Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop

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Both experimental and theoretical structure determinations of RNAs have remained challenging due to the intrinsic dynamics of RNAs. We report here an integrated nuclear magnetic resonance/molecular dynamics (NMR/MD) structure determination approach to describe the dynamic structure of the CUUG tetraloop. We show that the tetraloop undergoes substantial dynamics, leading to averaging of the experimental data. These dynamics are particularly linked to the temperature-dependent presence of a hydrogen bond within the tetraloop. Interpreting the NMR data by a single structure represents the low-temperature structure well but fails to capture all conformational states occurring at a higher temperature. We integrate MD simulations, starting from structures of CUUG tetraloops within the Protein Data Bank, with an extensive set of NMR data, and provide a structural ensemble that describes the dynamic nature of the tetraloop and the experimental NMR data well. We thus show that one of the most stable and frequently found RNA tetraloops displays substantial dynamics, warranting such an integrated structural approach.
OriginalsprogEngelsk
TidsskriftJournal of the American Chemical Society
Vol/bind145
Udgave nummer30
Sider (fra-til)16557-16572
Antal sider16
ISSN0002-7863
DOI
StatusUdgivet - 2023

Bibliografisk note

Funding Information:
This work was supported by DFG collaborative research center 902: Molecular principles of RNA-based regulation and the EU horizon program iNEXT-discovery. R.S. was supported by the Fonds der Chemischen Industrie. Work at BMRZ was supported by the state of Hesse. This research was also supported by the Lundbeck Foundation BRAINSTRUC initiative in structural biology (R155-2015-2666 to K.L.-L.). The authors also acknowledge access to computational resources from the ROBUST Resource for Biomolecular Simulations (supported by the Novo Nordisk Foundation; NNF18OC0032608) and Biocomputing Core Facility at the Department of Biology, University of Copenhagen. Funding for open access charge: institutional funds.

Publisher Copyright:
© 2023 The Authors. Published by American Chemical Society.

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