[Show abstract][Hide abstract] ABSTRACT: Despite the frequent observation of masking of HIV-1 neutralization epitopes, its extent has not been previously systematically assessed either for multiple epitopes presented by individual viruses or for individual epitopes across multiple viral strains. Using a recently developed method to identify amino acid sequence motifs required for recognition by HIV-1-neutralizing monoclonal antibodies (mAbs), we visualized the patterns of masking of specific epitopes targeted by mAbs in a diverse panel of HIV-1 isolates. We also calculated a specific masking intensity score for each virus based on the observed neutralization activity of mAbs against the epitopes in the virus. Finally, we combined these data with estimates of the conservation of each mAb-targeted epitope in circulating HIV-1 strains to estimate the effective neutralization potential (E(N)) for each mAb. Focusing on the V3 loop of gp120 as a prototype neutralization domain, we found that the V3 loop epitope targeted by mAb 2219 is one of the least masked mAbs and it has the highest E(N). Interestingly, although the V3 loop epitope targeted by mAb 3074 is present in over 87% of all viruses, it is 82.2% masked, so its E(N) is lower than that for mAb 2219. Notably, 50% of the viruses that mAb 3074 is able to neutralize are classified as subtype C viruses, while 70% or more of the viruses neutralized by mAbs 2219, 2557 or 447-52D are classified as subtype B. Thus, neutralization epitopes (in this case, in the V3 loop) have differential patterns of masking and also display distinct patterns of distribution among circulating HIV-1 viruses. Both factors combine to contribute to the practical vaccine value of any single epitope/mAb. Here we have developed a quantitative score for this value. These results have important implications for rational design of vaccines designed to induce neutralizing Abs by revealing epitopes that are minimally masked and maximally reactive with neutralizing Abs.
[Show abstract][Hide abstract] ABSTRACT: HIV-1 requires engagement of host co-receptor CCR5 or CXCR4 in order to infect human cells. Amino acid identity at positions 11 and/or 25 in the V3 loop of HIV-1 gp120 (positions 306 and 322 in terms of standard HXB2 gp120 numbering) has been shown to strongly influence which co-receptor is utilized by a viral strain. To identify additional sites in other gp120 regions that may influence co-receptor usage, we compared, position-by-position, the electrostatic charge distributions at each location in the D structure of X4-tropic gp120 core domains to each structurally equivalent location in R5-tropic gp120 core domains. Seven sites in the gp120 core showed a significant difference in charge distribution between the viral sets. The two strongest differences were positions 440 and 373, both located adjacent to the origin of the V3 loop, suggesting that the co-receptor binding surface of gp120 is a single hotspot formed by the V3 loop and adjacent gp120 core regions.
[Show abstract][Hide abstract] ABSTRACT: Effective antibody-mediated HIV-1 neutralization may be significantly diminished by factors such as epitope masking. Epitopes on HIV's surface envelope glycoprotein (gp120) may be masked either intrinsically, by glycans, or by occlusion by other protein regions. Previously, we quantitatively assessed neutralization epitope masking on a panel of HIV-1 pseudoviruses (psVs), with or without specific mAb epitopes, based on IC50 neutralization data and monoclonal antibody (mAb) epitope sequence motifs obtained from Hioe et al. (2010) and Cardozo et al. (2009), respectively. Here, we conducted a similar study using data from a novel and statistical neutralization analysis method: area under the neutralization titration curves (AUC), data from Hioe et al. (2010). Using the panel of HIV-1 pseudoviruses with and without specific mAb epitopes from our previous study, we were able to determine the epitope masking signatures for four mAbs: 2219, 3074, 447-52D and 2557 based on this AUC neutralization data. We also estimated the effective neutralization potential (EN) for each mAb. The effective neutralization score was calculated as: EN = (global conservation percentage) x [(100%-masked percentage)/100] where "global conservation percentage" is the percentage of circulating viruses containing the mAb targeted epitope, as taken from Swetnam et al. (2010); and "masked percentage" is the percentage of viruses containing a mAb-targeted epitope that were not neutralized. As in our previous study, we found the epitope targeted by mAb 2219 is the least masked overall, with the highest EN. Although interestingly, the neutralization epitope masking signature for each of the four mAbs was different when plotted from the AUC-based neutralization data versus from the IC50 values. Not only do different mAbs targeted to the same region of gp120 have different patterns of epitope masking in addition to a different distribution of their epitopes across circulating HIV-1 viruses, but different methods of neutralization activity analysis can also provide a different picture of effective neutralization and epitope masking.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, BCB 2010, Niagara Falls, NY, USA, August 2-4, 2010; 01/2010