Structural dynamics of COVID-19 main protease

Based on the importance of protease enzymes in functioning some viruses particularly coronaviridae, we have carried out an in silico investigation on the biologically important, yet unmapped phenomenon of activity and internal dynamics of COVID-19 main protease (M^pro) via applying finite-temperature all-atom molecular dynamics simulations. Temperature quench echoes generated by applying two successive cooling signals have therefore been analyzed in terms of the temperature-temperature correlation function of the protease within the harmonic approximation. An exponentially decaying brand of behavior has been found for the calculated echo depth values with increasing time, which has accordingly led to a much small dephasing time of about 150 fs, revealing a significant anharmonicity and therefore an overall structural stiffness for the COVID-19 main protease.

Keywords: COVID-19 main protease; Internal dynamics; Normal modes.