Computer Simulation of the interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals

Abstract

ABSTRACTA prominent feature of the SARS-CoV-2 virus is the presence of a large glycoprotein spike protruding from the virus envelope. The spike determines the interaction of the virus with the environment and the host. Here, we used an all-atom molecular dynamics simulation method to investigate the interaction of up and down conformations of the S1 subunit of the SARS-CoV-2 spike with the (100) surface of Au, Ag and Cu. Our results revealed that the spike protein is adsorbed onto the surface of these metals, being Cu the metal with the highest interaction with the spike. In our simulations, we considered the spike protein in both its up conformation Sup(one receptor binding domain exposed) and down conformation Sdown(no exposed receptor binding domain). We found that the affinity of the metals for the up conformation was higher than their affinity for the down conformation. The structural changes in the Spike in the up conformation were also larger than the changes in the down conformation. Comparing the present results for metals with those obtained in our previous MD simulations of Supwith other materials (celulose, graphite, and human skin models), we see that Au induces the highest structural change in Sup, larger than those obtained in our previous studies.GRAPHICAL ABSTRACT