ArticleiScience2023
Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike.
Article in iScience, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Switching Spike Plasticity Shapes ACE2 Engagement Across SARS-CoV-2 Variants.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Deep mutational scanning of recent SARS-CoV-2 variants highlights changing amino acid preferences within epistatic hotspot residues.PLoS pathogens · 2026Article
- Modulation of SARS-CoV-2 spike binding to ACE2 through conformational selection.Nature nanotechnology · 2025Article
- Charge distribution and helicity tune the binding of septin's amphipathic helix domain to membranes.Biophysical journal · 2025Article
- The Compensatory Effect of S375F on S371F Is Vital for Maintaining the Infectivity of SARS-CoV-2 Omicron Variants.Journal of medical virology · 2025Article
- Structural Immunology of SARS-CoV-2.Immunological reviews · 2025Review
- End-to-end Training of Latent Space Diffusion Models for Conformational Heterogeneity in Cryo-EM Reconstruction.International Conference Image and Vision Computing New Zealand : [proceedings]. International Conference Image and Vision Computing New Zealand · 2024Article
- Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach.Journal of chemical theory and computation · 2024Article
- Testing the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein.Biophysical journal · 2024Article
- Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2.Journal of nanobiotechnology · 2024Article
- Evolution of the SARS-CoV-2 Omicron spike.Cell reports · 2023Review
- Mutations in S2 subunit of SARS-CoV-2 Omicron spike strongly influence its conformation, fusogenicity, and neutralization sensitivity.Journal of virology · 2023Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Omicron BA.1 is a highly infectious variant of SARS-CoV-2 that carries more than thirty mutations on the spike protein in comparison to the Wuhan wild type (WT). Some of the Omicron mutations, located on the receptor-binding domain (RBD), are exposed to the surrounding solvent and are known to help evade immunity. However, the impact of buried mutations on the RBD conformations and on the mechanics of the spike opening is less evident. Here, we use all-atom molecular dynamics (MD) simulations with metadynamics to characterize the thermodynamic RBD-opening ensemble, identifying significant differences between WT and Omicron. Specifically, the Omicron mutations S371L, S373P, and S375F make more RBD interdomain contacts during the spike's opening. Moreover, Omicron takes longer to reach the transition state than WT. It stabilizes up-state conformations with fewer RBD epitopes exposed to the solvent, potentially favoring immune or antibody evasion.
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