2003-2004 Projects
Aquaporin
Kettle Moraine High School
Team Picture - Poster - Project Video
Students:
Ashley Bray, Rebecca Denison, Martie Dowis, Tony Schuler, Simon Schmidt, Nate Theobald, Trisha Williams
Teachers: Karen Deboer and Pete Nielsen
Mentors: Dr. Emad Tajkhorshid and Dr. Klaus Schulten, University of Illinois - Urbana
Consultants: Dr. Pete Agre, Dr. Jennifer Carbrey, Dr. David Kozono, Dr. Klaus Schulten
Function of Molecule: Transportation of water molecules.
PDB File: GlpF
Association of the Molecule with Disease: Nephrogenic diabetes, congenital cataracts and mercurial poisoning.
Abstract: Our SMART team has worked extensively with several scientists, including Nobel Laureate Dr. Peter Agre, to form an understanding of the protein aquaporin. This protein transports water molecules in and out of the cell in single file without letting anything else pass through it, not even ions. The computer model that Dr. Tajkorshid and Dr. Schulten created demonstrates this process in great detail. Dr. Tajkorshid sent this model to our team in the PDB file GlpF (E. coli glycerol facilitator).
Due to mutations or the absence of AQP proteins, diseases such as nephrogenic diabetes insipidus (kidney), congenital cataracts, and mercurial poisoning can occur. Other diseases related to this protein are edema, brain contusions, bacterial meningitis, and brain tumors, which happen because there are too many AQP proteins.
Dr. Peter Agre was attempting to find the mechanisms for human diseases when doing his research with AQP, while Dr. Tajkhorshid was interested in molecule dynamics and the mechanisms of proton exclusion.
Mammalian Cytochrome P450 2C5
Madison West High School
Team Picture - Poster - Project Video
Students:
Audra Amasino, Wriju Baattacharya, Elli Betlach, Hilary Cronon, Yuting Deng, Samuel Huang, Beckett Jackson, Olivia Judd, Iris Lee, Yaoli Pu, Harry Streckert, Peter Vander Velden
Teacher: Gary Graper
Mentor: Dr. Dave Nelson, UW-Madison Department of Biochemistry
Function of Molecule: Oxidoreductase found in endoplasmic reticulii and mitochondria that participates in detoxification, procarcinogen activation, and steroid hormone synthesis.
PDB File: 1DT6
Association of the Molecule with Disease: Because of the universal occurrence of this molecule in living organisms and the general oxidoreductase function, this molecule is involved with a myriad of diseases. In humans, many variations in drug reaction and many harmful drug interactions result from the 50 known polymorphisms of this molecule. Some of the better known are the varying toxicity and effect of acetaminophen, the harmful interaction of alcohol and acetaminophen. Many cytochrome researchers feel that in the future, physicians will do a cytochrome P450 assay on patients before prescribing medications to better determine proper dosage and possible toxicities.
Abstract: Proteins are essential catalysts in chemical reactions that are necessary for life. Cytochrome P450s are a large class of proteins that are expressed in every living organism. They generally metabolize foreign compounds and make them less toxic. The reactant for P450 2C5 is a steroid, progesterone, which in the process of hydroxylation is transformed into a more hydrophilic molecule that can be either flushed from the body or changed into another product. The little steps involving this is actually quite complex and requires the efforts of two other proteins, NADPH Cytochrome P450 Reductase and Cytrochrome B5, and a Heme group. The protein is located mostly in the endoplasmic reticulum membrane with small section that juts out. Because P450s are involved in reactions involving drugs and other toxins, it is important to study their function. Better understanding of P450s will improve the process of drug discovery and the ability to predict drug interactions, as well as developing the concept of “individualized medicine.”
Myelin Oligodendrocyte Glycoprotein - MOG
Riverside University High School
Team Picture - Poster - Project Video
Students:
Hannah Gottinger, Caitlin Keefe, Alyssa Latin-Kasper, Megan McChain, Christina O'Brien
Teacher: Jeffery Anderson
Mentor: Dr. Bonnie Dittel, Blood Research Institute
Function of Molecule: Protein is associated with the exterior of neural oligodendrocytes. Inappropriate recognition by the immune system may be associated with multiple sclerosis.
PDB File: 1PY9
Association of the Molecule with Disease: Currently being investigated in association with Multiple Sclerosis.
Abstract: The MOG protein is associated with the exterior of neural oligodendrocytes. MOG is an auto-antigen protein that when destroyed can result in a disease characterized by the demyelination of neurons. The exact mechanism for this mistaken self - nonself recognition sequence within the body is unknown. The location of MOG within the myelin sheath of attacked cells makes MOG a potential key protein that may initiate the self-destruction of the myelin sheath which results in irregular transmission patterns along affected dendrites. The MOG protein is currently being investigated for its effect on Multiple Sclerosis and related illnesses.
Dr. Bonnie Dittel of the Blood Research Institute of Southeastern Wisconsin is investigating the cellular and molecular interactions involved in the regulation of the immune response. Dr. Dittel’s research with mice and myelin sheaths along with the student’s interest in nervous system functioning resulted in the collaboration presented as – the Structure and Function of Myelin Oligodendrocyte Glycoprotein – MOG.
Factor VIII
Rufus King High School
Team Picture - Poster - Project Video
Students:
Mike McFadden, Beneva Myrick, Mike Piotrowski, Maixiong Thao, Yangyee Thao
Teacher: Dean Dolence
Mentor: Dr. Phil Krone, Medical College of Wisconsin
Function of Molecule: Factor VIII is a protein in the blood coagulation pathway.
PDB File: Stoylova2002.pdb
Association of the Molecule with Disease: Mutations or the absence of Factor VIII cause Hemophilia A.
Abstract: Factor VIII is connected to the hereditary bleeding disorder hemophilia. People with hemophilia may have absent or dysfunctional Factor VIII, a clotting protein. Factor VIII travels with Von Willebrand factor (VWF) through the bloodstream and is activated when a blood vessel is broken. Factor VIII is a key component in the blood coagulation process. Factor VIII consists of six domains, five when activated, B domain is clipped. A lack of healthy factor VIII results in symptoms such as swelling in the joints and hemorrhaging. Treatments include blood transfusions and soon gene therapy.
Histone Acetyltransferase, GCN5
St. Dominic School
Team Picture - Poster - Project Video
Students:
Kyle Bauer, Anthony Benz, Becky Berg,Lisa Breu, Blai Brophy, Megan Dougherty, Angela Limbach, Mike Masterson, Doug Miller, Kelly Moakley, Terri Mueller, Danny Polaski, Adam Puzach, Devon Rayburn, Michael Ruka, Justin Schmidt, Amy Solberg, Liz Spaits, Dan Tighe, Ben Tushaus, Kristi Volbrecht, Rebecca Widmann
Teacher: Donna LaFlamme
Mentor: Dr. Vaughn Jackson, Medical College of Wisconsin
Function of the Protein: To transfer acetyl groups to histones.
PDB File: 1M1D
Association of the Molecule with Disease: Cancer, including leukemia.
Abstract:The purpose of the St. Dominic SMART team project was to make a physical model of the enzyme GCN5 histone acetyltransferase and to learn about its function. We also wanted to make a model of GCN5 that our mentor, Dr. Vaughn Jackson, would find useful in his research and teaching at the Medical College of Wisconsin.
GCN5 is a very important enzyme in the cell because it is involved in making the DNA in the nucleus of cells available for replication (copying) and transcription (reading of genes). Histone acetyltransferases were first isolated in the mid-1990s. Scientists had already noticed that very active DNA was associated with highly-acetylated histones in nucleosomes. Our mentor, Dr. Jackson, is very interested in the chemical modifications to histones such as acetylation because they control the activity of genes.
This molecule is also interesting because histone acetyltransferases have been associated with several cancers including leukemia. This enzyme is overactive in some cancer cells causing them to keep dividing out of control. The scientists (A.N. Poux et al PNAS, October 2002) who determined the structure of our molecule also designed an inhibitor to stop the molecule from working. They made an inhibitor using Coenzyme A bonded to a piece of histone 3. This inhibitor stops the molecule from working by making it impossible for acetyl CoA to fit into the enzyme’s active site and then to acetylate histone 3. This is exciting because inhibitors like theirs could be used to stop cancer cells from reproducing.
Our design includes the important sidechains listed in the A.N. Poux paper and the Nature (Rojas, et.al) paper that our mentor advised us to include because of their importance in binding the inhibitor and the normal substrates. We decided on two models of CGN5, one without the inhibitor attached and one with the inhibitor in place so that the models could be compared.
UIA
West Allis Central High School
Team Picture - Poster - Project Video
Students:
Sara Daily, Cole Dremsa, Rebecca Easter, Amands Enders, Jessica Jacob, Megan Kaiser, Kim Kosobucki, Danielle Mattson, Erika Orth, Bai Yang
Teacher: Shari Gajria
Mentor: Dr. Mark McNally, Medical College of Wisconsin
Function of the Molecule: Part of the splicesome that splices RNA.
PDB File: 1DZ5
Association of the Molecule with Disease: Absence of this molecule results in embryonic lethality.
Abstract: U1A is a protein component of a very important RNA splicing-factor. It is one of many vital proteins that make up a splicesome, the cellular machinery that removes introns from RNA strands. U1A is self-regulatory. Since the U1A gene is always on and producing U1A mRNA, the regulation of U1A is done at a post-transcription level. This simply means that it is regulated after transcription. The code for the protein is transcribed into the RNA. In order to reach the ribosome (which constructs the protein) it must acquire a 5’-guanine cap and a 3’-polyadenine tail. These additions prevent the U1A from being degraded, or unraveled within the cytoplasm.
The U1A self-regulates by preventing the polyadenine tail from attaching to the mRNA. If this occurs, the mRNA of U1A will be degraded. This binding self-regulatory effect is produced when two U1A proteins bind to the poly-A polymerase, otherwise known as PAP (an enzyme that adds the poly-adenine tail onto the end of the U1A). When the two U1A bind to PAP, its function is inhibited. This restricts PAP from forming the polyadenine tails.
U1A is a novel protein because of these very functions. It only regulates the polyadenylation of itself, because the protein recognizes the very specific sequence within the RNA that codes for itself. This is called the polyadenylation inhibition element, or PIE. U1A recognizes its own PIE, binds to the RNA that codes for itself, and binds to PAP to stop the polyadenylation, or adding of the poly adenine tail. This process stops the U1A protein from being made, but only takes place when there are more U1A proteins than needed in the nucleus. The surplus is necessary because there must be enough U1A present for two of them to bind to the PAP, and therefore inhibit it.
Alpha-V-Beta-3 Integrin
Whitefish Bay High School
Team Picture - Poster - Project Video
Students:
Kira Brenner, David Brown, Seth Flaaten, Teg Grewal, Liz Hirschmann, Leana Moon
Teachers: Marisa Roberts, Laurie Stewart
Mentors: Dr. Debra Newman and Dr. Peter Newman, Blood Research Institute
Function of the Molecule: Involved in blood clotting.
PDB File: 1JV2
Association of the molecule with disease: Bleeding disorders, heart attacks.
Abstract: Integrins are involved in helping blood cells to stick to solid surfaces and to one another. The aVß3 integrin helps cells to stick tightly to, and then migrate through, the material that lines blood vessels, which may help cancer cells "metastasize," or leave the bloodstream. A related integrin, aIIbb3, helps platelets to stick to one another using, as a bridge, fibrinogen, which exists in the plasma and is the major ligand for aIIbb3. Because platelets must stick to one another, or aggregate, to close up a wound, bleeding disorders result when mutations in aIIbb3 make platelets unable to aggregate due to a lack of the integrin or to defects within it that make the portion of the integrin located outside of the cell membrane unable to bind fibrinogen. One of the bleeding disorders that is caused by a lack of the aIIbß3 integrin is Glanzman Thrombasthenia. A neonatal bleeding disorder that results when a mother makes antibodies against the aIIbb3 integrins on her baby's platelets is neonatal alloimmune thrombocytopenia, also known as NATP. Defects within the aIIbb3 integrin can also make it easier for platelets to stick together. When this happens, platelets can form a clump that's big enough to close up a blood vessel, which can cause a heart attack or stroke.
The Drs. Newman wish to understand aIIbb3 because it has so much to do with platelet aggregation. Understanding the integrin structure may lead to more effective treatments dealing with either generating or dissolving platelet clumps. At the moment, the use of these treatments is tricky because too much of either can easily compound the problem instead of reducing it.
A model of the molecule might be useful for seeing three dimensionally how integrins interact with the things to which they bind, for example, fibrinogen. Until now, all visualization has been on two-dimensional computer screens and paper. Also all the different aspects of the protein can be observed at once, which is impossible for such a complexly shaped protein when portrayed on a flat surface. For example, while watching the propellor’s action one cannot easily watch the actions of integrin aVß3’s other domains as well. Furthermore, computer representation of integrin aVß3 attempts to depict the protein’s three dimensional shape but in order to do so, computer programs rely on optical illusions to trick the eye into perceiving depth. Despite a program’s best efforts, its rendering can still be interpreted incorrectly. Hopefully a three dimensional model will remove any doubts about integrin aVß3’s structure.