ArticleNucleic acids research2009
Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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69 citing papers in PubMed, 118 citations in OpenAlex.
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- Virtual Screening of Hepatitis B Virus Pre-Genomic RNA as a Novel Therapeutic Target.Molecules (Basel, Switzerland) · 2023Article
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- Targeting RNA structures with small molecules.Nature reviews. Drug discovery · 2022Review
- Mining for Ligandable Cavities in RNA.ACS medicinal chemistry letters · 2021Article
- The structural plasticity of nucleic acid duplexes revealed by WAXS and MD.Science advances · 2021Article
- Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion.Biophysical journal · 2021Article
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- Targeting RNA structures in diseases with small molecules.Essays in biochemistry · 2020Review
- Target-Directed Approaches for Screening Small Molecules against RNA Targets.SLAS discovery : advancing life sciences R & D · 2020Review
- Exposing Hidden High-Affinity RNA Conformational States.Journal of the American Chemical Society · 2020Article
- Enhancing NMR derived ensembles with kinetics on multiple timescales.Journal of biomolecular NMR · 2020Article
- Salt Dependence of A-Form RNA Duplexes: Structures and Implications.The journal of physical chemistry. B · 2019Article
- Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The roles of structural dynamics in the cellular functions of RNAs.Nature reviews. Molecular cell biology · 2019Review
9 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
We describe a strategy for constructing atomic resolution dynamical ensembles of RNA molecules, spanning up to millisecond timescales, that combines molecular dynamics (MD) simulations with NMR residual dipolar couplings (RDC) measured in elongated RNA. The ensembles are generated via a Monte Carlo procedure by selecting snap-shot from an MD trajectory that reproduce experimentally measured RDCs. Using this approach, we construct ensembles for two variants of the transactivation response element (TAR) containing three (HIV-1) and two (HIV-2) nucleotide bulges. The HIV-1 TAR ensemble reveals significant mobility in bulge residues C24 and U25 and to a lesser extent U23 and neighboring helical residue A22 that give rise to large amplitude spatially correlated twisting and bending helical motions. Omission of bulge residue C24 in HIV-2 TAR leads to a significant reduction in both the local mobility in and around the bulge and amplitude of inter-helical bending motions. In contrast, twisting motions of the helices remain comparable in amplitude to HIV-1 TAR and spatial correlations between them increase significantly. Comparison of the HIV-1 TAR dynamical ensemble and ligand bound TAR conformations reveals that several features of the binding pocket and global conformation are dynamically preformed, providing support for adaptive recognition via a 'conformational selection' type mechanism.
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