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• W2998235890 abstract "Abstract Solution nuclear magnetic resonance (NMR) experiments allow RNA dynamics to be determined in an aqueous environment. However, when a limited number of peaks are assigned, it is difficult to obtain structural information. We here show a protocol based on the combination of experimental data (Nuclear Overhauser Effect, NOE) and molecular dynamics simulations with enhanced sampling methods. This protocol allows to (a) obtain a maximum entropy ensemble compatible with NMR restraints and (b) obtain a minimal set of metastable conformations compatible with the experimental data (maximum parsimony). The method is applied to a hairpin of 29 nt from an inverted SINEB2, which is part of the SINEUP family and has been shown to enhance protein translation. A clustering procedure is introduced where the annotation of base-base interactions and glycosidic bond angles is used as a metric. By reweighting the contributions of the clusters, minimal sets of four conformations could be found which are compatible with the experimental data. A motif search on the structural database showed that some identified low-population states are present in experimental structures of other RNA transcripts. The introduced method can be applied to characterize RNA dynamics in systems where a limited amount of NMR information is available." @default.
• W2998235890 created "2020-01-10" @default.
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• W2998235890 date "2019-12-31" @default.
• W2998235890 modified "2023-10-14" @default.
• W2998235890 title "Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data" @default.
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• W2998235890 doi "https://doi.org/10.1093/nar/gkz1184" @default.
• W2998235890 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/7026608" @default.
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• W2998235890 hasPublicationYear "2019" @default.
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