ArticleThe journal of physical chemistry. B2018
Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations.
Article in The journal of physical chemistry. B, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
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- Evaluating Force Matching as a Parametrization Strategy for the CHARMM36m Force Field Using Phosphorylation.The journal of physical chemistry. B · 2026Article
- Exploring the structure and dynamics of peptide nanodiscs through a synergistic approach with NMR spectroscopy, SAS and MD simulations.Communications chemistry · 2026Article
- Backbone rigidity of disordered protein linkers from NMR experiments and MD simulations.Biophysical journal · 2026Article
- Small-molecule inhibitor of C‑terminal HSP90 dimerization modulates autophagy and functions synergistically with mTOR inhibition to kill cisplatin-resistant cancer cells.Cell death & disease · 2025Article
- Gromacs MetaDump: a tool for extracting GROMACS simulation metadata.Journal of cheminformatics · 2025Article
- Molecular Dynamics of the Intrinsically Disordered Protein COR15A─A Force Field Validation on Structure and Dynamics.Journal of chemical theory and computation · 2025Article
- Quality Evaluation Based Simulation Selection (QEBSS) for analysis of conformational ensembles and dynamics of multidomain proteins.Communications chemistry · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.Journal of chemical information and modeling · 2025Article
- Rapid Interpretation of Protein Backbone Rotation Dynamics Directly from Spin Relaxation Data.The journal of physical chemistry letters · 2024Article
- Field-domain rapid-scan EPR at 240GHz for studies of protein functional dynamics at room temperature.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2024Article
- Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations.Communications chemistry · 2024Article
- Additively manufactured, solid object structures for adjustable image contrast in Magnetic Resonance Imaging.Zeitschrift fur medizinische Physik · 2022Article
- Accurate Simulations of Lipid Monolayers Require a Water Model with Correct Surface Tension.Journal of chemical theory and computation · 2022Article
- Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics.Journal of chemical information and modeling · 2021Article
- Bootstrap Aggregation for Model Selection in the Model-free Formalism.Magnetic resonance (Gottingen, Germany) · 2021Article
- NMR Structure and Dynamics of TonB Investigated by Scar-Less Segmental Isotopic Labeling Using a Salt-Inducible Split Intein.Frontiers in chemistry · 2020Article
- Structure and Dynamics of Spherical and Rodlike Alkyl Ethoxylate Surfactant Micelles Investigated Using NMR Relaxation and Atomistic Molecular Dynamics Simulations.Langmuir : the ACS journal of surfaces and colloids · 2019Article
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3 authors.
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Abstract
Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.
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