ArticleJournal of the American Chemical Society2009
Toward a unified representation of protein structural dynamics in solution.
Article in Journal of the American Chemical Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 105 citations in OpenAlex.
- Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles.Nature biotechnology · 2026Article
- NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins.Chemical reviews · 2022Review
- Article
- Applications of NMR and computational methodologies to study protein dynamics.Archives of biochemistry and biophysics · 2017Review
- Insights into Coupled Folding and Binding Mechanisms from Kinetic Studies.The Journal of biological chemistry · 2016Review
- Allosteric switch regulates protein-protein binding through collective motion.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations.Frontiers in molecular biosciences · 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
- Relating sequence encoded information to form and function of intrinsically disordered proteins.Current opinion in structural biology · 2015Review
- A minor conformation of a lanthanide tag on adenylate kinase characterized by paramagnetic relaxation dispersion NMR spectroscopy.Journal of biomolecular NMR · 2015Article
- NMR studies of dynamic biomolecular conformational ensembles.Progress in nuclear magnetic resonance spectroscopy · 2015Review
- Enhancing the quality of protein conformation ensembles with relative populations.Journal of biomolecular NMR · 2014Article
- Article
- Advances in the determination of nucleic acid conformational ensembles.Annual review of physical chemistry · 2014Review
- Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry.Journal of the American Chemical Society · 2013Article
- Measuring dynamic and kinetic information in the previously inaccessible supra-τ(c) window of nanoseconds to microseconds by solution NMR spectroscopy.Molecules (Basel, Switzerland) · 2013Review
- Ensemble-based interpretations of NMR structural data to describe protein internal dynamics.Molecules (Basel, Switzerland) · 2013Review
- A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.Journal of the American Chemical Society · 2013Article
- Mapping the structural and dynamical features of kinesin motor domains.PLoS computational biology · 2013Article
- Hot spots in a network of functional sites.PloS one · 2013Article
Corrections and comments
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Authors and funding
6 authors at 5 institutions in 2 countries.
Funding
Abstract
An atomic resolution description of protein flexibility is essential for understanding the role that structural dynamics play in biological processes. Despite the unique dependence of nuclear magnetic resonance (NMR) to motional averaging on different time scales, NMR-based protein structure determination often ignores the presence of dynamics, representing rapidly exchanging conformational equilibria in terms of a single static structure. In this study, we use the rich dynamic information encoded in experimental NMR parameters to develop a molecular and statistical mechanical characterization of the conformational behavior of proteins in solution. Critically, and in contrast to previously proposed techniques, we do not use empirical energy terms to restrain a conformational search, a procedure that can strongly perturb simulated dynamics in a nonpredictable way. Rather, we use accelerated molecular dynamic simulation to gradually increase the level of conformational sampling and to identify the appropriate level of sampling via direct comparison of unrestrained simulation with experimental data. This constraint-free approach thereby provides an atomic resolution free-energy weighted Boltzmann description of protein dynamics occurring on time scales over many orders of magnitude in the protein ubiquitin.
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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.