J'aime C. Moehlman's Week 9
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HIV Structure Research Project
- Our Question: Will there be specific differences between the protein sequences in subject 10 and 12 that results in different protein structures, which changes the function of the virus?
- We chose subjects 10 and 12; we chose them because their CD4 T cell rates had the widest range.
- We chose subject 10 because it had the largest decrease in CD4 T cell counts; of the 3 rapid progressors in our previous project 10 had the most visits and we chose it because we felt that would have the best data.
- We chose subject 12 because it had a an average rate of CD4 T cell increase within the nonprogressors.
- We chose all of the clones from visit 4 and 5 because both subjects were present and there are a total of 42 protein sequences.
- Include table 1 from the original markham paper in powerpoint.
Methods
- Run a multiple sequence alignment for subjects 10 and 12 (all clones from visits 4 and 5).
- Also, run a box shade color coded plot in order to more clearly see where the differences are located between the two subjects.
- From the boxshade we determined which amino acids were predominantly different between the two groups. We picked a clone from each subject to be the representative for PROSITE:
- Subject 10; visit 4 clone 2.
- Subject 12; visit 4 clone 4.
