Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions

Abstract

Subtype C human immunodeficiency vírus type 1 (HIV-1) is rapidly diversifying among populations, which display extensiva polymorphism of genes encoding class I human leukocyte antigen (HLA) proteins, as detected in different regions of the world. Broadly conserved HIV-1 cytotoxic T cell (CTL) epitopes considering 128 subtype C externai glycoprotein gp120 sequences selected from GenBank were identified to A*0201, A*0301, A*1101 and 8*07 HLA alleles using Epijen software. NetChop allowed to predict proteasome cleavage followed by prediction of binding to transport associated with antigen processing on TapPred. Glycosylation and positively selected sites within epitope sequences were also observed. Furthermore, three-dimensional structures of subtype C gp120 were predicted from consensus sequences in PHYRE and the PYMOL software was used to verify positions occupied by conserved epitopes. Finally, we predicted discontinuous B cell epitopes in DiscoTope 1.2. There is a recognized evolutionary force of HIV-1 to escape from B cells and CTL responses mutating sites that can negatively select the viral population. ' These types of analyses could be useful to understand HIV-1 epidemiology associated with polymorphisms in HLA alleles frequent in a determined region. 1t is expected that such knowledge may provide additional support for vaccine development.