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Integrating experimental data with molecular simulations to investigate RNA structural dynamics

Bernetti, Mattia
•
Bussi, Giovanni
2023
  • journal article

Periodico
CURRENT OPINION IN STRUCTURAL BIOLOGY
Abstract
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.
DOI
10.1016/j.sbi.2022.102503
WOS
WOS:000974483700001
Archivio
https://hdl.handle.net/20.500.11767/130351
info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85143494182
https://arxiv.org/abs/2207.08622
Diritti
open access
Soggetti
  • RNA

  • Molecular dynamics si...

  • Solution experiments

  • Settore FIS/03 - Fisi...

  • Settore PHYS-04/A - F...

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