ArticleProceedings of the National Academy of Sciences of the United States of America2014
Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
- Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes.Nature chemistry · 2026Article
- Semi-automated modeling of reaction states in time-resolved serial femtosecond crystallography using molecular dynamics sampled conformations.Structural dynamics (Melville, N.Y.) · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Scaling and merging macromolecular diffuse scattering with mdx2.Acta crystallographica. Section D, Structural biology · 2024Article
- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- Growth kinetics of amyloid-like fibrils: An integrated atomistic simulation and continuum theory approach.PNAS nexus · 2024Article
- Scaling and merging macromolecular diffuse scattering withbioRxiv : the preprint server for biology · 2024Article
- Robust total X-ray scattering workflow to study correlated motion of proteins in crystals.Nature communications · 2023Article
- Molecular-dynamics simulation methods for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light.Annual review of biophysics · 2022Review
- A Minireview on Temperature Dependent Protein Conformational Sampling.The protein journal · 2021Review
- Diffuse X-ray scattering from correlated motions in a protein crystal.Nature communications · 2020Article
- Advances in methods for atomic resolution macromolecular structure determination.F1000Research · 2020Review
- Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein.Structural dynamics (Melville, N.Y.) · 2019Article
- Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation.Journal of synchrotron radiation · 2019Article
- An introduction to classical molecular dynamics simulation for experimental scattering users.Journal of applied crystallography · 2019Article
- Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.Journal of the American Chemical Society · 2019Article
- Bringing diffuse X-ray scattering into focus.Current opinion in structural biology · 2018Review
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6 authors.
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Abstract
X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein-solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.
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