ArticleStructure (London, England : 1993)2008
De novo high-resolution protein structure determination from sparse spin-labeling EPR data.
Article in Structure (London, England : 1993), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions.Nature communications · 2025Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- Review
- Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations.Journal of chemical theory and computation · 2024Article
- Approximating conformational Boltzmann distributions with AlphaFold2 predictions.bioRxiv : the preprint server for biology · 2023Article
- A novel approach to modeling side chain ensembles of the bifunctional spin label RX.bioRxiv : the preprint server for biology · 2023Article
- Interdomain Linkers Regulate Histidine Kinase Activity by Controlling Subunit Interactions.Biochemistry · 2022Article
- Comparative evaluation of spin-label modeling methods for protein structural studies.Biophysical journal · 2022Article
- Protein functional dynamics from the rigorous global analysis of DEER data: Conditions, components, and conformations.The Journal of general physiology · 2021Article
- Methods for Molecular Modelling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Characterization of the ExoU activation mechanism using EPR and integrative modeling.Scientific reports · 2020Article
- Engineered chemotaxis core signaling units indicate a constrained kinase-off state.Science signaling · 2020Article
- Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement.Journal of chemical information and modeling · 2020Article
- Rapid Simulation of Unprocessed DEER Decay Data for Protein Fold Prediction.Biophysical journal · 2020Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta.Journal of chemical theory and computation · 2019Article
- Integrated Structural Biology for α-Helical Membrane Protein Structure Determination.Structure (London, England : 1993) · 2018Article
- Finding the needle in the haystack: towards solving the protein-folding problem computationally.Critical reviews in biochemistry and molecular biology · 2018Review
- Identification of a ubiquitin-binding interface using Rosetta and DEER.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
15 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
As many key proteins evade crystallization and remain too large for nuclear magnetic resonance spectroscopy, electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labeling offers an alternative approach for obtaining structural information. Such information must be translated into geometric restraints to be used in computer simulations. Here, distances between spin labels are converted into distance ranges between beta carbons by using a "motion-on-a-cone" model, and a linear-correlation model links spin-label accessibility to the number of neighboring residues. This approach was tested on T4-lysozyme and alphaA-crystallin with the de novo structure prediction algorithm Rosetta. The results demonstrate the feasibility of obtaining highly accurate, atomic-detail models from EPR data by yielding 1.0 A and 2.6 A full-atom models, respectively. Distance restraints between amino acids far apart in sequence but close in space are most valuable for structure determination. The approach can be extended to other experimental techniques such as fluorescence spectroscopy, substituted cysteine accessibility method, or mutational studies.
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