https://orcid.org/0000-0003-0753-3259
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Abstract
Mutations drive viral evolution and genome variability that causes viruses to escape host immunity and to develop drug resistance. SARS-CoV-2 has considerably higher mutation rate. SARS-CoV-2 possesses a RNA dependent RNA polymerase (RdRp) which helps to replicate its genome. The mutation P323L in RdRp is associated with the loss of a particular epitope (321-327) from this protein. We consider the effects of mutations in some of the epitope region including the naturally occurring mutation P323L on the structure of the epitope and their interface with paratope using all-atom molecular dynamics (MD) simulation studies. We observe that the mutations cause conformational changes in the epitope region by opening up the region associated with increase in the radius of gyration and intramolecular hydrogen bonds, making the region less accessible. Moreover, we study the conformational stability of the epitope region and epitope:paratope interface under the mutation from the fluctuations in the dihedral angles. We observe that the mutation renders the epitope and the epitope:paratope interface unstable compared to the corresponding wild type ones. Thus, the mutations may help in escaping antibody mediated immunity of the host
Communicated by Ramaswamy H. Sarma
Acknowledgements
AMG is thankful to the Technology Research Centre, S.N. Bose National Centre for Basic Sciences, Kolkata for the computational facilities.
Disclosure statement
No potential conflict of interest was reported by the authors.
Author contributions
AMG curate analyzed and interpreted the data and wrote the manuscript. SCM helped in writing the codes. SM reviewed and edited the manuscript. JC interpreted the data, reviewed and edited the manuscript.