ArticleNucleic acids research2020
Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Perspective - RNA Dynamics Today and Tomorrow.Journal of molecular biology · 2026Review
- Advances in Methods for Accurate Prediction of RNA-Small Molecule Binding Sites: From Isolated to AI-Integrated Strategies.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Internal ribosome entry sites enhance translation in trans in antisense non-coding SINEUP and circular RNAs.Nucleic acids research · 2025Article
- Structural heterogeneity and dynamics in the apical stem loop of s2m from SARS-CoV-2 Delta by an integrative NMR spectroscopy and MD simulation approach.Nucleic acids research · 2025Article
- Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems.Journal of chemical theory and computation · 2025Article
- Mechanistic insights into ASO-RNA complexation: Advancing antisense oligonucleotide design strategies.Molecular therapy. Nucleic acids · 2024Article
- RNA binding tunes the conformational plasticity and intradomain stability of TDP-43 tandem RNA recognition motifs.Biophysical journal · 2024Article
- Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation.Nature communications · 2024Article
- Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM.Nucleic acids research · 2023Article
- Decoding the dual recognition mechanism of the glucocorticoid receptor for DNA and RNA: sequence versus shape.Scientific reports · 2023Article
- Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments.RNA (New York, N.Y.) · 2022Article
- Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.Journal of chemical theory and computation · 2022Article
- Visualizing RNA Structures by SAXS-Driven MD Simulations.Frontiers in bioinformatics · 2022Article
- SINEUPs: a novel toolbox for RNA therapeutics.Essays in biochemistry · 2021Review
- Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.Current opinion in structural biology · 2021Review
- Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles.Nucleic acids research · 2021Article
- Data-Driven Molecular Dynamics: A Multifaceted Challenge.Pharmaceuticals (Basel, Switzerland) · 2020Review
- Integrating NMR and simulations reveals motions in the UUCG tetraloop.Nucleic acids research · 2020Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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