices within the membrane and an extracellular domain that binds GABA. Only the GBR1 subunit directly binds the GABA molecule and other ligands with a similar structure. However, recent studies have shown that GBR2 can affect the efficiency of GABA binding to GBR1. In addition, the GBR2 subunit activates the G protein after GABA binds, leading to various downstream effects. One well known effect is the opening of potassium channels, hyperpolarizing the cell, preventing action potentials from firing, and ultimately stopping neurotransmitter release. Using 3D printing technology, the Kettle Moraine SMART (Students Modeling A Research Topic) Team has modeled the GABAB receptor to study its structure to determine therapeutic possibilities. GABAB receptors' widespread importance in the nervous system may lead to new uses in the neurological and medical fields.

• Laconia High School
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Laconia

MscL: The Magic Behind theTouch


Laconia SMART Team model based on 2oar.pdb

Students:

• A. Garb
• D. Barbeau
• D. Ihrig
• N. Henke
• A. Opheim
• B. Hansen
• L. Respalje
• M. Schroeder

Teacher:

• Jodie Garb

Mentor:

• Andy Weyer, Ph.D. Candidate, Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin
• Katherine Zappia, Ph.D. Candidate, Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

The Institute of Medicine estimates $635 billion dollars are spent annually on people with chronic pain conditions. One debilitating symptom of these conditions is hypersensitivity to touch, where daily activities can be painful. Few therapeutics to ameliorate mechanical hypersensitivity exist because the mammalian ion channels that sense touch are poorly understood. The mechanosensitive channel of large conductance (MscL) is an ion channel in Mycobacterium tuberculosis which allows bacteria to respond to mechanical stimuli by electrochemical response, regulating membrane ion flow. Research shows structural changes in MscL causes the protein to open, allowing ions into the cell. Key amino acids include hydrophobic residues I14 and V21, creating a constriction at the cytoplasmic surface. R98, K99, K100, E102 and E104 are possibly a ligand binding site, potentially participating in the ion conduction pathway. Residues at the N-terminus of MscL, K3, F5, E7 and F8, may play a role in sensing membrane stretch. The Laconia SMART (Students Modeling A Research Topic) Team used 3D printing technology to model MscL. Understanding the structure-function relationships of the MscL channel protein may lead to better comprehension of how human mechanosensitive ion channels, like the Transient Receptor Potential Ankyrin 1, work and lead to a cure for hypersensitivity to touch.

• Madison West High School
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Madison West

Dopamine Reuptake Inhibition as the Means of Antidepressent Mechanism of Function


Madison West SMART Team model based on 4m48.pdb

Students:

• H. Deng
• T. Luo
• S. Vorperian

Teacher:

• Christine Petzold

Mentor:

• Dave Nelson, Ph.D., Department of Biomolecular Chemistry, University of Wisconsin – Madison

Abstract:

Maintaining the equilibrium of neurotransmitters (NT) at neural synapses is essential for normal brain functioning. Lack of regulation of NT levels is associated with disorders including depression, Parkinson's disease, ADHD, and epilepsy. The dopamine transporter (DAT) is the primary removal mechanism of the NT, dopamine, from the synaptic cleft. The regulation of NT reuptake is critical for preventing chemical imbalance and the inhibition of reuptake has become the primary target for antidepressants. The Drosophila melanogaster DAT was crystallized in complex with a tricyclic antidepressant (TCA) and found induced in an outward-open conformation towards the synaptic cleft. Three factors contribute to inhibiting the inward-facing conformation required for DAT activity: the antidepressant nortriptyline bound at the substrate-binding site blocks important helix movement, a cholesterol molecule stabilizes the outward conformation, and lastly the C-terminus caps the cytoplasmic gate. The Madison West SMART (Students Modeling a Research Topic) modeled the DAT structure using 3D printing technology. The structure of TCA-bound DAT provides new knowledge of eukaryotic transporters and enables a better understanding of the critical factors and conformational changes associated with NT transport inhibition to allow for targeted drug research.

• Marquette University High School
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Marquette University

Standing in the Way of the Common Cold Pleconaril – Is it the "Key" to Keeping Rhinovirus Locked Out of Cells?


Marquette University SMART Team model based on 1c8m.pdb

Students:

• J. Fuller
• D. Kim
• R. Sung
• E. Arnold
• A. Borden
• L. Ortega
• R. Johnson
• H. Albornoz-Williams
• C. Gummin
• A. Martinez
• N. Boldt
• D. Ogunkunle
• P. Ahn
• B. Kasten
• Q. Furumo
• N. Yorke
• J. McBride
• I. Mullooly
• M. Tripi
• D. Hutt

Teacher:

• Keith Klestinski
• Carl Kaiser

Mentor:

• William Jackson, Ph.D., Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to World Health Organization statistics, the common cold is the most prevalent known disease of humans. The majority of colds are caused by the human rhinovirus--an enterovirus genetically similar to dangerous viruses like polio and hepatitis A. Rhinovirus infection can lead to 72-hour periods of morbidity, including symptoms like sore throat, runny nose, and muscle weakness, often causing people to miss school or work. Rhinovirus is inert until infection occurs causing the immune system to combat the virus. Rhinovirus transmission is usually via aerosolized respiratory droplets or contact with contaminated surfaces. Once in the body, the virus binds to the cell surface, allowing it to enter cells. Cells use the Intercellular Adhesion Molecule 1 (ICAM-1) signaling protein to latch on to each other, but viruses bind to ICAM-1 using a site on the virus surface known as the "canyon." Since there are over 150 rhinovirus serotypes, it is impossible to put every serotype in one vaccine. Instead, scientists are developing new drugs, such as pleconaril, that bind to the canyon and prevent the virus from attaching to the host cell. This prevents the virus from replicating thus eliminating the spread of the virus and the symptoms caused by it. The Marquette University High School SMART Team modeled a portion of the human rhinovirus capsid bound to pleconaril using 3D printing technology.

• Messmer High School
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Messmer

Second Verse, Same as the First Structures of Thioredoxin Proteins TrxA and TrxC from Mycobacterium tuberculosis


Messmer SMART Team models based on trxc.pdb and trxa.pdb

Students:

• I. Osademe
• M. Cobb
• J. Gonzalez Cruz
• A. Richmond
• J. Rios Llamosa
• B. Rios Llamosa
• A. Junior
• A. Camacho

Teacher:

• Carol Johnson

Mentor:

• Terrence Neumann, Ph.D., Concordia University Wisconsin School of Pharmacy

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the World Health Organization, 8.6 million people became ill and 1.3 million died in 2012 from tuberculosis (TB). Thioredoxin A (TrxA) is a binding protein in the bacterium, Mycobacterium tuberculosis, the causative agent for TB. TB is prevalent in countries where infectious diseases have a high incidence due to weakened immune systems. TB mainly affects the lungs, but can also affect the lymphatic, circulatory, and central nervous systems. When a host organism is infected, the Mycobacteria in the lungs multiply often resulting in pneumonia, chest pain, and prolonged coughing. In response to this infection, host macrophages, a part of the natural immune system, engulf the Mycobacteria and attempt to destroy it by oxidizing bacterial proteins. To protect itself against this attack, the bacterial thioreductase system, consisting of the redox protein thioredoxin reductase (TrxR) and the thioredoxin proteins TrxA, TrxB, and TrxC, gives electrons back to the oxidized proteins. As this system works to maintain cellular redox homeostasis, finding ways to stop it might provide a new method for treating people with TB. TrxA whose function is unknown and TrxC, whose function has been well studied, have similar structures, thus it can be hypothesized that their functions are similar. Comparing binding sites between the proteins could provide insight if TrxA reacts with TrxR similarly to TrxC. By modeling TrxA and TrxC with 3D printing technology, the Messmer SMART (Students Modeling A Research Topic) Team can compare the structures of the two thioredoxins, which may lead to new strategies for curing or preventing TB.

• Milwaukee Academy of Science High School
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Milwaukee Academy of Science

The Emergence of a Superbug: NDM-1 and Its Role in Carbapenem Resistance


Milwaukee Academy of Science SMART Team model based on 3q6x.pdb

Students:

• L. Barns
• C. Bester
• C. Burrows
• B. Daubon
• D. Davis
• N. Hall
• J. Jackson
• J. Jones
• T. Jones
• J. Kendrick
• V. McCotry
• N. Payne
• R. Taylor
• Q. Tyra
• E. Walls
• D. Washington

Teacher:

• Kevin Paprocki
• Tyler Reed

Mentor:

• Lance Presser, Ph.D. & Sanjib Bhattacharyya, Ph.D., City of Milwaukee Health Department Laboratory

Project Files:

• Poster
• Model Description Sheet

Abstract:

Imagine going to the doctor to be treated for a normally treatable infection only to find that no effective treatments exist because all conventional antibiotics are ineffective. In some regions of the world, antibiotic prescription isn't regulated and overuse has lead to antibiotic resistance. Carbapenems are a class of antibiotics that inhibit bacterial cell wall synthesis and are often used as a last resort treatment for bacterial infections. New Delhi metallo-ß-lactamase-1 (NDM-1) is an enzyme that occurs in several types of bacteria and conveys resistance against carbapenems. The Milwaukee Academy of Science SMART Team (Students Modeling A Research Topic) modeled the NDM-1 protein using 3D modeling technology. NDM-1 is a single-chain polypeptide consisting of 270 amino acids found in the bacterial periplasmic space. The NDM-1 active site consists of two loops (L10 and the highly flexible L3) and two zinc ions. These zinc ions are held in place by three histidine amino acids (H120, H122, H189) on L3 and a triplet of amino acids on L10. The zinc ions bind to and sever the ß-lactam ring on carbapenems, inhibiting its antibiotic properties. It's the flexibility of L3 that gives NDM-1 the ability to hydrolyze the full spectrum of carbapenems. Researchers are concerned because the gene for NDM-1 is located on a plasmid that's frequently passed via horizontal gene transfer among various species of bacteria. An understanding of NDM-1's structure and function may prevent an outbreak of bacteria equipped with the NDM-1 enzyme.

• Saint Dominic Middle School
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Saint Dominic

The Human RhD Protein and Hemolytic Disease of the Newborn


Saint Dominic SMART Team model based on 3hd6.pdb

Students:

• J. Austin
• G. Gundrum
• G. Hilbert
• C. Hildebrand
• B. Hughes
• S. Jaskolski
• M. Kahler
• W. Klingsporn
• D. Lagore
• K. MacDonald
• T. Mark
• J. Minessale
• S. O'Brien
• M. Peterman
• S. Reinbold
• A. Rusnak
• L. Scott
• R. Storts
• M. Vuckovich
• M. Weisse
• N. Wilke
• C. Wormington

Teacher:

• Donna LaFlamme

Mentor:

• Matthew Karafin, M.D., Associate Clinical Investigator, Blood Center of Wisconsin, Assistant Professor of Pathology, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Hemolytic disease of the newborn (HDN) occurs during pregnancy when the red blood cells of an RhD positive (RhD+) baby comes in contact with the immune system of an RhD negative (RhD-) mother. The mother's immune system identifies the RhD protein on the baby's erythrocytes as foreign, and produces anti-D antibodies, which cross the placenta causing destruction of the baby's red cells. Resulting symptoms range from mild jaundice and anemia to perinatal death. The RhD protein belongs to an ancient family of ammonia channels and is found on RhD+ erythrocytes, but is missing from RhD- red cells. The St. Dominic S.M.A.R.T. Team has modeled RhD using 3-D printing technology. Our model highlights RhD's twelve transmembrane helices and the sidechains of its nonfunctional ammonia channel. Extracellular loops 3, 4, and 6 carry clusters of D antigen epitopes while loops 1, 2, and 5 do not play a major role in RhD antigenicity due to their sequence identity with RhCE. The RHD gene arose from gene duplication of the RHCE gene and has 93.8% homology. Along with RhAG (Rh associated glycoprotein) both RhD and RhCE are part of the trimeric Rh complex on erythrocytes, essential to the cell's structural integrity. HDN research led to the discovery of RhD and to the highly complex Rh blood group system whose major antigens are D, C/c, and E/e. Hemolytic disease of the newborn is now preventable by injecting RhD- mothers with anti-D immunoglobin to prevent them from developing active immunity to their babies RhD+ erythrocytes.

• Saint Joan Antida High School
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Saint Joan Antida

Exoenzyme U and Ubiquitin: A Fatal Attraction


Saint Joan Antida SMART Team model based on 4akx.pdb

Students:

• O. Adewale
• A. Ali
• J. Allen
• V. Ammons
• J. Gonzalez
• A. Ray
• I. Roberts
• T. Woods

Teacher:

• Emily Harrington

Mentor:

• Dara M. Frank, Ph.D., Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

Exoenzyme U is the most toxic and destructive effector of the pathogen Pseudomonas aeruginosa, an omnipresent, strategic pathogen found in soil. Exoenzyme U (ExoU) is a strong phospholipase, a catalytic enzyme that targets the cleavage of phospholipids, which is activated inside mammalian cells by ubiquitin. ExoU is inactive in P. aeruginosa as prokaryotic cells do not have ubiquitin, a regulatory protein used in post-translational modification vital for processes in cells. The function of ExoU is to destroy immune cells, which allows the bacterium to replicate in vivo without being attacked by the immune system. ExoU injects toxins into a host cell that serve to destroy the cell's membrane. In this way, ExoU acts similarly to venom. Scientists have discovered that when ExoU interacts with ubiquitin, it is activated. Research has highlighted the C-terminal four-helix bundle of ExoU, principally located between residues 600 and 683, because it is a probable binding site between ExoU and ubiquitin. It is also known that Tyr-619 and Arg-661 (located near the end of the C-terminal) play a role in the binding and activation of ExoU. Arg-661 may also function as a substrate interaction or in binding. ExoU is problematic in people who use artificial breathing machines and have weak immune systems. The Saint Joan Antida SMART (Students Modeling a Research Topic) Team modeled the ubiquitin binding domain of ExoU using 3D printing technology.

• Saint Thomas More High School
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Saint Thomas More

It's a Wonderful Metabo(life): The Story of Estrogen Sulfotransferase


Saint Thomas More SMART Team model based on 4jvn.pdb

Students:

• B. Drew
• M. Wengelewski
• B. Boren
• M. Peter
• K. Howell
• M. Lezama
• C. Sikora
• R. Cabigting
• F. Bowman
• A. Bollis
• S. Olmos

Teacher:

• Kathy Stelling

Mentor:

• Joseph McGraw, Ph.D., Pharm. D., Concordia University Wisconsin School of Pharmacy
• Cameron Patterson, Pharm. D. Candidate, Concordia University Wisconsin School of Pharmacy

Project Files:

• Poster
• Model Description Sheet

Abstract:

Hypoplastic left heart syndrome is a disorder of the fetal heart in which the ventricles and aorta are formed improperly. As a result, infants with this condition will die shortly after birth unless they receive immediate surgery. According to the World Health Organization, this syndrome affects about 1 in every 4,000 babies born each year. Further research by Dr. Joseph McGraw and Dr. Andrew Pelech has linked this condition to brominated flame retardants, or BFRs. BFRs are a class of chemicals that have bromine atoms attached to them in a specific sequence. Estrogen sulfotransferase (EST) is a metabolic enzyme that metabolizes various fatty acids, neurotransmitters, and hormones. The Saint Thomas More SMART (Students Modeling A Research Topic) Team modeled EST using 3D printing technology to further investigate the structure-function relationship. One function of EST is to attach a sulfate group to thyroid hormone, thyroxin, in a developing fetus. This process changes the thyroid hormone from a non-polar to a polar substance. The polar form of thyroxine may be absorbed into the fetus and later metabolized back to the thyroid hormone for use in fetal organ development. BFRs can closely mimic thyroxin, which causes EST to attach sulfate groups to BFRs rather than thyroxin itself. However, BFRs do not function in the same way as thyroxin, and adversely sulfation in thyroid hormone metabloism. Further research may result in effective prevention or treatment of fetal developmental disorders such as hypoplastic left heart syndrome.

• Wauwatosa West High School
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Wauwatosa West

A Vertebral Variation Mystery: The Case for Missing Collagen-8A1


Wauwatosa West SMART Team model based on 1o91.pdb

Students:

• P. Bonner
• Z. Hassan
• A. Ho
• A. Lau
• J. Mody
• A. Rowley
• Z. Stack
• K. Thao
• A. Zielonka

Teacher:

• Mary Anne Haasch

Mentor:

• Michael Pickart, Ph.D., Concordia University Wisconsin School of Pharmacy

Project Files:

• Poster
• Model Description Sheet

Abstract:

Scoliosis affects 6 to 9 million people in the United States, and collagen-8a1 may contribute to the disease's development. Collagen-8a1, a structural protein, is found throughout the body, generally serving as a connection at the base of endothelial cells, which line blood vessels and are critical to immune response and growth regulation. The molecule plays a role in angiogenesis, the development of new blood vessels, and smooth muscle cell migration. Collagen-8a1 is a highly conserved protein, meaning there are few variations of the amino acid sequence in different organisms. The only crystallized part of the molecule is a wide conical shape at the end of the uncrystallized rope-like structure. A trimer made of chains A, B, and C, collagen8a1 is held together by hydrogen bonds among sidechains such as Tyr660 and Tyr738 and water molecules in the central shaft. A single-point mutation at Tyr660 on the C chain of the molecule results in a mutant called gulliver in zebrafish, causing a distortion of the notochord. Thus, preliminary research in zebrafish suggests a new role for collagen-8a1 in bone formation during development of vertebrae. Research is currently in progress to understand how the absence or mutation of the molecule results in spinal malformations in zebrafish and if this is true for other organisms, including humans. This research could result in further knowledge as to whether dysfunctional collagen-8a1 results in spinal deficiencies. The Wauwatosa SMART (Students Modeling A Research Topic) Team modeled collagen-8a1 using 3D printing technology.

• Westosha Central High School
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Westosha Central

Deleterious Deoxyguanosine Kinase (dGK) Double Destruction


Westosha Central SMART Team model based on 2ocp.pdb

Students:

• J. Alberth
• N. Bielski
• D. Clements
• J. Holloway
• E. Kirsch
• M. Kirsch
• B. Lawrence
• J. Mellor
• M. Murphy
• A. Papendick
• S. Quist
• A. J. Reeves
• Z. Wermeling
• J. Williams

Teacher:

• Jonathan Kao

Mentor:

• Jason Kowalski, Ph.D., Department of Biological Sciences, University of Wisconsin-Parkside and Department of Physics and Chemistry, Milwaukee School of Engineering

Project Files:

• Poster
• Model Description Sheet

Abstract:

Mitochondrial Deficiency Syndrome (MDS) is characterized by a deficient amount of mitochondrial DNA (mtDNA). Without sufficient copies of mtDNA, the mitochondria cannot manufacture an adequate amount of ATP, leading to failure of energy expensive tissues such as the brain, skeletal muscle, and liver, ultimately causing death in early infancy. Deoxyguanosine kinase (dGK), an enzymatic protein, plays a role in regulating the replication of mtDNA by attaching a phosphate to a sugar/nitrogen-base nucleoside at the active site, amino acids Glu70 and Arg142. Once phosphorylated, the assembly of mtDNA proceeds. Mutations in dGK prevent the phosphorylation of mtDNA and lead to a decrease in mitochondrial function. Two point mutations have been shown to have a deleterious impact on dGK: the R142K mutation is 0.2% active when compared to the wild type, and the E227K mutation is 5.5% active when compared to the wild type. The 3D model designed by the Westosha Central SMART (Students Modeling A Research Topic) Team displays the active site, two specific mutations and additional mutations reported in MDS patients. Screening for MDS is difficult because the condition can be caused by a wide variety of dysfunctional proteins. One such protein is dGK; therefore identifying its structure can hasten an accurate diagnosis.

• West Bend High School
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West Bend

CaM You Remember?


West Bend SMART Team model based on 3cln.pdb

Students:

• S. Boggs
• L. Dommisse
• R. Fisher
• C. Kannenburg
• S. Kassin
• B. Laufer
• J. Myers
• T. Olwig
• D. Sanfelippo
• K. Vachuska

Teacher:

• Judy Birschbach

Mentor:

• Audra Kramer, Ph.D. Candidate, Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin
• Nashaat Gerges, Ph.D., Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

According to the Alzheimer's Association, more than 5 million Americans are living with Alzheimer's. One in three seniors dies with this disease or another type of dementia. The potential to eliminate this painful disease lies within calmodulin, an intra-cellular receptor protein that is found throughout the body but functions in the brain to affect learning and memory. Calmodulin (CaM) plays a role in cell growth, proliferation and movement of electrons within the electron-transport chain. It enters from the post-synaptic side of the spine of a dendrite within the brain and automatically binds to calcium causing a conformational changing of the calmodulin itself. Calcium binds to the EF hand motif (a conserved helix–loop-helix sequence) found in calmodulin. The action of the calcium binding induces a conformational change to calmodulin, which forms a calmodulin-complex. An enzyme, CaM Kinase 2 binds to and activates the calmodulin-complex. Activation causes an influx in the amount of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPAR), which increases the amount of calcium entering the cell. Researchers believe that an increase in calcium absorbed directly impacts the durability and stability of the brain. The West Bend SMART (Students Modeling A Research Topic) Team modeled CaM using 3D printing technology. Further calmodulin studies could prove to be the key to developing therapeutic treatments for mental illness, as well as finding ways to increase mental function.

• Whitefish Bay High School
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Whitefish Bay

NO S-nitrosylation, NO Memorization


Whitefish Bay SMART Team model based on 2dgv.pdb

Students:

• S. Broadnax
• J. Heo
• J. Schroeder
• M. Shin
• F. Zhang
• N. Longo
• B. Donaldson Morton
• J. Johnson
• M. Phillips
• B. Grych
• K. Xiong
• R. Davis
• L. Prekosovich
• C. Middleton
• T. Cho
• G. Von Paumgartten
• P. Flejsierowicz
• J. Ebert

Teacher:

• Katie Brown
• Paula Krukar

Mentor:

• Dmitry G. Khomyakov, Ph.D. Candidate, Department of Chemistry, Marquette University
• Qadir K. Timerghazin, Ph.D., Department of Chemistry, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

Nitrogen and oxygen are two components of the air we breathe. Bonded together as nitric oxide, they are an important signaling molecule that is involved in numerous physiological processes including the protein S-nitrosylation. The human body cannot function without this effective process, but if the regulation of this process breaks down, it can lead to common diseases such as Parkinson's and Alzheimer's. Irregular nitroslyase and denitrolayse activities may be involved in these diseases, so they are important therapeutic targets. This important process also allows blood vessels to expand, so they can transport more blood and retain more oxygen. The key component, nitric oxide (NO), attaches to glutathione to give the S-nitrosoglutathione molecule (GSNO). The NO from the GSNO then travels to a specific cysteine in a protein, which can affect the properties of that protein. Using 3D printing technology, the Whitefish Bay SMART (Students Modeling A Research Topic) Team is aiding its mentors as they research to figure out why the NO attaches to one cysteine specifically and what exactly this process does. Dr. Timerghazin and Mr. Khomyakov hypothesize that a positive amino acid, such as arginine, catalyzes the NO transfer and causes it to jump to the specific cysteine. Discovering what S-nitrolysation's physiological role as well as why one cysteine is chosen over others could lead to developments in our understanding of certain diseases that are linked to the erratic regulations of S-nitrolysation in the human body.

• Wisconsin Virtual Learning Academy
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Wisconsin Virtual Learning Academy

Vitamin D Receptor: An Underrated Hero


Wisconsin Virtual Learning SMART Team model based on 1db1.pdb

Students:

• J. Amro
• N. Amro
• C. Gad
• E. Merkel
• C. Minter
• S. Stuebs
• H. Van Gorden

Teacher:

• Karen O'Donnell

Mentor:

• Allie Reeme, Ph.D. Candidate, Microbiology and Molecular Genetics, Medical College of Wisconsin
• Richard Robinson, Ph.D., Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster
• Model Description Sheet

Abstract:

For over a century, vitamin D (vit. D) has been used as therapy for the bacteria Mycobacterium tuberculosis (Mtb) due to its effects on the immune system. Interest has risen for vit. D's ability to modulate immune responses by signaling through the vitamin D receptor (VDR). Vit. D is obtained through dietary sources, like seafood, or exposure to sun's UVB rays. Vit. D in its active form can passively diffuse into multiple cell types, such as lymphocytes, while the VDR, a transcription factor for vit. D regulated genes, can regulate the effects of the hormone in these cells. Vit. D has been shown to modulate the immune response during Mtb infection by controlling production of cytokines and antimicrobial peptides and its interactions with the VDR is critical for these effects. In order to recognize VDR's role during the immune response to Mtb, the Wisconsin Virtual learning SMART Team (Students Modeling A Research Topic) is using 3D printing technology to model the structure, primarily highlighting amino acids Arg274 and His305 which are required for ligand binding to the VDR. Scientists, recognizing vit. D's positive role during an immune response, will continue to investigate vit. D as a therapeutic agent to treat this significant plight.

• Valders High School
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Valders

"Good Vibrations" Differential Hydrogen Bonding in Human CYP17A1 Determines Hydroxylation versus Lyase Chemistry


Valders SMART Team model based on 3ruk.pdb

Students:

• R. Ansorge
• A. Brandl
• R. Bushman
• E. Evans
• T. Evenson
• A. Riederer
• I. Schmidt

Teacher:

• Joseph Kinscher

Mentor:

• James R. Kincaid, Ph.D. & Piotr J. Mak, Ph.D., Department of Chemistry, Marquette University

Project Files:

• Poster
• Model Description Sheet

Abstract:

Inhibiting Cytochrome P45017 (CYP17A1) could prevent androgen synthesis and treat prostate, breast, and other hormone responsive cancers. Cholesterol is the precursor of all steroid hormones including testosterone and estrogen. CYP17A1, an enzyme bound to the membrane of adrenal cells, plays a critical role in the biosynthesis of steroid hormones. This enzyme determines whether corticoids, which control metabolism, or androgens such as testosterone, will form. CYP17A1 catalyzes the hydroxylation of its substrates pregnenolone (PREG) and progesterone (PROG) to form 17-OH pregnenolone (17-OH PREG) and 17-OH progesterone (17-OH PROG), respectively. Most interestingly, it can further process the 17-OH PREG by catalyzing the cleavage of the carbon 17, 20 bond as a next step, which is the first committed step in androgen biosynthesis. While the enzyme can similarly transform the 17-OH PROG, it does so with much lower efficiency, and it is this difference which has attracted the interest of researchers. Attention has been focused on a key amino acid, asparagine 202 (N202), whose amide fragment can provide differential H-bonding interactions with these two substrates. The technique of resonance Raman spectroscopy can provide structural insight into the mechanisms that direct the reaction along a given pathway. Improved structural resolution at the active site of CYP17A1, may help lead scientists to better anticancer drug development. The Valders SMART (Student Modeling A Research Topic) Team used 3D printing technology to model the protein CYP17A1.

2012-2013 SMART Teams

Twenty-one schools participated in the local SMART Team program during the 2012-2013 school year. The remote SMART Teams and HHMI SMART Teams also expanded, for a total of over sixty SMART Teams nationwide. Completed projects are described below.

Final Presentations Abstract Book (890 Kb .pdf file)

• Brookfield Academy
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Brookfield Academy

Basis of Prokaryotic Selectivity in the Antibiotic Paromomycin




Students:

• Simar Puri
• Satvir Kalsi
• Ricky Singh
• Neil Chand
• Vipul Singh
• Sangwoo Park
• Chi Aguwa
• Moid Ali
• Anshul Dhingra
• Justin Zhu
• Griffin Gill
• Mike Sportiello

Teacher:

• Robbyn Tuinstra, Ph.D.

School:

• Brookfield Academy, Brookfield, Wisconsin

Mentor:

• Madhusudan Dey, Ph.D., Department of Biological Sciences, University of Wisconsin — Milwaukee

Project Files:

• Poster

Abstract:

Ribosomes are responsible for protein synthesis and are a major target of antibiotics. While translation is a universally conserved cellular process, the ability of drugs to target prokaryotic ribosomes depends on subtle variations from eukaryotic ribosomes. The ribosome is composed of ribosomal RNA (rRNA) and protein. The small ribosomal subunit, called 30s in prokaryotes, contains 21 proteins and one rRNA (16S) and the large subunit, called 50S, contains 31 proteins and two rRNAs (23S and 5S). Recent crystal structures reveal that the rRNAs adopt a 3D fold generating (I) decoding center for codon-anticodon recognition, (II) a peptidyl-transfer center (PTC) for a peptide bond formation and (III) an exit tunnel through which the nascent protein emerges. Paromomycin, used in the treatment of intestinal infections, inhibits prokaryotic ribosomes at the decoding site. Paromomycin physically restructures helix H44 of the 16S rRNA, preventing proper rotation of A1492 and A1493 during anticodon:codon recognition, decreasing tRNA selection accuracy in prokaryotic ribosomes. However, paromomycin fails to affect eukaryotes due to an A to G transition at position 1408. The Brookfield Academy SMART Team (Students Modeling A Research Topic) modeled a prokaryotic ribosome, highlighting nucleotides responsible for the prokaryotic specificity of paromomycin.

• Brookfield Central High School
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Brookfield Central High School

The Inhibition Mission: DHQase and the Shikimate Pathway of Mycobacterium tuberculosis




Students:

• Esha Afreen
• Deepti Ajjampore
• Brad Bartelt
• Krishti Bhowmick
• Anthony Fung
• Kamya Gopal
• Karin Jorgensen
• Ramprasad Karanam
• Harshi Mogallapalli
• Erik Nesler
• Nikil Prasad
• Rishi Sachdev
• John Scanlon
• Hafsa Shereen
• Nikita Sood

Teacher:

• Louise Thompson

School:

• Brookfield Central High School, Brookfield, Wisconsin

Mentor:

• Sanjib Bhattacharyya, Ph.D., Deputy Laboratory Director, City of Milwaukee Health Department

Project Files:

• Poster

Abstract:

In 2011, nearly 9 million people became sick with tuberculosis, of which 1.4 million died worldwide, according to the World Health Organization. Tuberculosis (TB) is an infectious, airborne disease caused by a pathogenic bacterium, Mycobacterium tuberculosis. This bacterium primarily attacks the lungs and is often fatal if not treated promptly. 3-dehydroquinate dehydratase (3-DHQase) is an enzyme that catalyzes the third step of the shikimate pathway, which is essential to M. tuberculosis. The shikimate pathway creates a precursor to the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Inhibition of 3-DHQase will block the shikimate pathway and the TB bacteria will die. Inhibitors can be used for drug development to treat tuberculosis, especially people affected by multi-drug-resistant strains, called MDR TB. Since DHQase is absent in human cells, the drug will only affect bacteria cells, where the enzyme is inactive until substrate binds to its active site. 3-dehydroshikimate, a natural ligand, and six inhibitors can interact with DHQase. Effectively inhibiting this enzyme would render tuberculosis harmless. 3-DHQase has a flexible catalytic loop at residues 19-24. Arg19 and Tyr24 are the two key conserved residues. The ligand binding induces closure of the loop through its interaction with the side-chain atoms of loop residues: Tyr24 and Arg19. 3-DHQase may hold the key to saving the lives of those infected by MDR TB. The Brookfield Central High School SMART Team (Students Modeling a Research Topic) created physical models of 3-DHQase dodecamer and monomer to show active-site binding molecules and inhibitors using 3-D modeling printing technology.

• Brown Deer High School
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Brown Deer High School

Feel the Burn, then Feel the Death. ExoU as a Phospholipase




Students:

• Evan Bord
• Zack Farrell
• Wongsai Heur
• William Keslin
• Robert Laughlin
• Hannah Leedom
• Andrew LeMense
• Seriah Lucre
• Chad Marable
• Suzie Mielke
• Sara Olk
• Carlos Orozco
• Charlie Rosio
• Jordan Schubert
• Sarah Smith
• Gina Wade
• Mike Weeden

Teacher:

• David Sampe

School:

• Brown Deer High School, Brown Deer, Wisconsin

Mentor:

• Dara W. Frank, Ph.D., Department of Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

A major cause of infection-related deaths in immunocompromised patients is the protein toxin ExoU, encoded by the bacterium Pseudomonas aeruginosa. The Brown Deer SMART (Students Modeling A Research Topic) Team has modeled ExoU using 3D printing technology to have a better grasp on how the toxin interacts with eukaryotic cells. P. aeruginosa uses a type 3 secretion system (T3SS) to inject toxins including ExoU into the cell to disrupt its functionality. The T3SS is a needle-like structure comprised of proteins that allow the bacterium to transfer effector proteins into innate immune cells. ExoU travels through the T3SS using a chaperone protein (SpcU). Once inside the eukaryotic cell, ExoU interacts with ubiquitin, where it refolds into an active potent phospholipase that breaks down cellular membranes using Ser142 and Asp344 as the catalytic amino acids. The exact mechanism is unknown but the C-terminus (residues 580-683) helps in targeting the membrane, allowing ExoU to break it down. P. aeruginosa is able to freely reproduce inside the environment of the host organism as the immune system is not able to compensate for the infected cells and bacterium. Left unchecked, this infection will prove fatal. Research is being conducted to create an ExoU inhibitor to reduce the deaths it causes in patients with compromised immune systems.

• Cedarburg High School
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Cedarburg High School

Calcium-calmodulin Dependent Protein Kinase II: An Unforgettable Story




Students:

• Laura Tiffany
• Alex Bothe
• Sarah Dyke
• Theresa Eggleston
• Savannah Kenny
• Erin Kuhn
• Alex Satchie
• Kathryn Tiffany
• Emily Zietlow

Teacher:

• Karen Tiffany

School:

• Cedarburg High School, Cedarburg, Wisconsin

Mentors:

• Audra Kramer, Ph.D. Candidate, Department of Cell Biology, Neurology and Anatomy, Medical College of Wisconsin
• Nashaat Gerges, Ph.D., Department of Cell Biology, Neurology and Anatomy, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

According to the National Institutes of Health, 5.1 million Americans have Alzheimer's disease (AD), which affects memory and the ability to learn. In long-term potentiation (LTP), a correlate of learning and memory, the number of receptors at the synapse increases. Calcium/calmodulin dependent protein kinase II (CaMKII), a large dodecameric enzyme comprising 1-2% of all proteins in the brain, is part of a signaling pathway implicated in LTP. In this pathway, Ca+2 binds calmodulin (CaM) and the Ca+2/CaM complex activates CaMKII, which then phosphorylates other proteins in the cell, like α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. To investigate the role of CaMKII, the Cedarburg SMART (Students Modeling A Research Topic) Team used 3D printing technology to design a CamKII model, highlighting the catalytic, self-association, and autoinhibitory domains. The Ca+2/CaM complex activates CaMKII by displacing a portion of the autoinhibitory domain that blocks the active site of the enzyme, exposing both the catalytic base and Thr286, the residue involved in autophosphorylation. When CaMKII phosphorylates AMPA receptors, their numbers increase in the post synaptic neuron and they are more sensitive to glutamate. Impaired LTP may lead to the cognitive decline seen in AD.

• Cudahy High School
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Cudahy High School

Wrinkle Release: The Entry Mechanism of Botulinum Neurotoxin




Students:

• Sara Kutcher
• Jazmin Jones
• Abby Jones
• Katherine MacDonald
• Katya Tolbert
• Alex Romfoe
• Amber Perkins
• Paige Broeckel
• Virginia Lachenschmidt

Teacher:

• Dan Koslakiewicz

School:

• Cudahy High School, Cudahy, Wisconsin

Mentor:

• Joseph Barbieri, Ph.D., Department of Microbiology and Molecular Genetics, Medical College of Wisconsin
• Andrew Karalewitz, Ph.D., Department of Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Botulism is a potentially fatal disease or therapeutic for muscular disorders, which results from intoxication of cells by the protein botulinum neurotoxin (BoNT). BoNT, produced by the bacteria Clostridium botulinum, paralyzes humans through inhibition of neuromuscular synaptic transmission. BoNT cleaves the Soluble NSF Attachment Protein Receptor (SNARE) proteins responsible for guiding synaptic vesicles carrying neurotransmitters for muscle stimulation to the neural plasma membrane, resulting in the muscle relaxation. BoNTs must first gain entry to the neuron using a ganglioside binding domain (GBP) that recognizes a specified ganglioside, a complex of carbohydrates and sialic acid within the neural plasma membrane. The sialic acid region of the ganglioside binds with specific residues on the BoNT GBP2: Tyr1115, Ser1275, Ile1240, Tyr1243, and Ser1242, modeled by the Cudahy SMART (Students Modeling A Research Topic) Team using 3D printing technology. After binding, the toxin is able to access a vesicle, crossing into the cytoplasm of the neuron, where the light chain of the toxin can cleave the SNARE proteins, causing a loss of muscular function due to lack of neural stimulation. In the case of a systemic BoNT intoxication, lack of muscle function can lead to respiratory failure but when used as a therapeutic BoNT relaxes specific muscles. While the action of the neurotoxin BoNT is well understood inside the neuron, the mechanism of entry is not well known. Understanding how BoNT recognizes and enters the neuron allows researchers to develop better treatments for infections and improved therapies to treat spastic muscle disorders.

• Grafton High School
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Grafton High School

TB or Not TB: That is Our Question The Role of Interleukin-12 Receptor in the Immune System and Preventing Tuberculosis




Students:

• Grace George
• Brandon Itson-Zoske
• Lelaina Evans
• Mariah Fox
• Megan Alascio
• Molly Schmidt
• Shabi Haider
• Brendon Konon

Teachers:

• Fran Grant
• Dan Goetz

School:

• Grafton High School, Grafton, Wisconsin

Mentor:

• Richard Robinson, Ph.D., Department of Microbiology and Molecular Genetics, Medical College of Wisconsin
• Halli Miller, M.S., Department of Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

According to the National Network for Immunization, the first tuberculosis (TB) vaccine was given in 1921 and has been administered to over 4 billion people. Unfortunately, the vaccine is not as effective as it once was because tuberculosis is becoming increasingly resistant to antibiotic treatments. As a result, new methods of treating and/or preventing this disease are underway. One method that could be used to prevent tuberculosis is to study the Interleukin-12 Receptor (IL-12R) an essential protein in initiating the immune response. When a pathogen invades the host, T-helper cells send signals to initiate an attack against the pathogen. IL-12, a cytokine, binds to IL-12R, which can signal macrophage activation to mount an attack against the invading pathogen. Some people have a mutated IL-12R which causes the patient to be infected by tuberculosis upon vaccination with BCG which contains live bacteria. IL-12 is a heterodimer with two glycoprotein subunits, p40 and p35, that are bound to the IL-12R via two disulfide bonds. If the IL-12R is mutated, the IL-12 will not bind properly to IL-12R, and the Helper T Cell's immune response to destroy the TB Cell will not commence. Although IL12R has not yet been crystallized, the Grafton SMART Team (Students Modeling A Research Topic) modeled gp130, a homolog of IL12R, using 3D printing technology. Ser 122 and Trp142 are highlighted on our model because this is where gp130 binds to IL-6, the homolog of IL-12.

• Greenfield High School
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Greenfield High School

The Future of Whole-Genome Sequencing: MGMT Mutations in a Family Could be Linked to Cervical Cancer




Students:

• Panfua Thao
• Robin Sandner
• Hannah Flees
• Joey Krasovich
• Morgan Borchardt
• Francis DeLeon-Camacho
• Alyssa Gerwig
• Zoe Osberg
• Mary Wojczulis

Teacher:

• Julie Fangmann

School:

• Greenfield High School, Greenfield, Wisconsin

Mentor:

• Elizabeth Worthey, Ph.D., Human and Molecular Genetics Center, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

In 2008 the CDC reported 4,008 cervical cancer-related deaths in the US. Researchers at MCW used Whole Genome Sequencing technology to sequence the DNA of a mother and daughter diagnosed with a rapidly progressing form of cervical cancer. Identifying the genetic underpinnings could explain how their cancer developed and progresses, and help develop a specific treatment for this cancer. One candidate gene,O-6-methylguanine-DNA-methyltransferase (MGMT), is a DNA repair enzyme that removes a methyl group from methylated guanines via a cysteine residue (Cys145), creating a normal guanine that properly pairs with cytosine in DNA. Alteration of MGMT, such as the mutations found in this family (Ile143Val and Lys178Arg), may prevent this reaction, leaving improperly pairing methylguanines. Altered MGMT may lead to an increased rate of DNA mutations, which may lead to accumulation of mutations altering molecules responsible for regulation of cell growth, leading to cancer development. Understanding MGMT's structure, specifically at these altered positions, will assist MCW researchers in determining whether the mutated MGMT is a likely cause of disease. The Greenfield SMART Team (Students Modeling A Research Topic) modeled MGMT using 3D printing technology to analyze the likely effect of these mutations to understand its possible role in the development of cervical cancer.

• Kettle Moraine High School
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Kettle Moraine High School

Gone with the Wnt: Role of GSK-3




Students:

• Jenna Greene
• Matthew Griesbach
• Grant Hoppel
• Thomas Hougard
• Daniel Lawniczak
• Pierce Lindell
• Samantha Miller
• Rachel Reiter
• Grant Sadowski
• Morgan Stachowski
• Nicholas Tolson

Teacher:

• Stephen Plum

School:

• Kettle Moraine High School, Wales, Wisconsin

Mentor:

• Anil Challa, Ph.D., Biotechnology and Bioengineering Center, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

According to the Centers for Disease Control every year more than 60,000 Americans die of excessive blood clots or thrombophilia, and many more suffer from this disorder. Clotting disorders pose unique problems for women because of their impact on reproductive health and pregnancy. Thrombin, a protease that cleaves fibrinogen and activates platelets, plays a key role in the generation of blood clots. Several mechanisms prevent excessive thrombin activity. Thrombin that diffuses away from the clot binds to its receptor, thrombomodulin. Thrombomodulin-bound thrombin can no longer generate blood clots. Instead, it cleaves and activates Protein C which shuts down further thrombin generation. The substitution Gln387Pro in thrombomodulin inhibits Protein C activation and interferes with this feed-back inhibition. The Laconia SMART (Students Modeling A Research Topic) Team used 3D printing technology to model thrombin in association with thrombomodulin. Amino acid residues within the catalytic site (Ser195, His57, and Asp102) and the two substrate binding sites, exosite I (Lys36- Arg77), and exosite II (Arg 93-Lys240 of thrombin, involved in these interactions are highlighted. Understanding the relation between structure and function of the thrombin-thrombomodulin complex may lead to new therapeutics for clotting disorders.

• Laconia High School
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Laconia High School

Cascading into the Thrombin-Thrombomodulin Complex: Comprehending a Substitution in Thrombomodulin




Students:

• Cole Tidemann
• Brady Beekman
• Amanda Leichtfuss
• Alex Parsons
• Jonathan Opheim
• Ashley Garb
• Noah Henke

Teacher:

• Jodie Garb

School:

• Laconia High School, Rosendale, Wisconsin

Mentor:

• Rashmi Sood, Ph.D., Department of Pathology, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

According to the Centers for Disease Control every year more than 60,000 Americans die of excessive blood clots or thrombophilia, and many more suffer from this disorder. Clotting disorders pose unique problems for women because of their impact on reproductive health and pregnancy. Thrombin, a protease that cleaves fibrinogen and activates platelets, plays a key role in the generation of blood clots. Several mechanisms prevent excessive thrombin activity. Thrombin that diffuses away from the clot binds to its receptor, thrombomodulin. Thrombomodulin-bound thrombin can no longer generate blood clots. Instead, it cleaves and activates Protein C which shuts down further thrombin generation. The substitution Gln387Pro in thrombomodulin inhibits Protein C activation and interferes with this feed-back inhibition. The Laconia SMART (Students Modeling A Research Topic) Team used 3D printing technology to model thrombin in association with thrombomodulin. Amino acid residues within the catalytic site (Ser195, His57, and Asp102) and the two substrate binding sites, exosite I (Lys36- Arg77), and exosite II (Arg 93-Lys240 of thrombin, involved in these interactions are highlighted. Understanding the relation between structure and function of the thrombin-thrombomodulin complex may lead to new therapeutics for clotting disorders.

• Madison West High School
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Madison West High School

Indispensable Replication Restart Helicase PriA Aids Bacterial Survival: A SMART Team Story




Students:

• Zoë Havlena
• Amy Hua
• Thomas Luo
• Sevahn Vorperian

Teacher:

• Basudeb Bhattacharyya, Ph.D. Candidate, Department of Biomolecular Chemistry, University of Wisconsin — Madison

School:

• Madison West High School, Madison, Wisconsin

Mentor:

• James L. Keck, Ph.D., Department of Biomolecular Chemistry, University of Wisconsin — Madison

Project Files:

• Poster

Abstract:

Approximately one disruption in DNA replication occur every cell cycle in bacteria leading to partially duplicated chromosomes. Since unfinished replication can result in genome instability and cell death, bacteria need a mechanism to reload the replication machinery onto the genome. Known as the replication restart primosome (RRP), several proteins function to reload the replicative helicase onto abandoned replication forks, restarting DNA replication. PriA is the most conserved member of the RRP, initiating the dominant replication restart pathway. A helicase, PriA remodels collapsed forks and serves as a platform for binding of other primosomal proteins. The Madison West High School Students Modeling a Research Topic (SMART) Team modeled PriA using 3D printing technology. PriA is a multi-domain protein and residues important for DNA binding, ATP hydrolysis, and helicase activity are modeled. Since DNA replication restart pathways are essential in preserving genomic integrity and cell viability in bacteria, studies of PriA offer an approach to developing novel antibacterial compounds.

• Marquette University High School
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Marquette University High School

One Indole Ring to Rule Them All: How Modeling of Naltrindole Bound to the Delta Opioid Receptor Can Aid the Development of Novel Analgesics




Students:

• Ernst Arnhold
• Nicholas Bell
• Theodore Boesen
• Nathan Boldt
• Alexander Borden
• Judson Bro
• Marlon Douglas
• John Fuller
• Quinlan Furumo
• Christian Gummin
• Andrew Keuler
• Daniel Kim
• Alexis Martinez
• Daniel Moldenhauer
• Ian Mullooly
• Ryan Nelsen-Freund
• Daniel Ogunkunle
• Luis Ortega
• Scott Palmersheim
• Thomas Sabatino
• Benjamin Schwabe
• Ryan Sung
• Karsten Trzcinski
• Cade Ulschmid

Teachers:

• Keith Klestinski
• Carl Kaiser

School:

• Marquette University High School, Milwaukee, Wisconsin

Mentor:

• Christopher W. Cunningham Ph.D., School of Pharmacy, Concordia University

Project Files:

• Poster

Abstract:

According to the Institute of Medicine, 116 million Americans currently suffer from chronic pain, costing our nation over $500 billion annually. As such, the use of pain-killing drugs like morphine and oxycodone has increased dramatically over the past decade. Analgesic effects are produced through agonism, or activation, of the body's mu (MOR) and delta (DOR) opioid receptors, which are G-coupled protein receptors. Tolerance, the decreased analgesic effect of MOR agonists after prolonged use, is a major problem facing opioid pain management. A drug that antagonizes, or inhibits, DOR can greatly reduce the development of tolerance to MOR agonists, offering new pain therapy potentials. One example of a selective DOR antagonist is naltrindole (NTI), which has a similar structure as morphine, except for a cyclopropylmethyl group on its nitrogen substituent and a bulky indole group. The large indole ring interacts with the W318 residue on MOR but is able to bond with W284 residue on the DOR, producing DOR-selective antagonism. Co-administration of NTI with morphine represents a potential new approach to producing analgesics with less tolerance. Understanding the structure of this ligand and enzyme may lead to structure based drug design. The Marquette University High School SMART Team is modeling naltrindole bound to DOR using 3-D printing technology.

• Messmer High School
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Messmer High School

R61 D,D-peptidase bound to a Helen-1 Penicillin Substrate or One "Hel"-en of an Antibiotic




Students:

• Sonia Sosa-Gonzalez
• Michaun Cobb
• Ngozi Osadame
• Isioma Osademe
• Kyler Campbell
• Merari Marin
• Jhordy Rios Llamosa
• Brigitte Rios Llamosa
• Kasaundra Jones

Teachers:

• Carol Johnson
• Meg Garland

School:

• Messmer High School, Milwaukee, Wisconsin

Mentor:

• Nicholas R. Silvaggi, Ph.D., Department of Chemistry and Biochemistry, University of Wisconsin — Milwaukee

Project Files:

• Poster

Abstract:

Although antibiotics like penicillin save lives, antibiotic-resistant bacteria are a growing issue. According to Purdom (2007), over 70% of infections acquired by hospital patients post-admission, are resistant to at least one prescribed antibiotic. Penicillin, a β-lactam antibiotic, treats bacterial infections caused by bacteria producing toxins within a host. Many pathogenic bacteria need a peptidoglycan cell wall for normal functionality. Enzymes in the cell membrane help form this cell wall by cross-linking peptidoglycan units. β-lactam antibiotics hinder bacterial cell wall biosynthesis by competing with the peptide substrate for the active site in these enzymes. While not the main enzyme used to produce bacterial cell walls, R61 DD-peptidase, a cytoplasmic enzyme, is easily crystallized to show bacterial enzyme chemistry. The active site of R61 consists of amino acid residues Ser62, Lys65, Lys159, Arg285, Thr299, and Thr301. The Messmer SMART Team modeled R61 complexed with Helen-1, a species-specific β-lactam, highlighting the functionality and chemistry of the active site amino acids and their interaction with the beta-lactam. Understanding the structure and function of the active site of penicillin binding proteins, like R61, could lead to new, species-specific antibiotics that could prevent antibiotic resistance in bacteria.

• Milwaukee Academy of Science
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Milwaukee Academy of Science

Cut, Copy, & Mutate: EcoRI and its Function in Genetic Engineering




Students:

• Cameron Bester
• Norris Campbell
• Jonte Jackson
• Jessie Jones
• Tim Jones
• Jailyn Kendrick
• Stephon Phillips
• Eddie Walls

Teachers:

• Kevin Paprocki
• Tyler Reed

School:

• Milwaukee Academy of Science, Milwaukee, Wisconsin

Mentor:

• Vishwakanth Y. Potharla, Ph.D., Department of Biological Sciences, University of Wisconsin — Milwaukee

Project Files:

• Poster

Abstract:

While farmers plant insect resistant corn, millions with diabetes inject themselves with the hormone, insulin. Despite the extraordinary differences between these practices, they have a common root: genetic engineering. Genetic engineering allows genes of interest to be moved from one species to another to create a desired protein or trait. This is accomplished through using restriction enzymes to cut DNA at a specific recognized sequence. Bacteria naturally use restriction enzymes to shred and destroy viral DNA. One of these restriction enzymes, EcoR1 endonuclease, is commonly used to genetically engineer insulin. In the early 1900s, insulin extraction and purification from a cow's pancreas was a time consuming and expensive process that yielded only a small amount of the hormone. More efficient production of insulin occurred in the 1950s when EcoR1 was used to cut the insulin gene from the human genome. Insertion of the gene into the genome of the bacteria, Escherichia coli did not disrupt normal bacterial division but did reprogram the bacteria to produce human insulin which could be collected for use. To investigate the structure of EcoR1, the Milwaukee Academy of Science SMART (Students Modeling A Research Topic) Team used 3D printing technology to design a model of the protein. EcoR1 is a homodimer composed of two polypeptide chains. Amino acids Asp91, Glu111, and Lys113 bind to the DNA sequence, GAATTC and cut between the guanine and adenine, allowing for gene insertion. Successfully engineered bacteria will now be able to use the inserted DNA sequence to create the desired protein. Genetic engineering with EcoRI is used to transfer genes between two organisms, whether it be bacteria, corn or even humans, thereby unlocking a variety of useful genetic combinations.

• Saint Dominic Middle School
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Saint Dominic Middle School

2A Protease from Human Rhinovirus 2




Students:

• Sara Achatz
• Luke Brown
• Thomas Brzozowski
• Jessica Diez
• Danny Drees
• Maddie Illman
• Brian Jerke
• Andy Kahler
• Lauren Kohl
• Vincent Marchese
• Harrison Ott
• John Otten
• Kyle Phelps
• Elizabeth Rowen
• Brianne Sherman
• Taylor Venuti
• Elena Valentyn

Teacher:

• Donna LaFlamme

School:

• Saint Dominic Middle School, Brookfield, Wisconsin

Mentor:

• William Jackson, Ph.D., Department of Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Human rhinoviruses (HRVs), a major cause of the common cold, usually produce mild illness, but in children they can trigger serious asthma exacerbations requiring hospitalization. HRVs belong to the Picornavirus family and like their close relative, the poliovirus, their short single-stranded positive-sense RNA genomes code for one polyprotein that is cleaved by the virus' two proteases into several viral proteins. The St. Dominic S.M.A.R.T. Team has modeled the 2a protease (2apro) of HRV2 using 3D-printing technology. 2apro is a homodimer with an active site and structurally essential zinc ion in each chain. 2apro promotes viral replication in host cells by shutting down both protein synthesis and nuclear-cytoplasmic import and signaling. By cleaving eIF4G (eukaryotic initiation factor 4G), 2apro prevents localization of host mRNAs to ribosomes, which are then free to synthesize the viral polyprotein using the viral RNA's IRES (internal ribosome entry site). Nuclear-cytoplasmic signaling and import is inhibited when 2apro cleaves specific nucleoporins (nups) in the nuclear pore complex (NPC). Proteolytic damage to Nup 62, Nup153, and Nup98 prevents the host cell's first responder, activated NFϰB (Nuclear Factor kappa B), from being imported into the nucleus where it turns on stress genes needed to signal warnings to immune system. The HRV-A, HRV-B, and HRV-C species differ in their abilities to cleave both NPC nups and eIF4G. HRV-A and HRV-C 2a proteases are more efficient at cleaving Nup 62 and eIF4G in vitro than HRV-B 2a proteases. Since HRV-A and HRV-C are also significantly better at triggering asthma exacerbations in children than HRV-B, it has been proposed that the effectiveness of a virus strain's 2a protease can predict the likelihood of that strain to cause asthma exacerbations.

• Saint Joan Antida High School
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Saint Joan Antida High School

Three Blind Mice: A Mutation in ADAM17 is Responsible for Embryonic Eyelid Closure Defect in woe Mice




Students:

• Omolola Adewale
• Velari Araujo
• Ashli Harris
• Erika Johnson
• Oluwatomisin Ladeinde
• Ivory Roberts
• Darneisha Virginia

Teacher:

• Cindy McLinn

School:

• Saint Joan Antida High School, Milwaukee, Wisconsin

Mentor:

• Duska Sidjanin, Ph.D., Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

During embryogenesis, in all mammals, the eyelids grow across the eye anterior, fuse together, and subsequently reopen. This process is essential for proper eye development. ADAM17 is a Zn2+ metalloprotease that has a role in cleaving numerous proteins including growth factors involved in EGFR signaling, a molecular pathway essential for cell migration. Mice with mutations in genes encoding ADAM17, EGFR, and EGFR ligands exhibit defects in embryonic eyelid closure. Recently, woe (wavy with open eyelids) mice, also exhibiting defects in embryonic eyelid closure, were identified. Genetic analysis of woe mice identified a mutation in ADAM17 leading to three different ADAM17 mutant proteins. Two of these mutant proteins were catalytically inactive; however, the third mutant protein exhibited normal ADAM17 catalytic activity. Further molecular analysis showed that this catalytically active mutant protein exhibited T265M substitution and was expressed at very low levels. The T265 residue is within the ADAM17 Zn2+ catalytic domain (215-473 aa). The T265M mutant protein exhibits normal ADAM17 catalytic activity most likely because T265 residue is not in the Zn2+ active site. The Saint Joan Antida SMART Team modeled ADAM17's catalytic core using 3-D printing technology. In addition SMART Team identified the location of the T265 amino acid residue within the catalytic core and its position relative to the active site. A better understanding of which amino acids are essential for the ADAM17 catalytic function will ultimately lead to a better understanding of ADAM17-mediated EGFR pathway and the role of this pathway in cell migration and organ development.

• Shorewood High School
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Shorewood High School

Red Rover, Red Rover, Send BCCP Over: Coordinating Catalysis in Pyruvate Carboxylase




Students:

• Monica Dix
• Emille Lozier
• Ananya Murali
• Anjana Murali
• Daniel Whittle
• Kelly Whittle

Teacher:

• Lalitha Murali

School:

• Shorewood High School, Shorewood, Wisconsin

Mentor:

• Adam D. Lietzan, Ph.D. Candidate, Department of Biological Sciences, Marquette University

Project Files:

• Poster

Abstract:

Cells exist in a state of continuous metabolic flux. The Krebs cycle, a central metabolic hub in the cell, is responsible for supplying precursors for the synthesis of amino acids, nucleotides, and compounds required for energy transfer. During periods of increased metabolic flux, metabolites in the Krebs cycle become depleted and must be replenished. Pyruvate carboxylase (PC), a multifunctional enzyme, replenishes the Krebs cycle by catalyzing the conversion of pyruvate to oxaloacetate, a Krebs cycle intermediate. The Shorewood SMART Team (Students Modeling A Research Topic) created a model of PC using 3D printing technology. PC contains four distinct domains: biotin carboxylase (BC), central allosteric, carboxyltransferase (CT), and biotin carboxyl carrier protein (BCCP). The overall reaction is initiated by BCCP-biotin carboxylation in the BC domain. BCCP-carboxybiotin physically translocates to the CT domain to transfer its carboxyl group to pyruvate. The active site of the CT domain undergoes a reconfiguration upon pyruvate binding to accommodate the docking of BCCP-carboxybiotin for pyruvate carboxylation. With the rise in antibiotic resistance, understanding how PC functions may provide a target in developing new antibiotics, whereby the new drug would eliminate critical metabolic activity, thus killing the bacteria.

• Valders High School
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Valders High School

Two Birds, One Stone": Reduction of HMBPP by the Iron-Sulfur Protein (IspH) for Isoprene Synthesis




Students:

• Rebecca Ansorge
• Angie Brandl
• Grace Ebert
• Elizabeth Evans
• Theresa Evenson
• Brianna Glaeser
• Phoenix Kaufmann
• Zach Leschke
• Mitchel Meissen
• Paige Neumeyer
• Alexis Patynski
• Ian Schmidt
• Christopher Singer

Teacher:

• Joe Kinscher

School:

• Valders High School, Valders, Wisconsin

Mentor:

• Eric Singsaas, Ph.D., Associate Professor of Biology, University of Wisconsin — Stevens Point, Research Director, Wisconsin Institute for Sustainable Technology

Project Files:

• Poster

Abstract:

A global natural rubber shortage may exceed one million tons by 2020, according to the International Rubber Study Group. While global demand is increasing for rubber, a fungus Microcyclus ulei, is killing rubber trees in South America and reducing supply of rubber globally. This has resulted in new monoculture plantations being developed in Southeast Asia where rainforests once existed. In order to satisfy demand for rubber in the future, renewable isoprene, a hydrocarbon produced by the nonmevalonate pathway used by bacteria, may be polymerized and used to create natural rubber and biofuels. Renewable isoprene production requires the iron-sulfur protein IspH, which reduces the substrate HMBPP (1-hydroxy-2-methylbut-2-enyl-4-diphosphate) to produce IPP (isopentyl diphosphate) and DMAPP (dimethylallyl diphosphate), the two precursors in the nonmevalonate pathway. The Valders SMART Team used 3D printing technology to model IspH. The substrate HMBPP enters the active site, and the rotation of HMBPP's hydroxymethyl group allows a complex to form with the Fe4-S4 cluster. The complex is further stabilized by the IspH amino acid Thr167 and HMBPP hydrogen bonding with Glu126. Electron transfer from the Fe4-S4 cluster and the protonation of HMBPP by Glu126, results in IPP or DMAPP in an approximate ratio of 6:1 at equilibrium. Industrial production of isoprene would be favored by shifting the IPP/DMAPP equilibrium towards DMAPP, as DMAPP is directly catalyzed into isoprene. By understanding how DMAPP production may be increased, the mass production of isoprene could be made more efficient to generate rubber and biofuels.

• Wauwatosa West High School
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Wauwatosa West High School

Transthyretin (TTR): Carrier of Thyroxine and Its Evil Twin (Environmental Pollutants)




Students:

• Zaynab Hassan
• Madeline Jordan
• Leah Rogers
• Zoe Stack
• Kayla Thao
• Cheung Wongtam
• Aleksandra Zielonka

Teacher:

• Mary Anne Haasch

School:

• Wauwatosa West High School, Wauwatosa, Wisconsin

Mentor:

• Cameron Patterson, School of Pharmacy, Concordia University
• Joseph McGraw, Ph.D., School of Pharmacy, Concordia University

Project Files:

• Poster

Abstract:

Transthyretin (TTR) is a carrier protein in the blood that binds to and transports the thyroid hormone thyroxine throughout the human body. The thyroid hormone is necessary for fetal development and metabolism regulation. TTR is a tetramer formed from two dimers. Ala-108, Ser-117, Thr-119, Lys-15, Leu-17, Thr-106, and Val-121 all play a role in binding the thyroxine in a hydrophobic channel formed where the two dimers come together. Polybrominated diphenyl ethers (PBDEs), found in flame retardants, which are in numerous household products, are converted in the body to hydroxy-PBDEs. Hydroxy-PBDEs mimic the shape of thyroid hormones allowing them to bind with TTR. Hydroxy-PBDEs can have a stronger affinity to bind to TTR, disrupting the transport of the thyroid hormone necessary for developmental and metabolic processes. An initial study shows a possible correlation between high levels of PBDEs and hypoplastic left-heart syndrome, a condition found in four out of 10,000 newborns (Lucile Packard Children's Hospital at Stanford) in which the left side of the heart does not fully develop. Wauwatosa West SMART Team (Students Modeling A Research Topic) modeled TTR using 3D printing technology.

• Westosha Central High School
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Westosha Central High School

Transportin' with Transportin (Trn1): A Nuclear Import Mechanism




Students:

• Julia Alberth
• Jonah Arbet
• Nick Bielski
• Monica Ceisel
• Sam Colletti
• Evan Kirsch
• Mitchell Kirsch
• AJ Reeves
• Julia Williams

Teacher:

• Jonathan Kao

School:

• Westosha Central High School, Salem, Wisconsin

Mentor:

• Mark McNally Ph.D., Department of Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Proteins manufactured in the cytoplasm play an important role in nuclear processes such as RNA splicing. Immediately after transcription, precursor (pre-) mRNA contains introns that are removed in making mature mRNA. Splicing proteins like hnRNP A1 (A1), manufactured in the cytoplasm, are transported into the nucleus and influence RNA splicing decisions. Some proteins in eukaryotic cells use the receptor Transportin (Trn1) for import. Cytoplasmic Trn1 is found in a configuration that allows for the pick-up of cargo proteins. A1 has a nuclear localization signal (NLS) to which Trn1 can bind. Once bound, the Trn1/A1 complex enters the nucleus through a nuclear pore. The protein Ran, when associated with GTP, binds to the complex and causes a loop of approximately 60 amino acids to move and expel the cargo. With the cargo delivered, Trn1 returns to the cytoplasm as a Trn1/RanGTP complex. GTP is then hydrolyzed into GDP signaling Ran to release Trn1. The amino acid loop returns to its original position allowing for another round of transport. The model constructed using 3D printing technology by the Westosha Central HS Smart team in cooperation with MSOE features Trn1 in complex with RanGTP, the mechanical state of cargo unloading. The NLS of A1 can be modified such that Trn1 cannot bind and deliver A1 to the nucleus. Failure of A1 to reach the nucleus results in altered splicing of mRNA, which can lead to diseases like cancer. Therefore, targeting the interaction between Trn1 and its cargo may provide an option for treating diseases.

• Whitefish Bay High School
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Whitefish Bay High School

GABAA Receptor: Knocked Out




Students:

• Jackson Middleton
• Shawn Wang
• Na'il Scoggins
• John Schroeder
• Sam Broadnax
• Jieun Heo
• Marissa Korte
• Morgan Phillips
• John Park
• Frank Zhang
• Wentong Zhang
• Alice Zhao

Teachers:

• Paula Krukar
• Katie Brown
• Lisa Krueger
• Marisa Roberts

School:

• Whitefish Bay High School, Whitefish Bay, Wisconsin

Mentor:

• Robert Peoples, Ph.D., Department of Biomedical Science, Marquette University

Project Files:

• Poster

Abstract:

Today, surgeons and dentists would not consider operating without the use of anesthetics, drugs that help numb pain and induce unconsciousness by inhibiting the transmission of signals in nerve cells. The GABAA receptor is a transmembrane receptor protein activated by the neurotransmitter gamma-aminobutyric acid (GABA) that plays a crucial role in the action of proprofol as an anesthetic. The Whitefish Bay SMART (Students Modeling A Research Topic) Team is modeling the GABAA receptor protein using 3D printing technology. When activated, the GABAA receptor selectively allows chloride ions to pass through the membrane and into the cell, creating a more negative overall charge inside the cell. When a nerve cell is excited, a sudden change in ion concentrations triggers an electrochemical potential across the cell membrane, ultimately resulting in the passage of the original signal to the next neuron. However, the GABAA receptor acts as an inhibitor, and impedes the spreading of the message by making the cell less likely to be in an excited state, causing the cell to relay a neural signal less frequently. Propofol produces its effects by enhancing the activity of the GABAA receptor. Currently, researchers are trying to pinpoint how propofol acts on the GABAA receptor protein because its molecular mechanism is not fully understood. It has been found that a phenylalanine at position 385 on the GABAA receptor is necessary for proprofol to produce its effects. Research targeting how propofol alters the function of the GABAA receptor may lead to the development of more effective anesthetics with fewer side effects.

• Wisconsin Virtual Learning Academy
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Wisconsin Virtual Learning Academy

PEDF: An Angiogenesis Inhibitor and Its Role in Glioblastoma Multiforme




Students:

• Emily Billin
• Hardy Liesener
• Holly Van Gorden
• Kiera Yohe
• Michael Mitchell

Teacher:

• Becki Van Keuren

School:

• Wisconsin Virtual Learning Academy, Northern Ozaukee School District, Fredonia, WI

Mentor:

• Shama P. Mirza, Ph.D., Department of Biochemistry, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Glioblastoma multiforme (GBM) is a cancerous brain tumor with almost 100% recurrence rate even after surgery, radiation and chemotherapy. Pigment epithelium-derived factor (PEDF) has been found in areas where these tumors do not grow as aggressively. PEDF slows the growth of tumors by inhibiting angiogenesis, a physiological process involving growth of new capillaries from pre-existing blood vessels in the body. Restricting blood flow to the tumor starves it of oxygen and nutrients. The mechanism of PEDF-mediated inhibition of angiogenesis is unknown. Research has shown that PEDF undergoes posttranslational modifications (PTM), chemical changes to a protein after translation, such as the addition of carbohydrates (glycosylation) or phosphate groups (phosphorylation), which may occur during various cellular events in tumors. PEDF is phosphorylated at Ser227, Ser114 and Ser24 and glycosylated at Asn285. Glycosylation may also occur on amino acids within a specific region of the protein (amino acids 371-383). The Wisconsin Virtual Learning SMART (Students Modeling A Research Topic) Team modeled PEDF using 3D printing technology. Identifying the PTMs of PEDF in GBM tumors and plasma samples may further the understanding of angiogenesis inhibition and in turn, may lead to the development of treatments for these lethal cancers.

2011-2012 SMART Teams

Nineteen schools participated in the local SMART Team program during the 2011-2012 school year. The remote SMART Teams and HHMI SMART Teams also expanded, for a total of over sixty SMART Teams nationwide. Completed projects are described below.

• Brookfield Central High School
X

Brookfield Central High School

Uncoupling Protein 2: A Mitochondrial Detour




Students:

• Deepti Ajjampore
• Krishti Bhowmick
• Tess Hammer
• Ramprasad Karanam
• Raga Komandur
• Kingshuk Mazumdar
• Nikil Prasad
• Sahana Ravindran
• Rishi Sachdev
• John Scanlon
• Nikita Sood
• Emily Strack
• Brian Zhu

Teacher:

• Louise Thompson

School:

• Brookfield Central High School, Brookfield, WI

Mentor:

• Martin Bienengraeber, Ph.D., Department of Anesthesiology, Pharmacology and Toxicology, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Heart diseases are the leading cause of death for Americans today. Mitochondria play a crucial role in recovery following ischemia (blood flow restriction) and reperfusion (blood flow return) injury, when a surge of reactive oxygen species (radicals) originating from the mitochondrial electron transport chain causes damage to proteins, lipids and DNA. Uncoupling protein 2 (UCP2), an inner mitochondrial membrane transport protein, is speculated to participate in this protection. The presumed function of UCP2 is carrying protons into the mitochondrial matrix along a concentration gradient generated by the electron transport chain. Normally, this proton gradient is used by ATP synthase to phosphorylate ADP to ATP. Under certain conditions, protons may preferentially be transported through UCP2, creating a detour past ATP synthase ("uncoupling"). Such uncoupling reduces damaging reactive oxygen species whose presence may actually activate UCP2 by residue modification. There are two proposed mechanisms for the transport of protons into the matrix. One is the direct transport of protons through UCP2. Alternatively, a fatty acid anion is transported out of the matrix through UCP2, while the protonated fatty acid permeates through the membrane into the matrix. UCP2 must be tightly regulated so it is only active when required, enabling the mitochondria to produce ATP. Understanding transport mechanism and regulation of UCP2 could lead to effective prevention of tissue injury due to heart attack. The Brookfield Central High School SMART Team created a physical model of UCP2 using 3-D modeling printing technology in order to better understand the structure-function relationship of UCP2.

• Brown Deer High School
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Brown Deer High School

Cation-Dependent Mannose 6-Phosphate Receptor: Tag, You're It!




Students:

• Maxwell Bord
• Carolyn Hermsen
• Wongsai Heur
• Christopher Jones
• Erica Kennedy
• William Keslin
• May Khang
• Hannah Leedom
• Andrew LeMense
• David McMurray
• Evan Naber
• Danielle Parish
• Mary Elizabeth Rice
• Alana Rodgers
• Charles Rosio
• Jordan Schubert
• Alexandra Smith

Teacher:

• Gina Vogt

School:

• Brown Deer High School, Brown Deer, WI

Mentors:

• Nancy Dahms, Ph.D., Department of Biochemistry, Medical College of Wisconsin
• Linda Olson, Ph.D., Department of Biochemistry, Medical College of Wisconsin
• Jung-Ja Kim, Ph.D., Department of Biochemistry, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Approximately 50 different lysosomal storage disorders affect one in every 5000 births, limiting life expectancy and quality of life. Therapies are available for a handful of these disorders. Sixty different lysosomal enzymes are responsible for recycling macromolecules in cells. In normal functioning cells, lysosomal enzymes are synthesized in the endoplasmic reticulum and are transported to the lysosome. Transportation of lysosomal enzymes occurs when a mannose 6-phosphate (Man-6-P) tag is placed on these enzymes, which is recognized by the cation-dependent mannose-6-phophate receptor (CD-MPR). The CD-MPR binds to the Man-6-P tags through a recognition site (Y45, Q66, H105, R111, E133, R135, Y143) and transports the enzymes from the Golgi apparatus to an endosome where enzymes are released from CD-MPR due to a more acidic environment. Enzymes are finally transported via vesicles to the lysosome to accomplish their function. Without the Man-6-P tags, CD-MPR cannot bind to the enzymes, prohibiting transportation to an endosome and ultimately the lysosome. If lysosomal enzymes are not properly transported, they are secreted out of the cell, causing lysosomal storage disorders due to buildup of macromolecules in the lysosome. The Brown Deer SMART Team (Students Modeling A Research Topic) created a physical model of CD-MPR using 3D printing technology.

• Cedarburg High School
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Cedarburg High School

I Like to Move It, Move It: The Role of Kif3B of Kinesin II in Primary Cilia




Students:

• Kyle Kohlwey
• Meredith Kuhn
• Nicole Lang
• Kathryn Tiffany
• Laura Tiffany
• Jacqueline Albrecht
• Sarah Clapp
• Kayla Fenton
• Austin Gallogly
• Rebecca Jankowski

Teacher:

• Karen Tiffany

School:

• Cedarburg High School, Cedarburg, WI

Mentor:

• Minde Willardsen, Ph.D., Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Primary cilia are structures found on the surface of most cells and are important for cell signaling. For cilia to develop and function properly, materials must be transported in and out of these structures by motor proteins that travel along microtubules in the cilia. The Kinesin II motor protein transports cargo toward the tip of the cilia. Our interest lies in a motor subunit of Kinesin II, Kif3B. Kif3B binds to both ATP and microtubules; hydrolysis of ATP causes Kif3B to change its shape and move up the microtubules. Cilia development depends on the movement of materials into the cilia, and research indicates that if Kif3B is not functioning, cilia formation will not occur properly. Diseases called ciliopathies result if primary cilia production is altered. These diseases include Bardet-Biedl syndrome (BBS), Joubert syndrome, and MORM syndrome. Using 3D printing technology, the Cedarburg SMART (Students Modeling a Research Topic) Team has designed a model of Kif3B to investigate the interaction of amino acid residues 96 through 104 of Kif3B with ATP and to visualize the neck region in Kif3B important for dimerization with Kif3A and for microtubule motility.

• Cudahy High School
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Cudahy High School

Over the Limit, Under Arrest: The NMDA Receptor and the Effect of Alcohol




Students:

• Becky Fansler
• Sara Kutcher
• Amber Perkins
• Liz Michalzik
• Laura Harrold
• Roxanne Thiede
• Virginia Lachenschmidt
• Amber Haapakoski
• Paige Broeckel
• Jazmin Jones

Teacher:

• Dan Koslakiewicz

School:

• Cudahy High School, Cudahy, WI

Mentor:

• Robert Peoples, Ph.D., Department of Biomedical Sciences, Marquette University

Project Files:

• Poster

Abstract:

Alcohol, or ethanol, is one of the most abused drugs worldwide, dating back to ancient cultures including Mesopotamia. Effects of alcohol on behavior are well-known, such as incoherence and lack of coordination. Overconsumption of ethanol can lead to alcoholism, which is related to genetic variations and brain chemistry. In the brain, proteins such as the N-methyl-D-aspartate (NMDA) receptor are responsible for multiple cognitive functions. The NMDA receptor binds glutamate, a major neurotransmitter, transferring signals from one neuron to another across the synapse, or gap between neurons. When ethanol is not present in the system, glutamate binds to the NMDA receptor on the post-synaptic cell and opens the ion channel, allowing sodium and calcium to enter and excite the cell. Ethanol, when present, crosses the protective blood-brain barrier and appears to bind to specific amino acid side chains: Ala825, Phe637, Met823, Val820, Phe639, and Leu824, which are in the transmembrane portion of the NMDA receptor GluN1 and GluN2A subunits. Ethanol limits NMDA receptor function by inhibiting the ion channel gate from opening and depolarizing the membrane. When ethanol binds to sites in the transmembrane domain, the conformational change of the NMDA receptor is inhibited, blocking the flow of sodium and calcium into the neuron, preventing synaptic transmission. By learning how ethanol interacts with the NMDA receptor to change its function, researchers hope to discover better treatments for alcoholism. The Cudahy SMART Team (Students Modeling A Research Topic) modeled the NMDA receptor, highlighting important structures, using 3D printing technology.

• Grafton High School
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Grafton High School

EPCR: The Role of Endothelial Protein C Receptor in Blood Clotting and the Immune System




Students:

• Lisa Borden
• Mariah Fox
• Sean Gasiorowski
• Grace George
• Lucas Mullens
• Emily Volkmann
• Jacob Zirbel

Teachers:

• Dan Goetz
• Fran Grant

School:

• Grafton High School, Grafton, WI

Mentor:

• Andrea Ferrante, M.D., Blood Research Institute, Blood Center of Wisconsin

Project Files:

• Poster

Abstract:

The coagulation of blood is essential to normal bodily function, but is especially important upon blood vessel injury. An excess of coagulation can lead to complications as well. One regulatory mechanism between pro- and anti-coagulant mechanisms involves Protein C. Protein C assists in the regulation of blood clotting by acting in a negative feedback response to the production of thrombin, a protein with procoagulant activity in the serum. Thrombin loses its procoagulant functions when it interacts with a membrane-bound protein expressed on endothelial cells called thrombomodulin. The thrombin/thrombomodulin complex promotes conversion of Protein C into Activated Protein C (APC). If protein C binds to the thrombin/thrombomodulin complex in the presence of endothelial protein C receptor (EPCR), the rate of this activation increases twentyfold. As a soluble molecule in the bloodstream, APC functions as an anti-coagulant factor. When APC remains bound to EPCR, the APC/EPCR complex can interact with the receptor protein, Protease-activated Receptor 1 (PAR1), resulting in decreased tissue damage during inflammation. Because EPCR is similar in structure to the Major Histocompatibility Complex (MHC), an important receptor in activating an immune response by presenting antigens to T-cells, it may have a similar function. While the MHC binds to peptides to perform its immune activation function, EPCR is thought to bind to lipids and may potentially be involved in cytoprotective mechanisms during sepsis. Because of its importance in blood clotting and its possible immune function, the Grafton High School SMART (Students Modeling A Research Topic) Team chose to model EPCR using 3D printing technology.

• Greenfield High School
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Greenfield High School

GatCAB: A Potential Target for Bacterial Destruction




Students:

• Amanda Miller
• Tania Alvarez
• Morgan Borchardt
• Haleigh De Smet
• Srinidhi Emkay
• Hannah Flees
• Pooja Keshvala
• Joey Krasovich
• Phat Nguyen
• Robin Sandner
• Panfua Thao
• Tammy Tian

Teacher:

• Julie Fangmann

School:

• Greenfield High School, Greenfiled, WI

Mentor:

• Martin St. Maurice, Ph.D., Department of Biological Sciences, Marquette University

Project Files:

• Poster

Abstract:

Staph infection is caused by the bacteria Staphylococcus aureus, which have become increasingly resistant to a broad spectrum of antibiotics. New ways to combat these bacteria are needed. The Greenfield High School SMART (Students Modeling A Research Topic) Team is modeling the enzyme GatCAB using 3D printing technology. GatCAB is found in certain bacteria and archaea and could be a target for new antibiotics. During protein synthesis, ribosomes bring together aminoacylated-tRNA molecules to form proteins needed for survival. Some bacteria have tRNAs that always have an incorrect amino acid attached. Staphylococcus aureus contains such misacylated tRNA molecules with aspartate where asparagine should be attached. GatCAB's three proteins (GatA, GatB, and GatC) correct these misacylations. GatA's active site produces ammonia, which travels through a tunnel leading to GatB. GatC holds GatA and GatB together. GatB's hinge recognizes and binds to the T loop of the misacylated tRNA, so GatCAB will not correct a tRNA that should have aspartate. The aspartate on the tRNA enters GatB's active site, where the aspartate reacts with ATP and the ammonia from GatA to form asparagine, ensuring the correct amino acid is on the proper tRNA. If the misacylated tRNAs were left uncorrected, protein synthesis would be severely disrupted, and the bacteria would die. If scientists produce a drug to prevent GatCAB from fixing the misacylated amino acids, the world would have a new weapon to fight antibiotic resistant bacteria.

• Kettle Moraine High School
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Kettle Moraine High School

The Day and Night of Grb2 in Glioblastoma Multiforme




Students:

• Grant Hoppel
• Tyler Holman
• Harrison Plum
• Bailey Rockwell
• Kevin Zhang
• Sean Murray
• Zella Christensen
• Alberto Patti
• Matt Griesbach
• Kimberly Stalbaum

Teacher:

• Steve Plum

School:

• Kettle Moraine High School, Wales, WI

Mentor:

• Shama Mirza, Ph.D., Department of Biochemistry, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Growth Factor Receptor Binding Protein-2 (Grb2) is an essential protein in cell motility, signaling, and most importantly, cell division. In a healthy cell, Grb2 interacts with various growth factors, stimulating the Ras signal transduction pathway, which facilitates cell growth and division. One such growth factor is VEGF (vascular endothelial growth factor), which promotes capillary branching, or angiogenesis. In a cancerous cell, this process goes horribly wrong. Overproduction of VEGF causes overexpression of GRB2 and overstimulation of the Ras pathway, leading to tumor growth. The growing tumor requires greater amounts of oxygen, supplied through angiogenesis, to sustain itself, causing increased production of VEGF and ultimately more tumor growth. Through this process, Grb2's ability to link angiogenesis and tumor growth can result in deadly cancers, including one of the most severe forms of brain cancer, Glioblastoma Multiforme (GBM). One method of treating this form of cancer targets VEGF, inhibiting both angiogenesis and tumor growth through the Grb2-Ras pathway. One medicine developed for this purpose is Bevacizumab (commonly called Avastin), which has been shown to lower the function of VEGF. By inhibiting the production of VEGF, the overstimulation of Grb2 is negated and, under ideal circumstances, the tumor is deprived of oxygen and nutrients, resulting in atrophy.

• Laconia High School
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Laconia High School

Prions Gone Mad: Insight into Prion Diseases; Structural Lessons Learned from Fungus




Students:

• Kea Schmuhl
• Tyler Foote
• Laura Block
• Ashley Toll
• Erin Cunningham
• Cole Tidemann
• Dakota Moore
• Ashley Garb

Teacher:

• Jodie Garb

School:

• Laconia High School, Rosendale, WI

Mentor:

• Anita Manogaran, Ph.D., Department of Biological Sciences, Marquette University

Project Files:

• Poster

Abstract:

Prion diseases, including bovine spongiform encephalopathy (mad cow) and Creutzfeldt-Jakob disease in humans, are caused by a misfolded protein in the brain that has the ability to convert the normal protein to the misfolded form. Prions in the brain lead to the formation of aggregates of misfolded protein, which are thought to be infectious and toxic to the cell. Additionally, these aggregates are resistant to detergents or heat, and are difficult to destroy. While reliable structural studies of human prion proteins have been unsuccessful, the structure of the [HET-s] prion in the fungus Podospora anserina has been solved. The HET-s protein misfolds and assembles into a higher order structure called a "solenoid", a tube of circular beta sheets. The Laconia SMART Team (Students Modeling A Research Topic) modeled the HET-s protein with 3D printing technology, illustrating its solenoid structure. Each "turn" of the solenoid consists of 21 amino acids. A pocket of hydrophobic (V244, L276, F286, W287), hydrophilic (Q240, E280), and glycine amino acid side chains is thought to stabilize the solenoid structure. Since human prion proteins are thought to share a similar solenoid structure with HET-s, studying HET-s provides insight into the molecular structure of human prions, which could potentially lead to advances in treatment of prion-related diseases.

• Madison West High School
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Madison West High School

Pumping Mechanism and Function of AcrAB-TolC Complex in E. coli




Students:

• Elijah Carrel
• Zoë Havlena
• Amy Hua
• Thomas Luo
• Xiangyi Tan
• Sevahn Vorperian

Teacher:

• Basudeb Bhattacharyya

School:

• Madison West High School, Madison, WI

Mentor:

• David Nelson, Ph.D., Department of Biochemistry, University of Wisconsin — Madison

Abstract:

Bacterial disease treatment has become a serious problem in clinical medicine due to antibiotic resistance. One way E.coli acquires resistance against otherwise effective antibiotics is through the over expression of the multidrug efflux pump AcrAB-TolC. The natural function of AcrAB is to pump out bile salts and their derivatives to increase survival during the presence of high detergent concentrations in E. coli's natural habitat in the human digestive system. However, the AcrAB-TolC system also has the capability to pump out a wide variety of foreign compound, such as antibiotics, due to the broad specificity of the pump. AcrB forms a homo-trimeric structure that uses cyclical conformational changes powered by ATP to transport foreign compounds into the TolC pore, which eventually expels the compounds from the bacteria. The role of AcrA is less defined, perhaps providing structural support to AcrB. We modeled the interactions between AcrB and associated proteins in the E. coli pump, AcrA and TolC, using 3D printing technology. The study of the detailed structures of AcrAB-TolC may be of paramount importance in the development of novel pharmaceuticals against bacterial infections.

• Marquette University High School
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Marquette University High School

Cytochrome P450: The Metabolizer




Students:

• Alex Borden
• John Fuller
• Daniel Kim
• Alex Martinez
• Joe Puchner
• Nick Bell
• Jud Bro
• Sam Broadnax
• Joel Gebhard
• Nate Griffin
• Christian Gummin
• Andrew Keuler
• Daniel Moldenhauer
• Tommy Sabatino
• Randy Spaulding
• Ryan Sung
• Caden Ulschmid

Teachers:

• Keith Klestinski
• David Vogt

School:

• Marquette University High School, Milwaukee, WI

Mentors:

• James Kincaid, Ph.D., Department of Chemistry, Marquette University
• Piotr Mak, Ph.D., Department of Chemistry, Marquette University
• Kazik Czarnecki, Ph.D., Department of Chemistry, Marquette University

Project Files:

• Poster

Abstract:

Why can't Grandpa drink grapefruit juice with his Lipitor? Why is John hypersensitive to aspirin? The answers lie in a study of cytochrome P450s (CYP101), a family of enzymes that are responsible for the transformation of vitamins, pharmaceuticals and other foreign chemicals into soluble and readily excreted molecules. This goal is achieved primarily by hydroxylation reactions, which occur in these molecules through a series of extremely fast sequential reactions, called an enzymatic cycle. In order to better understand certain intermediates in the cycle, the reaction must be stopped at given points. In a particular variant of cytochrome P450s, the presence of an aspartic acid near the active site causes immediate protonation of the peroxo group, making it impossible to stop the hydroxylation reaction. However, in the mutant form, CYP101 D251N, the aspartic acid is replaced with an asparagine, which blocks protonation on an atomic level. Scientists need to study these molecules and characterize the molecular structures of the reaction intermediates in order to understand what factors affect the process, such as mutation of particular protein sites and blockage by interfering chemicals. The Marquette University High School SMART Team (Students Modeling A Research Topic) modeled both the wild-type and the D251N mutant of P450cam using MSOE’s 3D printing technology.

• Messmer High School
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Messmer High School

The Role of Sterol Carrier Protein 2 in the Endocannabinoid System




Students:

• Anwuri Osademe
• Sonia Sosa-Gonzalez
• Briana Miller
• Gabriella Leachmon
• Ngozi Osademe
• Michaun Cobb
• David Gonzalez

Teacher:

• Carol Johnson

School:

• Messmer High School, Milwaukee, WI

Mentors:

• Elizabeth Sabens Liedhegner, Ph.D., Neuroresearch Center, Medical College of Wisconsin
• Cecilia J. Hillard, Ph.D., Neuroresearch Center, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

The endocannabinoid system (ECS) plays a role in diverse disorders such as anxiety, addiction, eating and memory disorders. The ECS is found throughout the body and consists of two lipid signaling molecules, N-arachidonylethanolamine (AEA) and 2-arachidonoylglycerol (2-AG), and their target receptor, CB1R. In the brain, these ligands bind to CB1R and modulate the release of neurotransmitters from nerve cells resulting in changes in synaptic transmission. Disorders result when levels of AEA and 2-AG are either too high or too low. While 2-AG is synthesized at the plasma membrane (PM), AEA is produced in the ER and may require an intracellular carrier protein to move through the cytoplasm to the PM where it is released. The lipid binding protein, sterol carrier protein 2 (SCP-2) is hypothesized to transport AEA due to its ability to bind to membranes and its nonspecific hydrophobic binding pocket. This proposed binding pocket is composed of 2 alpha helices, 3 beta sheets and the core hydrophobic amino acid residues F13, F27, F35, F37 and F80. The Messmer SMART Team (Students Modeling A Research Topic) created a model of SCP-2 using 3D printing technology. Understanding the structure of SCP2 and how this protein might regulate AEA and 2-AG levels could lead to possible new treatments for debilitating mood, appetite, memory and anxiety disorders.

• Milwaukee Academy of Science
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Milwaukee Academy of Science

To Stick or Not to Stick: PKA and Its Role in Platelet Coagulation




Students:

• Cameron Bester
• Norris Campbell
• Shaaliyah Friar
• Breeonna James
• Jessie Jones
• Timothy Jones
• Eddie Walls
• Erykah Williams

Teacher:

• Kevin Paprocki

School:

• Milwaukee Academy of Science, Milwaukee, WI

Mentors:

• Jackie Wisinski, Blood Research Institute, Blood Center of Wisconsin
• Gil White, M.D., Blood Research Institute, Blood Center of Wisconsin

Project Files:

• Poster

Abstract:

Have you ever gotten a cut and wondered how and what makes it heal? When you get a cut, platelets stick together, or aggregate to form a scab in a process called coagulation. A platelet is a cell fragment that is found in the blood and is involved in blood clotting. Too little blood clotting can end in wounds not healing properly. Too much clotting can cause heart attacks and strokes. Protein Kinase A (PKA) regulates the ability of platelets to aggregate. The Milwaukee Academy of Science SMART Team (Student Modeling A Research Topic) modeled the PKA protein using 3D printing technology. Kinase proteins are responsible for adding a phosphate group to other proteins to activate them through a process called phosphorylation. PKA is made up of four subunits: two Regulatory Subunits (R-Subunits) and two Catalytic Subunits (C-Subunits). When the R-subunits are bound to the C-subunits, PKA is inactive. When a small molecule, cyclic adenosine monophosphate (cAMP), binds to the R-subunits, the C-subunits are released, thus activating the kinase. When active, the C-subunit attaches a phosphate to a target protein, such as Rap1b. Rap1b is an important player in the regulation of platelet aggregation and is located on the inner cell membrane. When Rap1b is phosphorylated, it detaches from the cell membrane and enters the cytosol. As a result, the platelets are not able to aggregate. In essence, it is the behavior of PKA that determines whether platelets aggregate or remain free floating, which in turn makes PKA an incredibly important factor in understanding heart attacks and strokes.

• Shorewood High School
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Shorewood High School

Cadmium Inhibition of the Sodium-Dependent Glucose Co-Transporter




Students:

• Emilie Lozier
• Ananya Murali
• Anjana Murali

Teacher:

• Lalitha Murali

School:

• Shorewood High School, Shorewood, WI

Mentors:

• Rajendra K. Kothinti, Ph.D., Kidney Disease Center, Medical College of Wisconsin
• Niloofar Tabatabai, Ph.D., Kidney Disease Center, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Cadmium (Cd²⁺) is a toxic metal found in the environment, a product of industrial pollution, and can enter the body through inhalation. Chronic exposure to Cd²⁺ causes kidney failure characterized by Fanconi-like Syndrome, in which an array of sodium-dependent nutrient transport is inhibited. Cd²⁺ causes a concentration-dependent reduction in sodium-glucose co-transport that is correlated to the sodium-glucose transporter (SGLT1) gene expression in kidney proximal tubule epithelial cells. SGLT1 is regulated by the zinc finger transcription factor, Sp1. In the presence of Cd²⁺, the zinc ion is displaced by a Cd²⁺ ion, resulting in the loss of transcriptional regulation of SGLT1. The structure of human SGLT1 is not known; as such the Shorewood SMART Team (Students Modeling A Research Topic) modeled a bacterial homolog of SGLT1 using 3D printing technology. The SGLT1 protein transmembrane helices (TM2E, TM3, TM7E, TM8, and TM11) and amino acids on these helices vital for Na+ dependent glucose co-transport are conserved. SGLT1 undergoes a conformational change enabling Na+ dependent glucose transport across the apical membrane of proximal tubule of kidney. In order to understand the glucose transport in the face of Cd²⁺ and to understand the underlying molecular mechanism responsible for SGLT1 glucose transport, it is essential to know the protein structure of SGLT1

• St. Dominic Middle School
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St. Dominic Middle School

Kinesin I: Freaky Fast Delivery (100 Steps per Second!)




Students:

• Ellen Bruhn
• Aaron Chaffee
• Vienna George
• Nicholas Gequillana
• Ryan Hadland
• Meaghan Lagore
• Gabby Marchese
• Kelsey O'Brien
• Tyler Parker
• Erin Rieger
• Caroline Sauer
• Matthew Schmude
• McKenna Scott
• Danny Storts
• Abby Weisse
• Matthew Wickeham

Teacher:

• Donna La Flamme

School:

• St. Dominic Middle School, Brookfield, WI

Mentor:

• Jason Bader, Ph.D., Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Kinesin is a multi-subunit motor protein which, through the use of ATP hydrolysis, moves along microtubules (MTs) carrying cargo too big to diffuse but needed in cellular processes. Microtubules (MTs) are protein polymers, forming the cytoskeleton of the cell, that extend outward in railroad style away from the microtubule organizing center (MTOC) near the nucleus. Kinesin walks away from the MTOC toward the plus ends of the MTs while another motor protein, dynein, moves cargo toward the minus ends located near the MTOC. Kinesin is essential to axonal transport in neurons and carries cargo from the cell body toward the end of the axon, which can be a meter long. Axonal transport is the transportation of cargos within axons along MT tracks and consists of a bustling two way traffic of motor proteins. Cargo can include mitochondria, vesicles, microtubules, proteins, and other molecules. Neurodegenerative diseases such as Alzheimer's are caused by disruptions in this long distance transport. Conventional kinesin, active in axons, has two motor heads connected to a cargo binding region by a coiled-coil neck. A neck linker connects the coiled coil to each motor head. When a kinesin motor head binds to a microtubule, ADP is released and ATP immediately replaces ADP. The neck linker then zippers onto the catalytic core, which throws the trailing motor head forward. This motor head then attaches to the next MT binding site, and the trailing motor head hydrolyzes ATP and releases Pi. This process repeats as kinesin "walks" along microtubules. Using 3D printing technology, the St. Dominic S.M.A.R.T. Team (Students Modeling A Research Topic) modeled the motor domain of conventional kinesin to further explore the relationship between its structure and function.

• St. Joan Antida High School
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St. Joan Antida High School

Meet SbADC, The Secret Ingredient to Green Chemistry




Students:

• Velari Araujo
• Lissette Delatorre
• Erika Johnson
• Alexis Lockett-Glover
• Darneisha Virginia
• Ashley Volmer
• Fatima Yacoob

Teacher:

• Cynthia McLinn

School:

• St. Joan Antida High School, Milwaukee, WI

Mentor:

• Nicholas Silvaggi, Ph.D., Department of Chemistry and Biochemistry, University of Wisconsin — Milwaukee

Project Files:

• Poster

Abstract:

Scientists continue to seek eco-friendly methods and materials to be used in chemical synthesis, since there are many harmful solvents such as benzene currently in use. The use of certain enzymes could make syntheses "greener" because they work in water at room temperature and near neutral pH. However finding an enzyme that does exactly what you need it to is very difficult, so it is important that scientists try to identify new enzymes with potentially useful catalytic activities. Streptomyces bingchenggensis acetoacetate decarboxylase (SbADC) may be useful in some green chemistry applications. The enzyme SbADC comes from the same family as acetoacetate decarboxylase (ADC) which cleaves acetoacetate into the products carbon dioxide and acetone. While it is not known what SbADC does in a living bacterium researchers know what SBADC can do in a test tube. SbADC functions as an aldolase-dehydratase, forming a double-bond between pyruvate and a range of aldehydes. SbADC has been shown to bind to the substrate 4-nitro-cinnamylidenepyruvate. Our mentor would like to know what other analogs of this compound might bind with SbADC. Specifically, he is interested to know if the enzyme will accept substrates with groups on the ortho- and meta-positions of the cinnamyl ring. Since these “green” compounds are not available and are difficult to make, the St. Joan Antida SMART (Students Modeling a Research Topic) Team has used 3-D printing technology to create models of the protein and a selection of potential substrates in order to learn more about the substrate specificity of SbADC.

• Valders High School
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Valders High School

The Guanine Trap: RNA Guanine-Tract Recognition and Encaging by hnRNP F quasi-RRM2




Students:

• Paige Neumeyer
• Phoenix Kaufmann
• Theresa Evenson
• Alexis Patynski
• Ian Schmidt
• Elizabeth Evans
• Mitchel Meissen
• Grace Ebert
• Nicole Maala

Teacher:

• Joseph Kinscher

School:

• Valders High School, Valders, WI

Mentor:

• Mark McNally, Ph.D., Department of Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

RNA splicing, the process where mRNA exons are ligated together after the introns are cut out, is required for the production of mature mRNA. Exons are the regions of mRNA that are translated into protein, and introns are noncoding regions. Alternative splicing, the process where different combinations of exons can be ligated together to generate many mRNAs from one gene, accounts for protein diversity and affects over 90 percent of human genes. Alternative splicing regulation is important because many diseases can arise if it occurs improperly. A molecular machine called the spliceosome performs RNA splicing to ligate exons, and hnRNP F (heterogeneous nuclear ribonucleoprotein) influences the spliceosome's alternative splicing decisions. hnRNP F binds to guanine-(G) rich sequences in mRNA targets, resulting in their alternative splicing. Modeling shows a 'cage' formed around three G residues, which explains why hnRNP F binds G-rich sequences. Using 3D printing technology, the Valders SMART team (Students Modeling A Research Topic) modeled hnRNP F binding via arginine 116, phenylalanine 120, and tyrosine 180. Research suggests that too much hnRNP H, a close homologue of hnRNP F, plays a role in promoting brain cancer. Understanding how hnRNP F binds G-rich RNA to cause alternative splicing may lead to the development of therapies for genetic diseases.

• Wauwatosa West High School
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Wauwatosa West High School

Fibrinogen: Nature's Duct Tape




Students:

• Maddy Jordan
• Alec Kirtley
• Natalie Mullins
• Leah Rogers
• Sara Stevbe
• Jordan Voit
• Jack Wongtam

Teacher:

• Mary Anne Haasch

School:

• Wauwatosa West High School, Wauwatosa, WI

Mentor:

• Kevin Sienbenlist, Ph.D., Department of Biomedical Sciences, Marquette University

Project Files:

• Poster

Abstract:

Fibrinogen, the precursor to fibrin, is the last protein in the blood clotting process. Fibrin forms the clot that is stabilized by factor XIII (clotting protein), causing fibrin molecules to link together. Without fibrin, a person would bleed to death. Fibrinogen is made up of three unique polypeptide chains: α, β, and γ. These chains are twisted together, forming two terminal barbell-like D domains with a smaller central E domain in between. Thrombin, another essential clotting protein, forms fibrin by removing alpha and beta chain amino termini peptides in the E domain, exposing amino acid "knobs" that interact with "holes" always present on D domains of neighboring molecules. Van der Waals forces keep the α and β chains together between the E and D domains. Cross-linking occurs between D domains of adjacent molecules at residues Gln398/399 of one D domain and Lys406 of the other. There is currently controversy within the scientific community over whether fibrin D domains cross-link longitudinally (end-to-end) or transversely (between parallel molecules). Cross-linking transversely allows for greater elasticity, allowing the clot to stretch with the skin or blood vessels. Studies with fibrinogen in physiological solution strongly suggest cross linking occurs in a transverse manner. Although the cross-linking residues (381-411) in the crystalline structure appear to be too short to link transversely, if the loop on the γ chain could flip out, it would provide an extension. Using 3D printing technology, the Wauwatosa West SMART Team (Students Modeling A Research Topic) designed a fibrinogen model to visualize this loop.

• Whitefish Bay High School
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Whitefish Bay High School

ExoU: The Hugging Destroyer




Students:

• Corinne Kenwood
• Marissa Korte
• Lazura Krasteva
• Jack Middleton
• Andrew Phillips
• Zack Serebin
• Shawn Wang
• Alice Xia

Teachers:

• Michael Krack
• Paula Krukar
• Marisa Roberts
• Judy Weiss

School:

• Whitefish Bay High School, Whitefish Bay, WI

Mentor:

• Dara Frank, Ph.D., Department of Microbiology and Molecular Genetics, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Nascent proteins are folded into matured forms in the endoplasmic reticulum (ER). Stress inside the ER due to metabolic disorder (for example, diabetes) and/or pathogen infection, can lead to accumulation of misfolded/unfolded proteins. When this occurs, cells respond through a network of signal transduction pathways called the Unfolded Protein Response (UPR). This pathway includes IRE1 (inositol requiring kinase/endonuclease 1), which is an ER transmembrane protein. The Wisconsin Virtual Learning SMART Team (Students Modeling A Research Topic) modeled the cytoplasmic domain of IRE1 using 3D printing technology. The ER lumenal domain of IRE1 senses the unfolded proteins inside the ER and consequently IRE1 self-organizes into a polymer of several dimers. The kinase and the ribonuclease domains of the cytoplasmic domain of IRE1 are then activated, and the ribonuclease domain removes an intron in Xbp1 mRNA (or yeast homolog Hac1 mRNA). The spliced mRNA encodes a transcription factor that activates expression of proteins associated with proper protein folding. Defects in the UPR are associated with many diseases, including diabetes, Alzheimer's disease, and certain types of cancer. In fact, the IRE1-Xbp1 pathway is a survival pathway for cancer cells and promotes cancer cell progression. Therefore, molecular understanding of the IRE1 structure could result in small-molecule therapeutics for these diseases.

• Wisconsin Virtual Learning Academy
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Wisconsin Virtual Learning Academy

IRE1: Proofreading Proteins




Students:

• Emily Billin
• Michael Dieffenbach

Teachers:

• Trish Strohfeldt
• Becki Van Keuren

School:

• Wisconsin Virtual Learning Academy, Northern Ozaukee School District, Fredonia, WI

Mentor:

• Madhusudan Dey, Ph.D., University of Wisconsin—Milwaukee

Project Files:

• Poster

Abstract:

Nascent proteins are folded into matured forms in the endoplasmic reticulum (ER). Stress inside the ER due to metabolic disorder (for example, diabetes) and/or pathogen infection, can lead to accumulation of misfolded/unfolded proteins. When this occurs, cells respond through a network of signal transduction pathways called the Unfolded Protein Response (UPR). This pathway includes IRE1 (inositol requiring kinase/endonuclease 1), which is an ER transmembrane protein. The Wisconsin Virtual Learning SMART Team (Students Modeling A Research Topic) modeled the cytoplasmic domain of IRE1 using 3D printing technology. The ER lumenal domain of IRE1 senses the unfolded proteins inside the ER and consequently IRE1 self-organizes into a polymer of several dimers. The kinase and the ribonuclease domains of the cytoplasmic domain of IRE1 are then activated, and the ribonuclease domain removes an intron in Xbp1 mRNA (or yeast homolog Hac1 mRNA). The spliced mRNA encodes a transcription factor that activates expression of proteins associated with proper protein folding. Defects in the UPR are associated with many diseases, including diabetes, Alzheimer's disease, and certain types of cancer. In fact, the IRE1-Xbp1 pathway is a survival pathway for cancer cells and promotes cancer cell progression. Therefore, molecular understanding of the IRE1 structure could result in small-molecule therapeutics for these diseases.

2010-2011 SMART Teams

Nineteen schools participated in the local SMART Team program during the 2010-2011 school year. The remote SMART Teams and HHMI SMART Teams also expanded, for a total of over sixty SMART Teams nationwide. Completed projects are described below.

Final Presentations Abstract Book(1.3 Mb .pdb file)

• Brookfield Central High School
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Brookfield Central High School

A Molecular Weapon Against Viral Infection: The Puzzle of Protein Kinase R Structure Solved




Students:

• Justin Fu
• Zach Gerner
• Shariq Moore
• Nickhil Nabar
• Vickrum Nabar
• John Scanlon
• Josh Speagle
• Sai Vangala
• Nikil Prasad

Teacher:

• Louise Thompson

School:

• Brookfield Central High School, Brookfield, WI

Mentor:

• Madhusudan Dey, Ph.D., University of Wisconsin — Milwaukee

Project Files:

• Poster

Abstract:

One common mechanism against viral infection is to inhibit cellular protein synthesis, thus preventing viral propagation. The protein kinase R (PKR) is one of several enzymes involved in cellular immunity against viral infection through the phosphorylation of translation factor eIF2α. PKR is composed of two domains: two double stranded RNA binding domains (dsRNA) and a kinase domain (KD). The crystal structure of the PKR KD bound to its substrate eIF2α revealed that each KD is composed of two lobes: an N-terminal lobe (N-lobe) and C-terminal lobe (C-lobe). The active site lies between these two lobes where the ATP is bound. The two N-lobes of each PKR KD interact to form a dimer whereas the C-lobe is bound to eIF2α composed of an S1 domain and a helical domain. Upon viral infection, PKR senses the dsRNA inserted by the virus, and is dimerized and activated. The active PKR molecule then binds to eIF2α. Upon binding, a conformational change in eIF2α brings the helix insert containing Ser51 (phospho-acceptor residue) closer to the ATP. The γ phosphate of ATP is then transferred to the Ser51. The phosphorylated eIF2α inhibits cellular protein synthesis in infected cells. Such fundamental insights into the mechanisms of substrate recognition and phosphorylation by PKR will help design a small molecule that will activate PKR more effectively leading to improved immunity against multiple viral infections. In addition, the general mechanism of PKR function may be applied to cancer therapy due to its role in controlling cell differentiation.

• Brown Deer High School
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Brown Deer High School

Of Mice and MAGL (Monoacylglycerol Lipase)




Students:

• Sophia Andera-Cato
• Amanda Arnold
• Samuel Bach
• Aaron Blumberg
• Taylor Bombinski
• Maxwell Bord
• Matthew Daniels
• Ariel Feiertag
• Mark Greaves
• Danielle Gross
• Alexander Her
• Trevor Hogg
• Erica Kennedy
• Keirra Lewis
• Trevor Martin
• David McMurray
• Evan Naber
• Carlos Orozco
• Nickolas Perez
• Collin Rice
• Alana Rodgers
• Andreas Sauer
• Jordan Schubert
• Amanda Schulman
• Colin Tubbs
• Shavon Tucker
• Taylor Wray

Teacher:

• Gina Vogt

School:

• Brown Deer High School, Brown Deer, WI

Mentors:

• Lalita Shrestha, Medical College of Wisconsin
• Cecilia Hillard, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

About 18.8 million American adults suffer depressive disorders that may occur with anxiety and substance abuse. Tetrahydrocannabinol (THC), a compound in marijuana, is a cannabinoid chemical that binds to and activates cannabinoid receptors (CB1) in the pre-synaptic cell membrane as part of neuron-to-neuron transmission in the endocannabinoid system (ECS). Glutamate in the pre-synaptic cell is released and binds to the post-synaptic cell triggering the synthesis and release of 2-arachidonoylglycerol (2-AG). 2-AG returns to the pre-synaptic cell binding to and activating CB1 receptors. THC mimics 2-AG action, and is used to study the ECS retrograde signaling system and its effect on appetite and mood. A protein from the pre-synaptic cell, monoacylglycerol lipase (MAGL), hydrolyzes 2-AG into arachidonic acid (AA) and glycerol controlling 2-AG levels. When MAGL is hyperactive, too much 2-AG degrades, which is hypothesized to contribute to depression and anxiety. Hypoactive MAGL activity creates an excess of 2-AG. It is hypothesized that this can contribute to obesity and addictive behaviors. The Brown Deer Students Modeling a Research Topic Team, in alliance with MSOE, built a MAGL model using a 3D printer. Study of MAGL crystal structure may provide the key to regulating MAGL's enzymatic activity leading to therapies that will prevent neurodegenerative disorders.

• Cedarburg High School
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Cedarburg High School

Coming to a Location Within You: Localization of Protein Kinase A and DPY-30




Students:

• Beth Bougie
• Brooke Bolin
• Sarah Christon
• Kelly Cooper
• Austin Gallogly
• Noah Going
• Rebecca Houdek
• Rebecca Jankowski
• Kyle Kohlwey
• Meredith Kuhn
• Nicole Lang
• Allen Moltzan
• Katie O'Reilly
• Claire Olsen
• Shaylyn Pritchard
• Laura Tiffany
• Lindsay Wilfong
• Sam Wolff

Teacher:

• Karen Tiffany

School:

• Cedarburg High School, Cedarburg, WI

Mentor:

• Pinfen Yang, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

Signal transduction is an essential process in cells. One critical signaling molecule, protein kinase A (PKA), phosphorylates target proteins, thereby changing their conformations and modifying their functions. PKA is a component of multiple signaling pathways that regulate a variety of proteins. Since the broad substrate specificity of PKA can lead to phosphorylation of unintended proteins, PKA activity must be limited to specific times and places. A-kinase anchoring proteins (AKAPs) bind and help localize PKA to specific areas. The RIIa domain in PKA provides a shallow groove for an amphipathic helix of AKAP to bind via interactions of hydrophobic side chains. A similar binding motif is found in the DPY-30 domain, which suggests this domain may also play a localization role. The ability of AKAP to interact with PKA and regulate its activity is essential for the specificity of many cellular responses. The ability of a cell to localize proteins containing a DPY-30 domain may also be important for proper function. If localization is disrupted, serious problems like heart disease and cancer may result. To further understand the impact of structural interactions on localization, physical models of RIIa, DPY-30, and AKAP amphipathic helix have been designed and built by the Cedarburg High School SMART (Students Modeling a Research Topic) Team using 3D printing technology.

• Cudahy High School
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Cudahy High School

Gluten for Punishment — The Role of HLA DQ2 in Celiac Disease




Students:

• Rebecca Fansler
• Julie Casper
• Maggie Duris
• Sara Kutcher
• Liz Michalzik
• Amber Perkins
• Laura Harrold
• Roxanne Thiede
• Vince Rolbeicki
• Kyle Buckner
• Nour Kalbouneh
• Sam Preiser
• Jake Casper

Teacher:

• Dan Koslakiewicz

School:

• Cudahy High School, Cudahy, WI

Mentor:

• Andrea Ferrante, M.D., Blood Research Institute, Blood Center of Wisconsin

Project Files:

• Poster

Abstract:

Celiac disease is an inflammatory disease of the gastrointestinal tract. Many people are affected by this disease, but are undiagnosed. They dismiss the digestive and neurological symptoms as nothing more than malaise. Those who are diagnosed need a controlled, gluten-free diet to alleviate symptoms, since there is currently no medical treatment. The HLA-DQ2 allele is the second highest risk factor for celiac disease. HLA-DQ2 is a MHCII molecule, which presents antigens to a specific subset of T cells (T helper). An MHCII molecule is a protein exposed on the membrane of antigen presenting cells; these cells populate several body districts like small bowel mucosa. In a physiological setup, T cells are able to distinguish between "self" and "non-self" antigens, and they can be stimulated only upon recognition of "non-self" antigens bound to a "self" MHCII. Structurally, HLA-DQ2 has a binding groove, composed of two alpha helices and a beta sheet floor, where peptides from undigested gluten (gliadins) bind. The interaction of gliadins with this particular HLA allele relies specifically on the presence of Tyr-22, Leu-53, Arg-70 and Lys-71, leading to HLA-DQ2-gliadin complex formation. This complex may be recognized by T helper cells as "non-self", with subsequent activation and initiation of an autoimmune response. The ensuing inflammation causes disruption of the structure and function of the small intestine. By learning about binding of gliadins to MHCII, scientists may find a drug that can block the binding groove from gliadins or modify the gliadins to prevent their interactions with HLA-DQ2.

• Grafton High School
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Grafton High School

Rollin' Like a Tank — The Critical Function of Wzc in Gliding Motility




Students:

• Lisa Borden
• Kelsi Chesney
• Elizabeth Fahey
• Alex Konop
• Gabrielle Kosloske
• Kaleigh Kozak
• Michaela Liesenberg
• Chris Rose
• Nick Scherzer

Teacher:

• Dan Goetz

School:

• Grafton High School, Grafton, WI

Mentor:

• Ryan Rhodes, Ph.D., University of Wisconsin—Milwaukee

Project Files:

• Poster

Abstract:

Cells of Flavobacterium johnsoniae move over surfaces using gliding motility. Gliding motility is widespread among the phylum Bacteroidetes, and several members cause disease in fish. In gliding motility, surface-exposed adhesins mediate attachment and movement of cells, and are propelled around the cell surface by motor proteins anchored in the periplasm. Evidence suggests that exopolysaccharides secreted by F. johnsoniae coat the substratum and provide a substrate for binding of the cell surface adhesins. Polysaccharide secretion across the outer membrane of Gram negative bacteria is facilitated by the pore-forming protein Wza and regulated by Wzc. The proteins involved in F. johnsoniae gliding motility are novel, and the structures have not been determined. Consequently, we modeled the tyrosine kinase domain of E.coli tyrosine kinase (Etk), a protein domain homologous to Wzc in E. coli and F. johnsoniae. In E.coli, Wzc protein forms a tetrameric oligomer, and reversible, two-step phosphorylation regulates polysaccharide secretion. In the first step, autophosphorylation of Tyr569 occurs through an intramolecular process resulting in the removal of Arg614 from the kinase active site. Unblocking the active site of Tyr569 activates the protein kinase activity of Wzc, allowing for the intermolecular phosphorylation of the tyrosine cluster on a neighboring Wzc protein. Interaction of the phosphorylated and dephosphorylated Wzc tetramer with Wza in E.coli results in the regulation of polysaccharide export, and researchers hypothesize that a similar mechanism controls polysaccharide secretion in F. johnsoniae. Elucidating the molecular mechanisms involved in gliding motility and cell adherence will advance understanding of disease pathogenesis and aid in vaccine development.

• Greenfield High School
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Greenfield High School

Detecting B-Type Natriuretic Peptide to Better Diagnose Congestive Heart Failure




Students:

• Matt Trapp
• Tammy Tian
• Jordan Tian
• Panfua Thao
• Robin Sandner
• My Nguyen
• Tiann Nelson-Luck
• Maggie Munoz
• Guetzie Maya
• Elizabeth Konieczny
• Amber Inman
• Chi Huynh
• Marlene Hagen
• Hope Gueller
• Nick Evers
• Brayden Campagna
• Tania Alvarez
• Jodi Allison

Teachers:

• Julie Fangmann
• Martin Volk

School:

• Greenfield High School, Greenfield, WI

Mentor:

• Shama Mirza, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

There are about 400,000 new cases of Congestive Heart Failure (CHF) every year in the United States. CHF is a disease that interferes with the heart's ability to pump blood efficiently throughout the body. Major symptoms of CHF are fatigue, shortness of breath, nausea, sleeplessness, and swelling of the heart, lungs, and legs. One indicator of CHF is B-type Natriuretic Peptide (BNP), a hormone released due to stress on heart ventricles. A biologically active BNP molecule consisting of 32 amino acids (BNP-32) results from proteolytic cleavage of the precursor protein (originally 134 amino acids long). While CHF patients have a high concentration of BNP, this protein does not cause the disease. BNP-32 indirectly regulates sodium and water levels to reduce swelling. Natriuretic peptides, like BNP, do this by causing vasodilation and decreasing levels of certain chemicals that cause swelling. One of the receptors of BNP is Natriuretic Peptide Receptor-C (NPR-C), a clearance receptor found in the heart and other organs. When BNP binds to NPR-C, BNP is removed from the bloodstream and broken down, and swelling in that area reduces. Since CHF patients have a large amount of BNP, the receptors are unable to break down all of it and the swelling remains. Continual stress and swelling can be fatal. A way to measure the level of BNP in vivo could diagnose CHF before it becomes serious. Scientists are currently working on this through quantification of BNP using mass spectrometry-based technology.

• Kenosha Bradford High School
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Kenosha Bradford High School

Calcineurin-NFAT Complex: The Connection to Alzheimer's Disease




Students:

• Joe McKillip
• Ben Wipper
• Madeline Bullmore
• Abigail Bullmore
• Sara Bolyard
• Peter Capelli
• Brittany Snowden
• Michelle Melotik
• Martha Green
• Stephanie Funk
• Eric Ireland
• Morgen Mueller
• Britney Anthony

Teacher:

• Jean Lee

School:

• Bradford High School, Kenosha, WI

Mentor:

• Dena Hammond, University of Wisconsin — Milwaukee
• Ava Udvadia, Ph.D., University of Wisconsin — Milwaukee

Project Files:

• Poster

Abstract:

Patients with Alzheimer's disease (AD), a progressive neurodegenerative disorder, exhibit neuronal degeneration. High levels of the protein calcineurin (Cn) have been found in regions of earliest pathology in AD. Elevated Cn signaling results in symptoms associated with AD. NFAT proteins are a family of transcription factors activated by calcineurin. Inappropriately active NFAT 3 is associated with intermediate to severe AD. One NFAT target gene is GAP 43 which is involved in axon growth and guidance. Transcription of this gene is negatively regulated by NFAT 3. Reduced GAP 43 expression has been found in post-mortem AD brains. NFAT molecules have a nuclear localization sequence (NLS) to which an importin protein attaches and then carries NFAT into the nucleus. In a resting cell the NLS is masked due to phosphorylation on serine residues. In a stimulated cell there is an increase in the intracellular calcium ion concentration. Calcium activates Cn, which then dephosphorylates the serine residues, exposing the NLS and allowing the nuclear transport of NFAT. In a region distinct from the phosphorylation sites of NFAT lies a conserved PxIxIT motif which acts as a calcineurin docking site. This model shows the complex between activated calcineurin and a synthetic 14 amino acid peptide containing a PxIxIT-like segment, VIVIT. The VIVIT peptide, represented in red, fits into a hydrophobic cleft on calcineurin and blocks Cn-NFAT interactions and NFAT activation. Targeting this calcineurin/NFAT interaction site with blocking peptides like VIVIT is a possible strategy for inhibition of Cn-NFAT signaling and treatment of AD symptoms.

• Kettle Moraine High School
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Kettle Moraine High School

ExoU: A Poor Clinical Outcome




Students:

• Samantha Cinnick
• Maggie Davies
• Alexandra Greene
• Anna Henckel
• Grant Hoppel
• Sridevi Prasad
• Matt Wright

Teacher:

• Steve Plum

School:

• Kettle Moraine High School, Wales, WI

Mentor:

• Jim Feix, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Pseudomonas aeruginosa, the bacterium which is a major cause of pneumonia and other infections, is especially fatal to cystic fibrosis patients with an excessive build-up of mucous in the lungs. This in turn creates favorable conditions for the P. aeruginosa to invade and release the protein ExoU. ExoU, one of the key proteins in P. aeruginosa's invasion process, is a phospholipase which breaks down lipids. If a cystic fibrosis sufferer acquires P. aerguinosa, the ExoU produced by the bacterium will digest the membranes in the lung cells, leading to poor clinical outcome. ExoU can be found on the surface of the P. aeruginosa bacterium and is transported into the host cell through the type III secretion system. Next, ExoU kills the host cell by destroying the integrity of the plasma membrane, cleaving the lipids in the membrane. If ExoU is defective or blocked, P. aeruginosa is completely unable to attack the host cell. Given that the structure of ExoU is mostly unknown, Patatin, a phospholipase similar to ExoU is being studied by scientists in order to develop a better understanding of the structure and function of ExoU. From this understanding, scientists may then be able to create drugs to lessen the severity of P. aeruginosa infection, thus increasing the chances of survival for infected cystic fibrosis patients.

• Laconia High School
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Laconia High School

Sepsis Takes a Toll on Human Health: Understanding the Role of Toll-like Receptor 4




Students:

• Sarah Tetzlaff
• Mary Larson
• Molly Toll

Teacher:

• Jodie Garb

School:

• Laconia High School, Rosendale, WI

Mentors:

• Ben Tourdot, Blood Research Institute, Blood Center of Wisconsin
• Debra Newman, Ph.D., Blood Research Institute, Blood Center of Wisconsin

Project Files:

• Poster

Abstract:

Sepsis, the tenth leading cause of death in the United States, is a whole-body inflammatory response to infection. Sepsis leads to septic shock, a condition with a 30-40% mortality rate caused by multiple organ failure and development of hypotension. Lack of understanding of the pathophysiology of sepsis limits successful treatment options. Gram-negative bacteria are a major cause of sepsis. The outer membrane of Gram-negative bacteria contains lipopolysaccharide (LPS). LPS is recognized by a receptor complex expressed by certain immune cells that includes the transmembrane glycoprotein, Toll-like receptor 4 (TLR4), and myeloid differentiation factor-2 (MD-2). Over-stimulation of immune cells by LPS through TLR4/MD-2 results in sepsis. TLR4-mediated activation of immune cells is also responsible for allergic contact dermatitis due to nickel, a common and less fatal condition than sepsis. The crystal structure of TLR4-MD-2-LPS has elucidated residues involved in LPS binding to TLR4/MD-2 and in TLR4 dimerization, which are essential events involved in immune cell activation and induction of sepsis. A better understanding of interactions between TLR4, LPS and MD-2 will help create better drugs to disrupt the interactions. The Laconia SMART (Students Modeling A Research Topic) Team used 3-D printing technology to model the TLR4 dimer in collaboration with MSOE.

• Marquette University High School
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Marquette University High School

VDAC: Voltage Dependent Anion Channel




Students:

• Patrick Jordan
• Alexander Borden
• John Fuller
• Christian Gummin
• Joe Puchner
• Judson Bro
• Kevin Bustos
• Keegan English
• Andrew Keuler
• Qateeb Khan
• Daniel Kim
• Hasaan Munim
• Ryan Sung
• Nicholas Zausch

Teachers:

• Keith Klestinski
• David Vogt
• Mike Caballero

School:

• Marquette University High School, Milwaukee, WI

Mentors:

• Yi Fan Zhou, Medical College of Wisconsin
• Wai-Meng Kwok, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

VDAC (Voltage Dependent Anion Channel) is a channel protein located on the outer mitochondrial membrane. It regulates mitochondria functions and cell respiration through the exchange of molecules between the cytoplasm and the organelle, such as ADP, ATP, anions, cations, and other small, hydrophilic molecules. VDAC has been implicated in cardiac ischemia-reperfusion injury as well as cancer cell survival. Yet, the precise functional roles of VDAC in cardiac injury and cancer have not been elucidated. Recent structural information of VDAC obtained at a high resolution provides essential clues to the molecular mechanism that governs this protein. Movement of the positive N Terminus voltage sensor into and out of the protein coupled with putative sites of phosphorylation facing both the cytoplasm and the intermembrane space give VDAC greater regulatory abilities. In fact, VDAC may regulate several cell survival and cell death signals, as it can potentially prevent the release of Cytochrome C and, consequently, prevent apoptosis. If scientists learn more about the functions of this protein, it very well could represent a viable target for new therapeutics to treat ischemia-reperfusion injury in the heart and cancer. The Marquette University High School SMART Team (Students Modeling A Research Topic) created a physical model of VDAC using 3D printing technology.

• Messmer High School
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Messmer High School

People Sulfur Because of A Disulfide Bond; The Role of Thioredoxin in Tuberculosi




Students:

• Giovanni Rodriguez
• Kevonna Nathaniel
• Anwuri Osademe
• David Gonzalez

Teacher:

• Carol Johnson

School:

• Messmer High School, Milwaukee, WI

Mentors:

• Dan Sem, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

Tuberculosis, a disease caused by the bacterium, Mycobacterium tuberculosis, affects about one-third of the world's population, killing 2 million people each year. The bacteria reside in macrophages of the respiratory tract of infected individuals. Macrophages are a type of immune cell whose function is to engulf and kill foreign substances such as bacteria that invade the body. Macrophages do this by bleaching, or oxidizing, bacterial cell proteins, rendering the bacterial cell susceptible to cell death. To protect against these lethal oxidative attacks by macrophages, two bacterial cell proteins, Thioredoxin C (TrxC) and Thioredoxin Reductase (TrxR), function to reduce the oxidized proteins, thus stabilizing them and enabling the survival of the bacteria. To accomplish this protective reduction and maintain redox homeostasis in the bacterial cell, TrxC donates electrons to the oxidized bacterial cell proteins, becoming oxidized in the process. In order to continue to donate electrons to protect the cell, TrxC itself must now gain electrons (be reduced). TrxR is the protein that donates electrons to oxidized TrxC converting it back to the reduced form, continuing the redox cycle. NADPH then reduces the oxidized TrxR with its electrons stored in a tightly bound FAD. To accomplish this redox cycle, TrxC binds to TrxR through a disulphide bond, and stabilized by a hydrophobic pocket on TrxC that fits into a crevice on TrxR. If this reaction can be prevented, the protective redox cycle of TrxC/TrxR could be stopped thus leading to cell death of the Mycobacterium tuberculosis, preventing many deaths.

• Milwaukee Academy of Science
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Milwaukee Academy of Science

Pax3-Fox01: Forbidden Transcription by Fusion Protein




Students:

• Cameron Bester
• Carolyn Turner
• Javeoni Buford
• Kurtisha Jackson
• Tim Jones

Teacher:

• Kevin Paprocki

School:

• Milwaukee Academy of Science, Milwaukee, WI

Mentors:

• Fengjie Liu, Medical College of Wisconsin
• Sarah Kohler, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Alveolar Rhabdomyosarcoma (aRMS) is a type of aggressive muscle cancer that is the number one most common non-cranial childhood cancer. For 90% of all rhabdomyosarcomas, the Pax3-Fox01 fusion protein is detected and implicated. A fusion protein results from a chromosomal translocation event in which a piece of one chromosome breaks off and attaches to another chromosome, generating a hybrid genetic code that is translated to create a new protein. In the case of aRMS, two transcription factors, Pax3 from the 2nd chromosome and Fax01 from the 13th chromosome, are fused together and generate the Pax3-Fox01, a new transcription factor which can initiate genes on strand of DNA to be read to make mRNA, which in turn is read to make protein. Pax3-Fox01 contains the DNA binding domain of Pax3, which is involved in the early human development of the eyes, ears, face, nerves, and muscles. This fusion protein also contains the Fox01 transactivation domain containing DNA remodeling abilities that help unravel chromatin for potential transcription. Together, the activities of these two proteins allow the fusion proteins to activate genes that should only be activated during early stages of human development. This leads to oncogenesis in aRMS. Pax3-Fox01 is capable of binding to Pax3 binding sites on several muscle genes' regulatory elements, including the enhancer of MyoD, the master regulator for muscle development. The Cirillo lab has demonstrated that Pax3-FoxO1 can open compacted chromatin. Together, this data suggests that the Fox01 portion of the protein untangles chromatin, and the Pax3 portion recognize and read DNA both at Pax3 normal binding sites and at additional, non-Pax3 binding sites, leading to activation of embryonic genes and cancer genes in aRMS. If this hypothesis is true, this research on Pax3-Fox01 will elucidate a potential target for treatment of aRMS.

• St. Dominic Middle School
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St. Dominic Middle School

Cytoplasmic Dynein: It Walks the Walk




Students:

• Jesse Austin
• Jenna Brockman
• Hannah Brown
• Ben Caballero
• Ryan Chaffee
• Luke Emery
• Amanda Hodgson
• Finola Hughes
• Jackie Jarosz
• Kevin Kohl
• Connor Lagore
• Chris Malliet
• Kerri Jo Mark
• Emily Ott
• Drew Rusnak
• Mitchell Sauer
• Josh Schmirler
• Graydon Schroeder
• Katie Seim
• Aaron Siehr
• Joe Valentyn
• Keegan von Estorff
• Michael von Estorff
• Evan Wetzel

Teacher:

• Donna LaFlamme

School:

• St. Dominic Middle School, Brookfield, WI

Mentor:

• Jason Bader, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Cytoplasmic dynein is a multi-subunit motor protein powered by ATP hydrolysis that "walks" along the microtubules (MTs) of a cell's cytoskeleton carrying cargo that is too large to diffuse such as lysosomes, endosomes and parts of the Golgi complex. With the help of accessory proteins dynein can transport cell components as large as the nucleus. During mitosis dynein associates with the kinetochore of chromosomes and captures spindle MTs so that chromosomes can be positioned correctly. Because of this crucial role in cell division, lack of dynein is lethal for mammalian embryos and death occurs 5-7 days after fertilization. Cytoplasmic dynein assembles as a homodimeric complex consisting of a tail where cargo is attached and a force producing head known as the motor domain. The head consists of a motor domain composed of six AAA+ ATPase subunits arranged in a ring. In addition, the head contains two microtubule binding domains (MTBD's) which are connected to the motor domain by coiled coil stalks. The MTBD, stalk, and motor domain form the "legs" of dynein that walk along microtubules. The stalks are composed of two anti-parallel alpha helices that can move relative to each other. Changes in conformation in the motor domain caused by ATP binding to the AAA+ ring are thought to be transmitted along the stalk to the MTBD causing it to be pulled off the microtubule while conformational changes in the six helices of the MTBD upon binding to the microtubule are thought to be transmitted back along the stalk to the motor domain readying it for ATP binding.

• St. Joan Antida High School
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St. Joan Antida High School

An Integrin with Integrity -- The Manipulated Interactions of alpha_vbeta₃




Students:

• Beanca Buie
• Brianna Castanon
• Neli Jasso
• Alexis Lockett-Glover
• Shinny Vang
• Fatima Yacoob
• Sukaina Yacoob

Teacher:

• Cynthia McLinn

School:

• St. Joan Antida High School, Milwaukee, WI

Mentors:

• Emily Andreae, Medical College of Wisconsin
• Sally Twining, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

In order for a cell to interact and adapt to its environment, the cell needs receptors to recognize and respond to external signals. These signals tell a cell to migrate, proliferate, or specialize. Without receptors, a cell would be unable to function within its environment. One group of receptors that enable a cell to interact with its environment are the integrins. There are several families of integrins, one of which is the β3 family. Cyr61, a protein associated with breast cancer, wound healing, and vascular diseases such as atherosclerosis and restenosis, is an activation-dependent ligand of the β3 integrin family. This group of adhesive receptors mediates cell-cell and cell-extracellular matrix interactions. One of the two family members is αvβ3, an integrin expressed on the surfaces of endothelial cells, smooth muscle cells, monocytes, platelets, and osteoclasts. Binding of Cyr61 to αvβ3 stimulates angiogenesis, the creation of blood vessels, and migration of tumor cells. αvβ3 integrin commonly binds to the amino acid sequence RGD (arginine, glycine, and aspartic acid) on many extracellular molecules such as vitronectin and fibronectin, however, Cyr61 binds to αvβ3 via a unique sequence. When a ligand binds to αvβ3 integrin, a conformational change in αvβ3 initiates a signaling cascade that results in increased cell migration. Over-expression of αvβ3 can lead to life-threatening cancers such as breast cancer, melanoma, and colon cancer. Understanding and finding a way to restrict the expression and activation of αvβ3 integrin may lead to a new treatment of tumors with decreased side effects compared to conventional chemotherapy.

• Valders High School
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Valders High School

"Bad Roommate!" 3A: An Inhibitor of ER to Golgi Traffic




Students:

• Grace Ebert
• Nicole Maala
• Joe Nagel
• Paige Neumeyer
• Stacie Pearson
• Gavin Schneider
• Luke Schuh
• Kayla Walsh
• Emily Weyker
• Alyssa Yindra

Teacher:

• Joe Kinscher

School:

• Valders High School, Valders, WI

Mentor:

• Bill Jackson, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Acute respiratory illnesses (colds), Hepatitis, Poliomyelitis, and livestock diseases are caused by members of the viral family Picornaviridae. The common cold is the most prevalent infectious disease in humans and results in major economic impact through loss of productivity and strain on healthcare systems. 3A is a membrane protein produced by these viruses that is necessary for forming viral replication complexes which could be targeted to combat these diseases. Normally, cells communicate with each other using the secretory pathway. Proteins from the endoplasmic reticulum (ER) enter the Golgi apparatus where they are processed and packaged into vesicles for secretion. When cells are infected by viruses, the cells produce cytokines and display viral peptides on major histocompatibility complex molecules to induce an immune response. Picornovirus 3A inhibits the host cell immune response by interrupting this communication pathway. 3A binds to Golgi-specific-brefeldin-factor 1, which inhibits protein transport. This is thought to inactivate secretion and promote the remodeling of the endoplasmic reticulum membranes into replication complexes for viral RNA synthesis. Studies have found that some 3A amino acids have been evolutionarily conserved and therefore important to 3A function. Knowing the significance of these amino acids could lead to an attenuated vaccine encoding a mutated form of 3A.

• Wauwatosa West High School
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Wauwatosa West High School

DOPA Decarboxylase: It's Dope! Using DOPA decarboxylase to understand the production effects of dopamine and serotonin




Students:

• Jimmy Kralj
• Jordan Llanas
• Natalie Mullins
• Leah Rogers
• Jordan Voit
• Jack Wongtam

Teachers:

• Mary Anne Haasch
• Petra Vande Zande

School:

• Wauwatosa West High School, Wauwatosa, WI

Mentor:

• Ed Blumenthal, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

Dopamine and serotonin are neurotransmitters that affect a myriad of behaviors including basal locomotive activity and aggression in animals. The synthesis of both neurotransmitters involves the enzyme DOPA decarboxylase (DDC). In humans DDC will decarboxylate several different substrates; in flies, DDC is selective in that it decarboxylates only a few substrates. One of the main differences in the structure of fly DDC compared to mammalian DDC is the presence of a loop that may account for the substrate specificity of fly DDC. For the decarboxylation reaction to occur in flies, this loop must move out of the way. The DOPA can then access the active site, which contains PLP (pyridoxal-5'-phosphate) bound to the enzyme. At this site, DDC decarboxylates DOPA by breaking a carbon-carbon bond and releasing a carboxyl group. During this reaction an unstable negative charge is created. This charge is stabilized by PLP, allowing the reaction to proceed. In this way DDC is essential to the production of dopamine as well as serotonin. By studying the effects of serotonin and dopamine in flies, scientists can further investigate the biochemistry of basal locomotive activity and aggressive behavior.

• West Allis Nathan Hale High School
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West Allis Nathan Hale High School

Urokinase Plasminogen Actovator Receptor (uPAR) and Its Role in Metastasis




Students:

• Karmenleen Bajwa
• Ashley Brost
• Nick Gonzalez
• Sukhwinder Kaur
• Callan Loberg
• Joelle Pietrzak
• Rachel Pietrzak
• Jamie Rypel
• Samantha Toth
• Kyle Tretow

Teachers:

• Sue Getzel
• Anne Xiong

School:

• Nathan Hale High School, West Allis, WI

Mentor:

• Nancy Dahms, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Cancer is spread by the plasminogen activation system which is also responsible for biological processes including clearance of fibrin clots, cell migration, and activation of growth factors. The key role is played by urokinase plasminogen activator receptor (uPAR) which is a tethered membrane protein receptor having three domains, one of which is critical in activating its substrate, the serine protease urokinase plasminogen activator (uPA). uPA activation begins when two of uPA's domains (an N-terminal growth factor domain (GFD) and a kringle domain) interact with domain one of uPAR, creating a tight bond which converts uPA to its active form. The proteolytic cascade reaction continues when activated uPA converts inactive plasminogen to the active protease plasmin. Plasmin is a multi-use protease that can activate several matrix metalloproteinases, which along with plasmin, leads to digestion of extracellular matrix (ECM) and enhanced cellular migration. The binding of uPA to uPAR localizes these proteolytic cascades to the migrating edge of the cell, thereby clearing a path in the extracellular matrix that the cells can move through. Tumor cells often express high levels of uPA and uPAR, facilitating metastasis. uPA-uPAR expression can change a benign tumor into a malignant tumor. The activity of uPAR can be regulated by the proteolytic removal of its N-terminal D1 domain. When uPAR's N-terminal D1 domain is disabled or removed it cannot bind to uPA, therefore the cancer cells lack the ability to metastasize. This prevention technique could lead to the cure for cancer.

• Whitefish Bay High School
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Whitefish Bay High School

Rap1b: Stopping Blood Everywhere




Students:

• Colleen Ackermann
• Isaiah Kaplan
• Lazura Krasteva
• Shannon Mahony
• Andrew Phillips
• Zack Serebin
• Alice Xia

Teachers:

• Paula Krukar
• Michael Krack

School:

• Whitefish Bay High School, Whitefish Bay, WI

Mentors:

• Jackie Porath, Blood Research Institute, Blood Center of Wisconsin
• Gil White, M.D., Blood Research Institute, Blood Center of Wisconsin

Project Files:

• Poster

Abstract:

Blood clotting is crucial for maintaining homeostasis, or equilibrium of internal conditions. However, unintended consequences may result if blood is unable to clot or clots excessively. The protein Rap1b plays a key role in the process of regulating blood clotting, which is facilitated by platelets sending activation signals. When endothelial cells are damaged, matrix proteins are exposed; hence, activation signals are sent to Rap1b. In its inactive state, Rap1b is bound to GDP. Through the replacement of GDP with GTP, two switch regions on the now-activated Rap1b change shape. With the help of guanine nucleotide exchange factors (GEFs) and GAP proteins, Rap1b then binds to an effector protein, activating integrins, which control the attachment of cells to matrix proteins. In turn, the activated integrins located on the cell membrane of a platelet will allow platelets to stick together, forming a blood clot. Research has shown that if a mutation occurs at amino acid N17, the protein is permanently set to an inactive state. However, when amino acid G12 mutates into valine, Rap1b is constitutively active. An imbalance in the signaling cascade of blood clotting leads to health risks, such as strokes or bleeding disorders. Studying Rap1b brings us one step closer to understanding how the body regulates platelet activation and clotting.

• Wisconsin Virtual Learning Academy
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Wisconsin Virtual Learning Academy

Nek7: A Kinase with Self-Control




Students:

• Michael Dieffenbach
• Brok Davis
• Kira Gookin
• Aaron Dimeo
• Robert Herget

Teacher:

• Trish Strohfeldt

School:

• Wisconsin Virtual Learning Academy, Northern Ozaukee School District, Fredonia, WI

Mentor:

• Kerstin Janisch, Dr. rer. nat., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Blindness, polycystic kidney disease, cancer, and more can result from problems with the primary cilia of cells. Cilia are long, slender protuberances extending from the cell body. Although certain cells of human tissue (e.g. lung epithelium) have many motile cilia, most human cells typically possess one non-motile primary cilium. Primary cilia are responsible for receiving important signals for cells. They form from a basal body, which also doubles as a centromere during mitosis. The basal body forms the base of the cilia (where it connects to the cell body) and organizes the construction of the cilia from microtubules. Within retinae, specialized primary cilia connect the outer part of rod photoreceptor cells to the cell body. The length of these cilia is important in receiving the correct amount of light to allow proper vision. Nek7 is a kinase involved in mitosis and the formation and length of a primary cilium. As a kinase, Nek7 transfers a phosphate group from a high-energy ATP molecule to a protein (though the specific substrate of Nek7 is unknown). This essentially activates or deactivates the target protein. Normally, Nek7 has an auto-inhibitory tyrosine complex which blocks the active site until the conformation is altered and the protein is activated. When mutations alter this tyrosine complex, Nek7 remains active and can cause cells to multiply uncontrollably, leading to cancer. Abnormalities in Nek7 can also alter cilia length in retinae, negatively affecting and possibly eliminating vision. Further research on Nek7 could lead to new cancer and vision treatments.

2009-2010 SMART Teams

Fifteen schools participated in the local SMART Team program during the 2009-2010 school year. The remote SMART Teams and HHMI SMART Teams also expanded, for a total of over sixty SMART Teams nationwide. Completed projects are described below.

Final Presentations Abstract Book(1.3 Mb .pdf file)

• Brookfield Central High School
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Brookfield Central High School

HFE: An Iron Uptake Regulation Molecule




Students:

• Yuhan Chen
• Bryan Dongre
• Justin Fu
• Zach Gerner
• Shariq Moore
• Nick Nabar
• Vick Nabar
• Nikil Prasad
• Joshua Speagle
• Sai Vangala

Teacher:

• Louise Thompson

School:

• Brookfield Central High School, Brookfield, WI

Mentor:

• Andrea Ferrante, M.D., Blood Center of Wisconsin

Project Files:

• Poster

Abstract:

Accumulation of excess iron results in a common hereditary disease, Hereditary Haemochromatosis (HH). There are various genetic mutations that lead to different forms of the disease. HH-I is a form of this disease in which iron accumulates in hepatocytes and intestinal epithelial cells and is associated with a mutation in the HFE (high iron protein) gene. The Brookfield Central SMART Team (Students Modeling A Research Topic) developed a model of HFE using 3D printing technology. The HFE gene encodes for a non-classical MHC class I protein. In physiological conditions, HFE is expressed and translocated to the cell surface where it may interact with a transferrin receptor (Tfr). The binding of the α1/β2 domains of HFE to the Tfr allows for controlled release of iron bound to transferrin-transferrin receptor complex. A mutation (845G>A) causes the replacement of a cysteine with a tyrosine (C282Y). This replacement prevents the α3 subunit of HFE from folding properly and from interacting with β2 microglobulin, abrogating the translocation of the HFE-microglobulin complex to the cell membrane and promoting its rapid degradation. This defect hinders the regulatory capability of HFE. Current treatments include phlebotomy to prevent organ damage from accumulated iron. Further study to increase understanding of the regulatory mechanism may lead to improved treatment design.

• Brown Deer High School
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Brown Deer High School

I'm a PC (Pyruvate Carboxylase) ... and diabetes was not my idea!




Students:

• S. Andera-Cato
• A. Arnold
• S. Bach
• J. DeSwarte
• A. Faught
• E. Frisch
• A. Her
• A. Keller
• E. Kennedy
• T. Martin
• D. McMurray
• C. Mitch
• C. Orozco
• C. Rice
• B. Roberts
• A. Rodgers
• A. Sauer
• A. Schulman
• G. Sekhon
• A. Suggs
• K. Surfus
• S. Tucker
• T. Wray

Teacher:

• Gina Vogt

School:

• Brown Deer High School, Brown Deer, WI

Mentor:

• Martin St. Maurice, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

NIH estimates that 23 million Americans have diabetes, and 6.2 million are undiagnosed. If untreated, diabetes can cause complications, including heart disease and neuropathy. Type two diabetes patients cannot regulate glucose due to insulin resistance or deficiency. Pyruvate carboxylase (PC) plays an important role in insulin release from pancreatic β cells. Abnormal PC activity has been correlated with type two diabetes. PC is a dimer of dimers, each monomer a single chain with four domains: N-terminal biotin carboxylase (BC), central carboxyltransferase (CT), C-terminal biotin carboxyl carrier protein (BCCP), and allosteric domains. PC catalyzes the conversion of pyruvate to oxaloacetate (OAA). The process begins when biotin is carboxylated at the BC active site. The BCCP domain transfers the carboxybiotin to an active site in the CT domain. OAA is formed at the CT domain by adding a carboxyl group to pyruvate. Researchers concluded that the BCCP domain swings between active sites on opposite chains, instead of sites on the same chain. The Brown Deer SMART Team (Students Modeling A Research Topic), in collaboration with MSOE, built a model of PC using 3D printing technology illustrating this movement of the BCCP domain. Current research is focused on increasing PC activity through controlling a binding site in the allosteric domain, which may increase insulin production.

• Cedarburg High School
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Cedarburg High School

Isovaleryl-CoA Dehydrogenase: Dehydrate This!




Students:

• Beth Bougie
• Matt Cira
• Colin Erovick
• Anne Fahey
• Nick Grabon
• Kelsey Jeletz
• Eleanore Kukla
• Matt Murphy
• Tim Rohman
• Alyssa Sass
• Michelle Sella
• Laura Tiffany
• Sam Wolff

Teacher:

• Karen Tiffany

School:

• Cedarburg High School, Cedarburg, WI

Mentor:

• Jung-Ja Kim, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Although rare, isovaleric acidemia (IVA) is a potentially fatal metabolic disorder that affects one in every 250,000 people in the US. IVA results from lack of an enzyme, isovaleryl-CoA dehydrogenase (IVD), involved in the breakdown of leucine. Without this enzyme, leucine catabolism stops and organic acids accumulate within the body, causing symptoms of IVA, including vomiting, diarrhea, and fatigue. IVD belongs to a family of related enzymes called acyl-CoA dehydrogenases. IVD catalyzes the dehydrogenation, or removal of a pair of hydrogen atoms, of a small, branched-chain substrate, isovaleryl-CoA, during the third step of leucine catabolism. Glutamate 254 of IVD removes one hydrogen as a proton from the substrate, and flavin adenine dinucleotide, FAD, a cofactor of the enzyme, takes away the other hydrogen from the substrate. The three-dimensional structure of IVD, as determined through X-ray diffraction, illustrates how a small-branched chain substrate is able to fit into the active site of this enzyme and enables further investigation of how mutation of the IVD gene could affect IVD function, thus resulting in IVA. To further understand the structural impact on substrate specificity, a physical model of IVD has been designed and built by the Cedarburg High School SMART (Students Modeling A Research Topic) Team using 3D printing technology.

• Grafton High School
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Grafton High School

An OveRASsertive Mutation: The Uncontrolled Signaling in Cancer-Causing Ras




Students:

• Katie Best
• Lisa Borden
• Kelsi Chesney
• Emily Dufner
• Elizabeth Fahey
• Matt Harter
• Alex Konop
• Gabi Kosloske
• Kaleigh Kozak
• Michaela Liesenberg
• Sadie Nennig
• Nick Scherzer

Teacher:

• Dan Goetz

School:

• Grafton High School, Grafton, WI

Mentor:

• Casey O'Connor, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Ras is a signaling protein that acts to control certain cell functions, such as cell division, gene expression, or cell-to-cell communication. Ras is located in the cytoplasm near the cell membrane and is activated by the exchange of GDP for GTP. Ras deactivation is accomplished by hydrolysis of GTP to GDP. A mutation in Ras that prevents hydrolysis of GTP is found in a staggering number of cancerous cells and results in uncontrolled signaling of Ras-regulated pathways. Understanding the multiple structures and dynamics of RasGTP may lead to treatments for cancers with a permanently active Ras. When Ras is activated, it binds to other signaling proteins called effectors, which determine the cell functions to be carried out. The effector RalGDS is activated when bound to RasGTP, and leads to exchange of RalGDP for RalGTP. A single amino acid mutation in Ras permanently traps the protein in an active state with GTP, leading to increased association with RalGDS, resulting in an exchange of RalGDP for RalGTP. When Ral is activated, excessive signaling for cell proliferation and anti-tumor suppression is favored along with a change in cell shape. A critical step for developing possible anti-Ras cancer treatments lies within a complete understanding of the interaction between RasGTP and its effectors like RalGDS.

• Greenfield High School
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Greenfield High School

Cabin1's Control of MEF2 in the Developing Central Nervous System




Students:

• Robert Bhatia
• Ellen Campbell
• Chelsea Herr
• Leticia Gonzalez
• Alohani Maya
• Danielle Murphy
• Tiann Nelson-Luck
• Kara Stuiber
• Jordan Tian

Teachers:

• Julie Fangmann
• Martin Volk

School:

• Greenfield High School, Greenfield, WI

Mentor:

• Dena Hammond, University of Wisconsin—Milwaukee, WATER Institute

Project Files:

• Poster

Abstract:

Cabin1 (calcineurin binding protein) is predicted to play an important role in maintaining the nervous system, which regulates important functions such as breathing, heart rate, thinking, and movement. Mice lacking Cabin1 die early in development, and other Cabin1 malfunctions have been linked to cancer. As the nervous system develops, neurons require guidance to determine their growth. The expression of specific proteins influences this neuronal growth. Transcription factors, proteins that bind to DNA and other proteins, regulate the production of these neuronal growth proteins. MEF2 (myocyte enhancer factor 2), a protein known to bind to Cabin1, is involved in nervous system development. MEF2 is a transcription factor necessary for neuronal growth and survival. MEF2 activates transcription when it binds to DNA, causing proteins involved in neural development to be made. MEF2 has a hydrophobic binding pocket that attracts four amino acids found on Cabin1: Ile106, Thre110, Ile116, and Leu119. When Cabin1, a transcription repressor found in the nucleus, binds to MEF2's hydrophobic binding pocket, transcription is turned off. This prevents the proteins from being produced and causes neurons to stop growing or to potentially die. Since cell death and survival are both necessary for nervous system development, Cabin1 is hypothesized to play a major role in this process. Current research is examining what happens to neuronal growth and survival when there is a shortage or an excess of Cabin1, eventually leading to a better understanding of the precise way Cabin1 functions.

• Homestead High School
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Homestead High School

"Like a Boss" The Role of FoxD3 in Pluripotency




Students:

• Laura Auiar
• Claudia D'Antoine
• Sophia D'Antoine
• Lisa Liu
• Sarah Lopina
• Sahitya Raja
• Nikhil Ramnarayan
• Daniel Schloegel
• Ross Schloegel
• Claire Songkakul
• Rahul Subramanian
• Bryanna Yeh

Teachers:

• Chris Schultz
• Rick Hubbell

School:

• Homestead High School, Mequon, WI

Mentor:

• Sarah Kohler, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Stem cells play a major role in biological research due to their pluripotency, or ability to differentiate into various types of cells. Stem cells are essential for proper development and maintenance of systems. Therefore, it is imperative that adequate numbers of stem cells are produced during embryogenesis. During the initial stages of embryogenesis, differentiation must be suppressed until enough stem cells are produced. Several transcription factors, including FOXD3, help inhibit differentiation in order to produce the large numbers of cells required by the organism prior to differentiation. FOXD3 relies on a signaling pathway initiated by another transcription factor called Nanog to maintain the cell's pluripotency. Upon activation, the fork-head binding of domain of FOXD3 attaches to the DNA, causing the DNA to unwind and thereby making the DNA accessible to other transcription factors. This results in the activation of target genes, which are responsible for the maintenance of pluripotency in the stem cells. Once sufficient stem cells have been produced, FOXD3 is turned off, thus inhibiting the genes needed to maintain pluripotency and therefore allowing differentiation to occur. Determining how FOXD3 co-operates with other transcription factors, as well as how this protein is suppressed, could enhance understanding of stem cell development during embryogenesis. This research may be a source of new therapeutic treatments, such as using somatic cells that have been induced to a pluripotent state as a source for organ/tissue transplants, which would potentially eliminate host rejection during transplant procedures.

• Kettle Moraine High School
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Kettle Moraine High School

Plexin: Putting Together the Pieces




Students:

• Jacob Angst
• Samantha Cinnick
• Greg Dams
• Allie Greene
• Anna Henckel
• Bronson Jastrow
• Nick Merritt
• Bradley Wilson
• Aaron Zupan

Teacher:

• Steve Plum

School:

• Kettle Moraine High School, Wales, WI

Mentor:

• Shama Mirza, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

The cause of Proteus Syndrome, characterized by uncontrolled cell division leading to tumor formations, is currently not understood. Recent work suggests that cells from Proteus Syndrome patients express a higher level of a protein called Plexin D1. Plexin D1 has been found in angiogenic vessels during embryogenesis and may play an important role during embryonic development. Exploring the structure and function of Plexin D1 may contribute to a further understanding of Proteus Syndrome. Mass spectrometry can be used to compare the types and amounts of proteins found in diseased and healthy cells. Using Trypsin, the proteins in a healthy control cell and a diseased cell can be cleaved at basic residue groups along the polypeptide chains, such as arginine and lysine. Performing trypsin digestion in presence of heavy water (H₂¹⁸O) produces peptides with a +4 da mass shift. If ¹⁸O labeled peptides from diseased cells are mixed with unlabeled peptides from control cells, the ratio of labeled: unlabeled protein can indicate a change in protein expression between the two samples. The molecular weight of peptides from Proteus cells can be found through the process of electrospray ionization mass spectrometry (ESI-MS). This process involves a fine spray of protein fragments that can be analyzed by a computer. The data is then recorded in order to find the molecular weight of the peptides. Comparing the observed masses to a database of known proteins allows researchers to identify the peptide fragments. Plexin D1 may be the key to unlocking the mystery of Proteus Syndrome; the higher frequency of Plexin D1 in Proteus cells versus healthy cells remains promising. By collecting and analyzing data through mass spectrometry the uncertainty surrounding this elusive protein and obscure disease could be dissolved.

• Marquette University High School
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Marquette University High School

Cofacially-Arrayed Polybenzenoid Nano Structures




Students:

• Zeeshan Yacoob
• Caleb Vogt
• Patrick Jordan
• Jose Rosas
• Kienan Knight-Boehm
• Hector Lopez
• Fernando Buchanan-Nogueron
• Nicholas Zausch
• Qateeb Khan
• Judson Bro
• Payton Gill
• Jacob Klusman
• Alexander Lessila
• Jed Sekaran
• Caden Ulschmid

Teachers:

• Keith Klestinski
• David Vogt

School:

• Marquette University High School, Milwaukee, WI

Mentor:

• Rajendra Rathore, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

Based on Moore's Law, every 18 months the number of transistors that can be placed per unit area on a microchip will double. However, by the year 2017 this trend will cease to exist due to the size restrictions imposed by silicon, the main component of microchips; this has led to the birth of molecular electronics. An organic molecule that has been extensively tested for its potential in molecular electronics is DNA. However, recent research has shown that DNA cannot function as a molecular wire due to its fragile nature. This is why Raj Rathore's group is developing organic molecular wires based on robust macromolecular structures. The specific assembly designed to study the wire behavior consists of a triad which is made up of polyfluorenes as an electron donor site, a spacer unit (or wire) made of polyphenylenes, and an electron donor-acceptor complexation site composed of hexamethylbenzene (HMB). A chloranil molecule - an electron acceptor - complexes with the HMB of the triad, and when a laser is shined on HMB/CA complex, a hole is introduced in the molecular wire which will travel 30 Å to the polyfluorene donor, via an electron hopping mechanism. The Marquette University High School SMART Team (Students Modeling A Research Topic) created a physical model of this molecular wire using 3D printing technology.

• Messmer Catholic High School
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Messmer Catholic High School

The Role of β-Catenin in Cell Division and Colon Cancer




Students:

• Nancy Alba
• Darrell Anderson
• TeAngelo Cargille Jr.
• Sara Kujjo
• Giovanni Rodriguez
• Karla Romero

Teacher:

• Carol Johnson

School:

• Messmer Catholic High School, Milwaukee, WI

Mentors:

• Malathi Narayan, Medical College of Wisconsin
• Sally Twining, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Colon cancer is the fourth most lethal cancer in the U.S. As food passes through the colon, water and vitamins are absorbed and epithelial cells are sloughed off and replaced by a tightly regulated cell division process. Unregulated cell division can lead to the formation of polyps and tumors. β-catenin plays a role in regulating cell division and was modeled by the Messmer SMART Team (Students Modeling A Research Topic) using 3D printing technology. In non-dividing cells, a multi-protein complex of APC, GSK-3 and Axin phosphorylates β-catenin, signaling its degradation and preventing cell division. When cell division is needed, a Wnt signal cascade causes the complex to release β-catenin, stabilizing the protein for nuclear translocation and binding to TCF, a transcriptional activator, thus triggering cell division. Competitive binding of the inhibitor proteins, ICAT and Chibby, to β-catenin negatively regulates this process. In colon cancer, mutations in APC or Axin impede binding of the complex to b-catenin, preventing degradation, leading to increased nuclear localization, binding to TCF and deregulated cell division. Additionally, survivin, an anti-apoptotic protein that enables tumor cell survival, is upregulated. Understanding β-catenin's structure could help design drugs to promote binding of inhibitors to prevent the unregulated cell division of cancer.

• St. Dominic Middle School
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St. Dominic Middle School

Lighting Up Science: Firefly Luciferase




Students:

• Elana Baltrusiatis
• Allyson Bigelow
• Rachel Brielmaier
• Pamela Burbach
• Jacob Dowler
• John Fuller
• Caroline Hildebrand
• Teagan Jessup
• Molly Jordan
• Josh Kramer
• Jenna Lieungh
• Alex Mikhailov
• Patrick O’Grady
• Andrew Pelto
• Quin Rowen
• Rachelle Schmude
• Robert Schultz
• Katherine Seubert
• Alex Sherman
• Parker Sniatynski
• Alex Venuti
• Erin Verdeyen
• Molly Wetzel

Teacher:

• Donna LaFlamme

School:

• St. Dominic Middle School, Brookfield, WI

Mentors:

• Nathan Duncan, Medical College of Wisconsin
• Françoise Van den Bergh, Ph.D.,, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Luciferase is the generic name for an enzyme responsible for bioluminescence reactions and is commonly associated with fireflies. It is also found in many other organisms including bacteria, fungi, anemones, and dinoflagellates. Since the gene for the North American firefly (Photinus pyralis) luciferase was cloned in 1985, scientists have been genetically engineering the gene into living cells. The luciferase reaction is now widely used in scientific research to study protein production in cells, to analyze gene promoter activity, to study stem cell function in vivo, and in cancer studies, to trace the metastasis of cancer cells in living test animals. The scientific study of the luciferase enzymes themselves is also continuing. In recent research, single amino acid mutations to the active site cause the emission of different colored light in a predictable way. The uses of and improvements in bioluminescent imaging are increasing exponentially in cell biology, molecular biology, and in medical research.

• St. Joan Antida High School
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St. Joan Antida High School

Go with the Flow: The Importance of VEGF-B




Students:

• Beanca Buie
• Maritza Campos
• Brianna Castanon
• Kateri Duncklee
• Jagnoor Grewel
• Monica Harris
• Neli Jasso
• Meghan Krause
• Malayia Roper
• Shinny Vang
• Sukaina Yacoob

Teachers:

• Linda Krause
• Cynthia McLinn

School:

• St. Joan Antida High School, Milwaukee, WI

Mentor:

• Mary Holtz, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Blood vessels are such a vital part of out body that without them we would not progress from the embryo stage in the womb and our wounds would never heal. In addition, they are extremely helpful for the transportation of nutrients and oxygen and the removal of waste from cells in our body. In order for blood vessels to function correctly, Vascular Endothelial Growth Factor Type-B [VEGF-B] needs to be present. Unlike VEGF-A, which controls the development of blood vessels, VEGF-B controls the functions and prevents apoptosis. Though this protein does not make the blood vessels, VEGF-B stops apoptosis, or cell death, of endothelial cells, making it one of the main factors to the survival and development of blood vessels. VEGFs are a family of secreted glycoproteins, critical for development and function of blood vessels. The structure of VEGF-B consists of two cysteine knots, meaning two monomers, each of which contains eight cysteine residues and four disulfide bonds. The monomers are attached to form the dimer known as VEGF-B. VEGF-B promotes blood vessel survival by blocking apoptosis, in three kinds of cells that make up blood vessels: endothelial cells, smooth muscle cells, and pericytes. VEGF-B is sent between vascular endothelial cells (VEC) in the vessel connecting to the target cell in a locking fashion, assessing whether cells need to migrate, proliferate, specialize, or survive. Further understanding of the role that VEGF-B plays in vessel formation could be potentially used therapeutically against tumor formation. Tumors require angiogenesis, the production of new blood vessels, to enable blood transport to the tumor cells for continued growth. As a result, VEGF-B's abilities are taken advantage of by invading malignant tumors. Knowing more about VEGF-B is potentially life-saving and can be used to help maintain healthy blood vessels without encouraging vessel growth in tumors.

• Valders High School
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Valders High School

Inhibiting Dihydrofolate Reductase as a Treatment for Tuberculosis




Students:

• Corrine Brandl
• Kaylin Kleinhans
• Emily Weyker
• Nicole Maala
• Lauren Brandl
• Grace Ebert
• Paige Neumeyer
• Ryan Jirschele
• Gavin Schneider
• Luke Schuh

Teacher:

• Joe Kinscher

School:

• Valders High School, Valders, WI

Mentors:

• Andrew Olson, Marquette University
• Dan Sem, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

One-third of the world's population is infected by Mycobacterium tuberculosis (M.tb). Two million people die each year from tuberculosis (TB), the disease caused by this bacterium. TB primarily affects the lungs and is easily transmitted. One way to kill M. tb might be to inhibit the enzyme dihydrofolate reductase (DHFR). DHFR catalyzes the production of tetrahydrofolate by transferring a hydrogen ion (H^-) from NADPH to dihydrofolate, thereby releasing tetrahydrofolate and NADP⁺. Tetrahydrofolate is essential to the bacteria's survival, and is a cofactor that is needed for the synthesis of the DNA base thymine. Isoniazid is one antibiotic already used to treat TB by targeting several TB proteins that are necessary for building M. tb cell walls and inhibiting DHFR. Unfortunately, strains of M. tb are evolving resistance to isoniazid, so next generation antibiotics are needed. A variation of isoniazid could be designed to avoid resistance, and to inhibit DHFR, thereby targeting bacterial DNA synthesis. The Valders SMART Team (Students Modeling A Research Topic), using 3D printing technology, created a physical model of DHFR and a possible inhibitor of tetrahydrofolate production.

• Wauwatosa West High School
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Wauwatosa West High School

EnvZ: Triggering Steinernema carpocapsae's Secret Weapon




Students:

• Waj Ali
• Jimmy Kralj
• Jordan Llanas
• Leah Rogers

Teacher:

• Mary Anne Haasch

School:

• Wauwatosa West High School, Wauwatosa, WI

Mentor:

• Steve Forst, Ph.D., University of Wisconsin—Milwaukee

Project Files:

• Poster

Abstract:

The bacterium Xenorhabdus nematophilia participates in an unusual and fascinating mutualistic relationship with the nematode, Steinernema carpocapsae, which could not complete its lifecycle without the bacteria's help.  EnvZ, a kinase protein located in the cell membrane of the bacterium, is critical to both organisms' success. Xenorhabdus resides quietly in a specialized pouch in Steinernema's intestines. To reproduce, the juvenile nematode enters an insect host via the anus or the mouth, and bores a hole though the intestine wall to get into the insect's blood. In response to the environmental signals in the blood, the nematode's pharynx begins to pump, forcing the Xenorhabdus out of the intestinal pouch and into the insect's blood. Xenorhabdus begins to act as an insect pathogen - killing the host insect, while simultaneously secreting antibiotics to eliminate its bacterial competitors. In killing the insect host, Xenorhabdus provides its symbiotic partner, Steinernema, with a carcass in which to reproduce. EnvZ helps Xenorhabdus sense the higher solute concentrations in the insect's blood through a currently unknown mechanism. EnvZ functions as a dimer. In response to appropriate environmental signals, a phosphate from ATP bound to the cytoplasm section of one EnvZ molecule is transferred to the HIS243 of another EnvZ. The phosphate group on HIS243 is then transferred to OmpR, a gene-regulating protein in Xenorhabdus that regulates genes that produce the antibiotics used to kill bacterial competitors. OmpR also regulates genes for exoenzymes that degrade insect tissues providing nutrients that help the nematode to reproduce.

• West Allis Nathan Hale High School
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West Allis Nathan Hale High School

APC: The Key to Colon Cancer (The APC Protein and its role in controlling the cell cycle)




Students:

• Melissa Gall
• Laenzio Garrett
• Nick Goldner
• Zach Koepp
• Valerie Lamphear
• Peter Nguyen
• Vivek Patel
• Stefan Pietrzak
• Evan Rypel
• Ajay Sreekanth
• Kyle Tretow
• Tyler Zajdel

Teachers:

• Sue Getzel
• Anne Xiong

School:

• Nathan Hale High School, West Allis, WI

Mentor:

• William Berger, M.D., Clement J. Zablocki VA Medical Center

Project Files:

• Poster

Abstract:

Colorectal cancer affects 1 in 18 Americans, and is linked to mutations in the Adenomatous Polyposis Coli (APC) gene. The rapid division of colonocytes is regulated by the Wingless Type (WnT) signaling pathway, mediated by β-catenin. In the nucleus, β-catenin binds to Transcription Cell Factor (TCF) and initiates transcription of cell cycle proteins. Alternatively, β-catenin binds to the 20-amino acid repeat region of the APC protein with the help of the scaffold protein axin. The enzyme GSK-3 then phosphorylates threonine and serine residues of the APC protein and subsequently β-catenin. Phosphorylated β-catenin is degraded, slowing mitosis. Mutations in APC allow β-catenin to accumulate, resulting in hyperproliferation of colonocytes, an early step in colon cancer development As such, better understanding of APC and its function could potentially lead to better diagnosis and treatment in colorectal cancer.

• Whitefish Bay High School
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Whitefish Bay High School

The Dirt is Mightier than the Sword: Tetanus Toxin in the Human Body




Students:

• Cara Ahrenhoerster
• Quinn Beightol
• Gabe Drury
• Xavier Durawa
• Riley Gaserowski
• Shirley Hu
• Domi Lauko
• Ciara Otto
• Andrew Phillips
• Helen Wauck

Teachers:

• Paula Krukar
• Michael Krack

School:

• Whitefish Bay High School, Whitefish Bay, WI

Mentor:

• Joseph T. Barbieri, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Tetanus neurotoxin (TeNT), one of the most potent toxins known to humans, causes paralytic death to thousands of humans annually. TeNT is produced by the bacterium, Clostridium tetani, an anaerobic bacterium usually found as spores in soil. C. tetani often infects humans through open wounds where the bacterium colonizes the infected tissues. There are two domains of TeNT: the A domain possesses catalytic activity, while the B domain is made up of two sub-domains: the translocation sub-domain and receptor-binding sub-domain.

The SNARE protein contains VAMP-2, the target of the catalytic A domain of the TeNT. The SNARE protein regulates fusion of synaptic vesicles with the plasma membrane of the neuron, allowing the release of neurotransmitters that are responsible for relaying nerve signals such as inhibitory impulses to the body's muscle cells. TeNT binds to two gangliosides, on the presynaptic membrane of α-motor neurons. TeNT hijacks the trafficking machinery of the motor neuron and moves to the central nervous system, where it again binds to two gangliosides on the surface of neurons. Next, it enters the neuron by an endocytic mechanism to release the catalytic A domain into the host cell cytosol. The catalytic A domain cleaves the SNARE protein, which inhibits neurotransmitter fusion to the host cell membrane and the release of inhibitory neurotransmitter molecules. The loss of inhibitory impulses results in reflex irritability, autonomic hyperactivity, the classic large muscle spasticity and lockjaw associated with tetanus.

2008-2009 SMART Teams

Twenty-two schools participated in the local SMART Team program during the 2008-2009 school year. The remote SMART Teams and HHMI SMART Teams also expanded, for a total of over fifty SMART Teams nationwide. Completed projects are described below.

Final Presentations Abstract Book(1.7 Mb .pdf file)

• Brookfield Academy
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Brookfield Academy

Modeling the Cell Adhesion Molecule E-Cadherin




Students:

• Anshu Aggarwal
• ZeeShan Chattha
• Amanda Doyle
• Stuart Hunter
• Natalie Profio
• Sheil Shukla
• Joey Steven

Teacher:

• Robbyn Tuinstra, Ph.D.

School:

• Brookfield Academy, Brookfield, WI

Mentor:

• Mary Holtz, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

E-cadherin is a transmembrane protein essential for cell adhesion in organ and tissue development and integrity. Cadherins form plasma membrane structures called adherens junctions. Adherens junctions provide direct connections between adjacent cells and are crucial to maintaining epithelial membranes and blood vessel integrity. Adhesion of neighboring cells via E-cadherin occurs through a salt bridge interaction between the N-terminal Aspartate-1 of an E-cadherin protein on one cell and a Glutamate-89 of the opposing E-cadherin protein from the adjacent cell. Additional contacts are provided by hydrophobic and hydrogen-bonding between residues Trp2, Asp90, and Met92 located at the binding interface. E-cadherin is a classical Ca2+-dependent cadherin and loss of function may contribute to developmental abnormalities and cancer progression. Balance between maintenance and remodeling of cell adhesion junctions is required for normal embryonic development. For example, in the development of the embryonic heart, E-cadherin proteins facilitate connections between adjacent epithelial cells of proepicardial tissue. The proepicardium is an embryonic structure from which the coronary vasculature is formed. Cells of the proepicardium must migrate over the surface of the developing heart and then differentiate into the endothelial and smooth muscle cells of the mature coronary vasculature. In contrast, cancer progression and tumor growth involve metastasis and new blood vessel formation, two processes that rely on dissolution of normal cell-cell contacts. Understanding the mechanisms of formation and dissolution of adherens junctions provides important insight into cardiac development and may provide direction for new cancer therapies.

• Brookfield Central High School
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Brookfield Central High School

Toxic! The role of scorpion toxin and BK channels in the Tobacco Hawkmoth




Students:

• Bryan Dongre
• Zach Gerner
• Emily Gerner
• Que Kim
• Josh Speagle
• Sai Vangala
• Darshan Shankar

Teacher:

• Louise Thompson

School:

• Brookfield Central High School, Brookfield, WI

Mentor:

• Jane Witten, Ph.D., University of Wisconsin—Milwaukee

Project Files:

• Poster

Abstract:

A partnership between the Brookfield Central High School students participating in the MSOE SMART Team (Students Modeling a Research Topic) program and a researcher enabled the team to explore the structure and function of a potassium channel bound to a toxin and to build a 3D physical model of the protein. In the larvae of the Tobacco Hawkmoth, the Tobacco Hornworm, the muscle under study is a posture muscle that has a slow recovery (repolarization) rate, and is classified as "slow-twitch". Metamorphosis transforms this muscle into a flight muscle requiring a fast repolarization rate, becoming a "fast-twitch" muscle. The repolarization rate of these muscle cells is directly linked to the muscle's rate of contraction. An explosive increase in the number of the Ca2+-gated K+ channels (BK) in these muscles corresponds to these metamorphic changes. The Chinese scorpion toxin BmP09, from Buthus martensi Karsch, will be used to identify the BK channel as responsible for the change from posture to flight muscle. This toxin binds specifically to the BK channel, preventing the channel from removing K+ from the cell, slowing repolarization. Binding the toxin to flight muscle, repolarization rates can be studied to determine if the BK channel is involved in the transformation from posture to flight muscle.

• Brown Deer High School
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Brown Deer High School

Get "Hooked" On Brugia malayi Asparaginyl tRNA Synthetase




Students:

• Amanda Arnold
• Charles Bach
• Sam Bach
• Andy Faught
• Sadie Haeflinger
• Alex Her
• Kristin Lillie
• Trevor Martin
• Kristi Noll
• Kate Peak
• Collin Rice
• Pat Rice
• Kaitlyn Rogacheski
• Amanda Schulman
• Aaron Suggs
• Samantha Weber

Teacher:

• Gina Vogt

School:

• Brown Deer High School, Brown Deer, WI

Mentor:

• Michael A. Kron, M.D., M.S., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

A partnership between the Brown Deer High School students participating in the MSOE SMART Team (Students Modeling A Research Topic) program and a scientist enabled the team to explore asparaginyl-tRNA synthetase (AsnRS), a potential drug target to treat lymphatic filariasis, and to build a 3D physical model of the protein. Lymphatic filariasis results from mosquitoes transferring the nematode, Brugia malayi, to host lymph nodes, leading to swelling of affected limbs. AsnRS hooks asparagine to tRNA, used during protein synthesis. AsnRS is a member of the aminoacyl tRNA synthetase (AARS) family, a set of structurally heterogeneous enzymes, specific for each amino acid. AARS are potential drug targets as they are essential for survival and are structurally different between species. AARS also functions as an immunosuppressant, blocking interleukin 8 receptors in humans. Current research for treatment targets parasitic AARS. If multiple functions could be mapped to the same region of the protein, a single drug could target these functions. Inhibition of the tRNA-aminoacylation function of AsnRS would prevent protein synthesis, thus causing death of the parasite. Preventing AsnRS from blocking interleukin 8 receptors, would act as an immunostimulant in humans. Further research on this family of enzymes could provide alternative therapies to treating parasitic diseases.

• Cedarburg High School
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Cedarburg High School

Plasminogen: The Clot Buster




Students:

• Daniel Greinke
• Jessica Knap
• Michelle Sella
• Elissa Hornick
• Kelsey Jeletz
• Kirsten Loberg
• Sara Panighetti

Teacher:

• Karen Tiffany

School:

• Cedarburg High School, Cedarburg, WI

Mentors:

• Richard Bohnsack, Ph.D., Medical College of Wisconsin
• Linda Olson, Ph.D., Medical College of Wisconsin
• Nancy Dahms, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Coagulation and fibrinolysis comprise a complex system involving many proteins designed to form fibrin clots when needed to repair a blood vessel and dissolve these clots when no longer needed. One key fibrolytic protein, plasmin, circulates in the blood as plasminogen, an inactive protein made of several domains. Five domains are kringle domains that help plasmin bind to lysine residues in fibrin, while the catalytic domain exhibits protease activity that fragments the fibrin network. Plasminogen is incorporated within the fibrin network as a clot forms, but the catalytic domain is only able to break down fibrin when plasminogen has been activated and converted to plasmin. One substance known to convert plasminogen into plasmin, tissue plasminogen activator (tPA), is a serine protease that cleaves the peptide bond between Arg561 and Val562 in plasminogen. The endothelial cells of damaged blood vessels slowly release tPA that activates the plasminogen embedded within a fibrin clot. Because increased plasmin levels help dissolve clots, tPA is given clinically to treat conditions caused by blood clots, like heart attack and stroke. To further understand the structural implications of activation, a 3D physical model of plasminogen has been designed and built by the Cedarburg High School SMART (Students Modeling a Research Topic) Team using 3D printing technology.

• Community SMART Team
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Community SMART Team

Who's Afraid of the Big, Bad, Misfolded Protein?




Students:

• Moses Misplon
• Meghan Murphy
• Christine Pollnow
• Joel Pollen
• Maia Stack

Teacher:

• David Stack, Ph.D.

Mentor:

• Anita Manogaran, Ph.D., University of Illinois—Chicago

Project Files:

• Poster

Abstract:

Fatal prion diseases, such as Creutzfeldt-Jakob disease in humans, are associated with the conversion of the normally folded mammalian PrP protein to a misfolded prion form that aggregates. Understanding how prions behave has been greatly facilitated by the study of prions in Saccharomyces cerevisiae, or baker's yeast. In yeast, the translation release factor, Sup35, misfolds to form the [PSI+] prion. Although the Sup35 protein has a significantly different primary sequence from PrP, its prion form behaves similarly to human prions. The N-terminus of Sup35 is Q/N-rich and responsible for prion formation. Determining the structure of this region has proven difficult since the N-terminus forms aggregates instead of the ordered crystals required for structural studies. However, a small seven amino acid sequence (GNNQQNY) from Sup35's N-terminus was crystallized by Nelson et al. (2005). We have constructed a 3D physical model of GNNQQNY as part of the MSOE SMART Teams program using 3D printing technology. GNNQQNY's structure suggests that multiple prion molecules assemble into strong fibrous aggregates through tightly structured interlocking parallel beta sheets called a cross-β spine. The structure of GNNQQNY suggests a potential model of how human prions assemble, which could potentially help in developing therapies that prevent aggregation.

• Edgewood Campus School
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Edgewood Campus School

The Effect of Nrf-2 in Parkinson's Disease




Students:

• Emma Johnson
• Cassidy McDonald
• Katie Wall
• Kira Dohrn-Jones
• Marcy Prince
• Zoe Havlena
• Sara Murphy

Teacher:

• Dan Toomey

School:

• Edgewood Campus School, Madison, WI

Mentor:

• Jeffrey Johnson, Ph.D., University of Wisconsin—Madison

Abstract:

Neurodegenerative diseases affect one's memory and the brain, specifically the substancia nigra, a part of the brain that regulates movement. Parkinson's disease, a neurodegenerative disease that affects nearly 1.5 million Americans, with about 60,000 new cases yearly, is a possibly disabling and fatal disease that many scientists have been investigating. Symptoms of this disease include belated movement and tremors. Recently, Jeffrey Johnson and his lab at the University of Wisconsin-Madison have released results from a study regarding Parkinson's disease. These results indicate that adding extra copies of a gene, Nrf-2, completely neutralizes the disease state in chemically treated mice. Mice are exposed to a chemical, MPTP, to induce Parkinson's disease. MPTP is contaminant found in synthetic heroin that caused young drug addicts to look like they were in the late stages of Parkinson's. MPTP normally attacks the dopamine neurons in the substancia nigra, the part of the brain that controls movement. The presence of extra Nrf-2 leads to the production of several protective antioxidant proteins that neutralize the toxicity of Nrf-2. Astrocytes make Nrf-2, which then attaches itself to DNA, starting the activity of hundreds of genes that can protect the neurons from oxidation, a combination of chemical reactions that can injure or kill cells, by releasing certain chemicals called reactive oxygen species. Clinical trials for this information are at least two years into the future; however, if the manipulation of Nrf-2 is effective in the treatment of Parkinson's disease, then it can effectively lengthen the lives of those 1.5 million people affected by Parkinson's disease.

• Grafton High School
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Grafton High School

When Good Guys Go Bad: FoxO3a Mediating Apoptosis in HIV-Positive T-Cells




Students:

• Dan Burghardt
• Lexi Chopp
• Ashley Emery
• Kaleigh Kozak
• Jenna Ostrowski
• Adam Schaenzer
• Lindsay Wendtlandt

Teacher:

• Fran Grant

School:

• Grafton High School, Grafton, WI

Mentor:

• Sarah Kohler, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Within every cell, DNA provides instructions needed to sustain life. DNA is used to make proteins which perform countless cellular functions. One example of a protein is FoxO3a, a transcription factor involved in regulating cell metabolism and apoptosis (cell death), among other processes. To perform these functions, FoxO3a binds to compacted chromatin and opens the DNA for access by other transcription factors and the transcriptional machinery. Because it can perform these functions, FoxO3a is known as a "pioneer" transcription factor. The H3 helix of FoxO3a recognizes its cognate binding sequence within the DNA (GTAAACA). Once bound, the N and C termini wrap around the DNA, causing the DNA to unwind, while the two wings help to secure FoxO3a to the DNA.

Understanding the connection between FoxO3a and cell function enables researchers to explore potential therapies. For example, researchers are examining the potential role that FoxO3a may play in treating patients with HIV. FoxO3a has been suggested to regulate apoptotic genes in T cells, which are a vital part to the immune system. In healthy humans, T cells protect the body by killing abnormal or virus-infected cells. When a person contracts HIV, their T cells are attacked, and their immune defense is compromised. Inhibiting FoxO3a may prevent the upregulation of the apoptotic pathway in T cells, thereby increasing the lifespan of the T cell slightly. Researchers hypothesize that inhibition of the apoptotic pathway may maintain the efficiency of the immune system for a short period of time and hopefully slow the progression of HIV.

• Homestead High School
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Homestead High School

"You Look Familiar…" How the Immune System Specifically Targets and Kills Infected Cells




Students:

• Sophia Dantoin
• Dhruv Metha
• Yelena Ostrerov
• Sahitya Raja
• Nikhil Ramnarayan
• Rahul Subramanian

Teacher:

• Christine Schultz

School:

• Homestead High School, Mequon, WI

Mentor:

• Andrea Ferrante, M.D., Blood Research Institute, BloodCenter of Wisconsin

Project Files:

• Poster

Abstract:

The Acquired Immune System offers highly specific protection from infection by viruses, bacteria and other microbes by recognizing the pathogen, triggering an immune response resulting in pathogen elimination, and establishing immunological memory for future recognition. It relies on two types of responses: cell-mediated and humoral.

Humoral responses are mediated by B-lymphocytes that produce antibodies, which bind to specific antigens on the pathogen, labeling it for destruction. Cell-mediated responses involve T-lymphocytes, which play regulatory and/or killing functions. In particular, cytotoxic T-lymphocytes (CTL) identify and kill infected cells by examining pieces of proteins (antigens) on the cell membrane as illustrated by the CTL response to the influenza virus. Upon infection, viral antigens from the cytoplasm are transported to the cell membrane and presented on the outside of the cell by class I HLA proteins as a viral antigen-class I HLA protein complex. Each CTL scans the peptide/HLA complex repertoire with its receptor (TCR), and upon binding with a cognate complex, destroys the infected cell. In the present model, an influenza-derived peptide (MP (58-66)) is complexed with HLA-A2, and binds to the TCR Vb17Va10.2.The portion of this TCR that interacts with the peptide-HLA-A2 complex has an arginine-serine-serine sequence which gives reason to the specificity of recognition. The structural modeling of this interaction aids in the understanding of TCR bonding at the molecular level, thereby allowing for the prediction of TCR binding to closely related peptides. This could explain how the immune system responds specifically to new pathogens after involution of T cell production.

• Kenosha Bradford High School
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Kenosha Bradford High School

Flippin' Lipids: Transport of Lipid A by MsbA, a Lipid Flippase




Students:

• John DeVroy
• Kevin Patel
• Ronak Patel
• Fred Seewald
• Beth Stebbins
• April Szfranski
• Jazzmyne Washington
• Mike Weber

Teacher:

• Jean Lee

School:

• Bradford High School, Kenosha, WI

Mentor:

• Candice Klug, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

MsbA is a member of the ABC transporter class of proteins, one of the largest found in nature. ABC transporters move solutes across the cell membrane. MsbA consists of two transmembrane domains and two nucleotide binding domains. The transmembrane domains consist of 6 α helices embedded in the phospholipid bilayer. The nucleotide binding domains are found in the cytosol and are the site of ATP hydrolysis, which provides the energy for the protein to function.

MsbA is a lipid flippase, which means it transports lipid A produced in the cytosol to the outer leaflet of the outer cell membrane, flipping it so the hydrophilic end faces out. Lipid A is essential to the outer cell membrane of Gram-negative bacteria. If MsbA does not function properly, lipid A can kill the bacteria by accumulating in the intracellular layer of phospholipids. This is important to researchers, as MsbA has homology to human multi-drug resistance proteins. Finding a way to render MsbA inactive could lead to antibiotics that kill bacteria, such as Salmonella, which have traditionally been hard to treat. This is of much concern in today's society, as bacteria outbreaks in food seem to be happening more and more often.

• Kettle Moraine High School
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Kettle Moraine High School

Good Vibrations?




Students:

• Greg Dams
• Disa Drachenberg
• Mike Goelz
• Allie Greene
• Bronson Jastrow
• Kris Krause
• Jake Laux
• Nick Merritt
• Nate Murray
• Kara Reese
• Bradley Wilson

Teachers:

• Kelly Beck
• Stephen Plum

School:

• Kettle Moraine High School, Wales, WI

Mentor:

• Evgenii Kovirgin, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Cancer is manifested by uncontrolled cell growth, which occurs due to mutations in signaling proteins. Ras GTPase (Ras) is one of the most important signaling proteins that help regulate cell growth and division. Mutations in Ras leading to its permanent activation and uncontrolled cell growth are responsible for nearly 30% of human cancers. When functioning normally, Ras binds guanosine triphosphate (GTP), and adopts active signaling conformation. When activated, Ras interacts with other proteins and activates them resulting in cell growth and cell division (proliferation). When GTP is hydrolyzed and turned into guanosine diphosphate (GDP), Ras adopts its non-signaling conformation and can no longer bind other proteins and activate them (signaling was 'turned off'). However, if Ras has a specific oncogenic mutation, it cannot hydrolyze GTP and instead permanently signals for cell growth, causing cancer. One of the keys to figuring out how Ras causes cancer might be to better understand how the protein changes its conformation while performing its signaling function. Structural and dynamic studies of Ras using NMR techniques suggest that the protein, when active and bound to GTP, has two majorly different conformations it can take. Understanding how the protein changes conformation and interacts with other proteins could shed light on how it signals for cell growth. This information could further cancer treatments and potentially lead to a cure for cancers caused by Ras mutations.

• Madison West High School
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Madison West High School

Preventing Cancer: p53 Tumor Suppressor Protein




Students:

• Dianna Amasino
• Axel Glaubitz
• Yang He
• Susan Huang
• Joy Li
• Junyao Song
• Connie Wang

Teacher:

• Basudeb Bhattacharyya, University of Wisconsin—Madison

School:

• Madison West High School, Madison, WI

Mentor:

• Dave Nelson, Ph.D., University of Wisconsin—Madison

Abstract:

Each year, nearly 40% of cancer patients die of the disease in the U.S., and more than 50% of human tumors contain a mutation or deletion of the TP53 gene. Tumor protein 53, also known as p53, is a transcription factor coded by TP53, and possesses many anti-cancer mechanisms, such as initiating apoptosis and inhibiting angiogenesis. Usually p53 is inactive, bound to protein HDM2, which promotes its degradation. Once activated by cancer-causing agents (such as UV radiation or oncogenes), p53 is released by HMD2 and binds with DNA, inducing the expression of the CDKN1A gene, which encodes for protein p21. These proteins then interact with a cell division-stimulating protein (cdk2) to arrest cell division. Therefore, under normal conditions, p53 is able to regulate the cell cycle to prevent cancer through this process. However, mutant p53 cannot bind to DNA, and thus cannot trigger the production of p21, resulting in uncontrolled cell division and, ultimately, tumors. If one has only one functional copy of TP53, it will most likely lead to Li-Fraumeni Syndrome, which entails tumor development in early adulthood. Also, pathogens, such as the Human Papillomavirus (HPV), can produce proteins that inactivate p53. In addition, p53 itself induces HDM2 in a negative feedback loop; mutant p53, however, don't often do so, and therefore accumulate within the cell, disrupting normal p53 levels. Increasing the amount of p53, however, does not hold therapeutic potential, since it causes premature aging; restoring the function of the protein may serve as a feasible treatment instead. Through a more thorough understanding of the function of p53, we hope to formulate better treatments for cancer patients.

• Manitowoc Lincoln High School
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Manitowoc Lincoln High School

Don't Forget It: Thrombin Related Alzheimer's Disease




Students:

• Eric Auchter
• Vanessa Heck
• Danielle Niquette
• Jenna Schuh
• Kira Schultz
• Jen Stenson
• Brandon Vance

Teachers:

• Ann Hansen

School:

• Lincoln High School, Manitowoc, WI

Mentors:

• Sally Twining, Ph.D., Medical College of Wisconsin
• Malathi Narayan, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Alzheimer's disease is an incurable and terminal neurodegenerative disorder and is the most common form of dementia. There are 5.2 million people in the United States living with Alzheimer's and it is projected that 10 million baby boomers will eventually develop the disease. One of the three major competing hypotheses explaining Alzheimer's disease involves thrombin, a serine protease involved in blood coagulation. Normally present inside the brain's neurons, thrombin cleaves tau, a microtubule protein. In the brains of Alzheimer's patients, thrombin is also present outside the brain cells, where it binds and cleaves PAR-1, a protease activated receptor embedded in the cell membrane. The interaction between thrombin and PAR-1 exposes a peptide sequence that initiates a series of reactions which activate kinase enzymes that add phosphate groups to tau. Intracellular thrombin is then unable to cleave the phosphorylated tau and the neuron microtubules become clumped, losing their ability to function. As Alzheimer's disease advances, microtubule clumping becomes more prominent throughout the brain, explaining the progression of symptoms from confusion and memory loss to eventual death. Scientists are interested in studying the binding of thrombin to PAR-1 because this interaction is a possible therapeutic target for developing treatments for Alzheimer's and other neurodegenerative disorders.

• Marquette University High School
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Marquette University High School

OmpR: Outer Membrane Protein Gene Regulator: Regulating Xenorhabdus nematophila's "Appetite for Destruction"




Students:

• Mohammed Ayesh
• John Basich
• Wesley Borden
• Alexander Brook
• John Day
• Mahmoud Elewa
• Grant Flesner
• Patrick Jordan
• Lucas Kuriga
• Hector Lopez
• Ben Maier
• David Moldenhauer
• Joseph Radke
• Caleb Vogt
• Brandon Wolff
• Zeeshan Yacoob

Teachers:

• Keith Klestinski
• David Vogt

School:

• Marquette University High School, Milwaukee, WI

Mentor:

• Steve Forst, Ph.D., University of Wisconsin—Milwaukee

Project Files:

• Poster

Abstract:

A partnership between Marquette University High School students participating in the MSOE SMART Team (Students Modeling A Research Topic) program and a researcher enabled the team to explore structure and function, and to build a physical model using 3D printing technology, of OmpR. OmpR is a transcription factor necessary for the nutrition gathering strategy of the bacterium Xenorhabdus nematophila. Bacteria absorb food through membrane pores, which change in size to optimize food intake and to protect themselves from toxins.

X. nematophila has sensor proteins in the outer membrane. When food touches an outer membrane receptor (EnvZ), the receptor transfers phosphate to OmpR forming OmpR-P, which can bind to DNA. When nutrients are abundant, OmpR-P binds to OmpC, a gene promoting formation of a small pore, allowing food yet limiting influx of toxins. When food is scarce, OmpR-P binds OmpF, a gene promoting formation of a large pore, allowing more food intake and growth of a flagellum enabling movement to a nutrient rich location.

The OmpR gene is also responsible for production of antibiotic compounds that combat a broad range of microorganisms. X. nematophila often forms a mutualistic relationship with nematodes. The bacterium-nematode pair seek to inhabit and eventually kill certain insects, benefiting from the nutrients provided by the insect's corpse.

• Messmer Catholic High School
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Messmer Catholic High School

The Role of B7-2 in the Regulation of T cell Activation in Multiple Sclerosis




Students:

• Carolina Herrera
• Lillian A. Rios
• Edna Blackman

Teacher:

• Carol L. Johnson

School:

• Messmer High School, Milwaukee, WI

Mentors:

• Bonnie N. Dittel, Ph.D., Blood Research Institute, BloodCenter of Wisconsin
• Ashley Conrad, Ph.D., Blood Research Institute, BloodCenter of Wisconsin

Project Files:

• Poster

Abstract:

Multiple Sclerosis (MS) is a disease of the central nervous system that affects individuals 20-40 years old. MS is thought to be an autoimmune disease in which T cells attack and destroy the myelin sheath surrounding neurons. Demyelinated neurons have a reduced capacity to transmit electrical impulses, causing symptoms from loss of muscle control to memory loss. One protein thought to play a role in MS is B7-2, a member of a family of proteins that regulate T cell functions expressed by antigen presenting cells (APC). Generation of an immune response by T cells requires two signals: binding of the T-cell receptor to the antigen/MHC complex on APC and binding of B7-1 to CD28 on the T cells. B7-2 is thought to be involved in suppression of the T cell response through binding to CTLA-4. Research using the mouse model of MS, EAE, demonstrated that injection of B7-2 specific antibodies resulted in a more severe disease course. These data suggest that B7-2 plays a role in negative regulation of the immune response during EAE, possibly by binding CTLA-4. To investigate how B7-2 interacts with CTLA-4, we developed a physical model of B7-2 based on its crystal structure (1ncn.pdb) using 3D printing technology that highlights the protein's ß sheet structure and amino acids thought to be important in CTLA-4 binding. This model was built as a part of the SMART team program at Milwaukee School of Engineering.

• Pius XI High School
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Pius XI High School

GABA_A Receptor's Role in Keeping the Brain Calm




Students:

• Steven Brzezinski
• James Carian
• Katie Eszes
• Bilal Garner
• Brittany Givens
• Jenna Motz
• Bernie Mulvey
• Richa Rathore
• Joseph Schwemmer
• Kathryn Sulik
• Stefan Thompson
• Jordan Zawacki
• Sydney Zettler

Teachers:

• Julie Fangmann
• Mimi Verhoeven

School:

• Pius XI High School, Milwaukee, WI

Mentor:

• David Wagner, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

Numerous neurological pathologies, such as anxiety disorders, epilepsy, and insomnia, are due to neurons in the brain malfunctioning by being overactive. Like a stop sign directing traffic, the activation of gamma-amino butyric acid (GABA_A) receptors reduces neural activity preventing neurons from firing excessively. When GABA binds to the GABA_A receptor, negative chloride ions flow into the neuron. This inhibits neural activity because neurons need a net positive charge inside them to send messages. GABA_A receptors are targets for depressants, including alcohol, benzodiazepines (such as Ambien™, Valium™, and Xanax™), and general anesthetics. These drugs bind to the GABA_A receptor to increase inhibition of neural activity. The specific GABA binding site(s) on the GABA_A receptor are unknown. Current research focuses on altering amino acids potentially involved in binding GABA. If one of these amino acids in the binding site is altered, GABA will unbind faster from this mutated GABA_A receptor than it does from the wild type (normal) receptor. Finding the specific amino acids involved in binding GABA could lead to breakthroughs in GABA_A receptor-related pathologies and allow for better design of new drugs.

• St. Dominic Middle School
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St. Dominic Middle School

Nucleosome Assembly Protein 1




Students:

• Tom Boffeli
• Maggie Carter
• Michael Drees
• Jake Emery
• Andrew Geisinger
• Julia Hilbert
• Greg Mattern
• Bridget Moore
• John Orgovan
• Christine Pelto
• Kellie Prince
• Claire Pytlik
• Danny Reit
• Alex Ritchie
• Conor Rowen
• Danny Sladky
• Riley Storts
• Abbey Tangney

Teacher:

• Donna LaFlamme

School:

• St. Dominic Middle School, Brookfield, WI

Mentor:

• Vaughn Jackson, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

The two meters of DNA in every human cell must be tightly packaged in order to fit in the nucleus and to protect the genetic information. NAP1 (Nucleosome Assembly Protein 1) is a histone chaperone that helps assemble and disassemble the nucleosomes used to package this DNA. A nucleosome consists of a core of eight positively charged proteins called histones around which are wrapped 147 base pairs of DNA. The eight histones are actually four heterodimers; there are two H2A/H2B dimers and two H3/H4 dimers. The histones' positive charges are attracted to the DNA's negative charge; this attraction causes the DNA to form left-handed super coils around the histones. The experiment shown on our poster demonstrates that, in vitro, NAP1 can assemble nucleosomes on DNA without the help of other chaperones. Histone chaperones like NAP1 are essential in cells because without them the first step in protein synthesis, transcription — the process of making RNA copies of the genes encoded in DNA — cannot occur because RNA polymerase needs to access the DNA strands. This would not be possible if the DNA remained super coiled around nucleosomes. Nucleosomes must also disassemble for replication — the process of copying DNA by DNA polymerase — to occur. Replication is important in cell division because the DNA must be copied and distributed to the two daughter cells. NAP1 is so vital to these cellular processes that evolution has conserved it in organisms from one-celled yeast to humans with trillions of cells.

• St. Joan Antida High School
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St. Joan Antida High School

The Blister Battle: The Application of Angiogenin in the Treatment of Bullous Pemphigoid




Students:

• Ava Al-Awami
• Essraa Amer
• Maritza Campos
• Meghan Krause
• Claire Marshall
• Corie Marshall
• Kayla Mazul
• Ana Schuessler
• Jade Taylor
• Kristen Wagner

Teacher:

• Linda Krause

School:

• St. Joan Antida High School, Milwaukee, WI

Mentors:

• Françoise Van den Bergh, Ph.D., Medical College of Wisconsin
• Nathan Duncan, Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Bullous pemphigoid (BP) is an autoimmune disease which primarily affects the elderly and is characterized by large, fluid-filled blisters on the surface of the skin. BP currently has only a general, invasive cure. In BP, the body's immune system produces antibodies to attack collagen XVII, also called BP180, in the skin's basement membrane. When inflammation cells flock to the distressed membrane, painful blisters result. Traditional treatments for severe cases of BP include immunosuppressant drugs, which suppress the patient's immune system while treating the blisters, increasing the risk of development of certain cancers and infections. Research centering on angiogenin, a naturally occurring member of the ribonuclease superfamily, has led scientists to believe that a cure for BP may be found in the coupling of angiogenin with a specific region of BP180.

Research suggests that if angiogenin is fused to NC16A, a domain of BP180 and the target of the body's B-cells, the angiogenin and NC16A complex would be absorbed by the B-cell as it attacks BP180. Angiogenin, normally playing a crucial role in the formation of new blood vessels, becomes toxic once directly introduced to a cell. The angiogenin, acting as a toxin inside the B-cell, would use its depolymerization mechanism to destroy the B-cell's RNA. With the B-cell unable to make protein due to the loss of its RNA, apoptosis [cell death] would occur. Any angiogenin-NC16A complex remaining after the apoptosis would neither elicit a negative immune response nor produce any toxic side effects as angiogenin is naturally present in the body. Relief may thus be provided for BP sufferers.

• Valders High School
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Valders High School

αIIbβ3: The Key to Platelet Aggregation (and Clotting)




Students:

• Corrine Brandl
• Andrea Herrmann
• Katarena Hubbartt
• Nicole Maala
• Alexandria Meidl
• Hallie Reznichek

Teacher:

• Joseph Kinscher

School:

• Valders High School, Valders, WI

Mentor:

• Daniel S. Sem, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

In 2008, the leading cause of death in the United States was heart disease. Familial hypercholesterolemia (genetically high blood cholesterol levels) is a major factor responsible for this unfortunate statistic. Phosphomevalonate kinase (PMK) is a cytoplasmic enzyme predominantly found in the liver that is involved in the process to synthesize cholesterol. Two ligands bind to PMK: mevalonate 5-phosphate and ATP. Using the γ-phosphate from ATP, PMK converts mevalonate 5-phosphate (M5P) to mevalonate 5-diphosphate, which is a precursor to cholesterol. ATP binds to the catalytic "Walker A" loop of the kinase, which results in a conformational change. Once bound, M5P causes the domains to move together, around certain hinge residues, so that the two ligands are positioned to react, creating mevalonate 5-diphosphate. The negatively charged phosphates present in both M5P and ATP make this process difficult as the molecules repel one another due to the negative charges on each; therefore, neutralization of the ligands is necessary for catalysis by means of positively charged residues in or near the "Walker A" loop (Arginine 18, 19 and 110, and Lysine 17, 19 and 22). Understanding how PMK catalyzes this reaction could lead to alternative therapies to statin drugs for the control of hypercholesterolemia. Statin drugs may have negative side-effects, like kidney damage; inhibiting PMK would be an option for patients intolerant of statins. Heart disease caused by hypercholesterolemia continues to be a major concern in the U.S. Manipulation (by means of phosphomevalonate kinase) of the rate-limiting pathway by which cholesterol is synthesized may lead to a treatment for this genetic condition.

• Wauwatosa East High School
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Wauwatosa East High School

αIIbβ3: The Key to Platelet Aggregation (and Clotting)




Students:

• David Covell
• Nate Deisinger
• Brian Hoettels
• Nate Kolpin
• Henry Mittelstadt
• Molly Rasper
• Lucia Roegner

Teachers:

• Phil Kroner, Ph.D.
• Terry Teske

School:

• Wauwatosa East High School, Wauwatosa, WI

Mentor:

• Gilbert White, M.D., Blood Research Institute, BloodCenter of Wisconsin

Project Files:

• Poster

Abstract:

Blood coagulation, or the clotting of blood, is a vital process in the body wherein a damaged area of a blood vessel is blocked by platelets and fibrin to stop bleeding until it can be repaired. This process involves proteins known as integrins, a kind of integral membrane protein, which mediate cell-cell and cell-surface interactions. Integrin αIIbβ3, comprised of two glycoprotein subunits and acting as a transmembrane protein, rests on and in the surface of platelets and plays a crucial role in the clotting process by acting as a receptor for proteins that mediate the interaction of one platelet to another.

When a blood vessel is damaged, proteins under the endothelial layer of the blood vessel are exposed at the site of injury. Other receptors cause platelets to bind to the site of damage. This initial binding causes the platelets to become activated, which causes the release of many substances supportive of the clotting process, and also results in the activation of αIIbβ3. It is vital that the activation of αIIbβ3 is controlled, as an overly large amount of activated αIIbβ3 would cause excess clotting. During activation, the structure of αIIbβ3 changes dramatically, converting from a bent, inactive conformation, into a comparatively "straight" protein. These changes occur in the integrin because a salt bridge between the intracellular domains of αIIb and β3 is broken. As a result of this conformational change, amino acids are exposed which form the binding site to several plasma proteins which adhere to the damaged blood vessel, including fibrinogen, von Willebrand Factor, fibronectin, and vitronectin. The binding of fibrinogen cross-links the platelets and results in platelet aggregation at the site of damage. Despite intensive study, the changes leading to the activation of αIIbβ3 functions are still being clarified. However, because blood clotting plays a role in cardiovascular diseases, scientists are working hard to fully understand the structure and function of αIIbβ3 and its role in platelet aggregation.

• Wauwatosa West High School
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Wauwatosa West High School

Carbonic Anhydrase: Breathe in, Breathe Out




Students:

• Matt Berggruen
• Ali Hassan
• Jimmy Kralj
• Kayla Lemmon
• Emily Myers
• Mariah Rogers

Teacher:

• Mary Anne Haasch

School:

• Wauwatosa West High School, Wauwatosa, WI

Mentor:

• Dale Noel, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

All animals breathe in oxygen and breathe out carbon dioxide (CO₂). Carbonic anhydrase, which is found within red blood cells, catalyzes a reaction converting CO₂ and water into carbonic acid, which dissociates into protons, and bicarbonate ions. Said to be "near perfection", carbonic anhydrase is able to catalyze at a rate of 10⁶ reactions per second. We modeled the alpha form, found in humans.

The enzyme contains a pocket of amino acids His94, His96, and His119 that hold a zinc ion. When a CO₂ enters the active site of the enzyme, it gains an OH^- that was bonded to the zinc, forming carbonic acid that is then released. In order to replenish the OH^-, water dissociates. The OH^- binds to the zinc and the H⁺ is released. The reaction can now repeat itself.

In the lungs, carbonic anhydrase reverses the reaction, turning the carbonic acid back into CO₂ to be exhaled. This process also maintains blood pH by controlling the amount of bicarbonate ions and protons dissolved in the blood.

Malfunctions in carbonic anhydrase's regulation can cause glaucoma, the second leading cause of blindness. This disorder can be treated with inhibitors of the enzyme that prevent over-secretion of fluid that presses on the optic nerve. Carbonic anhydrase inhibitors are also used to treat ulcers, neurological disorders, and osteoporosis.

• West Allis Nathan Hale High School
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West Allis Nathan Hale High School

Botulinum Neurotoxin B: The Biochemical Blade




Students:

• Rebecca Ruechel
• Nicholas Dolan
• Nicholas Goldner
• Samuel Hall
• Brenna Hanley
• Katelyn Milos
• Ajay Sreekanth

Teachers:

• Susan Getzel
• Anne Xiong

School:

• Nathan Hale High School, West Allis, WI

Mentor:

• Joseph T. Barbieri, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

Botulinum neurotoxins (BoNTs) are highly toxic proteins that cause the fatal neuroparalytic illness called botulism. BoNTs are produced by the anaerobic bacteria Clostridium botulinum. Although most prominently contracted from contaminated food, botulism can also be contracted from the soil, through the air, or from an open wound. BoNTs are AB toxins composed of three domains. The first domain, the A domain of BoNT, is the catalytic component, a Zinc-dependent protease. The second and third domain, or the translocation and receptor-binding domain respectively, comprise the B domain of the toxin, the binding component. Botulinum neurotoxin serotype B (BoNT/B) is a specific type of neurotoxin that binds to the neurons. The membrane of a neuron depolarizes which then stimulates the transport of calcium ions into the neuron. Proteins on the transmitter vesicle bind the calcium and the vesicles are then transported to the plasma membrane by SNARE proteins to release the neurotransmitter acetylcholine. BoNT/B enters the lumen of the neurotransmitter vesicle and binds to the luminal loop of synaptotagmin, causing the loop to change from a coil to an alpha helix. This represents the high affinity binding of BoNT/B to neurons. Inside the neuron, the A domain of the toxin is translocated across the vesicle membrane by the translocation domain in a pH-dependent mechanism and cleaves the vesicle associated membrane protein (VAMP). This prevents neurotransmitter vesicles from fusing to the plasma membrane and inhibits further release of acetylcholine. Since acetylcholine is important in movement and memory, a lack of acetylcholine causes the nervous system to slow down and causes flaccid paralysis of the muscles, otherwise known as botulism.

• Whitefish Bay High School
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Whitefish Bay High School

Fueling Up: Transporting ADP and ATP Across the Mitochondrial Membrane




Students:

• Zachary Kaplan
• Ian Gee
• Sami Luber
• Tess Nottoli
• Youngjoon Choi
• Xavier Durawa
• Shirley Hu
• Tim Murray
• Ana Novak
• Eric Schwartz
• Minh-Tam Trinh

Teachers:

• Marisa Roberts
• Judy Weiss

School:

• Whitefish Bay High School, Whitefish Bay, WI

Mentor:

• Rosemary Stuart, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

Cells store energy by transforming ADP into ATP in mitochondria. Across the outer mitochondrial membrane, ADP and ATP readily diffuse through the protein porin. Across the inner mitochondrial membrane, the Bovine Mitochondrial ADP-ATP carrier, an anti-port, transports ADP in and ATP out. When this protein malfunctions, the resulting inefficient distribution of ATP can cause certain neuromuscular disorders. One disorder, characterized by drooping eyelids and the inability to move the eyes, results from a mutation in the C1 portion of the carrier protein. Cells make multiple types of these carrier proteins, which compensate if one form of the protein is defective. In cells where the disease occurs, there is usually one dominant type of carrier protein, reducing the ability of the other types to compensate. However, the transport function of the carrier protein still has the capacity to transport ADP and ATP despite the mutation. Therefore, it is unclear why the mutation causes problems. The C1 mutation may interfere with the ADP-ATP carrier protein's ability to interact with its partner proteins such as TIM23, a voltage-gated channel, or the cytochrome bc1-cytochrome oxidase enzymes, an H⁺ pumping complex. Further research on the interaction of the carrier protein with neighboring proteins may provide insight into cures for such neuromuscular disorders.

2007-2008 SMART Teams

During 2007-2008, fourteen local teams and fifteen remote teams participated in the SMART Team program. The program culminated in a poster session and oral presentations hosted by the Medical College of Wisconsin. In addition to presenting locally, SMART Teams attended many meetings such as the Wisconsin Society of Science Teachers (WSST) in Lake Geneva, WI, National Science Teacher Association (NSTA) in Boston, MA, and American Society for Biochemistry and Molecular Biology (ASBMB) in San Diego, CA. See the completed projects below.

Local teams:

Final Presentations Abstract Booklet (4.3 Mb .pdf file)

• Brown Deer High School
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Brown Deer High School

Sticky Situations: A Story of the Rebel Mammary Serine Protease Inhibitor




Students:

• Charles Bach
• Piper Bancroft
• Elaine Brushafer
• Ellen Cahill
• Andrew Faught
• Sara Faught
• Benjamin Jaberg
• Adam Majusiak
• Daniel Matz
• Kristi Noll
• Amy Ramirez
• Collin Rice
• Karleisa Rogacheski
• Justin Schleicher
• Cameron Stoeger
• Aaron Suggs
• Jordan Tubbs

Teacher:

• Gina Vogt

Mentors:

• Sally S. Twining, Ph.D., Medical College of Wisconsin, Milwaukee, WI
• Malathi Narayan, Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

In 2007 alone, an estimated 180,000 women and 2,000 men were diagnosed with breast cancer. Malignant cells in breast tissue rapidly reproduce and can metastasize, thus spreading cancerous cells throughout the body. If cells metastasize, they detach from the extracellular matrix (ECM), but if they remain attached to the ECM, cells cannot metastasize. This behavior has been linked to the expression of maspin in mammary cells. Maspin, or Mammary Serine Protease Inhibitor, is a member of the serpin family, members of which deactivate serine proteases, enzymes that cleave proteins which contain serine residues. Serine proteases aid in many functions of the body, including blood clotting and digestion. Maspin adopts a classical serpin protein fold, but is classified as a non-inhibitory/non-classical serpin as it does not have any known serine protease targets to inhibit. Instead, the reactive site loop (RSL) of maspin stimulates the adhesion of cells to the ECM. This action prevents the migration of cells, thus preventing metastasis. It has been found that the RSL of maspin alone is capable of producing the increased adhesion of cells to the ECM. Recent research has determined that substituting alanine for arginine at position 340 in the RSL loop reduces the adhesion of cells to the ECM. Current research is attempting to determine the method by which maspin functions, and which key amino acids on the RSL loop are responsible for increasing cell adhesion. With this new research, scientists are one step closer to developing an effective drug to control the metastasis of breast cancer cells.

• Edgewood Middle School
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Edgewood Middle School

HIV-1 Protease: A Paradigm for Structure-Based Drug Design




Students:

• Clare Everts
• Emma Green
• Walter Grosenheider
• Michael Hetsko
• Rebecca Jensen
• Ana Lynn
• Miles Petchler
• Julia Pinckney
• Jake Power
• MacKenzy Price
• Kelsey Rayment
• Jake Scholz
• Connor Spencer
• Alex Wol

Teacher:

• Dan Toomey

Mentor:

• Hazel M. Holden, Ph.D., University of Wisconsin, Madison, WI

Project Files:

• Poster

Abstract:

Acquired immunodeficiency syndrome, or AIDS, was first recognized as a diseased state in 1981 and is associated with a depletion of T lymphocytes. It is caused by the human immunodeficiency virus (HIV). Since 1981 more than 25 million people have died of AIDS, and it is believed that over 40.3 million people are presently living with HIV. Proteins on the cell surface of HIV attach to the host cell, enabling the viral membrane and the host membrane to fuse, releasing the viral RNA into the cell. The RNA is then converted to DNA, which is then transcribed and translated. The resulting proteins are long chains that need to be cut into separate proteins by the HIV protease. This cleavage event is essential for the life cycle of the virus because it enables the HIV proteins to become functional. These proteins are then packaged into new viral capsids, which then bud off of the host cell, thus creating several new viruses capable of infecting other cells. The three-dimensional structure of the HIV protease was first solved in 1989, and since then more than 250 structures of it complexed with various inhibitors have been solved. Because of its critical role in viral maturation, scientists have used its structure as a starting point for drug development. Eleven different “protease inhibitors" have been approved by the Food and Drug Administration (FDA). For our project, we have chosen the structure of the HIV-1 protease complexed with Tipranavir (Aptivus^®), a nonpeptidic protease inhibitor.

• Grafton High School
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Grafton High School

Ubiquitination: The Garbage Cycle of a Cell




Students:

• Dan Burgardt
• Lexi Chopp
• Ashley Emery
• Alyssa Fletcher
• Kaleigh Kozak
• Adam Schaenzer
• Dustin Studelska
• Lindsay Wendtlandt
• Lindsay Zadra

Teacher:

• Fran Grant

Mentor:

• Namitha Vishveshwara, University of Illinois — Chicago

Project Files:

• Poster

Abstract:

Within every cell, there exists a system known as the ubiquitin-proteasome system (UPS) that eliminates damaged, misfolded or excess proteins. Unwanted proteins are tagged with ubiquitin, a small protein that identifies other proteins as being ready for degradation. The process of activating and transferring the ubiquitin to the protein is referred to as ubiquitination. Three proteins involved in this process are the ubiquitin activating enzyme (E1), the ubiquitin conjugating enzyme (E2), and the ubiquitin ligase (E3). Ubiquitination begins with ubiquitin being activated by and attaching to E1. E1 transfers ubiquitin to E2. Then E2 delivers ubiquitin to the unwanted protein, either directly or through E3. Finally, the tagged protein is broken down by the proteasome, which is the cell's protein-degrading complex. E2 plays a critical role in the ubiquitination process. Ubch5b is one of many E2s that is involved in tagging unwanted proteins with ubiquitin. Researchers are studying the relationship between the yeast Ubch5b and a specific form of misfolded protein called prions. Prions are unique because when one protein takes the prion form, correctly folded proteins also misfold into prions and aggregate. Prions are infectious proteins; they are not viral or bacterial. Mad cow disease is caused by the presence of prions. In yeast, when Ubch5b is deleted, it leads to increased prion formation. The exact role of the yeast Ubch5b in increased yeast prion formation is still unknown.

• Kenosha Bradford High School
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Kenosha Bradford High School

Brain Eater




Students:

• Maria Barnes
• Mahmood Cheema
• Tony Clark
• Michelle Goettge
• David Jensen
• Fred Seewald
• Steve Snowden
• Beth Stebbins
• Joshua Swenson

Teacher:

• Jean Lee

Mentor:

• Anita Manogaran, Ph.D., University of Illinois — Chicago

Project Files:

• Poster

Abstract:

Many proteins are misfolded and dysfunctional when first formed. Chaperone proteins are used to refold, protect and disaggregate misshapen proteins. While chaperones are traditionally beneficial, it has been recently found they play a role in the formation of infectious protein aggregates. These infectious proteins are called prions and the diseases they cause have no known cure. Prions are responsible for transforming healthy brain proteins into prion replicas, therefore spreading the disease and disrupting normal functions. This transformation occurs when the mainly alpha helical form of the PrPc protein changes into a beta sheet rich protein This conformational change is associated with neurodegenerative disorders in many organisms, such as Mad Cow in cattle, Scrapie in sheep, and Creutzfeldt-Jacob disease in humans. Prions are found not only in mammals, but in other organisms as well, and have been extensively studied in yeast. One prion in yeast is called [RNQ+] which is the misfolded aggregate form of the Rnq1 protein. The chaperone protein Sis1 binds to the ssa1 chaperone and appears to influence the prion aggregate. Chaperones break the protein aggregate into smaller pieces that can be passed on to many daughter cells. Because the pieces have more sticky ends than the original aggregate, they attract more prions, forming new aggregates. Scientists hope to explore the structure of Sis1 and its peptide binding fragment to further understand how prions work.

• Kettle Moraine High School
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Kettle Moraine High School

Botulinum Neurotoxin Serotype A (BoNT/A)




Students:

• Greg Dams
• Jeff Dougherty
• Disa Drachenberg
• Michael Goelz
• Alex Hoffman
• David Kasper
• Kris Krause
• Tom Lankiewicz
• Jacob Laux
• Melanie Mayes
• Nathan Murray
• Kaitlin Swanson
• Marsha Tessman
• Brandon Williams

Teachers:

• Peter Nielsen
• Karen DeBoer
• Steve Plum

Mentor:

• Joe Barbieri, Ph.D. Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

Clostridium botulinum, which causes botulism, is a bacterium found in soil and in improperly processed foods. Botulism causes neuroparalytic diseases, where paralysis results in a part of the body because the nerves that supply it are diseased. Common symptoms of botulism usually appear twelve to 36 hours after consumption and include a dry mouth, difficulty swallowing, slurred speech or difficulty speaking, muscle weakness, blurred or double vision, and drooping eyelids. Botulism works by blocking the release of neurotransmitters — chemicals that transmit information to, from, and within the brain — through the action of clostridal neurotoxins (CNTs) that break down soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins, which are essential for fusion of the vesicle carrying the neurotransmitters with the cell membrane, thus releasing the neurotransmitters. If the neurotransmitters are not released, communication between nerve and muscle cells is halted, thus leading to paralysis. Botulinum toxins (BoNTs) are composed of three domains: receptor, translocation, and catalytic. The receptor domain of BoNTs binds to receptors in the surface of neurons and enters the neuron by receptor-mediated endocytosis. Once inside the neuron, the catalytic domain is translocated across the membrane of the vesicle by the translocation domain, into the cytosol, where the catalytic domain cleaves SNARE proteins. This blocks the release of neurotransmitters and leads to paralysis.

• Madison West High School
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Madison West High School

The Human β2-Adrenergic Receptor Bound to a Beta Blocker and the Role of G Protein-Coupled Receptors




Students:

• Dianna Amasino
• Axel Glaubitz
• Susan Huang
• Joy Li
• Hsien-Yu Shih
• Junyao Song
• Esther Yoon
• Xiao Zhu

Teacher:

• Basudeb Bhattacharyya

Assistant:

• Peter Vander Velden

Mentors:

• David Nelson, Ph.D., University of Wisconsin — Madison, Madison
• Jim Keck, Ph.D., University of Wisconsin — Madison, Madison

Project Files:

• Poster

Abstract:

G protein-coupled receptors (GPCRs) are the largest family of integral membrane proteins coded by the human genome. GPCRs are important for signal transduction with the general structural characteristic of a plasma membrane receptor with seven transmembrane segments. More than 50% of human therapeutics act on GPCRs, but these drugs only interact with a fraction of the GPCRs. One example of a GPCR targeted by pharmaceutical companies is the β2-adrenergic receptor. Adrenergic receptors are found throughout the body and are triggered by the hormone epinephrine (also known as adrenaline, hence the name adrenergic). When epinephrine binds to the receptors, it causes a slight conformational change within the receptor. This change then triggers activation of a G-protein (proteins that bind GTP and are coupled to the receptor on the cytoplasmic side of the receptor) causing dissociation of the G-protein from the receptor). Through the transfer of GTP, G-protein activates an enzyme that converts ATP into cyclic AMP, which induces a response within the cell (for example, muscle contraction if the receptor is located on a muscle cell). When this signal transduction event functions normally in the body, it helps regulate heart rate and blood pressure and is important for the "fight or flight" response. It is important medically to be able to manipulate these functions in cases of high blood pressure or heart failure through the use of beta blockers, a medicine designed to bind to adrenergic receptors, thus inhibiting the binding of epinephrine, and resulting in a lack of effect of the hormone on the body. We have used rapid prototyping technology to model the interaction of the human β2-adrenergic receptor with the beta blocker, carazolol. The structure is dominated by seven alpha helices and is representative of the structure of GPCRs. By modeling the β2-adrenergic receptor, we hope to better understand GPCRs as well as understand the mechanism of hormone/drug binding, which will aid in developing better drug treatments.

• Marquette University High School
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Marquette University High School

H-Ras GTPase: Key to Understanding Cancer?




Students:

• Mohammed Ayesh
• Wesley Borden
• Andrew Bray
• Brian Digiacinto
• Patrick Jordan
• David Moldenhauer
• Thomas Niswonger
• Joseph Radke
• Amit Singh
• Alex Vincent
• Caleb Vogt

Teachers:

• Keith Klestinski
• David Vogt

Mentor:

• Evgenii Kovrigin, Ph.D., Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

The protein known as H-Ras GTPase is essential to proper biological functioning in the entire web of life. The main function of this protein is giving the "stop" signal to the process of cell reproduction. Unfortunately, this protein is not perfect and severe consequences, such as cancer, can arise when H-Ras GTPase malfunctions.
H-Ras GTPase is a protein from the large family of enzymes that bind and split GTP. H-Ras GTPase is vital in processes like cell-to-cell communication, protein translation in ribosomes, and programmed cell death (apoptosis). Its main fields of operation are determining stem cell into specific functioning cells, as well as replicating preexisting "specialized" cells. All G domain based proteins have a universal structure and two universal switch mechanisms, which consist of a mixed, six-stranded beta sheet and five alpha helices. H-Ras GTPase works by first dissociating from GDP and binding to GTP, activating the protein. Then it binds to another G-protein to enact a cell response. After interaction, the GTP is hydrolyzed to GDP, turning off the switch.
H-Ras GTPase has a high affinity for both GDP and GTP. This affinity for GDP impairs the switch from turning off, which can lead to serious problems, such as cancer. When GTPase bonds to GTP, the molecular switches change shape. This newly shaped GTPase now bonds to a protein to transmit instructions. Since H-Ras GTPase is central to cell division, slight mutations in the protein cause the switch to be "stuck-on," resulting in hyperactive cell growth and division. These oncogenic mutations in H-Ras GTPase are responsible for nearly 30% of all human-form cancers.

• Messmer Catholic High School
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Messmer Catholic High School

Heparin-Induced Thrombocytopenia & Thrombosis




Students:

• Carolina Herrara
• Maya Bates-Muhammad

Teacher:

• Carol Johnson

Mentor:

• Debra Newman, Ph.D., Blood Center of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

HIT, or Heparin-Induced Thrombocytopenia, is a life-threatening complication that can occur during major surgery when the anti-coagulant Heparin is administered. This complication occurs when Heparin binds to Platelet Factor 4, which is a protein that is released from activated platelets. Platelets circulate in the bloodstream, and are important for coagulating blood. When a blood vessel is damaged, platelets bind to and cover the damaged site, sticking together to form a "thrombus", and initiate vessel repair. Heparin is a negatively charged polysaccharide that binds tightly to the positively charged tetramer, PF4. This binding produces a conformational change in the PF4 protein that causes the body's immune system to produce antibodies against the newly shaped PF4. When the PF4-Heparin complex then binds to platelets, the antibodies produced against the PF4 bind to the PF4-Heparin-Antibody complex and can cause two things to occur. First, the antibody-coated platelets are removed from the circulation, resulting in thrombocytopenia. Second, the antibodies can activate the platelets to which they are bound, resulting in thrombosis. Thrombocytopenia is a condition in which platelets are too few or inactive resulting in excessive bleeding. Thrombosis is a condition in which platelets are too numerous or active and can block blood flow and result in heart attack, stroke, or loss of limbs. Researchers at BloodCenter of Wisconsin and elsewhere study how antibodies bind to PF4-Heparin complexes so that they can find ways to interfere with antibody binding and prevent the thrombocytopenia and thrombosis that complicate treatment of patients who take Heparin.

• Milwaukee Riverside University High School
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Milwaukee Riverside University High School

Construction of a physical model of a farnesyltransferase-inhibitor complex. Insight into a novel therapy for Hutchinson-Guilford Progeria




Students:

• Maikeng Her
• Ardyce Jackson
• Tracy Bradley
• Hydiza Hassan
• Amy Lee
• Tommy Lee
• Qualandra Brookens
• Jennifer Donahoe
• Jessica Jimenez
• Kenneth Caldwell
• Damaris Hurtado
• Elizabeth Montes
• Ia Moua
• Athee Xiong

Teacher:

• Jeff Anderson

Mentor:

• Bob Deschenes, Ph.D., Medical College of Wisconsin, Milwaukee, Wisconsin

Project Files:

• Poster

Abstract:

The Riverside SMART Team (Students Modeling A Research Topic) created a 3D physical model of a farnesyltransferase (FTase)-inhibitor complex and discussed its significance in the development of a novel therapy for Hutchinson-Guilford Progeria. Farnesyltransferase inhibitors (FTIs) were originally designed as anti-cancer drugs, but recently have been shown to slow premature aging resulting from Progeria (1). This premature aging syndrome is caused by a mutation that affects processing of the lamin A protein, a component of the nuclear lamina. A farnesylated prelamin intermediate accumulates, which in turn interferes with the assembly of a functional nuclear lamina. Farnesylation of prelamin A occurs on a CaaX box motif by the FTase. One class of FTIs structurally mimics the CaaX motif thereby inhibiting the enzyme. Inhibition of lamin A farnesylation prevents the accumulation of farnesyl-prelamin A and inhibition of lamina assembly. This surprising discover has given clinicians the first drug to treat this rare, but deadly premature aging syndrome. By studying the structure of FTIs bound to farnesyltransferase, more new specific drugs might be found.
(1) Meta, M, Shao, H., Yang, Bergo, M.O., Fong, L., Young, S.G. (2006) Protein farnesyltransferase inhibitors and progeria. Trends in Molecular Medicine 12:480-487

• St. Dominic Middle School
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St. Dominic Middle School

RNA Polymerase II: The Reader of the Secret Code!




Students:

• Grace Buting
• Teddy Delforge
• Meg Donovan
• Erika Engel
• Teddy Esser
• Ellen Fink
• Maura King
• Meredith Klinker
• Billy MacDonald
• Katie Mark
• Stephanie McGavin
• Vince Moldenhauer
• Paige Pichler
• Nathan Rein
• Katie Rieger
• Hailey Rowen
• Stephanie Seubert
• Rachel Sladky
• Ariana van Willigen

Teacher:

• Donna LaFlamme

Mentor:

• Vaughn Jackson, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

RNA polymerase II is essential to life in cells. Found in the nucleus of a cell, this molecule is a multi-subunit protein. RNA Pol II makes messenger RNA (mRNA) copies of genes. This process is called transcription and is the first step in protein synthesis. Genes are made of DNA and contain the codes for making proteins. Since DNA is unable to leave the nucleus, RNA Pol II makes an mRNA copy that can leave the nucleus. Ribosomes then attach to and read the mRNA. They synthesize a protein by joining amino acids in the correct order. RNA Pol II has 12 subunits and the two largest, Chain A and Chain B, contain the active site where the enzyme adds fifty to ninety nucleotides per second to the growing mRNA strand. Pol II is very accurate, only making about 1 mistake every 10,000 nucleotides. When it does make a mistake or finds DNA damage, it can backtrack to correct the error. Roger Kornberg and his research group hypothesize that during transcription the bridge helix changes shape to ratchet the DNA template and transcript through the active site while holding the end of the transcript in place. When the poison alpha-amanitin found in the Death Cap Mushroom paralyzes the bridge helix, transcription slows from 50 to 90 nucleotides per second to 2 to 3 nucleotides per minute. At this slow transcription rate, mRNA copies of genes do not get made, protein synthesis stops, and cells die. Untreated alpha-amanitin poisoning usually causes death within 10 days.

• Wauwatosa East High School
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Wauwatosa East High School

Dr. Helix and Mr. Sheet: The two faces of α-synuclein




Students:

• David Covell
• Nate Deisinger
• Neha Hasan
• Brian Hoettels
• Kelly Hubert
• Elyssa Kenagy
• Nate Kolpin
• Matt Marti
• Lucia Roegner

Teacher:

• Mary Anne Haasch

Mentor:

• Jason Kowalski, Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

α-synuclein is a protein that affects thousands of people, yet very little is known about it. This protein is associated with neurodegenerative diseases including Parkinson's Disease (PD) and Lewy Body Dementia (LBD). PD affects 500,000 people every year, and is linked to degeneration of motion control centers in the brain. LBD is a disorder that affects cognitive, autonomic, and sleep ability in people over 65. α-synuclein is involved in synaptic vesicle pools, dopamine regulation, formation of soluble N-ethylmaleimide-sensitive factor (SNARE) complexes which help vesicles fuse with the membrane, and other less studied regulatory functions. α-synuclein's most understood function is the regulation of vesicle pools in neurons. When no α-synuclein is present, vesicles dock with a membrane and are ready to fuse with it and release neurotransmitters, sending signals to the brain. When α-synuclein accumulates, the vesicles are prevented from fusing and releasing neurotransmitters. In varying environments, α-synuclein can take the shape of an α-helix, β-sheet, or be unstructured. For instance, α-synuclein is unstructured until it is brought near a membrane, when it takes an a-helical conformation, an advantage to fusing with a membrane. The β-sheet conformation is found primarily in Lewy Bodies in PD and LDB patients. In order to understand α-synuclein's role in PD and LBD, scientists must learn more about its structure and function.

• Wauwatosa West High School
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Wauwatosa West High School

DRB3*0101: Mother Doesn't Always Know Best




Students:

• Matt Berggruen
• Connor Grant
• Chris Hampel
• Jessica Hoffmann
• Sean Kundinger
• Rituparna Medda
• Katie Omernick
• Mariah Rogers
• Chandresh Singh

Teacher:

• Donnie Case

Mentor:

• Andrea Ferrante, MD, Blood Research Institute

Project Files:

• Poster

Abstract:

Fifteen to forty percent of intensive care infants have Neonatal Alloimmune Thrombocytopenia (NAIT). This disorder may result in intracranial hemorrhaging, potentially causing death. NAIT is commonly associated with depletion of fetal platelets due to maternal antibodies against a specific glycoprotein located on the platelet cell surface. Glycoprotein IIb/IIIa has a region known as HPA1, which has a specific dimorphism linked to NAIT. If the mother's platelet has a proline residue in position 33 (HPA1b), and the baby has leucine at this same position (HPA1a), the mother will mount an immune response against the baby's platelets, as she sees them as foreign. Maternal B cells produce antibodies anti-HPA1a. The antibodies bind to the platelets and these antibody-coated platelets are then marked for destruction, leading to clotting disorder. Interestingly, mother responders are characterized by the expression of class II HLA DRB3*0101 (also known as DRw52a with other nomenclature) on the surface of Antigen Presenting Cells. Class II HLA molecules play an important role in the initiation of the immune response presenting antigenic peptides and stimulating helper T cells. This high HLA association may suggest that the B cells require T cell help. Thus, under the hypothesis that the same dimorphism may generate both the B cell target and constitute the HLA-bound peptide, T cells specific for the HPA1 antigen have been identified, supporting the existence of a HLA II/HPA1a complex. Here we present the crystal structure of HLA DRB3*0101 in complex with HPA1a antigen, whose exploration may provide insights as to the understanding of this and other allele-associated diseases.

• West Allis Nathan Hale High School
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West Allis Nathan Hale High School

>21st Century Drug Design: Blocking Prokaryotic Cell Wall Synthesis by Stopping DHPR




Students:

• Pravleen Bajwa
• Kenton Chodara
• Nicole DeGoerge
• J.J. Garsombke
• Tim Jesse
• Rebecca Ruechel
• Kristin Zorr

Teachers:

• Sue Getzel
• Anne Xiong

Mentor:

• Dan Sem, Ph.D., Marquette University, Milwaukee, WI

Project Files:

• Poster

Abstract:

The bacteria Mycobacterium tuberculosis is the causative agent for tuberculosis (TB) and has been present since at least 2400 BCE. Two million people worldwide die from it annually, with the highest death rates in developing countries. This resurgence of TB can be attributed to many factors, one of which is the bacteria's increasing resistance to a broad spectrum of antibiotics. In TB, antibiotics act to cause leakage in the prokaryotic cell wall, which leads to cell death. Resistant bacteria have acquired mutations in key enzymes involved in cell wall formation, thus preventing antibiotics from inducing wall leakage. Therefore a need exists for development of new types of drugs to inhibit or kill infectious bacteria. One new path includes targeting an enzyme, Dihydrodipicolinate reductase (DHPR), which is used to produce prokaryotic cell walls. When this enzyme is inhibited, the cell wall of M. tuberculosis becomes unstable, killing the bacterium. DHPR catalyzes a chemical reaction in the metabolic pathway leading to diaminopimelate, an essential cell wall component. If DHPR can be inhibited by a substrate competitor, then a potential drug lead may be identified. Understanding how the enzyme's active sites function will facilitate the optimization of a recently designed inhibitor of DHPR. Specifically, the research will explain how this molecule may interact with the 4 binding pockets on DHPR. For this drug to work, is binding required at 1, 2, 3 or all 4 pockets, and why? Does binding at one pocket affect what goes on at the other 3? These questions need to be answered before a drug molecule can be rationally engineered against DHPR.

• Whitefish Bay High School
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Whitefish Bay High School

Initiating Cell Division: The Role of the Ternary Complex




Students:

• Zixiao Chen
• Youngjoon Choi
• Justin Fenzl
• Anna Gibson
• Alison Huckenpahler
• Zak Kaplan
• Tim Murray
• Sam Roth
• Martin Steren

Teachers:

• Marisa Roberts
• Judy Weiss

Mentors:

• Ravi Misra, Ph.D., Medical College of Wisconsin, Milwaukee, WI
• Mary Holtz, Ph.D., Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

DNA, the fundamental building block of cells, tells the cell how to produce proteins, regulate cell division, and pass genetic information from parent cell to daughter cell. However, a human's DNA is over three billion bases long, and transcribing the entirety of the DNA to get a duplicate of a small section is highly inefficient. To combat this, DNA contains specific sequences that work in conjunction with proteins to signal where to begin and end copying for a specific section. One such sequence of nucleotides is the Serum Response Element (SRE). The SRE is bound by a protein called Serum Response Factor (SRF). SRF binds as a dimer to the minor groove of DNA (red and green structures on gray DNA helix, above). SRF, in combination with SAP-1, another protein, bind to DNA at the SRE. The SAP-1 protein contains two parts: the SAP-1 b-Box that binds to SRF, and the SAP-1 ETS domain that binds to DNA. These two parts are linked with a flexible chain of amino acids, shown above as the gold dotted line. Together, SRF and SAP-1 form a ternary complex with DNA that marks the DNA for transcription. SRF regulation of gene transcription plays an important role in embryonic development, possibly aiding in heart development. Mouse embryos devoid of SRF die early in development, never coming to term. When transcription of the mRNA is misregulated, SRF can cause cancer. This specific ternary complex binds to a portion of the genome that starts the transcription of the human c-fos proto-oncogene when the cell is externally stimulated. Research on this complex is still continuing and scientists are getting closer to understanding its full potential.

Remote Teams:

• Pingry School, Martinsville NJ - Pingry team website

2006-2007 SMART Teams

In 2006 - 2007, the SMART Team Program saw a very successful year with a big jump in the number of local teams, totaling fifteen compared to last year's seven. View the local team projects are below.

Local teams:

Final Presentation Abstract Booklet (1.4 Mb .pdf file)

• Sheboygan North High School
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Sheboygan North High School

Glycoprotein VI: Thrombosis and Collagen Reaction




Students:

• Colleen Anson
• Matt Cain
• Sam Ehrenreich
• Zach Girdner
• Otto Kletzien
• Rachel Mayer
• Mark Robitaille
• Melanie Signer
• Zhexi Wang
• Logan Vander Wyst

Teacher:

• Amy Reinholtz

Mentor:

• Debra Newman, Ph.D., Blood Center of Wisconsin

Project Files:

• Poster

Abstract:

Platelets normally circulate in the bloodstream in an inactive state. When a blood vessel is damaged and proteins in the extracellular matrix surrounding the blood vessel are exposed, platelets become activated, stick to one another to form a thrombus, and close up the wound. One of the major components of the extracellular matrix is collagen. Glycoprotein VI (GPVI) is a protein that plays a major role in allowing platelets to bind to and become activated by collagen. GPVI is embedded in the membrane of platelets; the extracellular region of GPVI is the section that binds to collagen, whereas the intracellular region is active in sending a signal to the inside of the platelet that enables the platelet to become activated. Activation of platelets by collagen can be beneficial during wound healing but, if platelets are activated and form a thrombus on the inside of a blood vessel, a heart attack or a stroke can result. An example of situation associated with clinical thrombosis complications is the use of coronary angioplasty to open up blocked blood vessels. Patients undergoing coronary angioplasty may have damaged artery walls with exposed collagen, which can cause excessive formation of thrombi that block the blood vessel up again. Researchers in the laboratory of Dr. Debra Newman at BloodCenter of Wisconsin have discovered that individuals who have GPVI deficient platelets exhibit only minor bleeding disorders. They are therefore interested in trying to develop a drug that would shed GPVI molecules from the platelet’s surface so as to treat patients with clinical thrombosis complications, with the expectation that such a drug would not cause major bleeding disorders.

• West Bend East High School
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West Bend East High School

It’s Positive to be Negative: Electron Transfer and Cytochrome P450 Cam




Students:

• Ryan Prinz
• Jared Blommel
• Brian Fossum
• Paul Fossum
• Michelle Geidel
• Myranda Reimer
• Emily Bruckert
• Gib Flockert
• Jen Donagen

Teacher:

• Trish Strohfeltd

Mentors:

• Rajendra K. Kothinti, University of Wisconsin-Milwaukee, Milwaukee, WI

Project Files:

• Poster

Abstract:

Cadmium is an environmental pollutant that can be responsible for failures in the human body. Humans are exposed to cadmium through the smoke of cigarettes; both first and second hand, contaminated water, and plants grown in contaminated soils. The accumulation of this toxic metal, cadmium, from our environment can interfere with a specific DNA transcription factor responsible for coding a protein, sodium-glucose transporter (SGLT1), which regulates the re-absorption of glucose into the blood. Sp1 was found to lose its binding capability with specific GC rich DNA (Petering et. al.). The protein that we are modeling is transcription factor IIIA, which has a comparable structure to SP1, the protein in study. The transcription factor which helps control the production of Finger 3 of transcription factor SP1 readily accepts a cadmium ion in place of the normal zinc ion due to their identical charges. The cadmium ion is significantly larger than the zinc, so the structure of the protein is altered to accommodate the size difference. Both the tertiary and quaternary structures are affected by this shift. Some pertinent amino acids that are altered are his21, his25, cys8, lys15, met18, and cys5. The helix’s shift is especially notable because it causes the transcription factor to incorrectly bind to the DNA; thus, mRNA is not correctly transcribed and the glucose-regulating protein is not produced. The lack of this protein results in numerous health concerns, namely glucosuria (loss of glucose in the blood) and kidney failure. Our task is to show the specific differences caused by the binding of cadmium to transcription factor SP1. This research may help to expand knowledge of the specific health effects of toxic cadmium.
Tabatabai NM, Blumenthal SS, Petering DH. Toxicology. 2005 Feb 28;207(3):369-82.
Krepkiy D, Forsterling FH, Petering DH. Toxicology. 2004 Jul;17(7):863-70.

• St. Dominic Middle School
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St. Dominic Middle School

RNA Polymerase II

Students:

• Sam Andreski
• Julie Armstrong
• Greg Cigich
• Andrew Cobb
• Kevin Drees
• Mark Engel
• Matt Geisinger
• Joe Heckes
• Patrick Jordan
• Ryan Kohl
• Kevin Koprowski
• Michael Moakley
• Rachael Reit
• Tara Robey
• Andrew Ruka
• Michael Russell
• Lauren Schmidt
• Tyler Sherman
• Paige Siehr

Teacher:

• Donna LaFlamme

Mentors:

• Vaughn Jackson, Ph.D., Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

RNA Polymerase II (Pol II), a major up-keeper of our cells, is found in the nucleus of all eukaryotic cells and is one of the most important enzymes in our body. Pol II has twelve protein subunits, which also makes it one of the largest molecules. Its function is to surround the DNA, unwind it, separate it into two strands, and use the DNA template strand to create a messenger RNA (mRNA) copy of a gene. These mRNA copies of genes are needed by the cell to make proteins to keep the cell healthy. The mRNAs are the templates used by ribosomes to link amino acids into long chains in the correct order to form all the different proteins in our bodies. In fact, RNA Pol II is so essential to life that when the poison, alpha-amanitin, from the Death Cap mushroom attaches to RNA Pol II, death occurs within 10 days. The alpha-amanitin goes into the funnel portion of Pol II and inserts under the bridge helix. The poison is thought to limit the movement of the bridge helix and prevent a ratcheting movement that translocates the DNA template. When working properly, RNA Pol II can make RNA copies of DNA at speeds of 1000 to 1500 bases per minute. The alpha-amanitin slows this speed to 2 or 3 bases per minute. At this slow speed, RNA Polymerase II cannot do its job of making messenger RNA copies of our genes. Without mRNA molecules, the ribosomes cannot make the thousands of different proteins needed for life.

• Kettle Moraine High School
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Kettle Moraine High School

It’s Positive to be Negative: Electron Transfer and Cytochrome P450 Cam




Students:

• Disa Drachenberg
• Nicole Fischer
• Andy Flick
• Madelyn Homuth
• Tom Lankiewicz
• Matt Larson
• Melanie Mayes
• Kimi Struck
• Kaitlin Swanson

Teachers:

• Peter Nielsen
• Karen DeBoer
• Steve Plum

Mentors:

• Daniel Sem, Ph.D., Marquette University, Milwaukee, WI

Project Files:

• Poster

Abstract:

Cytochromes P450 perform many functions, predominantly creating steroid-like hormones and metabolizing various organic compounds, vitamins, xenobiotics, pharmaceuticals, and carcinogens. They are present in most prokaryotic and eukaryotic cells. In humans, many cytochromes P450 are found in the adrenal cortex, but are primarily in the liver, where they metabolize ninety percent of all pharmaceuticals. P450cam is one of the few P450s that have been widely studied. This particular P450 hydroxylates camphor molecules and through electron transfer, lowers the activation energy, creating an energetically favorable circumstance for camphor metabolism. P450cam requires an allosteric regulator and electron source, putidaredoxin, to activate this process. Allosteric regulators can act like a key to either lock or unlock a molecule, thereby disabling or enabling metabolism. Putidaredoxin (PDX) interacts with P450cam at three specific points. At two of these points, ionic bonds form to connect the two molecules, and at the third point, an amino acid on the PDX buries itself inside P450cam, which pushes against a specific helix in the P450, termed the I-helix, on the P450cam, forcing the helix to straighten. When the I-helix straightens, another pair of helices, referred to as the F-G helices, move, and camphor molecules that are bound to the outside of the P450cam can gain access to the heme group, because the F/G-helices open like a trap door. Metabolism can begin once the PDX transfers electrons from its two-Iron/two-Sulfur ferredoxin cluster to the Iron in P450cam's heme group, thereby reducing it in preparation for catalysis. There are two likely electron pathways in this redox reaction. By studying P450cam as a model, general knowledge of the electron transfer mechanism and the pathways for heme reduction can be gained.

• Kenosha Bradford High School
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Kenosha Bradford High School

Gleevec: Rational Drug Design for Cancer




Students:

• Jonathan Jara-Almonte
• David Jensen
• Vincent LaRosa
• Peter McGrain
• Jessica Sherman

Teachers:

• Jean Lee

Mentors:

• Robert Deschenes, Ph.D., Medical College of Wisconsin , Milwaukee, WI

Project Files:

• Poster

Abstract:

Chronic myelogenous leukemia (CML) results from a translocation between chromosomes 22 and 9. The translocation results in an abnormal fusion between the BCR and the c-ABL tyrosine kinase gene which leads to uncontrolled cell division. The structure of the Abl kinase provides an understanding of kinase activation and a strategy for the design of inhibitors. The key to activation of c-Abl is the region of the protein called the activation loop. Phosphorylation alters the position of this loop such that when the kinase is active, the loop is fully extended in an open position. An aspartic acid residue (Asp-381 in Abl) within a conserved Asp-Phe-Gly (DFG) motif at the NH2-terminal base of the loop is positioned to interact with the magnesium ion that coordinates the phosphate groups of ATP. The remainder of the loop provides an area for substrate binding. This continuously binds with ATP and leads to constitutive activation of the kinase. The drug Gleevec is designed base on the 3D structure to inhibit c-Abl. When Gleevec binds with the protein, the NH2 terminal rotates drastically compared to the active conformation, so that Phe-382 points towards the ATP binding site. The rest of the loop mimics a substrate binding to the enzyme, thereby blocking the enzyme active site for ATP and preventing tyrosine phosphorylation. Gleevec is an effective treatment for patients with CML. However, mutated forms of c-Abl have emerged that are resistant to Gleevec. By studying the structure of the drug-resistant variants, scientist hope to create alternative forms of Gleevec that can be used in Gleevec resistant cases.

• St. Joan Antida High School
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St. Joan Antida High School

The N-Terminal Carbohydrate Recognition Site of the Cation-independent Mannose 6-Phosphate Receptor: The Internal Bouncer




Students:

• Ashley Miller
• Affnan Mohammad
• Mary Sayles

Teachers:

• Mary Carlson

Mentors:

• Nancy Dahms, Ph.D., Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

In order for the human body to function properly, lysosomes are necessary. Lysosomes are found in virtually every cell in the body, and they rid cells of metabolic waste through the process of hydrolysis. Important assistants to the formation of lysosome are mannose 6-phosphate receptors, which guides the hydrolytic enzymes, to the lysosomes. These hydrolytic enzymes are tagged with a phosphorylated carbohydrate, mannose 6-phospate, which allows for the recognition by the mannose 6-phosphate receptors. The hydrolytic enzymes are responsible for breaking down the metabolic waste within the lysosomes and are therefore essential to be taken into the lysosome. Without the mannose 6-phosphate tag, the receptors cannot recognize the enzymes, thus denying the delivery of the enzymes into lysosomes. The receptor has three sites to which the mannose 6-phosphate binds. The 300-kDa receptor plays a vital role in trafficking newly synthesized mannose 6-phosphate containing acid hydrolases to the lysosomes. It is not yet understood how the three sites are able to interact with one another. Though rare, lysosomes can malfunction, causing a toxic buildup, which damages and eventually kills the cell. In this case, Lysosomal Storage Disorder (LSD) results. There are over 40 Lysosomal Storage Disorders, the most common being Tay-Sachs Disease. Tay-Sachs, a degenerative disease, occurs when lysosomes fail to rid the brain of lipid waste material. Most cases are diagnosed in infancy, and death occurs by the seventh birthday. There are no known cures for the Lysosomal Storage Disorders. However, enzyme replacement therapy is available for the treatment of four of the Lysosomal Storage Disorders. This expensive therapy is performed to alleviate symptoms and the pain caused by the LSD.

• Whitefish Bay High School
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Whitefish Bay High School

Sound the Alarm! How the Immune System Responds




Students:

• Zixiao Chen
• Anna Gibson
• Mikki Harding
• Sylvia Janicki
• Tae-Eun Kim
• Shannon Murray
• Karen Wang
• Sarah Whaley

Teachers:

• Marisa Roberts
• Judy Weiss

Mentors:

• Andrea Ferrante, M.D., Blood Center of Wisconsin, Milwaukee, WI
• Jack Gorski, Ph.D., Blood Center of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

When antigens invade the body, we need a way to protect ourselves. One of the defenses that we have in place is envelope antigens into the cell via endocytosis and break the antigen into pieces. These antigen pieces are presented on Class II Major Histocompatability Complexes (MHC II), which are molecules present specifically in the human body in order to identify invaders. MHC II molecules are sometimes referred to human leukocyte antigen, or HLA molecules. Receptors located on T-cells recognize MHC II molecules and will mount an immune response against the antigen peptide piece which has been presented on the MHC II. The proteins which "cradle" the fragments during presentation are known as HLA-DR. The T-cell receptor binds to the antigen located in the HLA-DR and determines if the substance is harmful to the body. When the HLA-DR proteins are initially formed, they cradle a placebo antigen fragment, called CLIP. This fragment is essential for maintaining the structure of the HLA-DR protein in the absence of an antigenic peptide fragment. After an antigen has been endocytosed and broken into pieces, CLIP must be replaced by the best fitting fragment of antigen. HLA-DM is responsible for removing CLIP from HLA-DR and replacing it with a piece of the antigen. Additionally, HLA-DM also attempts to put in the best fitting peptide piece in order to produce the most stable complex to generate a long-lasting immune response. In facilitating the speed in which the removal and replacement of CLIP occurs, HLA-DM acts as a catalyst. With Andrea Ferrante and Dr. Gorski, our SMART Team has been researching exactly how HLA-DM and HLA-DR interact to produce the catalytic effect. By building models of certain parts of HLA-DM and HLA-DR, the researchers should find clues as to how their structures interact.

• Brown Deer High School
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Brown Deer High School

The Beta Bunch: A-Beta of Amyloid Precursor Protein




Students:

• Jason Baughman
• Elaine Brushafer
• Katie Easton
• Andrew Faught
• Sara Faught
• Ben Jaberg
• Adam Majusiak
• Catie Pfeifer
• Amy Ramirez
• Karleisa Rogacheski

Teacher:

• Gina Vogt

Mentor:

• Anita Manogaran, Ph.D., University of Illinois at Chicago, Chicago, IL

Project Files:

• Poster

Abstract:

The A-beta section of APP forms aggregates in the brain that are related to Alzheimer's disease. The year 2006 marks the 100th anniversary of the identification of Alzheimer's disease, an ailment affecting an estimated 4.5 million Americans, including, it is thought, approximately half of the population aged 85 and older. The ailment typically begins after age 60, and the risk of developing Alzheimer's disease increases with age since the disease is progressive in nature. A slow moving debilitating affliction, Alzheimer's disease causes mild forgetfulness in its early stages, but as the disease advances, Alzheimer's disease destroys nerve cells, disrupting connections between the cells in areas of the brain vital to memory. In addition, it chemically weakens their ability to send messages, which can impair thinking and memory. The subject of our study is the A-beta portion of the amyloid-beta precursor protein (APP), identified in the protein data bank as 1Z0Q; it may contain a potential link to the enigmatic nature of Alzheimer's disease. APP resides within the cell membrane and the A-beta portion is formed when APP is cleaved by the beta and gamma secretases, leaving a 42 amino acid peptide. After the protein is cut by these secretases sticky surfaces are exposed on the A-beta peptide. In the brain, the A-beta peptide aggregates in extracellular plaques. Presence of these plaques is associated with Alzheimer's disease; however, it is unknown whether the aggregates are a cause or an effect of the disease. Efforts to stop the progression of the disease target secretase identification and the resulting effect of selective drugs on these secretases as well as the aggregation of the A-beta peptide.

• Edgewood Middle School
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Edgewood Middle School

A Probable Treatment for Alzheimer's Disease: Somewhere Between Confusion and Clarity, The Transthyretin Protein




Students:

• Rebecca Cray
• Walter Grosenheider
• Sami Huntoon
• Taylor Johnson
• Corrie Lee
• Eric Madsen
• Claire McLaughlin
• Mariah Popp
• Jake Power
• Kathleen Ralph
• Sam Rothrock
• Neil Sekhon
• Emily Sharata

Teacher:

• Dan Toomey

Mentor:

• Jeff Johnson, Ph.D., University of Wisconsin - Madison, Madison, WI

Project Files:

• Poster

Abstract:

The amyloid beta protein and transthyretin are two proteins of interest to scientists trying to understand how Alzheimer's disease develops. The disease results from the accumulation of a specific fragment of the amyloid beta protein, referred to as the A-beta protein. When this small piece of protein is cut from the amyloid precursor protein, the smaller piece is referred to as A-beta protein. The A-beta peptide protein forms plaques by aggregating together, causing neurons in the brain to die, resulting in Alzheimer's disease. Transthyretin, however, is the "good protein" and prevents the A-beta protein from killing those neurons. Though researchers do not specifically know how the transthyretin does this, it is hypothesized that the transthyretin binds with the A-beta so that it cannot interact with the neurons. In a healthy cell, transthyretin proteins are though to be transport proteins the thyroid hormones. Though the A-beta protein is always being made in healthy cells, its regular function is not known. This has been an area of interest, because only some people get Alzheimer's disease. Researches believe this may be due to different amounts of defense mechanisms, such as transthyretin, in each person’s brain. Studies have shown that mice that have been genetically engineered to have higher levels of the A-beta protein also have more transthyretin, therefore preventing Alzheimer's disease. This increase in transthyretin, unfortunately, only happens in mice, and has not been seen in humans living with Alzheimer's disease. Because mice have dramatically increased transthyretin proteins, which block the A-beta toxicity, researchers are trying to find ways of increasing that protein in humans.

• Marquette University High School
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Marquette University High School

Serum Response Factor (SRF): The Key to Making or Breaking a Heart




Students:

• Wesley Borden
• Daniel Brodzik
• Patrick Carter
• Brian Digiacinto
• John Geary
• Thomas Niswonger
• Joseph Radke
• Matthew Shields
• Caleb Vogt

Teacher:

• Keith Klestinski

Mentor:

• Ravi Misra, Ph.D., Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

Serum Response Factor (SRF) is a protein transcription factor. Transcription factors use the information on DNA to regulate RNA production that ultimately encodes for proteins the body needs. SRF promotes the formation and growth of cardiac muscle cells. SRF functions as a "dimer" composed of two identical subunits. The SRF dimer works as a complex in cooperation with other associated factors to help control gene expression. The number and type of SRF-associated factors determines which genes are expressed, where they are expressed, and when they are expressed. SRF and the other factors bind a DNA sequence known as the Serum Response Element (SRE). The SRE region is known for its characteristic nucleotide sequence and is found in the promoters of SRF responsive genes in many different species. One way SRF is important for heart formation and function is based on its ability to regulate genes essential for the differentiation and growth of cardiac muscle cells. In mouse embryos, SRF is absolutely required for proper cardiac development. Research shows that embryos deprived of SRF die from underdeveloped hearts. Overexpression of SRF can result in cardiac hypertrophy (enlarged heart syndrome). Better understanding of SRF function holds the potential to develop therapies designed to repair human heart damage.

• Grafton High School
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Grafton High School

The Tale of Two Structures: Lymphotactin 10 (Ltn 10) and 40 (Ltn 40)




Students:

• Renee Buchholz
• Kyrstin Mueller
• Dustin Studelska
• Linday Zadra

Teacher:

• Fran Grant

Mentor:

• Robbyn Tuinstra, Ph.D., Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

Chemokines, like Lymphotactin (Ltn), are small proteins that direct lymphocytes to sites of injury or infection, aiding in the healing process. Chemokines bind sugars on the surface of epithelial cells that line the vascular and lymphatic systems, allowing chemokines to "catch" circulating lymphocytes. The interaction of chemokines with lymphocytes is mediated by the activation of cell surface receptors, signaling immune cell migration. HIV targets a chemokine receptor to infect and replicate within the T-cells. Alternatively, diseases such as Crohn’s disease and rheumatoid arthritis may result from a disregulation of chemokine production and lymphocyte migration. In chronic inflammatory conditions such as these, there is an inappropriate or uncontrolled T-cell infiltration driven by Ltn. Unlike other chemokines, Ltn exists under physiological solution conditions in two distinct, yet equally populated structures. The conversion between these structures is freely reversible, but can be stabilized by changes in solution conditions. At 10°C and high salt concentration, Ltn is a monomer (Ltn10) exhibiting the conserved chemokine fold of a 3-stranded ß-sheet and an a-helix. At 40°C, without salt, Ltn adopts a 4-stranded ß-sheet structure (Ltn40). Two Ltn10 proteins turn themselves inside out and bind together to form one Ltn40 protein. While the Ltn10 structure appears to activate the Ltn receptor on immune cells, Ltn40 is believed to contain the sugar binding site. The long term objective of the research is to determine the mechanism of Ltn rearrangement and the biological significance of each structural species.

• Wauwatosa West High School
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Wauwatosa West High School




Collagen: The Glue of Life

Students:

• Shazia Ali
• Jessica Hoffmann
• Rituparna Medda
• Katie Omernick

Teachers:

• Donnie Case
• Mary Anne Haasch

Mentor:

• Françoise Van den Bergh, Ph.D., Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

Collagen, a structural protein, makes up 25% by mass of all proteins in our bodies. It is essentially the "glue" that holds our tissues together by providing strength and flexibility to our skin, cartilage, tendons, ligaments, and bones. So far, 28 types of collagen have been discovered. Our model demonstrates the basic structure of collagen: a left-handed helix made from a repeating sequence of three amino acids. These amino acids follow the pattern Glycine-X-Y, or in our model, specifically Glycine-Proline-Proline. To make the complete collagen molecule, three of these strands come together in the endoplasmic reticulum and are "zipped up" creating a trimer. Together, the polypeptides will form a right-handed helix. The individual strands are held together by hydrogen bonds between the Glycine. The Glycine is situated in the center of the helix because it is small and can be tightly packed together. When the production of collagen I is flawed, bones become easily fractured. This is called "brittle bone" disease or osteogenesis imperfecta. Dystrophic epidermolysis bullosa is caused by mutations in collagen VII. This disease causes fragility in the dermis, which then results in blister formations when skin is exposed to friction because there is no collagen to adhere the layers of skin together. Problems with collagen can also be caused by dietary factors, as in scurvy. When people do not eat enough vitamin C, collagen cannot be hydroxylated and loses its strength, causing gum disease and skin hemorrhaging. Collagen can also be affected in autoimmune diseases. One example involving the skin is bullous pemphigoid. In this disease the immune system "decides" that collagen XVII does not belong and an immune response develops against this protein leading to its destruction and the formation of blisters on the patient. You can see from these diseases the importance of the structural role of collagen. Without it, common tissues in our body could not be held together and activities most people take for granted become impossible. Collagen truly is the glue of life.

• Wauwatosa East High School
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Wauwatosa East High School

NADPH-Cytochrome P450 Oxioreductase Catalyzing the Metabolism of Various Compounds




Students:

• Brittany Ladewig
• Katy Johnson

Teacher:

• MaryAnne Haasch

Mentor:

• Jung-Ja Kim, Ph.D., Medical College of Wisconsin, Milwaukee, WI

Project Files:

• Poster

Abstract:

NADPH-cytochrome P450 oxidoreductase (CYPOR) is found in the endoplasmic reticulum in the cell. CYPOR’s main function is to transfer electrons from NADPH to cytochromes P450, vital in the processes of all living things including the metabolism of drugs and steroid production in humans. CYPOR is a biomolecular machine. The enzyme opens up when it encounters NADPH, as if on a hinge; trytophan-677 moves, allowing NADPH to enter and transfer two electrons to the CYPOR. These electrons are transferred, one at a time, to P450 via FAD and FMN. Scientists have verified several diseases due to deficiency of CYPOR. One of the more severe diseases is called Antley Bixler Syndrome (ABS), which affects the skeletal structure of the body, creating malformations, mostly to the head or facial region. In affected children or infants, abnormalities may include prominent foreheads, protruding eyes, and underdeveloped midfacial regions. Also, fusion of adjacent bones in the arm, long, thin digits, bowing thigh bones, or certain joints permanently flexed or extended are additional abnormalities caused by ABS. Other less severe cases of CYPOR deficiencies include steroid hormone deficiencies; ranging from cases to under-masculinization in males or virilization in females. Since CYPOR is a vital enzyme to our body and other living things, research is continuing to find other diseases that could be caused by malfunctions in the process. However, as mice embryos died before birth when the enzyme was absent, isolating this process in living organisms proves difficult. Also, because of CYPOR's function of detoxifying and breaking down drugs, it's important to know its effects on certain drugs to prevent any complications. Being such a vital part of every organism’s system, the main question is how CYPOR's transfer electrons using NADPH via FAD and FMN to the cytochrome p450. From answering this question, hopefully we can learn more about this complicated process.

• Conserve High School
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Conserve High School

The Growing Problem of Antibiotic Resistance: How Kanamycin Nucleotidyl Transferase (KNTase) Inactivates the Antibiotic Kanamycin in Drug Resistant Bacteria




Students:

• Roy Currie
• Ben Evans
• Natasha Holmes
• Lauren Hughes
• Nate Reiners

Teacher:

• Patti Soderberg, Ph.D.

Mentors:

• Agnes Kanikula, University of Wisconsin-Madison
• Hans H. Liao, Ph.D., Biotechnology Development Center, Cargill Incorporated, MN

Project Files:

• Poster

Abstract:

The discovery of antibiotics revolutionized medical care as these powerful drugs enabled physicians to combat bacterial infections. Antibiotics became widely available in the 1940s. Kanamycin belongs to a family of antibiotics known as aminoglycosides. Kanamycin normally kills bacteria by binding to one of the ribosomal subunits, subsequently blocking the ability to produce proteins. Unfortunately, the overuse and misuse of these miracle drugs over the ensuing years has caused an alarming increase in the number of bacterial species that are resistant to one or more of our arsenal of antibiotics. The genes for resistance are typically found on plasmids, which are small circular pieces of DNA that can be transferred from one bacterium to another. One such plasmid encodes for an enzyme called kanamycin nucleotidyltransferase (KNTase) that inactivates kanamycin enabling bacteria to become resistant to it. This plasmid is widely used in the production of genetically modified organisms. KNTase was originally isolated from Staphlococcus aureus, a species of bacteria that is a major cause of hospital-acquired infections. An understanding of the molecular structure of KNTase is important in order to provide a model for the development of new, more effective drugs. In addition, a KNTase mutant isolated from thermophilic bacteria exhibits thermostability. It appears that a single amino acid mutation enables the enzyme to be stable at higher temperatures, making KNTase a good molecule for investigating the cause of enzyme thermostability.

• Madison West High School
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Madison West High School

How Penicillin and Streptomycin Kill Bacteria




Students:

• Audra Amasino
• Dianna Amasino
• Re-I Chin
• Yuting Deng
• Gabriela Farfan
• Axel Glaubitz
• Sam Huang
• Susan Huang
• Joy Li
• Hsien-Yu Shih
• JunYao Song
• Peter Vander Velden
• Connie Wang
• Mary Zhang
• Xiao Zhu

Teacher:

• Basudeb Bhattacharyya, School of Veterinary Medicine, University of Wisconsin

Mentors:

• David Nelson, Ph.D., University of Wisconsin
• Steve Goth, University of Wisconsin

Project Files:

• Penicillin Poster
• Streptomycin Poster

Abstract:

Prior to World War II, a bacterial infection would most likely lead to death. Especially crucial during the war, drugs were needed to combat infections that killed numerous wounded soldiers. Through an accidental discovery by Alexander Fleming in 1928, penicillin dramatically decreased the number of bacterial related deaths and amputations. Penicillin is an effective antibiotic that targets proteins (e.g. Penicillin Binding Protein 4—PBP4) responsible for cross-linking the components of the bacterial cell wall peptidoglycan layer. By targeting these bacterial specific proteins, penicillin weakens the cell wall of a dividing bacterium, thereby leading to the bacteria’s subsequent death without harming the patient. However, it is not effective against all types of bacterial infections because it can only target certain types of bacteria (i.e. Gram-positive bacteria which lack the lipopolysaccharide layers that surround and protect Gram-negative bacteria). Mycobacterium tuberculosis, the causative agent of tuberculosis (an airborne disease which left untreated can lead to death and was indeed a major cause of death in the United States prior to 1943) is an example of a bacterial species that is immune to the effects of penicillin. Streptomycin was the first antibiotic (discovered in October 1943 by Selman Abraham Waksman and Albert Schatz) found to combat tuberculosis. Isolated from the soil organism Streptomyces griseus, this antibiotic binds tightly to bacterial 16S ribosomal RNA (rRNA), causing a conformational change within the A-site of the ribosome, creating a higher affinity between the A-site and “incorrect” tRNAs (the A-site is generally restrictive and has a low affinity for incorrect tRNAs). This makes protein translation "error–prone" and therefore protein synthesis is inhibited in the target bacterium. This process does not affect human ribosomes which do not have the 16S rRNA and the specificity of streptomycin to this ribosomal subunit makes it an ideal treatment. We are using rapid prototyping to model the interaction between penicillin and PBP4 as well as streptomycin and the 16S rRNA in order to better understand the general mechanisms of bacterial infection and the variety of antibiotic treatments available as well as antibiotic resistance.

Remote Teams:

• Pingry School, Martinsville NJ - Pingry team website

2005-2006 SMART Teams

In 2005 - 2006, the SMART Team Program enlisted seven local teams from Wisconsin area high schools and eleven remote teams. View the local team projects below

Local teams:

Final Presentation Abstract Booklet

• St Dominic Middle School
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St Dominic Middle School

T7 RNA Polymerase: A Molecular Machine from a Virus




Students:

• David Baltrusaitis
• Lauren Bauer
• Derek Benz
• Josh Berg
• Pietro Boffeli
• Katelin Brockman
• Catherine Carter
• Kelsey Conlin
• Emily Drees
• Megan Henschel
• Katherine Hildebrand
• Caroline Klinker
• Troy Kostuch
• Jessica Lieb
• Matt MacDonald
• Mikaela McCarthy
• David Moldenhauer
• Sarah Newton
• Viktoria O’Leary
• Jordan Parker
• Stephanie Prince
• Sarah Rieger
• Joseph Ripple
• Katherine Russell
• Sally Scherrman
• Katherine Tighe

Teacher:

• Donna LaFlamme

Mentor:

• Vaughn Jackson, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

The purpose of the 2005-2006 St. Dominic SMART team was to create a model of the T7 RNA Polymerase (T7 RNAP) using data from the Protein Data Bank and a visualization program called RasMol. T7 is virus that infects bacteria, but its RNA Polymerase is a very important molecule to scientists. Scientists can use T7 RNAP to create large amounts of a specific protein for their research or to study transcription in vitro. This polymerase is also used by drug companies to produce human insulin for diabetics. Before this polymerase was used to make human insulin, people with diabetes had to use pig’s insulin. This caused problems because some immune systems rejected this insulin. T7 RNAP is not only useful to scientists, but also helps thousands of people affected with diabetes all around the world.

By designing this model, we were able to better understand the function and the chemical reactions of this polymerase. Our scientist mentor, Dr. Vaughn Jackson, gave us a presentation to help us understand how the molecule moves down the DNA and makes messenger RNA from the DNA template. He explained that T7 RNA Polymerase is shaped like a hand. There is a “thumb”, a “palm”, and “fingers”. The five-helix subdomain of the “fingers” domain pivots at a twenty-two degree angle. This movement threads the DNA through the hand-shaped part of the molecule and allows the enzyme to move down the DNA strand.

Dr. Jackson also showed us how the T7 RNA Polymerase makes the messenger RNA (mRNA) from the DNA. First a transcription “bubble” forms in the DNA separating the two strands and allowing the polymerase to transcribe one of the strands of the DNA. After this, one nucleoside triphosphate (NTP) floats into the T7 RNA Polymerase at a time to match with the template DNA’s nucleotide. The NTP moves into a position to be bound to the mRNA. The NTP has three phosphates contained in it that are then stabilized by two magnesium atoms, an arginine side chain, and a lysine side chain. This process is called the insertion process. Our first structure of T7 RNAP, 1s76, shows the molecule during the insertion process. After the NTP has been inserted, it is bonded to the mRNA by a hydrolysis reaction in which two of its three phosphates are removed. The pyrophosphate product of this reaction leaves the active site. The polymerase then moves further down the DNA, and another NTP is brought into the active site. The second structure of T7 RNAP, 1s77, shows the molecule after the nucleotide has been added and the pyrophosphate has been detached from the NTP. The T7 RNAP molecule then continues this process until it reaches the termination point. At this point, the mRNA floats away and ribosomes attach to it. The ribosomes then produce the protein that is coded for by this mRNA copy of DNA.

• St Joan Antida High School
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St Joan Antida High School

Get Hooked: Cross-Beta Structure Leads to Domino Effect in Prion Disease




Students:

• Joanne Chalhoub
• Christine Dargis
• Catherine Dornfeld
• Erica Garcia

Teacher:

• Anne Staab

Mentor:

• Anita Manogaran, Ph.D., University of Illinois-Chicago

Project Files:

• Poster

Abstract:

In the study of protein function, one of the most important factors to the outcome of a molecule is the way it folds. If a protein does not fold properly, it will be unable to meet its function. The cells in our body contain ways to correct or rid our body of these misfolded proteins. In some cases, when a protein misfolds, it can aggregate and/or form fibers to create a prion, which then can induce other proteins to misfold and aggregate. Baker’s yeast has been known to have a number of prions including [PSI+], which is the prion form of the Sup35 protein. The Sup35 protein is important in translational termination, but when in the prion form, it loses the ability to efficiently perform this process. Within prion domain of Sup35, located in the N-terminus, a seven amino acid region, GNNQQNY, has been found to form a “cross-beta spine” structure, which is thought to contribute to the fibrilar structure of the prion. The researchers at University of Illinois-Chicago's Laboratory for Molecular Biology are interested in the structure of GNNQQNY because it helps in understanding the structural change of Sup35 from a normal form to the prion form. Furthermore, it can provide insight to how prions fold in human/mammalian systems.

• West Bend East High School
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West Bend East High School

SHP-2 Has Awakened - Let’s Divide!




Students:

• Jared Blommel
• Jen Donegan
• Tyler Hinchey

Teacher:

• Trish Strohfeldt

Mentor:

• Debra K. Newman, Ph.D., Blood Center of Wisconsin

Project Files:

• Poster

Abstract:

The SYP tyrosine phosphatase, also known as SHP-2, is an enzyme that cleans phosphates off of the amino acid tyrosine. SYP has three sections, including an amino-terminal SH2 domain, a carboxyl-terminal SH2 domain, and a phosphatase domain. The amino-terminal SH2 domain of the SYP tyrosine phosphatase is a specific section that regulates the cleaning of phosphates off of tyrosine amino acids. When resting, the amino-terminal SH2 domain of SYP binds with the phosphatase domain of the same molecule and keeps it "off." When active, the amino-terminal SH2 domain of SYP binds with phosphate-containing tyrosine amino acids on other proteins, which releases the phosphatase domain of SYP and enables it to turn "on."

The SYP molecule is an indispensable regulator of cell division and reproduction. In animals that are SYP deficient (for example, experimental mice in which the SYP gene has been "knocked out"), cell division is so abnormal that even the embryo does not develop. Therefore, no SYP-deficient animals, either mice or humans, ever develop. In animals in which there is something wrong with SYP, such as a mutation that results in irregularity in the binding of the amino-terminal SH2 and phosphatase domains to one another, the animal will develop but will have defects due to abnormal cell growth. This is because the SYP enzyme will never rest and will continuously take phosphates off of proteins that control cell reproduction. This can lead to accelerated cell division. Mutations in the gene that encodes SYP in humans result in a condition called Noonan’s syndrome, where abnormal bone growth and leukemia result.

Our model represents the amino-terminal SH2 domain of the SYP enzyme. The model includes a piece of another protein, the PDGF receptor, which binds to the amino-terminal SH2 domain of SYP and activates it. Differently colored amino acids in our model represent differences that arise from mutations in the SYP gene in people who have Noonan's syndrome.

• Madison West High School
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Madison West High School

Kinesin and Myosin Travel Along Molecular Rails




Students:

• Audra Amasino
• Dianna Amasino
• Re-I Chin
• Yuting Deng
• Gabriela Farfan
• Axel Glaubitz
• Samuel Huang
• Jessie Lee
• Adeyinka Lesi
• Linus Marco
• Yaoli Pu
• JunYao Song
• Peter Vander Velden
• Min Yoo

Teacher:

• Basudeb Bhattacharyya, School of Veterinary Medicine, University of Wisconsin

Mentors:

• David Nelson, Ph.D., University of Wisconsin
• Steve Goth, University of Wisconsin

Project Files:

• Poster

Abstract:

Kinesin and myosin are motor proteins (driven by ATP) that walk along molecular rails in order to transport “cargo” within cells; kinesin moves along microtubules, myosin moves along actin microfilaments. Their cargos include proteins, membrane vesicles, and organelles. Myosin also produces the contraction of muscle cells. Although they have similar functions, the binding sites, the ATPase sites, and the cargo binding sites differ. There are many types of kinesin and myosin throughout the body that vary in load (bound to cables) and direction of motion. Kinesin is composed of two identical “feet,” attached to a cable, which walk using a hand-over-hand motion. Myosin is found as a string of connected feet that moves by lifting one foot, planting it farther down along the microfilament, pulling its cable forward, then lifting a foot up again and repeating the motion. There are several diseases linked to mutations of kinesin and myosin including Alzheimer’s disease, blindness, Retinitis Pigmentosa, Charcot-Marie-Tooth Disease, hypertrophic cardiomyopathy, and May-Hegglin anomaly. We used rapid prototyping technology to print the RP-Rasmol derived PDB files 2KIN (kinesin) and 1B7T (myosin) in order to compare and contrast the two proteins and to visualize more specifically how they move along their respective “rails.”

• Kettle Moraine High School
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Kettle Moraine High School

Cytochrome P450 2D6 Drugs: The Breakdown




Students:

• Kyla Barr
• Tristan Dudley
• Madelyn Homuth
• Talan Miller
• Lindsay Swanson
• Brian Wenzler

Teachers:

• Karen De Boer
• Peter Nielsen

Mentor:

• Daniel Sem, Ph.D., Marquette University

Project Files:

• Poster

Abstract:

Cytochrome P450 is a microsomal membrane-bound protein that metabolizes xenobiotic compounds, most commonly pollutants, environmental compounds, and drugs; and is located primarily in the liver. CYP2D6 is one of several liver P450s, and it primarily metabolizes pharmaceuticals, such as anti-arrhythmics, anti-depressants and beta-blockers. Research on P450s is extremely valuable to the pharmaceutical industry because CYP2D6 binds as substrates and inhibitors, drugs such as: codeine, quinidine, fluoxetine, ritonavir. This binding can lead to the metabolism of the drug, or the inhibition of the metabolism of another drug through interaction. Because of this, it is possible to predict how effective drugs will be, in terms of their lifetime in the blood, based upon how they fit into the CYP2D6 binding site.

The CYP2D6 active site includes a heme group and five amino acids that impact binding. These five include: glutamate 216 which is part of the F-G helix, aspartate 301 which is along the I-helix, and phenylalanines 102, 481, and 483. The heme present is responsible for carrying out hydroxylation on substrates. If a drug can fit well into the binding site, it will be metabolized before it has done its job; if a drug does not fit easily, interactions may result because it will block the binding site when another drug molecule needs access, so the system’s concentration of that drug will spike.

Our goal is to look at these amino acids and two helices to determine how drugs are cleared from the system through metabolism. We are using a homology molecule model that was made using Swiss-Model with CYP2C5 as a template.

• Whitefish Bay High School
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Whitefish Bay High School

Defending Against Influenza: How Our Body Protects Itself




Students:

• Mary Cieslewicz
• Nate Bolyard
• Jay Lim
• George Chao
• Tae-Eun Kim

Teachers:

• Judy Weiss
• Marisa Roberts

Mentor:

• Jack Gorski, Ph.D., Blood Center of Wisconsin

Project Files:

• Poster

Abstract:

T cells play a vital role in immune responses. Each T cell has a unique receptor (TCR) that can recognize a fragment of a pathogen such as a virus or bacteria. Class II Major Histocompatibility Complex (MHC II) proteins and antigen presenting cells (APC) are also integral to the immune response. In the first step of this immune response, the APC, typically a macrophage or dendritic cell, “swallows” the pathogen through endocytosis and digests it. Next, the MHC II accepts a digested peptide fragment of the pathogen and carries it to the surface of the APC. Here, the MHC II displays the antigen to a T cell, whose receptor examines the complex. If the T cell receptor is able to bind to the antigen-containing MHC II, the T cell notes the presence of a foreign substance. B cells in the body also have receptors that bind to a pathogen, bringing it into the cell where it is digested and displayed on the surface of the cell by an MHC II protein. The TCR may also examine the antigen displayed by an MHC II on a B cell. If this antigen matches the fragment earlier displayed by the APC, the T cell generates growth and maturation signals to allow the B cells to become antibody factories to fight the pathogen. Using the PDB file DR1-HA-TCR.pbd to construct our physical model of a TCR, we are studying the interactions between a TCR and an MHCII protein presenting a fragment of influenza virus. Our goal is to understand how the TCR binds to the MHCII and antigen, and how the virus might try to interfere with this interaction. Researchers like Dr. Gorski study T cell receptors because understanding a T cell’s ability to detect foreign substances will help reveal insights into how our immune system fights viruses and infection.

• Wauwatosa West High School
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Wauwatosa West High School

“Flipping on the Switch:” Ras & NF1




Students:

• Shazia Ali
• Jessica Huffmann
• Annie Davidson-Keup
• Ben Schrank

Teachers:

• Donnie Case
• Mary Anne Haasch

Mentor:

• Robert Deschenes, Ph.D., Medical College of Wisconsin

Project Files:

• Poster

Abstract:

According to the American Cancer Society, an estimated 1,368,000 Americans died of cancer and related complications in 2004. Cancer, which is characterized by an uninhibited growth of cells, is caused by mutation of genes that regulate cell growth. Mutations fall into two major classes, those that cause activation of a growth activator (oncogene) or those that result in loss of function of a growth inhibitor (tumor suppressor). Our project involves the oncogene protein Ras and a tumor suppressor, NF1, which regulates Ras.

RAS is a signal transducer, a molecular switch with two states: an “on” state, which contains the GTP nucleic acid, and an “off” state, which contains the GDP nucleic acid. The “switch” is turned on by growth factor receptors such as epidermal growth factor (EGF) and results in Ras binding GTP. Once in the “on” state, RAS interacts with another growth activator, the Raf oncogene. Activation of Raf initiates a cascade of kinases that leads to an increase in gene expression and stimulation of cell growth.

To terminate the Ras activatation signal, GTP is hydrolyzed to GDP resulting in Ras-GDP, the “off” state of Ras. This is accomplished with the help of a GTPase activating protein, NF1. The action of NF1 is to turn off Ras, hence it is a tumor suppressor. NF1 is also called Neurofibromin. The loss of NF1 via genetic mutations causes a cancer called neurofibromatosis.

Neurofibromatosis is a genetic disorder, which is associated with the nervous system. It causes tumor growth, skin lesions, and bone deformities. Neurofibromatosis is generally inherited by birth, although 30 and 50 percent of new cases arise through spontaneous mutations. Symptoms include headache, facial pain, or facial numbness from pressure from the tumors.

Our project explores how the Ras protein interacts with NF1 to stimulate the hydrolysis of GTP to turn off the Ras oncogene protein. Scientists are interested in this interaction because it contributes to the understanding of cancer and potentially the design of drugs for Neurofibromatosis.

Remote Teams:

• Pingry School, Martinsville NJ - Pingry team website

2004-2005 SMART Teams

Many local and remote SMART teams participated in the 2004-2005 program. Discovery World returned to assist teams in professional speaking, and also created videos of the team projects. Below is a list of the participating teams.

Local teams:

Final Presentation Abstract Booklet

• Mary Ryan Boys and Girls Club
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Mary Ryan Boys and Girls Club

S.W.A.T., Starched with Attitudes




Students:

• Dwaun Bailey
• Kyree Carter
• Joshua Carter
• Justin Drake
• LaQuencia Grant
• LeRonne Hill
• Ebonie Jackson
• Danielle Johnson
• Gabrielle Kelly
• Shakoda Love
• Antwaun Miller
• Carolyn Pearson
• Shaneal Pearson
• A'Lace Ward
• Chris Weightmann




Teacher:

• Amanda Lavoe

Mentors:

• Will Allen, Growing Power
• Tim Herman, MSOE Center for BioMolecular Modeling
• Jon Knopp, MSOE Center for BioMolecular Modeling
• Justin Snowden, MSOE Center for BioMolecular Modeling
• Jennifer Morris, MSOE Center for BioMolecular Modeling

Function:

Glucose is a carbohydrate produced by plants and is an important energy source for humans, animals, and plants.

Abstract:

We are the Mary Ryan Boys and Girls Club S.W.A.T Team, Starches With Attitudes. We have been working with Will Allen at Growing Power, an example of agriculture in the city using recyclable organic wastes. Will Allen uses hydroponics and vermiculture to break down the organic wastes into nitrogen and carbon which helps plants grow. We have been working on understanding how plants capture the energy of the sun, carbon dioxide, water, and create carbohydrates. This process is called photosynthesis and produces oxygen and glucose. Glucose is one of the most important carbohydrates and is used as a good source of energy in animals and plants.

• Kettle Moraine High School
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Kettle Moraine High School

Caspace: And the Death of a Cell




Students:

• Becca Denison
• Ian Flaws
• Claire Gannon
• Chris Pierzchalski
• Heather Rusk
• Tony Schuler




Teachers:

• Karen Deboer
• Pete Nielsen

Mentor:

• Dr. Jean-Yves Sgro, University of Wisconsin - Madison

Project Files:

• Poster

Function:

Capsaces are involved in the process of apoptosis, or programmed cell death.

Abstract:

"For every cell, there is a time to live and a time to die." Apoptosis, or programmed cell death, is a naturally occurring process that is vital to normal life and development. This cellular pathway eliminates damaged, dangerous or unwanted cells in organisms. Triggers can include radiation, poison, and viral infection. After a cells dies, surrounding cells engulf it to prevent the spread of its infected contents. A genetically controlled form of cell suicide, it is initiated by normally inactive enzymes, called caspases. These proteases and apoptosis can also play a role in many diseases including cancer, autoimmune disorders, viral infections, Alzheimer's disease, ischemic injuries, and osteoporosis.

Located in all cells, whether eukaryotic or prokaryotic, caspases are highly conserved and show little variation between species. The caspase involved in our study of baculoviruses is SF-caspase-1, located in Autographa californica. The baculoviral p35 protein blocks apoptosis in two distinct steps of caspase inhibition. Before cleavage, the p35 recognizes the caspase and then cleaves the protein leaving an irreversible complex. The N terminus of p35 bonds with the active site cysteine of the caspase that is opened during cleavage to prevent hydrolysis and the continuation of the reaction.

• Madison West High School
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Madison West High School

COX-1 and COX-2 Enzymes Catalyse Prostaglandin Synthesis and Are Inhibited by Nonsteroidal Anti-Inflammatory Drugs




Students:

• Audra Amasino
• Yuting Deng
• Samuel Huang
• Iris Lee
• Adeyinka Lesi
• Yaoli Pu
• Peter Vander Velden




Teacher:

• Gary Graper, Teacher Emeritus, University of Wisconsin-Madison

Mentors:

• Dr. David Nelson, University of Wisconsin-Madison
• Basudeb Bhattacharyya, Student, University of Wisconsin-Madison

Project Files:

• Poster

Function:

COX-1 and Cox-2 are enzymes that synthesize prostaglandins, which are proteins responsible for fever, pain and inflammation, as well as maintaining the stomach lining and preventing ulcer formation.

Abstract:

Prostaglandin Hormone Synthases (COX-1 and COX-2) are enzymes embedded in cell membranes that produce prostaglandins responsible for fever, pain, and inflammation, but also maintenance of the lining of the stomach and prevention of ulceration. COX is short for CYCLOOXYGENASE meaning that it is an enzyme that oxidizes a substrate. Prostaglandins are modified fatty acids attached to a 5-membered ring that act as local messengers near their site of synthesis, and are metabolized very rapidly. COX-1 is found mainly in the gastrointestinal lining, and COX-2 at sites of inflammation. NSAIDS (Nonsteroidal anti-inflammatory drugs) such as aspirin, naproxen, ibuprofen, and flurbiprofen inhibit both COX-1 and COX-2, and are taken regularly by over 33 million Americans for pain and inflammation. Some 10%-50% of these users suffer gastrointestinal side effects such as abdominal pain, diarrhea, bloating, heartburn, and ulcers. Thus, recent efforts to inhibit only COX-2 have resulted in COX-2 inhibitors such as Celebrex, Vioxx, and Bextra which do not have the unwanted side-effects, but have been linked to increased numbers of heart attacks and strokes. We are studying the interaction of the COX enzymes with NSAIDS and COX-2 inhibitors to see how the enzymes are inhibited from catalyzing prostaglandins, as well as the structural differences between COX-1 and COX-2. We are designing models of the active sites of COX-1 and COX-2 using pdb files 1Q4G and 1PXX, as well as models of the normal COX substrate, arachidonic acid, and NSAIDS and COX-2 inhibitors to better understand the actions and side-effects of NSAIDS and COX-2 inhibitors.

• Marquette University High School
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Marquette University High School

The Effect of 2,3 Diphosphoglycerate (DPG) on Hemoglobin




Students:

• Fritz Bartel
• Matthew Clark
• Jason Carr
• Patrick Carter
• Thomas Fleming
• Creston Flemming
• Raman Kutty
• Evan Lloyd
• Ashim Singh

Teacher:

• Keith Klestinski

Mentors:

• Dr. George Phillips and Mr. Roman Aranda, University of Wisconsin-Madison
• Dr. Michael Patrick, MSOE Center for Biomolecular Modeling

Function:

Interaction of DPG with hemoglobin promotes the movement of oxygen from red blood cells to body tissues.

Abstract:

Hemoglobin is among the most important molecules in biology, for it facilitates a complex, efficient transfer of oxygen which distinguishes the higher organisms. Hemoglobin is an allosteric protein; that is, it undergoes conformational changes that affect its function. The two primary allosteric states of hemoglobin are the "tense" (T) state, which is characteristic of a hemoglobin molecule without oxygen, and the "relaxed" (R) state, which is favored when the molecule is oxygenated.

The tendency of hemoglobin to assume either the T or R state is mediated by a number of environmental and molecular factors termed "allosteric effectors." One such molecule is 2,3-diphosphoglycerate, or DPG. DPG binds to hemoglobin within the molecule's central cavity, and forms rigid salt bonds with hemoglobin subunits that "lock" hemoglobin in the T-state. Because the T-state has lower oxygen affinity than the R-state, DPG-induced hemoglobin tends to release more oxygen at tissue-level than R-state hemoglobin, which holds on to oxygen more tightly.

DPG plays an important role in the body's adaptation to varying environmental conditions. At high altitude, DPG production is accelerated, allowing for an increase in hemoglobin's release of oxygen that counterbalances the lower oxygen concentration of mountain air. Human fetuses have a modified hemoglobin molecule that prevents the binding of DPG, thus giving fetal hemoglobin a great affinity for oxygen than maternal hemoglobin and allowing for oxygen transfer across the placenta. Increased DPG is also associated with diseases such as emphysema and congenital heart disease that reduce the efficiency of the body's oxygenation mechanisms.

• St. Dominic Middle School
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St. Dominic Middle School

Sir2 Histone H4 Deacetylase: A Key to Controlling DNA




Students:

• Mike Beining
• Katie Benz
• Brian Borges
• Ana Caballero
• Ryan Cisler
• Tyler Cobb
• Jimmy Delforge
• Meredith Dentice
• Megan Farley
• Drew Fink
• Kevin Kallinger
• John Lambert
• Jesse Mark
• Alex Mattern
• Jim Mirda
• Sarah Misna
• Becca Moore
• Ben Robey
• John Selas
• Joe Sladky
• Sam Sladky
• Stephen Varnum
• David VonRuden
• Jon Weisse

Teacher:

• Donna LaFlamme

Mentor:

• Dr. Vaughn Jackson, Medical College of Wisconsin

Project Files:

• Poster

Function:

Regulates DNA expression by removing acetyl groups from lysine 16 of the histone H4 tails of the nucleosome.

Abstract:

The purpose of the St. Dominic SMART Team project was to design a physical model of the enzyme yHst2 Histone H4 Deacetylase using data deposited in the Protein Data Bank and a molecular visualization program called RasMol. The designing process helped us to learn about this important enzyme's structure, its function in the cell, and also about the chemical reaction it catalyzes. Our mentor, Dr. Vaughn Jackson, helped us understand how yHst2 controls DNA expression by removing acetyl groups from the lysine 16 of the histone H4 tails of nucleosomes. Removing an acetyl group from lysine changes its charge from neutral to positive. This positively charged histone tail is attracted to the negatively charged backbone of the DNA wrapped around the histones. Scientists have known for some time that acetylated histone tails are associated with active DNA and deacetylated tails with inactive or silent DNA.

Our enzyme, yHst2, belongs to an important family of enzymes called sirtuins. yHst2 is the yeast homologue of human Sir two 2. All Sir2 deacetylases have amino acid sequences that are very similar in all organisms from bacteria to humans. They all remove acetyl groups from acetyllysine sidechains on the proteins that they target. They all use NAD+ to accomplish this.

Sir2 proteins are very important to cells because they are involved in essential activites such as turning off genes, promoting the repair DNA, maintaining genome stability, and in cell metabolism. They have even been linked to increased lifespan. For example, scientists have discovered that restricting calories can extend the life of several research organisms. They noticed that calorie restriction causes cells to have very active Sir2 enzymes. Maybe, in the future, drugs that activate Sir2 deacetylases may become a way to stay young! Doctors are already using Sir2 activators in research trials to treat the cancers, lymphoma and leukemia.

• St. Joan Antida High School
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St. Joan Antida High School

Eukaryotic Peptide Chain Release Factor (ERF3)




Students:

• Lina Abdulkarim
• Nadia Ali
• Elisa Krause
• Pamela Xiong




Teacher:

• Mary Carlson

Mentor:

• Dr. Anita Manogaran, University of Illinois-Chicago Laboratory for Molecular Biology, Illinois

Project Files:

• Poster

Function:

ERF3 plays a role in the termination of protein synthesis and has been known to misfold in yeast, leading to protein aggregates, or prions.

Abstract:

The building blocks of the entire human body-proteins-play many important roles in everyday processes. Proper folding of proteins is important to their function. In some cases, proteins misfold and cannot properly function. The misfolding of a protein can lead to the formation of prion disease. Prion disease is unique since the misfolded protein convinces other proteins to misfold. This self-perpetuating cycle leads to numerous health problems. Prions can be found in many organisms leading to disease like mad cow disease in cattle and Cruetzfeldt-Jacob's disease in humans. Prions can also be found in yeast. Prions can be studied easily in yeast because yeast undergoes prion aggregation, is well studied, and has a rapid duplication rate. Our molecule, eukaryotic peptide chain release factor GTP-binding subunit (ERF3), misfolds and aggregates into prions in yeast. ERF3 is involved in protein biosynthesis. It binds GTP and performs translational termination in yeast. The researchers of the University of Illinois at Chicago's Laboratory for Molecular Biology are interested in the M region because it is important to prion formation. Having a physical model of the area will allow researchers to understand the actual shape and potential misfolding activity of the molecule.

• Wauwatosa West High School
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Wauwatosa West High School

Neonatal Alloimmune Thrombocytopenia




Students:

• Shazia Ali
• Danielle Perszyk
• Ben Schrank




Teacher:

• Donnie Case

Mentors:

• Drs. Debra and Peter Newman, Blood Research Institute

Project Files:

• Poster

Function:

Integrins are a family of molecules on the surface of cells that mediate cell-matrix and cell-cell interactions. The PSI domain contributes to activation of integrin and genetic variation in the PSI domain is associated with NATP.

Abstract:

Platelets, also called thrombocytes, are required to control bleeding. Alloimmune thrombocytopenia is a disease that results when an individual makes antibodies that bind to proteins on another individual's platelets. Neonatal Alloimmune Thrombocytopenia (NATP) occurs when a mother makes antibodies that bind to her baby's platelets. In this disease, the mother's antibodies on the fetal platelets can cause them to be cleared by the immune system or prevent them from working properly, resulting in severe bruising and hemorrhaging. Once the antibodies are gone, the baby's platelets will then function properly and initiate clotting. The baby is in danger when the antibodies are present at or before birth because of the possibility of intracranial bleeding can lead to severe brain damage.

A major target for antibodies in NATP is the glycoprotein IIb-IIIa, (GPIIb-IIIa), which is made up of two subunits, GPIIb and GPIIIa, and is expressed only on platelets. NATP most commonly occurs when a mother has the amino acid proline (Pro or P) and her baby has a leucine (Leu or L) at position 33 of the GPIIIa subunit.

Scientists have struggled for years to solve the structure of the region within the GPIIIa subunit that contains the L33P polymorphism. They have recently determined that it folds into a structure called a PSI domain. We have built a model of the PSI domain of GPIIIa, which possesses a leucine at position 33. The ability to visualize the structure adopted by the PSI domain of GPIIIa will hopefully enable scientists to use their knowledge of that structure to find successful treatments for NATP.

• West Bend East High School
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West Bend East High School

FcRN: From Mother to Fetus




Students:

• Logan Riemer
• Christine Anhalt
• Megan Petri




Teacher:

• Trish Strohfeldt

Mentor:

• Dr. Jason A. Bubier, Post-doctoral researcher, Jackson Laboratory

Project Files:

• Poster

Function:

Transfer of IgG across placenta.

Association of the Molecule with Disease:

FcRn can be used as a possible therapeutic agent in the treatment of diseases.

Abstract:

Fc Receptor Neonatal or FcRn is a protein in mammals by which immunity is passed from mother to fetus before birth. FcRn is a heterodimer that consists of three identical beta-2-microglobuin chains and three Fc Receptor chain. FcRn binds to Immunoglobin G (IgG) and aides in transport of IgG across the placenta. FcRn's function is regulated by pH and is involved in the transport of IgG through transport vesicles. FcRn binds to IgG at a pH of 6.0 in the vesicles and releases at a pH of 7.4 in the fetal blood stream. FcRn is also important in the control of the catabolism of IgG. It prevents degradation of IgG, substantially increasing the half-life of IgG. IgG lasts 22-23 days in humans. Since FcRn has the ability to increase the half-life of IgG, research is being done with coupling of therapeutic agents to IgG to increase the stability of the therapeutic agent. Reaserch on FcRn and IgG is currently being done on mice and rat models.

• Whitefish Bay High School
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Whitefish Bay High School

Acceptance of the Influenza Pathogen into Class II MHC




Students:

• Charlie Brummitt
• Mary Cieslewicz
• Michael Krack
• Jay Lim
• Colin Monnat
• Alex Wauck




Teachers:

• Marisa Roberts
• Judy Weiss

Mentor:

• Dr. Jack Gorski, Blood Research Institute

Project Files:

• Poster

Function:

The immune response to viral and bacterial diseases is mediated by Class II MHC molecules. These molecules present peptide fragments to the T cells in order to mount an immune response against foreign particles.

Abstract:

The class II major histocompatibility complex (MHC II) molecule is involved in immune responses to viral and bacterial diseases. When a peptide fragment of a protein is "loaded" into the molecule, the alpha helices of the Class II MHC unwind and the peptide is inserted in the gap. The class II MHC molecule is critical in the production of antibodies to fight illness and prevent future infections. The class II MHC helps the body identify antigens by presenting antigen fragments to helper T-cells. The helper T-cells then instruct B-cells to produce antibodies, which in turn alert other cells to the presence of a pathogen and instruct them to fight the intruder. We are focusing on influenza and the way in which a fragment of the influenza protein fits into the class II MHC molecule. In the case of influenza, macrophages ingest the virus, producing peptide fragments that the MHC molecules collect. We have designed a physical model of the class II MHC protein and a peptide fragment of influenza in the PDB file DR1HATCR.pdb. Researchers like Dr. Gorski are working to understand how the MHC molecule opens for the peptide to be inserted. Understanding this peptide loading process is important for rational vaccine design, as vaccines should optimize the ability to load the class II MHC with pathogen-derived peptide fragments.

Remote teams:

• Pingry School, Martinsville, NJ
• Champlin High School, Champlin, MN
• Newburgh Free Academy, Newburgh, NY

2003-2004 SMART Teams

During 2003-2004, seven local teams and five remote teams participated in the SMART Team program assisted by Discovery World. In addition to accomplishing projects at a national level, SMART Teams attended many meetings such as, Wisconsin Society of Science Teachers (WSST) in Appleton, WI, National Science Teacher Association (NSTA) in Atlanta, GA, and American Crystallographic Association (ACA) in Chicago, IL. See the completed projects below.

Specific School Project Information Coming Soon!

2002-2003 SMART Teams

During the 2002 - 2003 school year, ten teams of students in the Milwaukee area completed the qualification stage of the program and were certified as SMART Teams. See the projects that were completed below.

• Kettle Moraine High School
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Kettle Moraine High School

Human Prion Protein Dimer




Students:

• Ken Brockman
• Aaron Eifler
• Matt Gehling
• Faith Hughes
• Jenny Morgan
• Scott Patson
• Eric Powleit
• Jacob Schmidt

Teachers:

• Karen Deboer and Pete Nielsen

Mentor:

• Vivien C. Yee, Lerner Research Institute, Cleveland, OH

Abstract:

We researched the human prion protein. Prions are associated with diseases such as Creutzfeldt-Jakob in humans, mad cow and chronic wasting disease in cattle and deer. In its normal conformation the prion protein is a folded monomer. By an unknown mechanism the protein changes shape and is able to interact with another "unfolded" prion to form a very stable complex of two prion proteins. The dimer of extended prion proteins is the pathogenic conformation. Our model tries to demonstrate this conformational change.

• Wauwatosa West High School
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Wauwatosa West High School

1-Mannose-6-Phosphate Receptor




Students:

• Saba Ali
• David Blackfield
• Megan Harney

Teacher:

• Donnie Case

Mentor:

• Dr. Nancy Dahms, Medical College of Wisconsin, Milwaukee, WI

Abstract:

We researched the Cation-Dependant Mannose-6-Phosphate Receptor with the help of Dr. Nancy Dahms of the Medical College of Wisconsin. This protein is responsible for transporting newly-synthesized lysosomsal hydrolases to the lysosome. The lysosome is responsible for inracellular digestion. When the Mannose-6-Phosphate Receptor is defective, the lysosome does not receive hydrolases needed for digestion and the individual afflicted eventually dies because the non-working lysosome fills up with cellular matter, leading to apoptosis of the cell. This can eventually lead to the death of the organism.

The Cation-Dependent Mannose-6-Phosphate Receptor protein is a dimer, however, we decided to create only the monomer to better show the details of the structure. On the molecule you will see three disulfide bonds that are created by cysteine residues. One of these bonds is the ligand-binding site of the molecule. In addition there is also a Manganese ion, which helps in the binding of the sugar.

• Madison West High School
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Madison West High School

Beta-amyloid Protein




Students:

• Elie Betlach
• YuTing Deng
• Beckett Jackson
• Yaoli Pu

Teachers:

• Gary Graper and Betsy Barnard

Mentor:

• Dr. Brendan Orner, University of Wisconsin-Madison, Madison, WI

Abstract:

The Madison West SMART Team modeled the three major theoretical models of the beta-amyloid protein which forms the amyloid fibrils associated with Alzheimer's and Parkinson's diseases, as well as at least 20 other diseases. These are only proposed models since the molecular structure is not known below the fibril level. It is not known whether the toxicity of the diseases is caused by the molecule, the fibril, or the plaque formed from fibrils. There is some evidence that amyloid forms pores in membranes which causes cell dysfunction and death. We worked with Dr. Brendan Orner, a research fellow in Dr. Laura Kiessling's Chemistry/Biochemistry Lab at the University of Wisconsin-Madison. Dr. Orner's research focus is developing molecules that bind to beta-amyloid peptides and inhibit aggregation and cellular toxicity. The most fascinating thing that the team learned in addition to knowledge about Alzheimer's disease and protein structure was how to modify pdb files and create new ones with WebLab. This was necessary since we were only given small parts of the protein models in some cases, and had to arrange and aggregate those parts to show the torsion in the fibrils and keep the three models similar in scale and size for in depth comparison.

• West Allis Central High School
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West Allis Central High School

Von-Willebrand Factor A1 Domain Bound to the GPIb-Alpha Domain




Students:

• Jennifer Hack
• Becky Habersat
• Kelly Schlicht
• Jeni Both

Teacher:

• Shari Gajria

Mentor:

• Dr. Phil Kroner, Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI

Abstract:

VWF is a protein that is important in the clotting process. When a person is cut, their collagen is exposed; VWF sticks to the collagen and then becomes activated. Then platelets roll across the VWF until they find a place that satisfies them and they stick. From here, layers can be built so that a clot can form. When a person has very few, or even no, VWF present in their blood, or malfunctioning VWF, they are diagnosed with Von Willebrand Disease (VWD). Therefore, a person with VWD has blood that clots poorly, and they may bleed continuously for extended amounts of time from even small wounds. Researchers are uncertain why some people are afflicted with this disease. We are hoping that the model we have made will help give researchers a closer look into what is the determining factor that makes VWF function correctly. Dr. Phil Kroner and his colleagues would like to know why platelets sometimes stick to the VWF and sometimes do not. Hopefully seeing an up-close, detailed view of VWF, especially the A-1 domain, will help them answer this question and give them insight into why VWF sometimes malfunctions.

Student Response: We feel that the entire process has been an amazing experience that has given us many rare, valuable experiences. To be able to work with scientists at such an intimate level is something that most high school students will never have the opportunity to encounter. We hope that the work we have put into our model will help the people who are researching VWF and VED to better understand what they are looking at, and maybe even help the people who are stricken with VWD. This will be an experience that I know we will all remember for the rest of our lives, and we are very thankful for this opportunity.

• St. Joan Antida High School
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St. Joan Antida High School

Adenosine Dependent Methyltransferase




Students:

• Vanessa Ali
• Zaynab Baalbaki
• Ninfa Martin
• Erin Schmeling

Teacher:

• Mary Carlson

Mentor:

• Dr. James Anderson, Marquette University, Milwaukee, WI

Abstract:

The molecule we have created is an ado-met-dependent methyltransferase, also called Rv2118c. It is a protein that depends on adenosyl methionine to transfer methyl groups and aid in tRNA modification. This molecule is being studied for a possible connection with helping stop HIV replication. Hopefully, by mutating or altogether stopping the role of Rv2118c in tRNA modification, the virus can no longer continue replicating, therefore ending HIV replication. By using this molecule, our science advisor can be able to physically manipulate the protein and compare it to a tRNA molecule to find out how the connection and therefore mutation can be made. This was the first time any of the students from St. Joan Antida High School were involved in the Smart Team program so everything we studied was fascinating. The RasMol program and learning about rapid prototyping was interesting, and trying to understand the function of our protein was a project in itself. Everything we did, we learned through our Smart Team involvement, so the experience as a whole was fascinating and interesting.

• St. Dominic Middle School
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St. Dominic Middle School

Nucleosome


St. Dominic SMART Team model based on 1eqz.pdb

Students:

• Sana Baltrusaitis
• Ashley Becker
• Kristin Holzhauer
• Jordan Kapke
• Shannon King
• Alex Knauf
• Allison LaGuardia
• Jennifer Limbach
• Sarajean Mahrt
• Jackie Marcello
• Kristen Pankow
• Jillian Picciolo
• Maureen Reardon
• Melissa Ruppert
• Andy Sinclair
• Sarah Sladky
• Katie Straub

Teacher:

• Donna LaFlamme

Mentor:

• Dr. Vaughn Jackson, Medical College of Wisconsin, Milwaukee, WI

Abstract:

The St. Dominic SMART Team designed a model of a nucleosome with the guidance of Dr. Vaughn Jackson at the Medical College of Wisconsin and using the pdb file 1eqz. The function of the nucleosomes is to package the long strands of DNA in the nucleus. A nucleosome is composed of an octomer of four different proteins called histones around which two loops of DNA (146 base pairs) are wrapped. Scientists are actively researching the functions of nucleosomes and are finding that they do much more than protect and compact the DNA. Enzymes interact with the N-terminal tails of the histones affecting whether genes on the DNA are silent or active. Our model of the nucleosome highlights the lysines that are involved in being methylated or acetylated. Deacetylated lysines on the histone tails are associated with silent DNA and turned-off genes. Acetylated lysines on the histone tails are associated with active DNA – turned-on genes. Our scientist mentor, Dr. Jackson, is doing research into “the specific mechanisms required to access DNA” that is wrapped around histones so that the DNA can be transcribed or replicated. One of the mechanisms he is studying, for example, is “the role of metabolic modifications such as acetylation. A common characteristic of active genes is the presence of highly acetylated histones.” Interestingly, a possible cure for a well-known dominant genetic disease called Huntington's has been suggested in recent issues of The Scientist reporting the work of Steffan and Thompson. The potential cure is related to histone acetylation. Apparently, the mutant huntington protein folds improperly, gets cleaved, and migrates to the nucleus where it has been shown to reduce acetylation of histones H3 and H4. It does this by binding to the acetyltransferase domains of several enzymes. Mutant Huntington protein has also been shown to reduce gene transcription. Steffan and Thompson have also shown that histone deacetylase inhibitors reverse the degeneration of neurons in Drosophila models of Huntington's disease offering hope of treatment for an incurable disease!

• New Berlin West High School
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New Berlin West High School

T Cell Receptor




Students:

• Ellery Brooks
• Kristin Jansen
• Stephanie Rindt
• Maciej Czarnecki
• Kim Wirth
• Scott Wirth
• Alison Marlin
• Ingrid Ericsson
• Kevin Malec
• Meghan McGinty
• Angela Ludwig
• Paul Carter

Teacher:

• Pamela Patterson

Mentor:

• Dr. Bonnie Dittel, Blood Research Institute, Milwaukee, WI

Abstract:

Our SMART team worked with Dr. Bonnie Dittel at the Blood Research Institute in Milwaukee. Her research goal is to find the cellular and molecular interactions involved in regulating immune responses. Dr. Dittel is working specifically with the autoimmune disease Multiple Sclerosis. We made a model of a T cell receptor, an important protein in regulating immune responses. An antigen presenting cell takes foreign particles in the body, breaks them up into small fragments called peptides. The peptides bind to another protein called the Major Histocompatibility Complex (MHC) and both are displayed on the cell surface. The T cell receptor recognizes the complex of MHC and the peptide fragment and initiates an immune response to help rid the body of the potentially dangerous substance.

Function: The TRCrecognizes foreign antigens displayed on MHC (major histocompatibility complex) molecules on the cell surface of antigen presenting cells.

Disease: Associated with Multiple Sclerosis; T-cells may recognize the body's own oligodendrocyte cells and initiate an immunce response that kills the oligodendrocyte. These cells are responsible for making myelin, a fatty protective covering on nerves. If these cells are killed, myelin won't be made and MS will soon result.

Research Goal: Dr. Bonnie Dittel is looking to find the cellular and molecular interactions involved in the regulation of the immune response.

Students' Response: We got a glimpse of research in the real world. We saw her lab and research area and all the equipment needed to do research. We realized how long it takes to make small steps in research. It takes a lot of little steps and discoveries to have a big effect on a long-term problem like MS.

2001-2002 SMART Teams

In 2001, CBM/SEPA was funded by Ameritech to run the SMART Team program (also known as the Ameritech Teams). View the variety of projects that the seven local area high schools completed below.

• Bay View High School
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Bay View High School

Hydrogenase


Fuel cells may one day be powered by
hydrogen generated by bacteria in bioreactors

Students:

• Charles Radomski
• Dinero Fudge
• Chue Yang

Teacher:

• Dan Wexler

Abstract:

Hydrogenases play a central metabolic role in various microorganisms. These enzymes catalyze the half-cell reaction 2H+/H2. The best studied of these is a heterodimeric protein from Desulfovibrio gigas. The enzyme active site is located in the large subunit and coordinates one atom each of nickel and iron. Hydrogen gas can be used to power fuel cells for the efficient and clean production of electricity. Currently, hydrogen is produced by the combustion of fossil fuels or through the use of solar battery-induced splitting of water. It has been known for some time that hydrogen can also be produced by certain algae and bacteria. If such biological methods could be adapted to bioreactors at high efficiency, they would provide low cost, environmentally friendly sources of hydrogen. These adaptations will depend on the ability of scientists to genetically engineer microorganisms to increase hydrogen production.

• Brown Deer High School
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Brown Deer High School

Alpha-Hemolysin


Brown Deer researched the mechanism by which
the a-Hemolysin protomer assembles into a heptamer,
and produces a b-barrel that spans the cell's bilayer

Students:

• Matt Kopp
• Matt Kuczynski
• Emily Majusiak
• Jon Kao
• Matt Derosier
• Ramon Smith
• Nick Russell
• Josh Belke
• Ryan Kautzer

Teacher:

• Brian Fortney

Abstract:

A current model that is being used for research into the Anthrax bacteria's mechanism of cell penetration is the mechanism that a-Hemolysin uses to produce a b-barrel. A single unit of the a-Hemolysin (called a protomer) attaches to the bilayer of a cell, and attracts six other protomers to form a heptamer. It is this heptamer that forms the transmembrane pore, which is called a b-barrel. The b-barrel is composed of fourteen strands of protein, with each protomer contributing two b-strands. It is this mechanism that is being used as a model for comparison of the Anthrax bacteria's mechanism. Our team will be describing the different parts of the a-hemolysin molecule, as well as the mechanism that each protomer uses to extend the two b-strands into the cell's bilayer.

• Kettle Moraine High School (2 teams)
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Kettle Moraine High School: Team I

The P680 Reaction Center of Photosystem II


This photosynthesis model is of the P680 reaction
center of photosystem II which collects photons of
energy and boosts electrons to a higher energy level

Students:

• Stacy Weber
• Joe Yatzeck
• Rebeca Buendia

Teacher:

• Pete Nielson

Abstract:

This protein model was chosen because it was felt that by seeing a model of the chlorophyll molecule p680 reaction center one could better explain the details of photosynthesis in the classroom. This model demonstrates that structure and symmetry directly relate to function as a series of chlorophyll molecules donate their photoexcited electrons to an electron transport chain. These electrons are passed to pheophytin and in turn to photosystem I. The four chlorophyll molecules and two pheophytin molecules are cradled in a symmetrical set of transmembrane alpha helices which also use four histidine residues to support a single atom of iron.

 

Kettle Moraine High School: Team II

Aquaporin, a Water Transporter


An aquaporin is a transmembrane protein in plants and animals
that allows water molecules to move into the cell's interior.

Students:

• Eric Powleit
• Chris Pinahs
• Jacob Schmidt

Teacher:

• Karen DeBoer

Abstract:

Aquaporin is a tansmembrane protein used in many cells including those of humans, which permits the passage of water molecules into the cell. The central feature permitting this is the hourglass-shaped pore created by several alpha helices. At the thinnest point in this structure, rests a pair of asparagine residues, which are able to use the water molecule's polar nature to restrict passage to one molecule at a time. This model can be used in a classroom setting, as it is relatively durable. Each color represents a different alpha helix, demonstrating how these formations are critical in maintaining molecular structure, giving students a physical representation of what previously was kept to theory and discussion.

• Riverside University High School (2 teams)
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Riverside University High School

Exo Enzyme S of Pseudominas Aeruginosa

Students:

• Courtney Nelson
• Maria Martinez
• Abigail McGraw
• Temitope Thompson

Teacher:

• Jeff Anderson

Abstract:

Team Joe used the computer program Rasmol and information pulled from the Protein Data Bank to construct a three dimensional model of the Exo enzyme S found in the bacteria Pseudominas aeruginosa.

We began the process of protein modeling by attempting to comprehend various articles from online sources which dealt with the bacteria Pseudomonas aeruginosa and its Exo enzyme S. From our studies we concluded that the enzyme is a GAP protein meaning that it is a GTP activating protein. It functions with Rac and Rho proteins to inhibit the cell from functioning by stopping vesicle traffic. We applied our understanding of the molecule to the construction of the N terminus on the Exo S that binds the Rac protein causing the breaking of GTP into a phosphate and GDP. To reach these ends, we downloaded the Rasmol file for Exo S and the information that came with it. We had to distinguish between hydrogen bonds and those added in to our altered downloaded version. Then we added the accessory bonds that formed between the various amino acids and monitor lines to stabilize the molecule. The molecule was built and, using the color code found on Rasmol, we painted our molecule to distinguish between different chains and termini.

• Rufus King High School (2 teams)
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Rufus King High School: Team I
Hyaluronate Lyase

Streptococcus pneumoniae hyaluronate lyase is a pathogenic
bacterial spreading factor that interacts with ascorbic acid
Students:
• Kayla Bunge
• Christina Vogel
• Brendan Sperandio
• Peter Marino
Teacher:
• Keith Zeisse
• Liz Substad
Abstract:
Streptococcus pneumoniae hyaluronate lyase is one of the most common causes of infections of neonates in the United States. The researchers noted in the Med-Line article are Li S, Kelly SJ, Lamani E, Farraroni M, and Jedrzejas MJ. It is so serious that in many cases when the infection is not fatal, the patient may suffer from seizures,blindness, and/or mental retardation. This enzyme rapidly degrades hyaluronan in an unusual manner. It makes an initial random cut in a hyaluranan chain and moves quickly along the chain, while releasing unsaturated disaccharide units. Ascobic aqcid (vitamin C) has recently been shown to bind to this enzyme…and inhibit it. So...drink your orange juice.
 
Rufus King High School: Team II
SV40 Capsid Comple

This is the structure of one of seventy-two
pentamers comprising the simian virus 40 capsid shell
Students:
• Mohammed Farhoud
• Adam Carr
• Laura Gerber
Teacher:
• Dean Dolence