Assignment 1:-Left ventricular assist device- A destination therapy
Assignment 2: Bioinformatics assignment
Assignment No 3:Compare and contrast mitosis and meiosis (include at least 3 comparisons and 3 differences
2. A woman who is a carrier for cystic fibrosis has children with a man that has cystic fibrosis.
a.What are the parental genotype?
b. What F1 phenotypic and genotypic ratios are produced from this cross? (Show your Punnett Square
c. Diagram the F2 results. (Show your Punnett Square).
3 R codes for red flower color and r codes for white flower color.
a.What color would Rr be if R has complete dominance?
b. What color would Rr be if R and r are codominant?
c. What color would Rr be if R has incomplete dominance?
Assignment 4: 10. The authors ultimately conclude that [Tyr123] Prepro Endothelin (110-130) is a promising inhibitor of DENV because:
a. it has a lower predicted binding affinity than standards, poor predicted ADME/Tox and is too expensive
b. it has a lower predicted binding affinity than standards, good predicted ADME/Tox and exhibited a stable MD trajectory
c. it has a lower predicted binding affinity than standards, good predicted ADME/Tox and exhibited an unstable MD trajectory
d. it has a higher predicted binding affinity than standards, good predicted ADME/Tox and exhibited an unstable MD trajectory
Part II Multiple choice questions based on 2P41 structure. You will have to use SPDBV, VegaZZ and Vina to answer some of the questions.
11. In terms of secondary structure, the 2P41 structure is best classified as:
a. alpha-helical
b. beta
c. mixed alpha helical and beta
d. unstructured
12. Using SPDBV calculate the number of hydrogen bonds formed between the SAH ligand and the dengue methyltransferase protein.
a. 10
b. 2
c. 5
d. 7
e. 0
13. The SAH OXT atom forms a hydrogen bond with the N Trp87 atom. Calculate the approximate electrostatic energy of the SAH OXT atom interaction with N Trp85, assuming the interacting atoms are completely buried and are surrounded by "oily" groups. Use SPDBV to calculate the inter-atomic distance and the partial charge on Trp87 N; assume the partial charge on OXT is -0.55.
a. 16.23 kcal/mol
b. 0.21 kcal/mol
c. 4.06 kcal/mol
d. none of the above
14. Prior to a docking calculations, protein structures are sometimes "regularized" or energy "minimized". Regularization of a protein structure often involves setting all of the bond lengths and angles to their equilibrium values. Assuming the 2P41 protein structure has been perfectly "regularized", what would it's SPDBV molecular mechanics bond energy be?
a. > 0 kJ/mol
b. < 0 kJ/mol
c. = 0 kJ/mol
d. = 761.848 kJ/mol
15. The coordinates of the SAH C4' atom are:
a. -11.306, 86.124, 8.985
b. 86.124, -11.306, 8.985
c. -11.306, 86.124, 19.98
d. -11.217, 84.676, 9.419
16. Using the coordinates of the SAH C4' atom to define to SAH binding site, and using the SAH ligand from the 2P41 file, use Vina to re-dock SAH into its binding site. The predicted binding affinity for the best Vina pose is approximately:
a. -12.3 kcal/mol
b. -8.0 kcal/mol
c. -6.5 kcal/mol
d. -4.7 kcal/mol
e. none of the above
17. Calculate the inter-atomic distances between the SAH ligand x-ray coordinates and pose 1 predicted coordinates for N6-N6, C4'-C4', and carboxyl C-C. Based on these distances, calculate the approximate average distance deviation between pose 1 and the x-ray SAH ligand.
a. 3.3 Å
b. 0.15 Å
c. 2.2 Å
d. 1.1 Å
Assignment 5:Short protein-protein docking research project: a comparative bound and unbound protein-protein docking exercise using the barnase-barstar complex.