Amanda N. Wavrin Week 9

From OpenWetWare
Jump to navigationJump to search

HIV Structure Research Project

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?


  • 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.

Structure Project

Useful Links

Weekly Journals