Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations

The 5? untranslated region (UTR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is a conserved, functional and structured genomic consisting several RNA stem-loop elements. While secondary structure such elements has been determined experimentally, their three-dimensional structures are not known yet. Here, we predict dynamics five stem loops in 5?-UTR SARS-CoV-2 by extensive atomistic molecular simulations, more than 0.5 ms aggregate simulation time, combination with enhanced sampling techniques. We compare simulations available experimental data, describe resulting conformational ensembles, identify presence specific structural rearrangements apical internal that may be functionally relevant. Our atomic-detailed predictions reveal rich these molecules, could help characterization systems, provide putative models for structure-based drug design studies.