Deamidation drives molecular aging of the SARS-CoV-2 spike receptor-binding motif

ABSTRACT: The spike is the main protein component of the SARS-CoV-2 virion surface. The spike receptor-binding motif mediates recognition of the hACE2 receptor, a critical infection step, and is the preferential target for spike-neutralizing antibodies. Post-translational modifications of the spike receptor-binding motif can modulate viral infectivity and immune response. We studied the spike protein searching for asparagine deamidation, a spontaneous event that leads to the appearance of aspartic and isoaspartic residues, affecting both the protein backbone and its charge. We used computational prediction and biochemical experiments to identify five deamidation hotspots in the SARS-CoV-2 spike. Asparagine residues 481 and 501 from the receptor-binding motif deamidate with a half-time of 16.5 and 123 days at 37 °C, respectively. Deamidation is significantly slowed down at 4 °C, pointing at a strong dependence of spike molecular aging on the environmental conditions. We demonstrate that topological constraints drive the conservation of deamidation hotspots among Sarbecoviruses spike proteins. Deamidation of the spike receptor-binding motif decreases the equilibrium constant for binding to the hACE2 receptor more than 3.5-fold, yet its high conservation pattern suggests some positive effect on viral fitness. We propose a model for deamidation of the full SARS-CoV-2 virion that illustrates how deamidation of the spike receptor-binding motif leads to the accumulation on the virion surface of a non-negligible chemically diverse spike population in a timescale of days. Our findings provide a mechanism for molecular aging of the spike, with significant consequences for understanding virus infectivity and vaccine development.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Severe Acute Respiratory Syndrome Coronavirus 2

DISEASE(S): Covid-19

SUBMITTER: Jennifer Schwarz  

LAB HEAD: Leonardo G.Alonso

PROVIDER: PXD027873 | Pride | 2022-02-17

REPOSITORIES: Pride