Structural rearrangements maintain the Glycan Shield of an HIV-1 envelope trimer after the loss of a glycan

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.IS

Exploiting glycan topography for computational design of Env glycoprotein antigenicity

Mounting evidence suggests that glycans, rather than merely serving as a “shield”, contribute critically to antigenicity of the HIV envelope (Env) glycoprotein, representing critical antigenic determinants for many broadly neutralizing antibodies (bNAbs). While many studies have focused on defining the role of individual glycans or groups of proximal glycans in bNAb binding, little is known about the effects of changes in the overall glycan landscape in modulating antibody access and Env antigenicity. Here we developed a systems glycobiology approach to reverse engineer the complexity of HIV glycan heterogeneity to guide antigenicity-based de novo glycoprotein design. bNAb binding was assessed against a panel of 94 recombinant gp120 monomers exhibiting defined glycan site occupancies. Using a Bayesian machine learning algorithm, bNAb-specific glycan footprints were identified and used to design antigens that selectively alter bNAb antigenicity as a proof-of concept. Our approach provides a new design strategy to predictively modulate antigenicity via the alteration of glycan topography, thereby focusing the humoral immune response on sites of viral vulnerability for HIV

Refining the HIV-1 glycan shield model: dynamics of a heterogeneous envelope trimer and empirical prediction of glycan processing

The HIV-1 surface protein, Envelope (Env), is covered in asparagine-linked glycans, which interact with the human immune system and are thus important as potential vaccine targets. Laboratory studies have shown that the glycan type and form can differ substantially at each glycan site on Env clones. However, these studies are limited by time and cost and rely on biosynthetic assumptions to elucidate the structure of branched glycans. Furthermore, glycan heterogeneity creates challenges when determining the three-dimensional structure of Env, which has resulted in the use of methods that restrict glycan processing to produce uniform glycans for these studies. Computational methods are used to complement the laboratory studies; however, due to the limitations of modelling software, even computational studies have focussed on uniformly glycosylated Env models using a limited set of high-mannose glycans, rather than a mix of glycan types. To bridge this gap, this study set out to examine the structural differences of two computationally glycosylated HIV-1 Env trimers, one uniformly glycosylated, and the other based on the heterogeneous glycosylation of a laboratory determined gp160 strain. A secondary aim was to estimate whether the type of glycan is predictable using computational techniques, since these are less expensive and time consuming than laboratory studies. Using 500 ns molecular dynamics (MD) simulations, it was found that the heterogeneously glycosylated trimer had 64% greater stability, likely due to the presence of 25% more hydrogen bonds, as well as stabilising bonds which appeared to prevent asymmetrical movements. Furthermore, by focussing on the heterogeneously glycosylated trimer, a computational method based on surface area was explored to estimate the accessibility to enzymes involved in glycan processing, and to use this measure as a predictor of the glycan type. The results of this study highlight the differences between a uniformly, and a heterogeneously, glycosylated trimer, and suggest that previous MD studies, which used uniformly glycosylated trimers, may not sufficiently describe the structural dynamics of HIV-1 Env. Notably, complex glycans appear to stabilise the trimer to a greater extent than the high-mannose glycans used in previous studies. Thus, it is evident that research on Env models should incorporate a more diverse set of glycans in order to deepen our understanding of the dynamics of Env, which will, in turn, further our understanding of its interactions with antibodies and anti-HIV compounds

Exploring the role of the “glycan-shield” of human immunodeficiency virus in susceptibility to, and escape from, broadly neutralising antibodies

Philosophiae Doctor - PhDThe 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. Despite the importance of the HIV- 1 Env glycans, limited computational analyses have been employed to analyse these glycans. Here, the Env glycans of two HIV-1 wild-type subtype C isolates are examined, in detail, using computational approaches. These particular strains were used since in vitro data showed that the removal of a single glycan had a substantially different impact on the neutralisation sensitivity of the two strains. Molecular dynamics simulations, and the subsequent analyses, were carried out on the computationally determined, fully glycosylated, Env structures of these two wild-type strains and their N301A mutant counterparts. Detailed comparison of the molecular dynamics simulations demonstrated that unique glycan dynamics and conformations emerged and that, despite shared HXB2 reference sequence positions, the glycans adopted distinct conformations specific to each wild-type model. Furthermore, different changes in conformations were observed for each wild-type model compared to its N301A mutant counterpart and, interestingly, these N301A mutant model-specific glycan conformations were directly associated with the protein residues ultimately found to be exposed, which may explain the varied resistance to neutralising antibodies observed, in vitro, for the two N301A mutant strains