Chloe Jones, Isabel Gonzaga, and Nicole Anguiano

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Presentation transcript:

Chloe Jones, Isabel Gonzaga, and Nicole Anguiano HIV Structure Project Chloe Jones, Isabel Gonzaga, and Nicole Anguiano BIOL368: Bioinformatics Laboratory October 28, 2014

Outline -Examining the V3 structure between the HIV-1 variants -V3 region of gp120 protein plays a critical role in HIV entry to CD4 T-Cells -Examining the V3 structure between the HIV-1 variants -Results for the different groups - will finish when everybody imputs data

V3 region of gp120 protein plays a critical role in HIV entry to CD4 T-Cells -Third variable region (V3) -Conformational Changes important for coreceptor binding :CCR5 or CXCR4 (necessary for viral entry) -Spikes on envelope allows for binding of receptors and virus entry, “molecular hook -Studying the V3 structure, the HIV virus it can be further examined and analyzed towards progression and neutralization ○Neutralization targets V3 region

Examining the V3 structure between the HIV-1 variants Question: How does HIV status (diagnosed, progressing or non-trending) affect the structure of the V3 protein region? Hypothesis: Diagnosed groups will express greater variability in the V3 region in their protein structure, in comparison to the non-trending groups. *Know that pogressing groups expressed greater genetic variability , also may be true of V3 region affecting the host's ability to adapt to the changes and generate sufficient immune response.

Progression groups defined from Markham et al. (1998) AIDS Diagnosed <200 TD4 C Cell Counts at final visit AIDS Progressing Developed AIDS within 1 year after final visit No Trend Two Times: First Visit (initial seroconversion) Final Visit Sequences selected at random

V3 region lies on the G domain of the gp120 protein Four domains: Glycoprotein CD4 cell surface X5 Heavy Chain X5 Light Chain

V3 sequence located and deduced from the gp120 structure V3 Region on gp120: 296:G and 331:G Sequence: C T R P N Q N T R K S I H I G P G R A F Y T T G E I I G D I R Q A H C

V3 region secondary structure prediction contains 1 beta sheet and alpha helix V3: 293 - 326 on gp120 Beta sheet: 20 - 22; Alpha helix: 30 - 33

AIDS progressing groups show increased diversity over time

Progressing group initial visit secondary structure highlights amino acid changes Beta sheet (20-22): 2 differences 20: Phe vs Lys 22: Ala vs Thr Alpha helix (56-61): 1 difference 56: Asp vs Asn

Progressing group initial visit secondary structure highlights amino acid changes Beta sheet (20-22): 2 differences 20: Phe vs Lys nonpolar, aromatic → (+) 22: Ala vs Thr nonpolar → polar

Progressing group initial visit secondary structure highlights amino acid changes Alpha helix (56-61): 1 difference 56: Asp vs Asn (-) → polar

Progressing group final visit diversity affects secondary structure Beta sheet (20-22): 2 a.a. differences no more conservation at residue 20 Alpha helix (56-61): 3 a.a. differences New strong conservation at 59 and 61

Progressing group loses consensus at B-sheets over time Beta sheet (20-22): 2 differences 20: Phe vs Lys vs Tyr np, arom → (+) → polar arom 22: Ala vs Thr nonpolar → polar

Progressing group alpha helix loses consensus over time Alpha helix (56-61): 3 differences 56: Asp vs Asn 59: Gln vs Lys: polar → (+) 61: His vs Tyr: (+) → polar, arom

Non-trending

Non-Trending groups show little to no change in diversity over time Table 1. The calculated percentage differences of amino acid and DNA residues for Progressor groups at the initial visits, final visits, and combined groups. DNA more conserved

No diversity or divergence present in phylogenetic tree of Non-trending groups Figure 1. Phylogenetic tree comparing all non-trending subjects from the first to final visit. -Clones from the same virus were more genetically similar to each other, than to clones from other subjects. -Each subject stayed with in a particular region -no divergence

Non-trending group initial visit secondary structure highlight amino acid changes

Non-trending group final visit secondary structure highlight amino acid changes

Methods/results here and stuff

Interpretation of results and answering of questions and things Interpretation of results and answering of questions and things. Was hypothesis right?

Acknowledgments Dr. Kam Dahlquist Stephen Louis