Structural Basis of Antibody Recognition in Emerging Viral Variants
DOI:
https://doi.org/10.5281/zenodo.22687742Keywords:
cryo-electron microscopy, neutralising antibodies, viral spike glycoprotein, receptor-binding domain, immune escape, epitope mappingAbstract
Successive antigenic variants of respiratory RNA viruses repeatedly erode the neutralising activity of antibodies
elicited by earlier infection or vaccination, and understanding the structural basis of that erosion at single-residue
resolution is central to designing next-generation vaccines and therapeutic antibodies with durable breadth. We
solved cryo-electron microscopy structures, at resolutions between 2.9 and 3.4 angstrom, of six broadly
neutralising and four variant-specific monoclonal antibodies in complex with the receptor-binding domain of a
panel of three sequentially emerged viral spike variants, and combined these structures with deep mutational
scanning of the receptor-binding domain surface to map antibody escape at every accessible residue. The six
broadly neutralising antibodies converged on a structurally conserved, functionally constrained epitope
overlapping the receptor-binding motif, contacting residues that tolerate substitution poorly because they
participate directly in host receptor engagement, whereas the four variant-specific antibodies targeted more
peripheral, structurally variable epitopes that accumulated escape mutations across the three variants studied.
Deep mutational scanning identified a small set of five residues at which single substitutions reduced binding by
more than tenfold for at least three of the four variant-specific antibodies while leaving broadly neutralising
antibody binding intact, and these residues were significantly enriched among substitutions that subsequently
emerged in circulating lineages sampled after our structural and escape-mapping analysis was completed, a
retrospective validation we regard as meaningful support for the predictive value of systematic escape mapping.
Structure-guided analysis of one broadly neutralising antibody's paratope identified a hydrogen-bond network with
the conserved core of the receptor-binding motif that we show, through targeted alanine-scanning mutagenesis of
the antibody itself, is largely responsible for its breadth. These findings identify a structurally and functionally
conserved vulnerability suitable for targeting by next-generation vaccine immunogens and antibody therapeutics
designed for durability against continued viral antigenic drift.
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