Research Article: Resistance of Subtype C HIV-1 Strains to Anti-V3 Loop Antibodies

Date Published: April 2, 2012

Publisher: Hindawi Publishing Corporation

Author(s): David Almond, Chavdar Krachmarov, James Swetnam, Susan Zolla-Pazner, Timothy Cardozo.


HIV-1’s subtype C V3 loop consensus sequence exhibits increased resistance to anti-V3 antibody-mediated neutralization as compared to the subtype B consensus sequence. The dynamic 3D structure of the consensus C V3 loop crown, visualized by ab initio folding, suggested that the resistance derives from structural rigidity and non-β-strand secondary protein structure in the N-terminal strand of the β-hairpin of the V3 loop crown, which is where most known anti-V3 loop antibodies bind. The observation of either rigidity or non-β-strand structure in this region correlated with observed resistance to antibody-mediated neutralization in a series of chimeric pseudovirus (psV) mutants. The results suggest the presence of an epitope-independent, neutralization-relevant structural difference in the antibody-targeted region of the V3 loop crown between subtype C and subtype B, a difference that we hypothesize may contribute to the divergent pattern of global spread between these subtypes. As antibodies to a variable loop were recently identified as an inverse correlate of risk for HIV infection, the structure-function relationships discussed in this study may have relevance to HIV vaccine research.

Partial Text

Subtype C infections now represent the majority of HIV-1 infections worldwide [1], suggesting greater in vivo or host-pathogen fitness. By contrast, in direct in vitro competition assays, R5 subtype B isolates outcompete R5 subtype C isolates [2], suggesting greater in vitro infective fitness. Thus, more rapid in vivo spread of subtype C infections may be occurring despite an apparent greater in vitro fitness of subtype B.

The experimental results described here indicate that a significant fraction of the anti-V3 antibody-mediated neutralization resistance of the conC sequence maps directly to the antibody-binding domain of the V3 crown. Furthermore, the epitope-independent structural feature by which the subtype C V3 crown resists neutralization by a variety of anti-V3 antibodies appears to be a rigid N-terminal non-β-strand conformation at positions 12 to 14 of the V3 loop. This effect is exclusive of the more commonly observed mechanism of antibody escape, that is, mutations of key neutralization epitope side chains, such as R18Q for 447-52D which we have shown results in a distinguishable, antibody-specific resistance. The combination of the loss of key neutralization epitope amino acid side chains with rigidity or non-β-strand structure results in total resistance of the psV bearing these V3 loop properties to neutralization by the antibody in question. Since these are intrinsic features of the V3 loop sequences, this phenomenon would apply to circulating viruses bearing these properties in their V3 loops as well, specifically subtype C viruses. Our dissection of the effects of single V3 loop point mutations shows that the effects of each point mutation is complex, and the backbone effect is combinatorial to all of the V3 loop positions simultaneously. Thus, no single amino acid position is solely responsible for the conC structural phenomenon. The convergence of three completely independent sets of data—(1) known crystallographic structures of V3 peptides bound to antibody, (2) patterns of psV neutralization, and (3) validated ab initio folding simulations—strongly supports these conclusions.




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