Section 3 - Building Your Physical Protein Models
The final step to successfully competing in the Science Olympiad Protein Modeling Event is to actually build your protein models. This section will cover how to construct a protein model, including information on:
- The visualization environment
- Folding a Mini-Toober model
- Taking your model further and judging tips
The Visualization Environment
Overall Layout of the Visualization Environment
Changing the Display Format and Color Schemes
Using the Select and Restrict Commands
Advanced Jmol Training Guide
For students that really want to push their understanding and knowledge of Jmol further, the advanced Jmol training web pages below will provide a more detailed review of commands and techniques for manipulating protein and DNA structures in the Jmol visualization environment.
- Getting Started in Jmol
- Finding Protein and Molecular Structures
- Changing Colors and the Display Format
- Saving and Reloading Your Work
- The Select Command and Boolean Operators
- Adding Sidechains to Your Structure
- Bonds and Structural Supports
- Working with Nucleic Acids
Folding a Mini-Toober Model
Every team competing in the Science Olympiad Protein Modeling Event will be expected to create at least two protein models of specific protein structures. This section contains three important video tutorials describing how to map out and fold these models.
Mapping Out the Mini-Toober ModelView video content as a PDF
Folding Secondary StructuresView video content as a PDF
Folding the 3-D ShapeView video content as a PDF
Taking your model further and judging tips
Pre-build models are expected to have additional added features and all models will undergo a judging process. This section contains two important video tutorials describing how to approach adding additional features on the pre-build model and how models will be judged.
Going Beyond Just the BackboneView video content as a PDF
How do you know which residues are important?
The protein that you are modeling may be large and complex. Here are a few simple ways to figure out which amino acid residues in the structure are important for its structure or function:
- Are there specific residues mentioned/discussed in the abstract and/or manuscript describing this protein structure? Here are some possibilities:
- These amino acids may be mentioned as the active site, catalytic, or binding site residues.
- They may also be discussed as sites of mutations that change the structure and/or function of the protein.
- Are there any ligands, drugs, ions, inhibitors or other small molecules bound to the protein structure?
- The residues within ~5 angstrom of the small molecule are likely to be non-covalently interacting with it. These amino acid residues may have an important role in the structure and function of the protein.
- Any residues covalently linked to the small molecule ligands, drugs etc. may be critical to the structure and function of the protein.
- Does your protein of interest interact with other proteins, nucleic acids?
- Look through the figures in the manuscript describing the protein structure. Pay attention to any additional proteins, DNA, RNA or other molecules shown in these figures.
- Read about these molecules and try to figure out how and why the interaction is shown.
- Can you figure out the interactions stabilizing these molecules?
- Examine residues at the interface between 2 proteins or a protein and DNA/RNA etc.
- These amino acids may have important roles in the functioning of the protein.
Judging the Protein ModelsView video content as a PDF