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

Abstract

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.

Figure 1

Neutralization of chimeric psVs by antibodies 447-52D (purple) and 2219 (blue). The psV consist of the SF162 strain with its V3 loop replaced by the indicated V3 loop sequence. Consensus B-R18Q is a psV consisting of the consensus subtype B V3 loop sequence with position 18 in the V3 loop mutated from a subtype B consensus arginine to a subtype C consensus glutamine. IC₅₀ is the amount of antibody in ug/mL required to achieve 50% neutralization. The negative base 10 logarithm of the IC₅₀ has been plotted for easier comparison: higher, positive bars towards the top of the graph indicate strong neutralization by the antibody. Antibodies were only tested to a concentration of 20 ug/mL for neutralization, so the negative value of 1.3 on the plot is maximal and indicated no detectable neutralization by the antibody. Adapted from [14].

Figure 2

(a) Top: lowest energy conformation of the subtype C V3 loop crown from V3 loop amino acid positions 10 to 22. The structure is shown in ribbon representation colored in a gradient from the N-terminal residue at position 10 (dark blue) to the C-terminal residue at position 22 (colored dark red). The side chain conformations of Ile12, Arg13, and Ile14 are shown in full-atom wire representation. Their backbone curvature and fanned orientation are inconsistent with β-strand secondary structure. Bottom: plot of 180 lowest energy conformations from the folding simulation. x-axis (ENER): energy score ranging from lowest at the left to higher at the right. y-axis (NVIS): number of visits by the simulation to the indicated conformation. For example, the lowest energy conformation was found again and again by the search over 150 times. The presence of a 4 kcal simulation energy unit gap in the subtype C simulation indicates a rigid structure as a 4 kcal energy barrier prevents exit from the lowest energy conformation most of the time on the biological time scale. (b) Top: lowest energy conformation of the subtype B V3 loop crown from positions 10–22 depicted as in A. The extended linear conformation of Ile12, Arg13, and Ile14 with alternating directions for the side chains is typical of canonical β-strand structure. Bottom: plot of 180 lowest energy conformations from the folding simulation as in A. Many conformations are present near the lowest energy conformation in this subtype B simulation predicting a flexible structure that flickers between ~10 conformations all the time (is flexible) on the biological timescale.