Amanda N. Wavrin Week 9

Proposed Research Questions

 * Will there be specific differences in the protein sequences of subjects 10 and 12 that will result in different structures and different functions?

Methods

 * We chose subjects 10 and 12 because they had a wide range of CD4 T cell rates
 * Subject 10 had the largest decrease in CD4 T cell counts. Of the rapid progressors in our previous project, subject 10 had the most visits.
 * We chose subject 12 because it had an average rate of CD4 T cell increase within the nonprogressors
 * We decidced to use all the clones for visits 4 and 5 of each subject because both subjects were present for that visit and there are a total of 42 sequences.
 * We used biology workbench run a CLUSTALW multiple sequence alignment
 * We ran a Boxshade color-coded plot to help us identify the differences between the subjects.
 * Using the boxshade we picked a clone from each subject to be the representitive for that subject while using PROSITE.
 * The clones we chose are subject 10; visit 4 clone 2 and subject 12; visit 4 clone 4.
 * We used PSIPRED to predict the secondary structures for our two representative clones.
 * Using the Kwong et. al article we located the V3 region of the gp120 protein.
 * We then ran multiple sequence alignments for the two representative clones. We then found the differences between those sequences and compared them to the V3 loop found using Kwong et. al.

[[Media:Bioinformatics HIV Structure Project1-final.ppt|Structure Project]]