A Preliminary Investigation in the Molecular Basis of Host Shutoff Mechanism in SARS-CoV

Pandala, Niharika; Cole, Casey A.; McFarland, Devaun; Nag, Anita; Columbia, Homayoun Valafar University of South Carolina; Upstate, University of South Carolina

Recent events leading to the worldwide pandemic of COVID-19 have demonstrated the effective use of genomic sequencing technologies to establish the genetic sequence of this virus. In contrast, the COVID-19 pandemic has demonstrated the absence of computational approaches to understand the molecular basis of this infection rapidly. Here we present an integrated approach to the study of the nsp1 protein in SARS-CoV-1, which plays an essential role in maintaining the expression of viral proteins and further disabling the host protein expression, also known as the host shutoff mechanism. We present three independent methods of evaluating two potential binding sites speculated to participate in host shutoff by nsp1. We have combined results from computed models of nsp1, with deep mining of all existing protein structures (using PDBMine), and binding site recognition (using msTALI) to examine the two sites consisting of residues 55-59 and 73-80. Based on our preliminary results, we conclude that the residues 73-80 appear as the regions that facilitate the critical initial steps in the function of nsp1. Given the 90% sequence identity between nsp1 from SARS-CoV-1 and SARS-CoV-2, we conjecture the same critical initiation step in the function of COVID-19 nsp1.