Scanning the RBD-ACE2 molecular interactions in Omicron variant

Soumya Lipsa Rath; Aditya K Padhi; Nabanita Mandal

doi:10.1016/j.bbrc.2022.01.006

Scanning the RBD-ACE2 molecular interactions in Omicron variant

Biochem Biophys Res Commun. 2022 Feb 12:592:18-23. doi: 10.1016/j.bbrc.2022.01.006. Epub 2022 Jan 6.

Authors

Soumya Lipsa Rath¹, Aditya K Padhi², Nabanita Mandal³

Affiliations

¹ National Institute of Technology, Warangal, Telangana, 506004, India. Electronic address: slrath@nitw.ac.in.
² Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
³ National Institute of Technology, Warangal, Telangana, 506004, India.

Abstract

The emergence of new SARS-CoV-2 variants poses a threat to the human population where it is difficult to assess the severity of a particular variant of the virus. Spike protein and specifically its receptor binding domain (RBD) which makes direct interaction with the ACE2 receptor of the human has shown prominent amino acid substitutions in most of the Variants of Concern. Here, by using all-atom molecular dynamics simulations we compare the interaction of Wild-type RBD/ACE2 receptor complex with that of the latest Omicron variant of the virus. We observed a very interesting diversification of the charge, dynamics and energetics of the protein complex formed upon mutations. These results would help us in understanding the molecular basis of binding of the Omicron variant with that of SARS-CoV-2 Wild-type.

Keywords: Covid19; Molecular dynamics; SARS-CoV-2; Variants.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Amino Acid Substitution
Angiotensin-Converting Enzyme 2 / chemistry*
Angiotensin-Converting Enzyme 2 / metabolism*
COVID-19 / metabolism*
COVID-19 / virology*
Host Microbial Interactions / genetics
Host Microbial Interactions / physiology
Humans
Molecular Dynamics Simulation
Pandemics
Protein Binding
Protein Interaction Domains and Motifs
SARS-CoV-2 / chemistry*
SARS-CoV-2 / genetics
SARS-CoV-2 / metabolism*
Spike Glycoprotein, Coronavirus / chemistry*
Spike Glycoprotein, Coronavirus / genetics
Spike Glycoprotein, Coronavirus / metabolism*
Static Electricity

Substances

Spike Glycoprotein, Coronavirus
spike protein, SARS-CoV-2
ACE2 protein, human
Angiotensin-Converting Enzyme 2

Supplementary concepts

SARS-CoV-2 variants