Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2

Priya Antony, Amie Jobe, Ranjit Vijayan

Research output: Contribution to journalArticlepeer-review

Abstract

Background: The COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions. Methods: To gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein’s receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics—generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant. Results: Though mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex.

Original languageEnglish
Article numbere13680
JournalPeerJ Computer Science
Volume10
DOIs
Publication statusPublished - 2022

Keywords

  • Angiotensin-converting enzyme 2
  • B.1.1.529
  • Molecular dynamics
  • Omicron
  • Sars-cov-2
  • Spike protein

ASJC Scopus subject areas

  • Computer Science(all)

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