AninditaVarshneya BIOL368 Week 11

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  • To find out more information about the types of amino acid mutations between clones, and the structural impacts those mutations might have.

Methods and Results

  • Clones from visit 1 and 4 were uploaded to Biology Workbench, Protein Tools
  • Upload Huang protein sequence as well
  • Select all clones from a single subject as well as the Huang protein sequence
  • Run ClustalW Multiple Alignment and import the alignment into the Alignment Tools section
  • Select the alignment under Alignment Tools and run BoxShade
  • Open the Huang protein structure file on Cn3D, as well as the amino acid sequence
  • Select all amino acids of interest to analyze their importance in the structure of the protein. Using the space-filling model is helpful.
    1. Highlight all amino acids in Cn3D that have corresponding amino acids in BoxShade that are not green
    2. Highlight only amino acids with grayed out mutations, not including Huang
    3. Highlight only amino acids with more than one grayed out mutations, not including Huang
  • Repeat these steps to analyze mutations in all other subjects against the Huang reference strain
  • After completing this work, my lab partner and I worked on our presentation for the following week (linked below).


Through structural analysis, I found that subjects from the moderate progressor group had significantly more amino acid substitutions along the surface of the gp120 protein compared to subjects from the rapid progressor group. Furthermore, I found that subject 14 has a single amino acid that multiple clones mutated. This was of especial interest to us because this amino acid was at a structural location that indicates that it interacts with the antibody proteins to some extent. While the extent of that interaction is unknown, the major mutations occurring at that place would affect the way gp120 sits in relation to the antibody. Furthermore, through research Matt and I found position 317 is a highly variant amino acid that also exists within the binding site for the antibody. This is interesting to us because we found that both subjects in the moderate progressor group had mutations in this region. Because it is within the binding site, mutations here would greatly affect the proteins ability to bind with the antibody. Considering the fact that this mutation was only found among moderate progressors, we can assume that, to a certain extent, the gp120 protein in moderate progressors did not bind with the antibody the same way that the gp120 protein in rapid progressors did. This means that the mutations we found in position 317 could represent some level of importance in the progression of HIV-1.

Data and Files


  • Edlefsen, P. T., Rolland, M., Hertz, T., Tovanabutra, S., Gartland, A. J., Magaret, C. A., et al. (2015). Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. PLoS Comput Biol, 11(2), e1003973.
  • Huang, C. C., Tang, M., Zhang, M. Y., Majeed, S., Montabana, E., Stanfield, R. L., ... & Wyatt, R. (2005). Structure of a V3-containing HIV-1 gp120 core. Science, 310(5750), 1025-1028.
  • Kirchherr, J. L., Hamilton, J., Lu, X., Gnanakaran, S., Muldoon, M., Daniels, M., Kasongo, W., et al. (2011). Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120. Virology, 409(2), 163-174. DOI: 10.1016/j.virol.2010.09.031
  • Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (1998). Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature, 393(6686), 648-659. DOI: 10.1038/31405
  • Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. doi: 10.1073/pnas.95.21.12568
  • Week 11 Assignment Page
  • Week 10 Assignment Page
  • Week 9 Journal Entry
  • Week 10 Journal Entry


Matt Allegretti and I met to work on our research product during lab on 11/8/16 and again on 11/12/16 for several hours. We also worked on our research presentation together over Google Drive throughout the week. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Other Links

User Page: Anindita Varshneya

Bioinfomatics Lab: Fall 2016

Class Page: BIOL 368-01: Bioinfomatics Laboratory, Fall 2016

Weekly Assignments Individual Journal Assignments Shared Journal Assignments

SURP 2015

Links: Electronic Lab Notebook