Integrating experimental data with molecular simulations to investigate RNA structural dynamics

TL;DR

This paper reviews how combining experimental techniques with molecular dynamics simulations enhances understanding of RNA structural dynamics, enabling validation, refinement, and force field improvements.

Contribution

It provides a comprehensive overview of recent advances in integrating experimental data with MD simulations to study RNA dynamics.

Findings

Experimental data validate MD simulations.

Data refinement improves structural ensembles.

Enhanced force fields transfer to new systems.

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 F\"orster 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.