Mutation Effects on Structure and Dynamics: Adaptive Evolution of the SARS-CoV-2 Main Protease

The main protease of SARS-CoV-2 (M^pro) plays a critical role in viral replication; although it is relatively conserved, M^pro has nevertheless evolved over the course of the COVID-19 pandemic. Here, we examine phenotypic changes in clinically observed variants of M^pro, relative to the originally reported wild-type enzyme. Using atomistic molecular dynamics simulations, we examine effects of mutation on protein structure and dynamics. In addition to basic structural properties such as variation in surface area and torsion angles, we use protein structure networks and active site networks to evaluate functionally relevant characters related to global cohesion and active site constraint. Substitution analysis shows a continuing trend toward more hydrophobic residues that are dependent on the location of the residue in primary, secondary, tertiary, and quaternary structures. Phylogenetic analysis provides additional evidence for the impact of selective pressure on mutation of M^pro. Overall, these analyses suggest evolutionary adaptation of M^pro toward more hydrophobicity and a less-constrained active site in response to the selective pressures of a novel host environment.