S373P Mutation Stabilizes the Receptor-Binding Domain of the Spike Protein in Omicron and Promotes Binding

A cluster of several newly occurring mutations on Omicronis foundat the & beta;-core region of the spike protein's receptor-bindingdomain (RBD), where mutation rarely happened before. Notably, thebinding of SARS-CoV-2 to human receptor ACE2 via RBD happens in adynamic airway environment, where mechanical force caused by coughingor sneezing occurs. Thus, we used atomic force microscopy-based single-moleculeforce spectroscopy (AFM-SMFS) to measure the stability of RBDs andfound that the mechanical stability of Omicron RBD increased by & SIM;20%compared with the wild type. Molecular dynamics (MD) simulations revealedthat Omicron RBD showed more hydrogen bonds in the & beta;-core regiondue to the closing of the & alpha;-helical motif caused primarily bythe S373P mutation. In addition to a higher unfolding force, we showeda higher dissociation force between Omicron RBD and ACE2. This workreveals the mechanically stabilizing effect of the conserved mutationS373P for Omicron and the possible evolution trend of the & beta;-coreregion of RBD.