Viruses, Volume 12, Issue 10
October 2020 - 144 articles
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Cover Story: Viral RNAs are shapeshifters. Rather than being trapped in one conformation, dynamic assemblies of metastable tertiary conformations carry-out the replication events and evade the host defense mechanisms. The conformational space of large RNAs is immense, even for supercomputers (α1.8N, N=nucleotides, nt) but herein, is winnowed down using secondary structure data gathered on individual viral RNA motifs. Experimentally-determined input constraints, theoretical metastable pairings, and 300 million iterations by the SimRNA algorithm were sufficient to classify major dynamic ensembles of an HIV 5’-untranslated region. The simulations predict dynamical equilibrium around the 5’-cap that is governed by metastable nt–nt pairings. View this paper