ArticleRNA (New York, N.Y.)2015
Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
16 citing papers in PubMed.
- Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.Nucleic acids research · 2023Article
- Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.Molecules (Basel, Switzerland) · 2022Article
- Using quantum chemistry to estimate chemical shifts in biomolecules.Biophysical chemistry · 2020Review
- Using All-Atom Potentials to Refine RNA Structure Predictions of SARS-CoV-2 Stem Loops.International journal of molecular sciences · 2020Article
- Integrating NMR and simulations reveals motions in the UUCG tetraloop.Nucleic acids research · 2020Article
- Maximizing accuracy of RNA structure in refinement against residual dipolar couplings.Journal of biomolecular NMR · 2019Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints.Communications biology · 2018Article
- MgBiophysical journal · 2017Article
- RNA structure refinement using NMR solvent accessibility data.Scientific reports · 2017Article
- Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.Physical chemistry chemical physics : PCCP · 2017Article
- Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs.Nucleic acids research · 2016Article
- RNA folding pathways in stop motion.Nucleic acids research · 2016Article
- VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.The Journal of chemical physics · 2016Article
- Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.Journal of the American Chemical Society · 2015Article
- Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.RNA (New York, N.Y.) · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
RNA hairpins are widespread and very stable motifs that contribute decisively to RNA folding and biological function. The GTP1G2C3A4C5U6U7C8G9G10U11G12C13C14 construct (with a central UUCG tetraloop) has been extensively studied by solution NMR, and offers and excellent opportunity to evaluate the structure and dynamical description afforded by molecular dynamics (MD) simulations. Here, we compare average structural parameters and NMR relaxation rates estimated from a series of multiple independent explicit solvent MD simulations using the two most recent RNA AMBER force fields (ff99 and ff10). Predicted overall tumbling times are ∼20% faster than those inferred from analysis of NMR data and follow the same trend when temperature and ionic strength is varied. The Watson-Crick stem and the "canonical" UUCG loop structure are maintained in most simulations including the characteristic syn conformation along the glycosidic bond of G9, although some key hydrogen bonds in the loop are partially disrupted. Our analysis pinpoints G9-G10 backbone conformations as a locus of discrepancies between experiment and simulation. In general the results for the more recent force-field parameters (ff10) are closer to experiment than those for the older ones (ff99). This work provides a comprehensive and detailed comparison of state of the art MD simulations against a wide variety of solution NMR measurements.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.