Structural Rearrangements Maintain the Glycan Shield of an HIV-1 Envelope Trimer After the Loss of a Glycan

Roux-Cil Ferreira,Thandeka Moyo,Robert J Woods,Jeffrey R Dorfman,Simon A Travers,Natasha T Wood,Oliver C Grant

doi:10.1038/s41598-018-33390-2

Abstract

The HIV-1 envelope (Env) glycoprotein is the primary target of the humoral immune response and a critical vaccine candidate. However, Env is densely glycosylated and thereby substantially protected from neutralisation. Importantly, glycan N301 shields V3 loop and CD4 binding site epitopes from neutralising antibodies. Here, we use molecular dynamics techniques to evaluate the structural rearrangements that maintain the protective qualities of the glycan shield after the loss of glycan N301. We examined a naturally occurring subtype C isolate and its N301A mutant; the mutant not only remained protected against neutralising antibodies targeting underlying epitopes, but also exhibited an increased resistance to the VRC01 class of broadly neutralising antibodies. Analysis of this mutant revealed several glycans that were responsible, independently or through synergy, for the neutralisation resistance of the mutant. These data provide detailed insight into the glycan shield’s ability to compensate for the loss of a glycan, as well as the cascade of glycan movements on a protomer, starting at the point mutation, that affects the integrity of an antibody epitope located at the edge of the diminishing effect. These results present key, previously overlooked, considerations for HIV-1 Env glycan research and related vaccine studies.

Highlights

Some HIV-1 infected individuals develop potent and broadly neutralising antibodies that target, or find ways to bypass, the glycan shield[12,18,19,20,21]
Since glycans N197, N262, N386, N442 and N446 were identified as the glycans nearest to the protein residues that had increased antibody accessible surface area (AASA) ratios and showed conformational changes, we investigated whether these conformations were viable when glycan N301 was present, i.e. whether or not they caused large conformational clashes with any of the wild-type glycans, which would imply that the N301A mutant glycan conformations are impossible in the wild-type model
We analysed two 500 ns molecular dynamics simulations (CAP45.G3 wild-type and CAP45.G3 N301A mutant) and show that the systems imitate in vitro neutralisation data – the glycan shield restores itself and retains its ability to protect key epitopes after the removal of glycan N30113. This was in contrast to a second isolate, Du156.12, where the laboratory results showed that this N301A mutant virus had increased sensitivity to a panel of sera from chronically infected individuals[13], and where the in silico simulations of the Du156.12 wild-type and N301A mutant models were vastly different to that of the CAP45.G3 models (Supplementary File 1)

Summary

Introduction

Some HIV-1 infected individuals develop potent and broadly neutralising antibodies (bNAbs) that target, or find ways to bypass, the glycan shield[12,18,19,20,21]. Our study demonstrates how a cascade of events could contribute towards the increased resistance to antibodies targeting an epitope distal to the point mutation, in this case the N301A mutation and the VRC01 epitope These in silico data provide a detailed investigation of the glycan shield’s ability to compensate for the loss of a glycan as well as the associated cascade of events that affect a distal epitope, which provides further important considerations and avenues of exploration for vaccine studies focussing on the HIV-1 Envelope

Methods

Results

Conclusion