Exercise 9

 

{A. Secondary Structure Prediction }

{1. Use GCG PEPTIDESTRUCTURE and PLOTSTRUCTURE to predict secondary structure by the Chou-Fasman method. }

{2. Use GCG PEPPLOT to predict secondary structure by the GOR method. }

{3. Compare and evaluate the predictions made by the above methods to each other and to the actual structure. }

 

{B. Transmembrane Sequences}

{1. Use one or more of the web services to predict transmembrane sequences. }

{2. Compare prediction to Kyte-Doolittle style hydrophobicity plot using the GCG program PEPPLOT. }

{3. Use PSORT and SignalP to predict signal peptides. }

 

{C. Homology Modeling }

{1. Use Swiss-model to get a homology based structure prediction }

 

{D. Protein 3D Structure Visualization}

{1. Use RasMol on your Sun Solaris Computer.}

{a. Activate RasMol on your Sun computer}

{b. RasMol Documentation and Tutorials}

{c. Use RasMol on a PDB structure or two.}

{Obtain at least two *.pdb structure files for use with RasMol}

{Open a *.pdb file in RasMol and see what RasMol can do}

{Try RasMol on the file 3cro.pdb that came with the RasMol download. Try to reproduce the image shown at the top of this Exercise.}

{2. Databases of annotated 3D images.}

{a. Use of the SWISS-3DIMAGE database of 3D images.}

{b. Use of the SCOP database of 3D images.}

{Learn about the SCOP database and facility}

{Maneuver up and down through the SCOP heirarchy.}

 

{E. Questions:}

Answer questions given in the Exercise text as well as the following:

1. Give at least two reasons why the molecular weight calculated for a protein based on its sequence may be wrong. How might your reasons be related to protein function?
2. How might post-translational modification events affect protein secondary structure?
3. How might such modification events be important to "proteomics"?
4. What is the main feature in "normal" globular proteins that could be confused with a transmembrane region when using the Kyte-Doolittle method? What distinguishes these regions from "true" transmembrane regions?
5. Are all transmembrane sequences extremely hydrophobic? Why or why not? What is an amphipathic protein?
6. What are the main alpha helix forming and breaking residues in the Chou-Fasman secondary structure prediction method?
7. What are the main beta sheet forming and breaking residues in the Chou-Fasman secondary structure prediction method?
8. Why is a proline a breaking residue for both alpha and beta structures?
9. What are the preferred residues at the central two positions of a turn? Are turns simply hydrophilic regions ? Explain, basing your answer on either the Chou-Fasman or GOR prediction method.
10. Describe at least two potential problems with the Profile approach to describing sequence motifs. What are the advantages of a position-specific weight matrix approach as compared to a regular expression appraoch?
11. What does the consensus sequence shown at the left-hand side of the profile represent? Would you expect to get equivalent (to PROFILESEARCH) results if you simply used the consensus sequence in a BLAST search?
12. What is the most difficult part of the unsupervised learning approach used by MEME? Finding the description of the motif, finding the locations of the motif, or determining the width of the motif. Why?
13. What are the major Display options found in RasMol? Why might one choose each of these options?
14. What do each of the Color options distinguish in their color patterns in RasMol?
15. What do each of the Options pulldown menu choices do in RasMol?
16. What Display and Color options were used to obtain the Cro Operator graphic at the top of this Exercise 9?
17. What are the basic steps used in Homology Modeling, for example, as done by Swiss-Model?
18. How do the Swiss-3DImages compare with those in RasMol?
19. What are the "Lineage" objects in SCOP?
20. What are the two primary visualization tools used in SCOP?