ArticleMethods (San Diego, Calif.)2009
Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.
Article in Methods (San Diego, Calif.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Synthesis, Characterization, and Nanodisc Formation of Non-ionic Polymers*.Angewandte Chemie (International ed. in English) · 2021Article
- Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion.Biophysical journal · 2021Article
- Natural-abundanceChemical communications (Cambridge, England) · 2020Article
- Information content of long-range NMR data for the characterization of conformational heterogeneity.Journal of biomolecular NMR · 2015Article
- Slowdown of Interhelical Motions Induces a Glass Transition in RNA.Biophysical journal · 2015Article
- Advances in the determination of nucleic acid conformational ensembles.Annual review of physical chemistry · 2014Review
- NMR studies of nucleic acid dynamics.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2013Article
- Advances in the REDCAT software package.BMC bioinformatics · 2013Article
- Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.Molecules (Basel, Switzerland) · 2013Article
- Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods.Journal of biomolecular NMR · 2013Article
- Imino hydrogen positions in nucleic acids from density functional theory validated by NMR residual dipolar couplings.Journal of the American Chemical Society · 2012Article
- Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings.Journal of chemical theory and computation · 2011Article
- Theory of nonrigid rotational motion applied to NMR relaxation in RNA.The journal of physical chemistry. A · 2011Article
- Constructing ensembles for intrinsically disordered proteins.Current opinion in structural biology · 2011Review
- Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.Current opinion in structural biology · 2011Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
A broad structural landscape often needs to be characterized in order to fully understand how regulatory RNAs perform their biological functions at the atomic level. We present a protocol for visualizing thermally accessible RNA conformations at atomic-resolution and with timescales extending up to milliseconds. The protocol combines molecular dynamics (MD) simulations with experimental residual dipolar couplings (RDCs) measured in partially aligned (13)C/(15)N isotopically enriched elongated RNA samples. The structural ensembles generated in this manner provide insights into RNA dynamics and its role in functionally important transitions.
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