ArticleThe journal of physical chemistry. B2014
Elucidating molecular motion through structural and dynamic filters of energy-minimized conformer ensembles.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.Nucleic acids research · 2017Article
- Ultraslow Domain Motions in HIV-1 TAR RNA Revealed by Solid-State Deuterium NMR.The journal of physical chemistry. B · 2017Article
- RNA folding pathways in stop motion.Nucleic acids research · 2016Article
- Integrative, dynamic structural biology at atomic resolution--it's about time.Nature methods · 2015Review
- NMR studies of dynamic biomolecular conformational ensembles.Progress in nuclear magnetic resonance spectroscopy · 2015Review
- Characterizing RNA ensembles from NMR data with kinematic models.Nucleic acids research · 2014Article
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Authors and funding
6 authors.
Funding
Abstract
Complex RNA structures are constructed from helical segments connected by flexible loops that move spontaneously and in response to binding of small molecule ligands and proteins. Understanding the conformational variability of RNA requires the characterization of the coupled time evolution of interconnected flexible domains. To elucidate the collective molecular motions and explore the conformational landscape of the HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized structures generated by the program "Fragment Assembly of RNA with Full-Atom Refinement (FARFAR)". We apply structural filters in the form of experimental residual dipolar couplings (RDCs) to select a subset of discrete energy-minimized conformers and carry out principal component analyses (PCA) to corroborate the choice of the filtered subset. We use this subset of structures to calculate solution T1 and T(1ρ) relaxation times for (13)C spins in multiple residues in different domains of the molecule using two simulation protocols that we previously published. We match the experimental T1 times to within 2% and the T(1ρ) times to within less than 10% for helical residues. These results introduce a protocol to construct viable dynamic trajectories for RNA molecules that accord well with experimental NMR data and support the notion that the motions of the helical portions of this small RNA can be described by a relatively small number of discrete conformations exchanging over time scales longer than 1 μs.
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Registered trials
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