Integrating experimental data with molecular simulations to investigate RNA structural dynamics.

Autor: Bernetti M; Computational and Chemical Biology, Italian Institute of Technology, 16152 Genova, Italy; Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy., Bussi G; Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136, Trieste, Italy. Electronic address: bussi@sissa.it.
Jazyk: angličtina
Zdroj: Current opinion in structural biology [Curr Opin Struct Biol] 2023 Feb; Vol. 78, pp. 102503. Date of Electronic Publication: 2022 Dec 01.
DOI: 10.1016/j.sbi.2022.102503
Abstrakt: Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule Förster resonance energy transfer, or even thermal or mechanical denaturation experiments probe RNA dynamics at different time and space resolutions. Their combination with accurate atomistic molecular dynamics (MD) simulations paves the way for quantitative and detailed studies of RNA dynamics. First, experiments provide a quantitative validation tool for MD simulations. Second, available data can be used to refine simulated structural ensembles to match experiments. Finally, comparison with experiments allows for improving MD force fields that are transferable to new systems for which data is not available. Here we review the recent literature and provide our perspective on this field.
Competing Interests: Conflict of interest statement Nothing declared.
(Copyright © 2022 Elsevier Ltd. All rights reserved.)
Databáze: MEDLINE
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