9sy4

NMR structure determination of a dynamic and thermodynamically stable CUUG RNA tetraloop without restrained loop base pair

spinqualitylabelsall models 9sy4 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9sy4 is a 1 chain structure with sequence from Synthetic RNA. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Solution NMR, 10 models Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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. Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop.,Oxenfarth A, Kummerer F, Bottaro S, Schnieders R, Pinter G, Jonker HRA, Furtig B, Richter C, Blackledge M, Lindorff-Larsen K, Schwalbe H J Am Chem Soc. 2023 Aug 2;145(30):16557-16572. doi: 10.1021/jacs.3c03578. Epub , 2023 Jul 21. PMID:37479220 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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