ArticleProceedings of the National Academy of Sciences of the United States of America2014
Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR.
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 99 papers.
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99 citing papers in PubMed.
- IDPForge: Deep Learning of Proteins with Global and Local Regions of Disorder.bioRxiv : the preprint server for biology · 2026Article
- Mapping functional dynamics hotspots for protein engineering with NMR peak intensity analysis.Protein engineering, design & selection : PEDS · 2026Article
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain.bioRxiv : the preprint server for biology · 2025Article
- Comparative Structural Analysis of Escherichia Coli Cyay at Room and Cryogenic Temperatures Using Macromolecular and Serial Crystallography.Chembiochem : a European journal of chemical biology · 2025Article
- Solvation Energetic Costs of Cognate Binding Site Formation.Journal of chemical information and modeling · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Mapping allosteric rewiring in related protein structures from collections of crystallographic multiconformer models.bioRxiv : the preprint server for biology · 2025Article
- Advances in uncovering the mechanisms of macromolecular conformational entropy.Nature chemical biology · 2025Review
- Anisotropic Dynamics of Protein Side Chain NHThe journal of physical chemistry letters · 2025Article
- Revealing Functional Hotspots: Temperature-Dependent Crystallography of K-RAS Highlights Allosteric and Druggable Sites.bioRxiv : the preprint server for biology · 2025Article
- bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties.Bioinformatics (Oxford, England) · 2024Article
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- Data-driven probabilistic definition of the low energy conformational states of protein residues.NAR genomics and bioinformatics · 2024Article
- A curated rotamer library for common post-translational modifications of proteins.Bioinformatics (Oxford, England) · 2024Article
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- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Contribution of protein conformational heterogeneity to NMR lineshapes at cryogenic temperatures.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
39 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Detailed descriptions of atomic coordinates and motions are required for an understanding of protein dynamics and their relation to molecular recognition, catalytic function, and allostery. Historically, NMR relaxation measurements have played a dominant role in the determination of the amplitudes and timescales (picosecond-nanosecond) of bond vector fluctuations, whereas high-resolution X-ray diffraction experiments can reveal the presence of and provide atomic coordinates for multiple, weakly populated substates in the protein conformational ensemble. Here we report a hybrid NMR and X-ray crystallography analysis that provides a more complete dynamic picture and a more quantitative description of the timescale and amplitude of fluctuations in atomic coordinates than is obtainable from the individual methods alone. Order parameters (S(2)) were calculated from single-conformer and multiconformer models fitted to room temperature and cryogenic X-ray diffraction data for dihydrofolate reductase. Backbone and side-chain order parameters derived from NMR relaxation experiments are in excellent agreement with those calculated from the room-temperature single-conformer and multiconformer models, showing that the picosecond timescale motions observed in solution occur also in the crystalline state. These motions are quenched in the crystal at cryogenic temperatures. The combination of NMR and X-ray crystallography in iterative refinement promises to provide an atomic resolution description of the alternate conformational substates that are sampled through picosecond to nanosecond timescale fluctuations of the protein structure. The method also provides insights into the structural heterogeneity of nonmethyl side chains, aromatic residues, and ligands, which are less commonly analyzed by NMR relaxation measurements.
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