ColinWikholm BIOL368 Week 11

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To complete the HIV-1 structural project and use in-class assistance to modify and improve on our current progress on the project. Also, to master and apply the tools we learned in protein sequencing and analysis to finalize our project and prepare the HIV-1 structure presentation.

Methods and Results

  • Feedback from the week 10 presentation was used to make slight alterations to the project
  • The powerpoint slide was constructed, and data analysis from week 10 was organized for proper presentation.
  • Structural analysis of the gp120 protein was narrowed to the V3 region, and its interactions with other structures was also considered.
  • We further outlined why we picked the samples we utilized in the analysis.
  • The outlier was considered, but not taken out for analysis
  • We used Boxshade for visual analysis of protein multiple sequence analysis produced from Markham et al. (1998).
  • The 3DcN software was used for structural visualization, particularly the amino acid side chains of the V3 region of gp120
  • The presentation was finalized and we discussed project issues and further areas of study.


Scientific Conclusion

We successfully completed out HIV-1 structural analysis project and found that simple analysis of gp120 amino acid diversity was not enough to describe dynamics of gp120 mutational evolution. No significant results were discovered between visits or between groups, but structural analysis and literature review suggests that focusing on the V3 region (and its dual beta-strand region in particular) may offer insight into possible modes of HIV-1 mutational evolution and its effects on protein structure. What is more, increasing sample size and considering all mutants may decrease standard error and show statistical significance for the trend seen during analysis. Specifically,


I would like to thank Isai Lopez for his assistance in this project. We worked together in-person everyday since week 10 in our apartment complex to perform data analysis, protein sequencing, and construction of the HIV-1 structure project. I would also like to thank Dr. Dahlquist for her assistance in focusing the project and utilizing structures in the presentation. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Colin Wikholm 02:48, 15 November 2016 (EST)

Important links

Bioinfomatics Lab: Fall 2016

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

Weekly Assignments Individual Journal Assignments Shared Journal Assignments

User:Colin Wikholm