Molecular dynamics and intrinsic disorder analysis of the SARS-CoV-2 Nsp1 structural changes caused by substitution and deletion mutations.

SARS-CoV-2 non-structural protein 1 (Nsp1) is a virulence factor that inhibits the translation of host mRNAs and interacts with viral RNA. To date, hundreds of mutations (base substitutions, deletions, and insertions) have been reported in SARS-CoV-2 Nsp1. Despite the relevance of Nsp1, a few studies have been conducted to understand the effect of those mutations on Nsp1 structure and function. In this study, the effects of the most frequent mutations were investigated using molecular dynamics simulations. We found that several mutations profoundly affect the local intrinsic disorder predisposition, with most deletions increasing disorder propensity and replacement mutations inducing variable effects. We found that deletions Δ80–90 and Δ156–158 destabilise the protein structure. For example, the Δ156–158 cause a higher root-mean-square deviation (RMSD) and Rg values than those of the wild-type of SARS-CoV-2 Nsp1. We also found that the SARS-CoV-2 Nsp1 is slightly more disordered than its counterpart from SARS-CoV. A better understanding of the complexity and dynamic nature of interactions between intrinsically disordered segments of Nsp1 and ribosome subunits might help develop novel therapeutic countermeasures against the SARS-CoV-2 variants. Highlights Multiple mutations have been found in the N/C-termini of the SARS-CoV-2 Nsp1. The effects of deletions are greater than substitutions on SARS-CoV-2 Nsp1. Δ80–90 and Δ156–158 destabilise the protein structure and may increase the SARS-CoV-2 virulence. F157S, E159D, L173P, and R175H mutations affect the structure of the SARS-CoV-2 Nsp1 and may cause increased infectivity. The most disorder-promoting mutations were F157L and M174 K, whereas E159D and E159 K were the most order-promoting. [ABSTRACT FROM AUTHOR]