Reevaluation of Amino Acid Variability of the Human Immunodeficiency Virus Type 1 gp120 Envelope Glycoprotein and Prediction of New Discontinuous Epitopes

Abstract

To elucidate the evolutionary mechanisms of the human immunodeficiency virus type 1 gp120 envelope glycoprotein at the single-site level, the degree of amino acid variation and the numbers of synonymous and nonsynonymous substitutions were examined in 186 nucleotide sequences for gp120 (subtype B). Analyses of amino acid variabilities showed that the level of variability was very different from site to site in both conserved (C1 to C5) and variable (V1 to V5) regions previously assigned. To examine the relative importance of positive and negative selection for each amino acid position, the numbers of synonymous and nonsynonymous substitutions that occurred at each codon position were estimated by taking phylogenetic relationships into account. Among the 414 codon positions examined, we identified 33 positions where nonsynonymous substitutions were significantly predominant. These positions where positive selection may be operating, which we call putative positive selection (PS) sites, were found not only in the variable loops but also in the conserved regions (C1 to C4). In particular, we found seven PS sites at the surface positions of the ␣-helix (positions 335 to 347 in the C3 region) in the opposite face for CD4 binding. Furthermore, two PS sites in the C2 region and four PS sites in the C4 region were detected in the same face of the protein. The PS sites found in the C2, C3, and C4 regions were separated in the amino acid sequence but close together in the three-dimensional structure. This observation suggests the existence of discontinuous epitopes in the protein's surface including this ␣-helix, although the antigenicity of this area has not been reported yet.The envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) interacts with receptors on the target cell and mediates virus entry by fusing the viral and cell membranes. To maintain viral infectivity, amino acids that interact with receptors are expected to be more conserved than other sites on the protein surface. Amino acid changes that reduce the affinity for the receptor will decrease infectivity or survivability, implying that negative selection is operating against amino acid changes on sites for receptor binding. The primary receptor for HIV is CD4 (9), and the secondary receptors are chemokine receptors. The main second receptor for the macrophage-tropic strains is CCR5 (11, 13) and that for T-celltropic strains is CXCR4 (15). In contrast to the functional constraint of amino acids for receptor binding, some amino acid changes in this protein may produce antigenic variations that enable the virus to escape from recognition by the host immune system. Variants with such mutations at antigenic sites will have a higher fitness than others, implying that positive selection is operating against amino acid changes at the antigenic sites. Therefore, both positive and negative selections against amino acid changes are taking place during the evolution of the surface proteins of parasites (48, 66).The relative importance of positive and ne...

Evidence for Heterogeneous Selective Pressures in the Evolution of the env Gene in Different Human Immunodeficiency Virus Type 1 Subtypes

“…This lack of lineage-specific model significance is most likely due to the much shorter sequence data used (150 codons) and the fact that the fragments covered the V3-V5 region, where only 20% of category II sites were observed in the full gene. A strong correlation was observed between sites identified as category II amino acids in this study and sites observed as undergoing strong evolutionary constraints in other studies (4,(27)(28)(29). For example, 50% of the subtype K category II sites in the gp120 three-dimensional structure were determined to be undergoing strong selective pressures in at least one of the other studies examined (4,(27)(28)(29) (Table 2).…”

“…There was little correlation between category I sites and amino acid sites identified in other studies (4,(27)(28)(29) as having undergone strong selective pressures. Previous intersubtype studies (4, 28) examined group M subtypes independently, looking at selective pressures within each subtype.…”

Genetic drift and within-host metapopulation dynamics of HIV-1 infection

“…4). Many analyses of the pattern of nucleotide substitution in the viral env gene have detected evolution in response to positive selection (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16), although relatively few studies have linked these patterns of viral genetic variation to selection by defined immune responses or for changes in viral phenotype associated with coreceptor usage. In the presence of antiretroviral agents that target viral protease and reverse transcriptase, positive selection has been described in numerous studies, which demonstrate convergent evolution in different individuals of mutations that confer drug resistance (17)(18)(19)(20).…”

Selection for Human Immunodeficiency Virus Type 1 Recombinants in a Patient with Rapid Progression to AIDS

“…While it is generally assumed that selection is responsible for the appearance of recombinant forms, other possibilities, such as neutral recombination and genetic drift, have not been rigorously evaluated. Despite evidence for selection in HIV-1 env across groups of human patients (65) and evidence for selection in specific cytotoxic T lymphocyte (CTL) epitopes encoded by gag and tat in simian immunodeficiency virus (SIV)-infected macaques (1), analyses of longitudinally sampled HIV-1 sequences from individual patients have thus far failed to reveal any statistically clear examples of natural selection acting during chronic infection in association with the development of AIDS (32; D. R. Shriner, R. Shankarappa, M. A. Jensen, D. C. Nickle, J. E. Mittler, J. B. Margolick, and J. I. Mullins, submitted for publication).…”