Molecular dynamics simulations of the flexibility and inhibition of SARS-CoV-2 NSP 13 helicase

Bryan A Raubenolt; Naeyma N Islam; Christoper M Summa; Steven W Rick

doi:10.1016/j.jmgm.2022.108122

Molecular dynamics simulations of the flexibility and inhibition of SARS-CoV-2 NSP 13 helicase

J Mol Graph Model. 2022 May:112:108122. doi: 10.1016/j.jmgm.2022.108122. Epub 2022 Jan 5.

Authors

Bryan A Raubenolt¹, Naeyma N Islam¹, Christoper M Summa², Steven W Rick³

Affiliations

¹ Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA.
² Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA.
³ Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA. Electronic address: srick@uno.edu.

Abstract

The helicase protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is both a good potential drug target and very flexible. The flexibility, and therefore its function, could be reduced through knowledge of these motions and identification of allosteric pockets. Using molecular dynamics simulations with enhanced sampling, we determined key modes of motion and sites on the protein that are at the interface between flexible domains of the proteins. We developed an approach to map the principal components of motion onto the surface of a potential binding pocket to help in the identification of allosteric sites.

Publication types

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

MeSH terms

Binding Sites
COVID-19*
Humans
Molecular Dynamics Simulation
Protein Binding
SARS-CoV-2*