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

Abstract

HIV-1 coreceptor usage plays a critical role in virus tropism and pathogenesis. A switch from CCR5-to CXCR4-using viruses occurs during the course of HIV-1 infection and correlates with subsequent disease progression. A single mutation at position 322 within the V3 loop of the HIV-1 envelope glycoprotein gp120, from a negatively to a positively charged residue, was found to be sufficient to switch an R5 virus to an X4 virus. In this study, the NMR structure of the V3 region of an R5 strain, HIV-1JR-FL, in complex with an HIV-1-neutralizing antibody was determined. Positively charged and negatively charged residues at positions 304 and 322, respectively, oppose each other in the ␤-hairpin structure, enabling a favorable electrostatic interaction that stabilizes the postulated R5 conformation. Comparison of the R5 conformation with the postulated X4 conformation of the V3 region (positively charged residue at position 322) reveals that electrostatic repulsion between residues 304 and 322 in X4 strains triggers the observed one register shift in the N-terminal strand of the V3 region. We posit that electrostatic interactions at the base of the V3 ␤-hairpin can modulate the conformation and thereby influence the phenotype switch. In addition, we suggest that interstrand cation-interactions between positively charged and aromatic residues induce the switch to the X4 conformation as a result of the S306R mutation. The existence of three pairs of identical (or very similar) amino acids in the V3 C-terminal strand facilitates the switch between the R5 and X4 conformations.447-52D ͉ gp120 ͉ NMR T he third variable (V3) region of the HIV type 1 (HIV-1) envelope glycoprotein gp120 binds to chemokine receptors CCR5 and CXCR4, which are involved in HIV-1 infection. The amino acid sequence of V3 determines whether the virus binds to CCR5 (''R5 viruses'') and infects predominantly macrophages or to CXCR4 (''X4 viruses'') and infects mostly T cells (1). The presence of a basic residue at V3 positions 306 or 322 is associated with X4 and dual-tropic, X4R5 viruses, whereas the presence of a negatively charged residue and a neutral residue at positions 322 and 306, respectively, is correlated with R5 viruses (the ''11͞25 rule'') (2). Numerous investigations have confirmed that mutation of a negatively charged residue at position 322 to a positively charged one converts an R5 strain into an X4 strain (2-4).To gain insight into the structure of the V3 region and the mechanism for phenotype conversion, we used solution NMR spectroscopy to study the conformation of synthetic V3 peptides in complex with V3-specific anti-gp120 antibodies. An assumption underlying this approach is that the native conformation of V3 is induced in linear V3 peptides upon binding to V3-directed antibodies that were elicited against the entire gp120 protein. We studied two V3-specific antibodies. The first, murine mAb 0.5␤, is a potent strain-specific HIV-1-neutralizing antibody that was raised against a full-length gp120 protein of the X4 virus HIV-1 IIIB (...

Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region

“…V3 mutations 4 and 7 have been implicated in affecting coreceptor usage in functional studies (de Jong et al 1992;Fouchier et al 1992;Hung et al 1999; and structural modeling studies (Cardozo et al 2007;Gorry et al 2007;Rosen et al 2006). These mutations had significant pairwise and higher-order interactions with mutations 1 and 3, as well as other mutations.…”

Selection with a Peptide Fusion Inhibitor Corresponding to the First Heptad Repeat of HIV-1 gp41 Identifies Two Genetic Pathways Conferring Cross-Resistance to Peptide Fusion Inhibitors Corresponding to the First and Second Heptad Repeats (HR1 and HR2) of gp41

“…Two patterns of resistance mutations defined by early acquisition of either the E560K mutation in HR1 (pathway I) or E648K mutation in HR2 (pathway II) emerged and were In one of these cultures, mutations arose in residues 319 and 306, which are located on antiparallel ␤-hairpin strands in the V3 loop and possibly influence each other in a compensatory manner (65). The two cultures in pathway I were characterized by the E560K mutation in HR1 together with mutations that may affect CD4 interactions, including L125 and E429 (38), and by the Q577R mutation (16).…”

Rabbit Anti-HIV-1 Monoclonal Antibodies Raised by Immunization Can Mimic the Antigen-Binding Modes of Antibodies Derived from HIV-1-Infected Humans

“…Several recently described highly potent human MAbs, including PGT128, are also against the C-terminal region of V3, as well as its associ-ated glycans (26). Many of the anti-V3 MAbs are characterized by structural methods, including protein crystallography and the nuclear magnetic resonance (NMR) method (19,(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40). These structural studies of MAbs against the V3 crown showed that they have, in general, two antigen-binding modes.…”