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• W3080783844 endingPage "1766" @default.
• W3080783844 startingPage "1755" @default.
• W3080783844 abstract "Ribonucleic acids (RNAs) play essential roles in living cells. Many of them fold into defined three-dimensional (3D) structures to perform functions. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have enabled structure determinations of RNA to atomic resolutions. However, most RNA molecules are structurally flexible, limiting the resolution of their structures solved by cryo-EM. In modeling these molecules, several computational methods are limited by the requirement of massive computational resources and/or the low efficiency in exploring large-scale structural variations. Here we use hierarchical natural move Monte Carlo (HNMMC), which takes advantage of collective motions for groups of nucleic acid residues, to refine RNA structures into their cryo-EM maps, preserving atomic details in the models. After validating the method on a simulated density map of tRNA, we applied it to objectively obtain the model of the folding intermediate for the specificity domain of ribonuclease P from Bacillus subtilis and refine a flexible ribosomal RNA (rRNA) expansion segment from the Mycobacterium tuberculosis (Mtb) ribosome in different conformational states. Finally, we used HNMMC to model atomic details and flexibility for two distinct conformations of the complete genomic RNA (gRNA) inside MS2, a single-stranded RNA virus, revealing multiple pathways for its capsid assembly." @default.
• W3080783844 created "2020-09-01" @default.
• W3080783844 creator A5009642414 @default.
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• W3080783844 creator A5075861212 @default.
• W3080783844 creator A5086525063 @default.
• W3080783844 date "2020-08-21" @default.
• W3080783844 modified "2023-10-16" @default.
• W3080783844 title "Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities" @default.
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• W3080783844 doi "https://doi.org/10.1261/rna.071100.119" @default.
• W3080783844 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/7668250" @default.

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