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

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)

HIV Infection

The Membrane Protein Gp160 Gp160: Gp120+Gp41

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

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

Expected Results SIGV1V2V3 CSFDHR1HR2TMCYT D 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

Results-conserved regions Domain,residuesExplanation 37-50,280,425, CD4 binding sites gp /1,418/9 421/2 CCR5 binding sites gp120 88,198,241,339 Glycosylation sites gp Cleavage site Trans membrane gp41

Conserved regions within groups Domain,residuesExplanation 1-36signal peptide -Targeting to and translocation across different membranes’ cells gp bridging sheet :is likely includes components of CCR5-binding site 283,370,368, CD4 binding sites gp Fusion domains gp , HR1 and HR2:two heptad repeats motifs results Cytoplasmic domain:contains sequences critical for CD4 degradation. (different groups have different levels of CD4 degradation)

Results-variable regions Domain,residuesExplanation (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) (V3) V3 loop,includes CCR5 binding sites.

multalin SIGCD4 binding site

multalin V1/V2 loops

MEME-finding motifs S A ? MF93BR e S A ? maibng 4.6e S A ? MDJY1 8.1e S A ? MGLBV217 1e S A ? MG92RU e S A ? MJSE e S A ? MJSE e S A ? MDNDK 2.7e S A ? masf e S A ? METN e S A ? METN e S A ? MF93BR e S A ? METN e S A ? OMVP e S A ? hiv2BUC1 5.5e S A ? hiv2AROD 3.1e S A ? hiv2ACAM2 1.6e S A ? hiv2BD e S A ? hiv2ANIHZ 2.4e S A ? hiv2AD e S ||||||||||||||||||||||||||||||||||||||||||||||

2D Structure Prediction of Gp Gp41 Gp120 v3v3 HR 1 HR 2 TMTM Cyto α,βC, ββ,α αβCαβC α,β,C α,C v1v1 v2v

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)

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).