Induced Fit in HIV-Neutralizing Antibody Complexes:  Evidence for Alternative Conformations of the gp120 V3 Loop and the Molecular Basis for Broad Neutralization^,

Abstract

Human monoclonal antibody (mAb) 447-52D neutralizes a broad spectrum of HIV-1 isolates, whereas murine mAb 0.5beta, raised against gp120 of the X4 isolate HIV-1(IIIB), neutralizes this strain specifically. Two distinct gp120 V3 peptides, V3(MN) and V3(IIIB), adopt alternative beta-hairpin conformations when bound to 447-52D and 0.5beta, respectively, suggesting that the alternative conformations of this loop play a key role in determining the coreceptor specificity of HIV-1. To test this hypothesis and to better understand the molecular basis underlying an antibody's breadth of neutralization, the solution structure of the V3(IIIB) peptide bound to 447-52D was determined by NMR. V3(IIIB) and V3(MN) peptides bound to 447-52D exhibited the same N-terminal strand conformation, while the V3(IIIB) peptide revealed alternative N-terminal conformations when bound to 447-52D and 0.5beta. Comparison of the three known V3 structures leads to a model in which a 180 degrees change in the orientation of the side chains and the resulting one-residue shift in hydrogen bonding patterns in the N-terminal strand of the beta-hairpins markedly alter the topology of the surface that interacts with antibodies and that can potentially interact with the HIV-1 coreceptors. Predominant interactions of 447-52D with three conserved residues of the N-terminal side of the V3 loop, K312, I314, and I316, can account for its broad cross reactivity, whereas the predominant interactions of 0.5beta with variable residues underlie its strain specificity.

Discrete conformations of epitope II on the hepatitis C virus E2 protein for antibody-mediated neutralization and nonneutralization

“…The flexibility conferred by this highly conserved glycine residue meets the requirements for permitting the spatial and temporal relationships of the C-terminal α-helix and the N-terminal loop. This finding is consistent with the generally accepted role of glycine in providing the freedom necessary for the regulation of both folding and function of a protein (22)(23)(24)(25)(26)(27)(28). In addition, it has been found experimentally that Gly 436 has a functional role in the entry process of the virus (6).…”

Molecular switch for alternative conformations of the HIV-1 V3 region: Implications for phenotype conversion

“…The structures of V3 JR-FL and V3 IIIB bound to 447-52D (the latter of which we previously postulated was the R5 conformation of V3) (10) are similar in the pairing of the ␤-hairpin residues, the side chain orientation, and the register of the hydrogen bond-forming positions in both the N-and C-terminal strands ( Fig. 3 A and B).…”

HIV-1 Glycoprotein Immunogenicity

“…Its core epitope is the Gly-Pro-Gly-Arg (GPGR) motif which is located at the center of the V3 region. This recognition is altered with the substitution of AA at the N-Term segment of the V3 region (Rosen et al, 2005). This Ab neutralize both X4 and R5 primary isolates, making it one of the most effective anti-V3 Ab.…”

“…The only side-chain interactions are with the Pro and Arg-residues in the GPGR sequence; the side chains from both residues form extensive interactions with residues in the Ab combining site. The side chain of the Arg residue in the GPGR sequence is oriented in the opposite direction in the 447-52D complex relative to its orientation in the other complexes with anti-V3 antibodies and V3 (Binley et al, 2004;Rosen et al, 2005). However, exposure of the V3 region during infection seems to occur exclusively in the context of gp120 oligomer on the virus and may be influenced by the presence of glycan moieties.…”