Third short-essay exam
(30% of the final grade)
covering lectures 9-15 and practical sessions 5 and 6.

 

1.      What is a "molecular mechanics model?"

2.      What is a "conformation?"  Describe briefly a-helix conformation.

3.      What is an "energy minimization?" Describe briefly force field components.

4.      Describe main steps in homology modeling of proteins.

 Practical exercise 1:

1.      Apply any two methods of secondary structure prediction for predicting a secondary structure of the bovine pancreatic trypsin inhibitor (BPTI).

2.      Compare your results with the crystal structure (PDB code: 5pti).

 Practical exercise 2:

1.      Login into system with your password.

2.      Load in SYBYL.

3. From BIOPOLYMER, build peptide (protein) sequence:

PHE ARG CYS ILE LEU SER GLU LYS SER

4. Set the Conformation to b-sheet.

5. Label all residues.

6. Set turn_1 conformation for residues LEU5-SER6.

7. Add to SER9: GLU LYS VAL ALA LEU SER ARG HIS GLN.

8. Set a-helix conformation for GLU10-GLN18.

9. Fix end groups as charged.

10. Add hydrogens (all).

11. Perform 100 steps of energy minimization with Tripos force field and Gasteiger-Huckel charges using Powell method. Compare the starting and final energies.

12. Highlight amino acid residues: a) a-helix - in green, b) b-sheet - in red, c) turn - in blue.

13. Measure distances between C-a atoms of ILE4 and LYS8

14. Measure all torsion angles for GLU7.

15. Display backbone conformation by Shaded Ribbon.

16. Print out this picture.