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

https://doi.org/10.1016/j.jmgm.2022.108122Get rights and content

Highlights

  • Molecular dynamics with advanced sampling reveals large scale motion of the SARS-CoV-2 NSP 13 helicase.

  • A method is presented that maps the major domain motion as indicated from principal component analysis onto binding pocket surfaces.

  • The analysis of the domain motion reveals potential allosteric sites.

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.

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