ArticleNucleic acids research2014
Characterizing RNA ensembles from NMR data with kinematic models.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.Current opinion in structural biology · 2021Review
- Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion.Biophysical journal · 2021Article
- Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.Biochemistry · 2016Article
- Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data.Journal of computational biology : a journal of computational molecular cell biology · 2016Article
- Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.PLoS computational biology · 2015Article
- Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations.Journal of the mechanics and physics of solids · 2015Article
- Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs.PLoS computational biology · 2015Article
- Integrative, dynamic structural biology at atomic resolution--it's about time.Nature methods · 2015Review
- GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.PloS one · 2015Article
- Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities.PloS one · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem-loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention.
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