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Molecular Explorations

Webpages with Interactive Molecular Visualizations

The Principles of Chemistry that Drive Protein Folding

This Jmol Exploration is meant to complement the Amino Acid Starter Kit from 3D Molecular Designs, and allows students to explore how the main principles of chemistry that drive protein folding are revealed in real protein structures.

Jmol Exploration Creator Web Pages
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Explorations Suitable for Introductory Courses

Polar Nature of Water: Explores the polar nature of water and how it interacts with nonpolar, polar and charged molecules. Includes video explorations of 3D Molecular Designs' Water Kit. (Appropriate for online learning)

Molecules of Life: Explores macromolecules and their building bloxks, with video explorations of 3D Molecular Designs kits. (Appropriate for online learning)

Molecules of Life and Water: Explores macromolecules and their building blocks, as well as the polar nature of water, with video explorations of 3D Molecular Designs kits. (Appropriate for online learning)

Functional Groups: Review of polarity and electronegativity, with Jmol exploration of organic functional groups.

Protein Structure: Exploration of four levels of protein structure, as well as chemical properties of amino acids.

Protein Structure (with animations): This exploration provides a little more background and includes animations of protein folding. It also includes the structures of all twenty amino acids.

Protein Primary and Secondary Structure: This exploration focuses on primary and secondary protein structure, featuring the Alpha Helix Beta Sheet Construction Kit. Suitable for online learning.

Protein Tertiary Structure: This exploration demonstrates the use of the Amino Acid Starter Kit to visualize how proteins fold in the watery environment of the cell. Suitable for online learning.

Basic Principles of Chemistry that Drive Protein Folding: Explores two chemical principles involved in protein folding: 1) hydrophobic core and 2) interaction of charged residues on surface of proteins. Examination of multiple proteins. (Combines and updates Principles of Chemistry Parts 1 and 2.)

Protein Structure (Madison): Exploration of protein structure with hemoglobin, green fluorescent protein, CIP4 and NF-ĸB as example proteins.

The Many Jobs of Proteins: Exploration of a variety of proteins (Many Jobs of Proteins Collection) to develop molecular visualization skills while reinforcing concepts of secondary structure and hydrophobic core.

Identifying Patterns in Proteins: Very brief introduction to some common protein folds, followed by a deeper exploration of the zinc finger fold.

Engineering Insulin For Better Treatment of Diabetes: Explores insulin modifications to create slow-, intermediate- and fast-acting insulins.

Introduction to Enzymes: This exploration uses the Enzymes in Action Kit from 3D Molecular Designs to explore terminology associated with enzymes: active site, substrate, product, induced fit vs. lock and key models, competitive and noncompetitive (allosteric) inhibitors. Written as a POGIL, this activity is suitable for online learning.

Substrate Specificity: This exploration was developed to be used with the Substrate Specificity Kit from 3D Molecular Designs. Videos included in this exploration make it suitable for online learning.

Enzymes: Explores how enzymes function, ranging from the enzyme-substrate interactions, enzyme specificity, cofactors and coenzymes, regulating enzymes and enzyme inhibitors.

DNA Structure: Includes videos of DNA Discovery Kit from 3D Molecular Designs. (Appropriate for online learning)

DNA Replication: Includes videos of Flow of Genetic Information Kit from 3D Molecular Designs. (Appropriate for online learning)

Protein Synthesis: Includes videos of Flow of Genetic Information Kit from 3D Molecular Designs. (Appropriate for online learning)

Exploring Fischer Projections: This exploration provides practice in representing chiral molecules as Fischer projections. It starts with generic colored and labeled structures that can be rotated in 3D space, then transitions to actual chiral compounds including glucose.

Advanced Topics

Potassium Channel and Scorpion Toxin: In depth exploration of how the potassium channel selects for potassium ions while filtering out larger sodium ions. Also explores how scorpion toxin binds to and blocks the flow of potassium ions through the channel.

Hemoglobin Structure and Function: Exploration of the structure of the heme group, comparison of myoglobin and hemoglobin, and conformational changes in hemoglobin in absence and presence of oxygen.

Comparison of Oxy-, Deoxy- and Fetal Hemoglobin Structures: Structures are compared to see conformational changes; very little text.

Structural Basis of Antibiotic Resistance: Exploring β-Lactamases: Appropriate for advanced level course. Models available on special request from MSOE Model Lending Library.

Cdc42 Interacting Protein (CIP4): Developed as part of the CREST Program for use in the UW-Madison BioCore Program, this tutorial explores how one protein's structure, location and dynamic interactions with other biomolecules regulate plasma membrane structure.

Exploration of Proteins in David Goodsell's Coated Pit Molecular Landscape: Identifies major proteins involved in endocytosis, pairing images from the molecular landscape Coated Pit (2012) by David Goodsell and interactive Jmol windows.

Alkaline Phosphatase: Detailed comparison of the structure of alkaline phosphatase from E. coli (EAP), human placenta (hPLAP) and rat intestine (rIAP).

Glycogen Phosphorylase: Glycogen Phosphorylase structure (four levels of protein structure) and function are explored.

Glycogen Phosphorylase Conformations: Side by side comparison of glycogen phosphorylase in active (open) and inactive (closed) conformations. No text.

NF-κB: Exploration of structure, function and regulation of NF-κB.

NF-κB Regulation: Side by side comparisons of NF-κB in two conformations: bound to DNA and bound to inhibitor. Color key but no text.

Exploration of Drug Targets: Molecular exploration of a variety of drugs bound to their drug target molecules. Appropriate for an introductory pharmacology course.