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Angela Garibaldi & Ryan Willhite Loyola Marymount University BIOL 398-01 March 23, 2010

Residue Sequence and Structure in the Re evaluation the Categorization of HIV Progression in Subjects Based on CD4 T cell Decline Rates. Angela Garibaldi & Ryan Willhite Loyola Marymount University BIOL 398-01 March 23, 2010. Outline. Review of previous experiment using CD4 decline rates

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Angela Garibaldi & Ryan Willhite Loyola Marymount University BIOL 398-01 March 23, 2010

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  1. Residue Sequence and Structure in the Re evaluation the Categorization of HIV Progression in Subjects Based on CD4 T cell Decline Rates Angela Garibaldi & Ryan Willhite Loyola Marymount University BIOL 398-01 March 23, 2010

  2. Outline • Review of previous experiment using CD4 decline rates • Structure based hypothesis • Methods and programs used • Results • Comparison to More Recent Studies • References

  3. Recap of past experiment • Evaluated the categorization of progressors based on CD4 decline rates • Analyzed two moderate progressors (6,7) with rates comparable to non-progressor 13 and rapid progressor 10. • Based on divergence and diversity subject 6 did not act as non-progressor • Subject 7 acted like a rapid progressor.

  4. Hypothesis • Subject 7’s protein structure and properties will be more similar to Rapid Progressor Subject 10 than to Moderate Progressor 5. • Looking at protein sequences and structure is a more efficient method of testing our CD4 T-cell decline rate categorization than nucleotide sequence.

  5. Methods • Create phylogenetic trees based on amino acid sequence using Biology Workbench • Use ProtPram to analyze residue composition in subjects 6,7,5,10,13 • Select 7, 10, and 5 for time point analysis • All clones used for selected visits • Use PSIPRED to analyze secondary structures of 7, 10 , 5, 13

  6. Phylogenetics based on amino acid sequence 10 vs 5 10 vs 7 5 vs 7

  7. Subject 6 v 13

  8. Subjects 6 v 7

  9. Subjects 13 v 5

  10. Subjects 6 v 5

  11. ProtParam Physico-chemical properties of a protein using ExPASy server

  12. Subject 5 Properties

  13. Subject 6

  14. Subject 7

  15. Subject 10

  16. Overall residue composition • No significant pattern in Negative/Positive Charged residues • Rapid Progressor Subject 10 is the only subject with Asn as its most prevalent residue

  17. Residue composition over time • Asn (Asparagine) is a carboxamide and is not an essential amino acid • Often found at the beginning and ends of helices • Provides key sites for N-linked glycosylation

  18. Residue composition over time • All clones from selected visits were used. • Subject 10, Rapid Progressor shows Asn as its prevalent residue over time. • Subject 7, Moderate Progressor begins with Asn as prevalent residue • Subject 10 showed sudden jump in Arg %. This may be an artifact. • Negative/Positive Charged residue ratio conserved over time

  19. Secondary Structure Subject 10 Visit 6 Subject 7 Visit 5 No Difference! Subject 13 Visit 6 Subject 5 Visit 5

  20. Conclusion • The highest percent of amino acids found in the moderates 5,6, and 7 is (Ile) • The highest percent of amino acids found in the rapid 10 to compare is (Asn) • These differences did not equate to significant secondary structure differences • While looking at these compositions along with protein structure is a questionable method of progressor categorization, it provides insight regarding qualities of progressors.

  21. More recent study by YS Ho et al • N-linked Glycosylation (NGL) important in minimizing virus neutralizing antibody response • Looked at env gp120 C2-V5 region (includes V3) in plasma, leukocyte and other compartments • Significant variation in numbers of NGL sites between patients • Found single cell/compartment-specific amino acid changes and differences in NLG patterns between plasma and blood leukocytes

  22. Prediction of NGL sites on gp120 • Figure 2. YS Ho et al

  23. V3 Region NGL sites • V3 region has 1 clearly significant NGL site along with 2 lesser NGL sites

  24. Conclusions in relation to YS Ho • The dominance of Asn % in Rapid Progressor amino acid composition across all time points may lead to the increase of NGL sites • Dominance of Asn % in Subject 7 during Time Point 1 suggests subject does share some Rapid Progressor qualities • Increase in NGL sites or changes in NGL sites may be a mechanism of dealing with HIV-1 in its later stages • May influence viral recognition by host antibodies

  25. Future Direction • Analyze amino acid composition in larger number of Rapid Progressors for Asn dominance • Based on subject sequences, predict NGL sites per individual • Compare these with that of Non-Progressors • Analyze the folding patterns of the gp120 protein based on differences in the V3 region where Asn% is dominant vs Ile%.

  26. References • Ho YS, Abecasis AB, Theys K, Deforche K, Dwyer DE, Charleston M, Vandamme AM, and Saksena NK. HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments. Virol J 2008 Jan 23; 5 14. doi:10.1186/1743-422X-5-14 pmid:18215327

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