ArticleJournal of the American Chemical Society2012
Interpreting protein structural dynamics from NMR chemical shifts.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed, 133 citations in OpenAlex.
- Allosteric Protein Chemical Shift Perturbations are Ubiquitous.bioRxiv : the preprint server for biology · 2026Article
- Dynamic-Structure Redesign of Calmodulin Reveals Mechanistic Constraints on Ryr2 Regulation.bioRxiv : the preprint server for biology · 2026Article
- Molecular driving force of a small molecule-induced protein disorder-order transition.Communications chemistry · 2026Article
- Beyond structures: solution NMR as the quantitative engine of integrated structural biology.Frontiers in molecular biosciences · 2026Review
- Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution.Nature communications · 2025Article
- Monomer binding modes of small molecules that modulate the kinetics of hIAPP amyloid formation.bioRxiv : the preprint server for biology · 2025Article
- Molecular Dynamics of the Intrinsically Disordered Protein COR15A─A Force Field Validation on Structure and Dynamics.Journal of chemical theory and computation · 2025Article
- Decoding phospho-regulation and flanking regions in autophagy-associated short linear motifs.Communications biology · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- AdvancingThe journal of physical chemistry. A · 2024Article
- Integrative Modeling of Protein-Polypeptide Complexes by Bayesian Model Selection using AlphaFold and NMR Chemical Shift Perturbation Data.bioRxiv : the preprint server for biology · 2024Article
- Resolution in cryogenic solid state NMR: Challenges and solutions.Protein science : a publication of the Protein Society · 2024Review
- Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics.The journal of physical chemistry letters · 2024Review
- Molecular basis for curvature formation in SepF polymerization.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Simulation Reveals the Chameleonic Behavior of Macrocycles.Journal of chemical information and modeling · 2023Article
- Global protein dynamics as communication sensors in peptide synthetase domains.Science advances · 2022Article
- Electronic Polarization at the Interface between the p53 Transactivation Domain and Two Binding Partners.The journal of physical chemistry. B · 2022Article
- Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations.Journal of chemical theory and computation · 2022Article
- Generating Ensembles of Dynamic Misfolding Proteins.Frontiers in neuroscience · 2022Review
- CheSPI: chemical shift secondary structure population inference.Journal of biomolecular NMR · 2021Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
In this investigation, semiempirical NMR chemical shift prediction methods are used to evaluate the dynamically averaged values of backbone chemical shifts obtained from unbiased molecular dynamics (MD) simulations of proteins. MD-averaged chemical shift predictions generally improve agreement with experimental values when compared to predictions made from static X-ray structures. Improved chemical shift predictions result from population-weighted sampling of multiple conformational states and from sampling smaller fluctuations within conformational basins. Improved chemical shift predictions also result from discrete changes to conformations observed in X-ray structures, which may result from crystal contacts, and are not always reflective of conformational dynamics in solution. Chemical shifts are sensitive reporters of fluctuations in backbone and side chain torsional angles, and averaged (1)H chemical shifts are particularly sensitive reporters of fluctuations in aromatic ring positions and geometries of hydrogen bonds. In addition, poor predictions of MD-averaged chemical shifts can identify spurious conformations and motions observed in MD simulations that may result from force field deficiencies or insufficient sampling and can also suggest subsets of conformational space that are more consistent with experimental data. These results suggest that the analysis of dynamically averaged NMR chemical shifts from MD simulations can serve as a powerful approach for characterizing protein motions in atomistic detail.
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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.