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Molecular Modeling and Protein Structure

Molecular Modeling

1. Define molecular modeling.

2. Be able to identify possible uses and applications of molecular modeling.

3. What are the advantages of computer models over physical models?

4. How are macromolecular structures solved experimentally? Be able to describe the details of each experimental approach.

5. What kind of information is contained in PDB files? Be able to interpret the ATOM records of a PDB file (i.e., know what the different columns are in the ATOM records).

1. Be able to draw the generalized structure of amino acids, and know the names of the different parts (amino group, carboxyl group, R-group, main chain, side chain).


2. How are two amino acids connected? Be able to draw the process of creating this bond given two amino acids.


3. What are some properties of amino acid side chains that are important to protein structure and folding?


4. What are the different levels of protein structure? Be able to define each level.


5. Be able to describe the torsion angles that occur in the main chain of proteins. What atoms define phi and psi dihedral angles?


6. Describe the information contained in Ramachandran plots. Know which regions are populated by various secondary structures.


7. Describe the two major secondary structures, and be able to identify them in molecular diagrams.


8. Be able to describe the network of hydrogen bonding in both alpha helices and beta sheets.


9. What are the different kinds of alpha helices and beta sheets?


10. What are turns? Where would you normally expect to find them?


11. Be able to describe the differences between globular proteins, membrane proteins, and fibrous proteins.


12. What are some common secondary structure motifs found in proteins?


13. What are the main forces that stabilize protein structure?


14. What is a protonation state? Which amino acids are concerned?

Structural Alignment

Describe the relationship between sequence and structure, in particular how similarity in one may imply similarity in another.

What is structural alignment? Why align molecular structures?

What are the basic operations of molecular transformation used to align structures? Describe each operation.

How do you evaluate a structural alignment? Describe RMSD, and be able to use the equation given the 3-D coordinates of a set of points.

How can structural alignment help in structure prediction?


Be able to do the following operations:

Download a PDB file from the PDB, and load it onto the VMD environment.

Display using different Drawing Methods, and know when commonly used methods such as CPK, NewCartoon, and others are useful in analyzing structure.

Use the “Selected Atoms” field to display only the protein or nucleic acid (if any), or only the backbone atoms or side chain atoms, or only hydrophobic or polar (or any other property of) side chains. (Hint: go through the various options in the “Selections” tab.)

Display only particular selected residues: for instance, residue 84, or residues 23-27, or all lysine residues (or any other amino acid type).

Calculate Phi and Psi angles

Generate Ramachandran plots for all the phi-psi angles of the protein structure, or for particular residues.

Load a second protein structure, structurally align the two structures, and compute the RMSD value of the resulting alignment.

Use the Tcl Console to load a structure onto the VMD environment, and use it to compute the phi and the psi dihedral angles of particular residues.

Know how to explain the sequence-structure-function relationship.

Know three experimental methods and three computational methods to obtain 3D models.

Why is it useful to have structural information?

Explain the steps of homology modeling in details (where are the coordinates of the backbone, the side chain are generated).

What are the limitations of experimental techniques and in which cases can computational approach help?

What are the two limiting steps of model generation by homology?

Enumerate ways to improve the quality of a model using additional features.

How can the model quality be checked?

How to refine the model quality?

Know how to use basic python scripts to generate a model by homology.

Know how to use basic linux and vi commands.

Still know how to use VMD to align your structures and calculate the RMSD.

Explain the change in protein conformation shape (lock and key versus induced-fit)

What are the 2 calculation methods to calculate protein motion

What is the advantage of classical mechanics versus quantum mechanics?

What are the steps of classical mechanics?

Define what a force field is.

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