Computational saturation mutagenesis to predict the effects of systematic mutations on the stability and binding affinity of nonstructural proteins ۷ and ۸ in SARS-CoV-۲

The replication of severe acute respiratory syndrome coronavirus ۲ (SARS-CoV-۲) is mediated by proteinproteininteractions of nonstructural proteins (nsps) and nsp-viral RNAs. The central component ofreplication machinery in SARS-CoV-۲ is nsp۱۲ with RNA-dependent RNA polymerase (RdRp) activity thatcatalyzes the synthesis of viral RNAs. Nsp۷ and nsp۸ as cofactors of RdRp play vital roles in stimulating thepolymerase activity of RdRp and promoting its processivity. In this study, we analyzed the effects of allpossible mutations (a total of ۳۷۲۴ mutations) generated by the computational saturation mutagenesis of allresidues in nsp۷ and nsp۸ proteins of SARS-CoV-۲ to all other ۱۹ residues on the stability of proteins andprotein-protein binding affinity. mCSM-PPI۲ server was used to predict the effects of missense mutations onnsp۷-nsp۸ binding affinity. The impacts of the generated systematic mutations on stability and flexibility ofinvestigated proteins were predicted by structure-based prediction tools including DynaMut, mCSM, SDM,and CUPSAT servers as well as PROVEAN and I-Mutant ۲.۰ as sequence-based prediction tools. ConSurfwas used for analyzing the evolutionary conservation of the residues. A significant majority of mutationshave the potential to destabilize the interaction of nsp۷ and nsp۸. K۲P, M۵۲D, and L۵۶G mutations in nsp۷and L۱۰۸D, I۱۱۱D, and L۹۶D mutations in nsp۸ were predicted to significantly decrease the nsp۷-nsp۸binding affinity. Mutations in highly conserved interface residues of nsp۷-nsp۸ were predicted toconsiderably decrease the stability and flexibility of proteins. This study provides comprehensive insightsinto the consequences of mutations in nsp۷ and nsp۸ proteins with importance in antiviral design anddevelopment for COVID-۱۹ or future possible outbreaks related to coronaviruses.

کلیدواژه ها:

SARS-CoV-۲ ، nsp۷-nsp۸ ، Computational Saturation mutagenesis ، COVID-۱۹ ، Missense mutation