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.

Automated summary

A cluster of newly occurring mutations on Omicron was found in the β-core region of the spike protein's receptor-binding domain, where mutations rarely occurred before. The mechanical stability of Omicron RBD was found to increase by approximately 20% compared to the wild type. Molecular dynamics simulations showed that Omicron RBD had more hydrogen bonds in the β-core region due to the closing of the α-helical motif caused by the S373P mutation. In addition, the dissociation force between Omicron RBD and ACE2 was higher. This study reveals the mechanically stabilizing effect of the conserved S373P mutation in Omicron and the possible evolutionary trend of the β-core region of the receptor-binding domain.