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Although it is known that SARS-CoV-2\u2019s own RNA evades nsp1\u2019s host translation shutoff, the molecular mechanism underlying the evasion was poorly understood. We performed an extended ensemble molecular dynamics simulation to investigate the mechanism of the viral RNA evasion. Simulation results suggested that the stem loop structure of the SARS-CoV-2 RNA 5\u2019-untranslated region (SL1) binds to both nsp1\u2019s N-terminal globular region and intrinsically disordered region. The consistency of the results was assessed by modeling nsp1-40\n                    <jats:italic>S<\/jats:italic>\n                    ribosome structure based on reported nsp1 experiments, including the X-ray crystallographic structure analysis, the cryo-EM electron density map, and cross-linking experiments. The SL1 binding region predicted from the simulation was open to the solvent, yet the ribosome could interact with SL1. Cluster analysis of the binding mode and detailed analysis of the binding poses suggest residues Arg124, Lys47, Arg43, and Asn126 may be involved in the SL1 recognition mechanism, consistent with the existing mutational analysis.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1009804","type":"journal-article","created":{"date-parts":[[2022,1,19]],"date-time":"2022-01-19T13:36:10Z","timestamp":1642599370000},"page":"e1009804","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Extended ensemble simulations of a SARS-CoV-2 nsp1\u20135\u2019-UTR 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