1. Project in BioInformatics Variability of Membrane proteins of different HIV strains By Emad Nimer Wisam Kadry

2. Hiv groups & subtypes hiv hiv2hiv1 OM A J Predominant Less easily transmitted Longer period between infection And illness (Cameron) (Europe) Hiv types Hiv1 groups M subtypes The 20 chosen strains: hiv1: O(1 strain), M(13 strains from subtypes A,D,E,F,G,J) hiv2(6 strains)

3. HIV Infection

4. The Membrane Protein Gp160 Gp160: Gp120+Gp41

5. Project goal explanation of regions of conservation/variability in the gp160 protein for different hiv strains

6. 1. Extracting the gp160 sequences. hiv sequence database- http://hiv-web.lanl.gov/ 2. Detect conserved/variable residues. Multiple alignment- multalin/clustw 3. Detect motifs. MEME 4. Detect conserved 2D-structure - PSIPRED Methodology & Tools

7. Expected Results SIGV1V2V3 CSFDHR1HR2TMCYT D 361131345185370509 510527512546579628655685705856 gp120 gp41 SIG-signal peptide V1/V2/V3-loops CS-cleavage site FD-fusion domain HR1/2-heptad repeats TM-trans membrane domain CYT D-cytoplasmic domain

8. Results-conserved regions Domain,residuesExplanation 37-50,280,425,124-130CD4 binding sites gp120 120/1,418/9 421/2 CCR5 binding sites gp120 88,198,241,339 Glycosylation sites gp120 511Cleavage site 685-705Trans membrane gp41

9. Conserved regions within groups Domain,residuesExplanation 1-36signal peptide -Targeting to and translocation across different membranes’ cells gp120 230-340 bridging sheet :is likely includes components of CCR5-binding site 283,370,368,472-474 CD4 binding sites gp120 512-527Fusion domains gp41 546-579,628-655HR1 and HR2:two heptad repeats motifs results 706-856 Cytoplasmic domain:contains sequences critical for CD4 degradation. (different groups have different levels of CD4 degradation)

10. Results-variable regions Domain,residuesExplanation 131-185 (V1,V2)V1/V2 loops, part of CD4 binding site, their variability disrupt blocking the CD4 binding by the antibodies. Loops have a flexible structure(that explains the low consensus). 345-370 (V3) V3 loop,includes CCR5 binding sites.

11. multalin SIGCD4 binding site

12. multalin V1/V2 loops

13. MEME-finding motifs S A ? MF93BR029.2 8.6e-43 10 10 1 7 2 9 7 5 2 1 5 5 4 6 9 7 10 10 6 3 3 8 3 8 4 4 S A ? maibng 4.6e-42 10 10 1 7 2 9 7 5 2 1 6 4 5 4 6 9 7 10 10 6 3 3 8 3 8 4 4 S A ? MDJY1 8.1e-42 10 10 1 7 2 9 7 5 2 1 2 5 5 4 6 9 7 10 10 6 3 3 8 3 8 4 4 S A ? MGLBV217 1e-41 5 10 10 1 7 2 9 7 5 2 1 6 4 5 4 6 9 7 10 10 6 3 3 8 3 8 4 4 S A ? MG92RU131.9 3.4e-41 10 10 1 7 2 9 7 5 2 1 6 4 5 4 6 9 7 10 10 6 3 3 8 3 8 4 4 S A ? MJSE702 4.9e-41 10 10 1 7 2 9 7 5 2 1 5 5 4 6 9 7 10 10 6 3 3 8 3 8 4 4 S A ? MJSE7887 2.6e-40 10 10 1 7 2 9 7 5 2 1 5 5 4 6 9 7 10 10 6 3 3 8 3 8 4 4 S A ? MDNDK 2.7e-40 10 10 1 7 2 9 7 5 2 1 5 5 4 6 9 7 10 10 6 3 3 8 3 8 4 4 S A ? masf1703 8.1e-40 10 10 1 7 2 9 9 7 5 2 1 6 4 5 4 6 9 7 4 10 10 6 3 3 8 3 8 4 4 S A ? METN239 1.4e-39 10 10 1 7 2 9 7 5 2 1 5 4 6 9 7 6 3 3 8 3 8 4 S A ? METN235 1.4e-39 10 10 1 7 2 9 7 5 2 1 5 4 6 9 7 6 3 3 8 3 8 4 S A ? MF93BR020.17 1.8e-38 5 10 10 1 7 2 9 7 5 2 1 5 5 4 6 9 7 10 10 6 3 3 8 3 8 4 4 S A ? METN242 3.5e-38 10 10 1 7 2 9 7 5 2 1 5 6 9 7 6 3 3 8 3 8 4 S A ? OMVP5180 4.8e-37 10 10 1 7 2 9 5 2 1 5 3 5 5 4 9 7 6 3 3 8 3 8 4 S A ? hiv2BUC1 5.5e-34 10 10 2 2 9 5 1 10 10 5 4 5 6 3 8 4 4 S A ? hiv2AROD 3.1e-33 10 10 2 9 5 1 10 10 5 4 5 6 3 8 4 4 S A ? hiv2ACAM2 1.6e-32 10 10 2 5 9 5 1 10 10 5 4 5 6 3 8 4 S A ? hiv2BD205 1.3e-31 10 10 2 2 9 5 1 10 10 5 4 5 6 3 8 4 4 S A ? hiv2ANIHZ 2.4e-31 10 10 2 9 9 5 1 10 10 5 4 5 6 3 8 4 S A ? hiv2AD194 4.2e-31 10 10 2 5 9 5 1 10 10 5 4 5 6 3 8 4 S |||||||||||||||||||||||||||||||||||||||||||||| 1255075100125150175200225250275300325350375400425450475500525550575600625650675700725750775800

14. 2D Structure Prediction of Gp160 856511 Gp41 Gp120 v3v3 HR 1 HR 2 TMTM Cyto α,βC, ββ,α αβCαβC α,β,C α,C v1v1 v2v2 131185345370546579628655685705

15. Conclusions 1.Conserved regions/residues have an important role in the functionality gp160 proteins,such as: trans membrane domain (high affinity to lymphocyte cell’s membrane), CD4/CCR5 binding sites and glycosation sites. 2. Conserved regions within the groups attribute group speciality such as different levels of infections : Why hiv1 is more dominant? More binding sites Higher level of CD4 degradation (Cytoplasmic domain) Different pre-fusion complexes (hiv1 has 6 heptads and hiv2 has 3) 3. Variable regions are loops near binding sites,their variability disrupt antibodies performance. (that is why HIV is so dangerous)

16. Future research 1. Investigate the variable regions V1/V2/V3, Is mutation random ? 3. Include more strains to yield better sampling. 4. Investigate the conserved/variable regions of the Gag protein. Is there any interaction or correlation between Gag protein and gp160 ? 2. Our results showed that hiv1 has 6 heptad repeats while hiv2 has only three. Is that true ? (try to use other tools).