Extended ensemble simulations of a SARS-CoV-2 nsp1–5’-UTR complex

Non-structural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 180-residue protein which blocks the translation of SARS-CoV-2 infected cells. Although it has been known that SARS-CoV-2's own RNA evades nsp1's host translation shutoff, its molecular mechanism has been poorly understood. We performed an extended ensemble molecular dynamics simulation to investigate the mechanism of the viral RNA evasion. Simulation results showed that the stem loop structure of SARS-CoV-2 RNA 5'-untranslated region is recognized by both nsp1's globular region and intrinsically disordered region.