Sequences in Glycoprotein gp41, the CD4 Binding Site, and the V2 Domain Regulate Sensitivity and Resistance of HIV-1 to Broadly Neutralizing Antibodies

Abstract

The swarm of quasispecies that evolves in each HIV-1-infected individual represents a source of closely related Env protein variants that can be used to explore various aspects of HIV-1 biology. In this study, we made use of these variants to identify mutations that confer sensitivity and resistance to the broadly neutralizing antibodies found in the sera of selected HIV-1-infected individuals. For these studies, libraries of Env proteins were cloned from infected subjects and screened for infectivity and neutralization sensitivity. The nucleotide sequences of the Env proteins were then compared for pairs of neutralization-sensitive and -resistant viruses. In vitro mutagenesis was used to identify the specific amino acids responsible for the neutralization phenotype. All of the mutations altering neutralization sensitivity/resistance appeared to induce conformational changes that simultaneously enhanced the exposure of two or more epitopes located in different regions of gp160. These mutations appeared to occur at unique positions required to maintain the quaternary structure of the gp160 trimer, as well as conformational masking of epitopes targeted by neutralizing antibodies. Our results show that sequences in gp41, the CD4 binding site, and the V2 domain all have the ability to act as global regulators of neutralization sensitivity. Our results also suggest that neutralization assays designed to support the development of vaccines and therapeutics targeting the HIV-1 Env protein should consider virus variation within individuals as well as virus variation between individuals.

Conserved Role of an N-Linked Glycan on the Surface Antigen of Human Immunodeficiency Virus Type 1 Modulating Virus Sensitivity to Broadly Neutralizing Antibodies against the Receptor and Coreceptor Binding Sites

“…Glycans on HIV-1 envelope proteins have been shown or postulated to play an important and multifaceted role in viral replication, including structural integrity of the virus, coreceptor usage, evasion of host immune responses, and as targets for bNAbs (21,23,57,70,76). Here, we report a conserved role for the N-linked glycan at amino acid position 197 (N7) in modulating the antigenicity of the CD4bs and epitopes in the V3 loop, a major determinant for coreceptor usage.…”

“…Because glycans on HIV-1 play an important role in the structure and function of Env (63,83,84) and because multiple studies have shown that carbohydrates modulate Env antigenicity (21,23,57,70,76,(85)(86)(87)(88)(89)(90), glycan modification may represent a rational approach for immunogen design. Although multiple studies have shown little or negative impact of glycan modifications on Env immunogenicity (91)(92)(93)(94)(95), we previously demonstrated that removal of specific glycans may enhance the ability of HIV Env to elicit neutralizing antibody responses (21).…”

Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5

“…D197, which results in loss of a PNGS located at the HIV Env trimer apex that determines neutralization sensitivity/resistance in several primary isolates (Kolchinsky et al, 2001b; Li et al, 2008; O’Rourke et al, 2012; Pantophlet et al, 2003; Rizzuto et al, 1998; Saphire et al, 2001), is a rare polymorphism that was detected in brain in some patients with HAD. Codon 200 was estimated to be under positive selection in both brain and lymphoid sequences from HAD patients.…”

Impact of the Maraviroc-Resistant Mutation M434I in the C4 Region of HIV-1 gp120 on Sensitivity to Antibody-Mediated Neutralization

“…M434 mutated to I434 might have an effect on stabilizing the CD4-bound conformation of the Env (53-55). Thus, it is possible that particular C4 mutations, such as M434I, impact the exposure of the CD4 binding site epitope for neutralizing antibodies (22,48,51,52). In the present study, the M434I mutation showed enhanced neutralization sensitivity to anti-CD4bs, b12, and 0.5d NMAbs.…”

“…M434I, for instance, was observed in escape variants from the attachment inhibitor BMS-378806 and its derivatives (49,50). Furthermore, some C4 mutations in the Env region also occur in neutralizing antibody sensitive variants (48,51,52). These C4 mutations, including M434I, are located in close proximity to the CD4 binding area.…”