Alex J. George Week 10

Structure Project

 * Bobby and I spent this class working and formulating our project for the structure of a protein


 * The question that we posed is: '''Within the variable regions of the V3 domain of HIV-1, what are the amino acid differences for progressors and nonprogressors alter its structure significantly enough to affect its function?

Results of Clustal W:
 * 1) For our data, we decided to use the same set of rapid and non progressors from the project that Bobby performed for the DNA Evolution project. For the rapid progressors, we have chosen subject 11, 10, and 4 because they had the highest rates of annual CD4 cell decline. For each subject we chose visits that had the biggest drop in CD4 T cell count. For subject 11 we chose visits 4,3, and 2. For subject 10 we chose visits 6,5,4 and for subject 4 we chose visits 4,3,2. We screened for the clones that had the greatest divergence amongst each other.  For the group of non-progressors, we have chosen 2-V3, 2-V4, 2-V5, 12-V3, 12-V5, 12-V6, 13-V5, 13-V6, 13-V10. These subjects were chosen because they were the only recorded nonprogressors in the experiment. These visits were chosen because they had the highest CD4 T cell count among all visits. These clones will be analyzed for each visit to find a difference in the nucleotide sequence. To convert our DNA sequences into protein sequences, we first had to obtain our amino acid sequences from each subject at www.bioquest.org/bedrock.  We know that the amino acid sequences obtained are correct because it came from the data generated during the study of these subjects by scientists.
 * 2) Perform a multiple sequence alignment on the protein sequences. There are fewer differences in the protein sequences than the DNA sequences because the amino acid code is degenerate which means that each amino acid has more than one codon that correlates to it. Are there more or fewer differences between the sequences when you look at the DNA sequences versus the protein sequences?
 * 1) Amino acid change S to F at position four Subject 13 V5 clone 1. Serine --> to phenylalanine goes from polar uncharged to hydrophobic side chain
 * 2) T -> M polar to phobic
 * 3) T to S: polar polar
 * 4) I to T: phobic to polar
 * 5) I to N: phobic to polar
 * 6) L to P: phobic to proline which is a ring strucurre can alter bonding
 * 7) S to A: polar to phobic
 * 8) S to T: polar to polar ''look at this one S to T and T to S
 * 9) S to F: polar phobic
 * 10) E to G: negative to glycine * look at this change also
 * 11) E to V: negative to phobic