Aljedani, S. | Search bioRxiv

bioRxiv2021

Structurally related but genetically unrelated antibody lineages converge on an immunodominantHIV-1 Env neutralizing determinant following trimer immunization

Understanding the molecular mechanisms by which antibodies target and neutralize the HIV-1 envelope glycoprotein (Env) is critical in guiding immunogen design and vaccine development aimed at eliciting cross-reactive neutralizing antibodies (NAbs). Here, we analyzed monoclonal antibodies (mAbs) isolated from non-human primates (NHPs) immunized with variants of a native flexibly linked (NFL) HIV-1 Env stabilized trimer derived from the tier 2 clade C 16055 strain. The antibodies displayed neutralizing activity against the autologous virus with potencies ranging from 0.005 to 3.68 ug/ml (IC50). Structural characterization using negative-stain EM and X-ray crystallography identified the variable region 2 (V2) of the 16055 NFL trimer to be the common epitope for these antibodies. The crystal structures revealed that the V2 segment adopts a {beta}-hairpin motif identical to that observed in the 16055 NFL crystal structure. These results depict how vaccine-induced antibodies derived from different clonal lineages penetrate through the glycan shield to recognize a hypervariable region within V2 (residues 184-186) that is unique to the 16055 strain. They also provide an explanation for the potent autologous neutralization of these antibodies, confirming the immunodominance of this site and revealing that multiple angles of approach are permissible for affinity/avidity that results in potent neutralizing capacity. The structural analysis reveals that the most negatively charged paratope correlated with the potency of the mAbs. The atomic level information is of interest to both define the means of autologous neutralization elicited by different tier 2-based immunogens and facilitate trimer redesign to better target more conserved regions of V2 to potentially elicit cross-neutralizing HIV-1 antibodies. Author summaryNHPs immunizations with an HIV-1 immunogen (native-like tier 2 clade C 16055 strain) elicit potent HIV-1 tier 2 autologous polyclonal neutralizing antibodies. To understand the basis of the autologous neutralization, we determined structures of antibodies isolated from the vaccinated NHPs in complex with their epitopes. Our structural analysis reveals that the V2 hypervariable region, unique to 16055, is immunodominant and targeted by antibodies from diverse lineages. Additionally, vaccine-elicited V2 NAbs use different binding angles to avoid Env N-glycan shield and the more negatively charged paratope displays potent autologous neutralizing function. In summary, detailed analysis of how vaccine-elicited monoclonal antibodies interact with the target antigen provide valuable information for the design of immunogens aimed to elicit more broadly HIV-neutralizing antibodies. The use of cocktail/prime-boost sequential regimens that include a range of sequence variation combined with the removal/shielding of unwanted immunodominant epitopes will likely be needed to reach this goal.

biochemistry↗

bioRxiv2020

Synergy and allostery in ligand binding by HIV-1 Nef

The Nef protein of human and simian immunodeficiency viruses (HIV and SIV, respectively) boosts viral pathogenicity through its interactions with host cell proteins. Nef has a folded core domain and large flexible regions, each carrying several protein interaction sites. By combining the polyvalency intrinsic to unstructured regions with the binding selectivity and strength of a 3D folded domain, Nef can bind to many different host cell proteins, perturbing their cellular functions. For example, the combination of a linear proline-rich motif and a hydrophobic core domain surface allows Nef to increase affinity and selectivity for particular Src family SH3 domains. Here we investigated whether the interplay between Nefs flexible regions and its core domain can allosterically influence ligand selection. We found that the flexible regions can bind back to the core domain in different ways, producing distinct conformational states that alter the SH3 domain selectivity and availability of Nefs functional motifs. The resulting cross-talk might help synergising certain subsets of ligands while excluding others, promoting functionally coherent Nef-bound protein ensembles. Further, we combined proteomic and bioinformatic analyses to identify human proteins that select SH3 domains in the same way as does Nef. We found that only 2-3% of clones from a whole human fetal library displayed a Nef-like SH3 selectivity. However, in most cases this selectivity appears to be achieved by a canonical linear interaction rather than a Nef-like tertiary interaction. This analysis suggests that Nefs SH3 recognition surface has no (or marginally few) cellular counterparts, validating the Nef tertiary binding surface as a promising unique drug target.

biophysics↗