ArticleThe journal of physical chemistry. B2013
Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Hidden protein disorder: Deciphering the structural organisation and dynamics of a non-canonical CP12 from the diatom Thalassiosira pseudonana.The FEBS journal · 2025Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- Expanded Functionality and Portability for the Colvars Library.The journal of physical chemistry. B · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Review
- Integration of Nanometer-Range Label-to-Label Distances and Their Distributions into Modelling Approaches.Biomolecules · 2022Review
- gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.PLoS computational biology · 2022Article
- AlphaFold2 predicts the inward-facing conformation of the multidrug transporter LmrP.Proteins · 2021Article
- Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints.PLoS computational biology · 2021Article
- Inference of Joint Conformational Distributions from Separately Acquired Experimental Measurements.The journal of physical chemistry letters · 2021Article
- How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations.Computational and structural biotechnology journal · 2021Review
- Data-guided Multi-Map variables for ensemble refinement of molecular movies.The Journal of chemical physics · 2020Article
- Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques.Biomolecules · 2019Review
- Hybrid Refinement of Heterogeneous Conformational Ensembles Using Spectroscopic Data.The journal of physical chemistry letters · 2019Article
- Interpretation of spectroscopic data using molecular simulations for the secondary active transporter BetP.The Journal of general physiology · 2019Article
- Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements.Structure (London, England : 1993) · 2019Article
- Refinement of Highly Flexible Protein Structures using Simulation-Guided Spectroscopy.Angewandte Chemie (International ed. in English) · 2018Article
- gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations.Bioinformatics (Oxford, England) · 2018Article
- Confidence Analysis of DEER Data and Its Structural Interpretation with Ensemble-Biased Metadynamics.Biophysical journal · 2018Article
- Conformational transitions of the sodium-dependent sugar transporter, vSGLT.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
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Abstract
DEER (double electron-electron resonance) spectroscopy is a powerful pulsed ESR (electron spin resonance) technique allowing the determination of spin-spin distance histograms between site-directed nitroxide label sites on a protein in their native environment. However, incorporating ESR/DEER data in structural refinement is challenging because the information from the large number of distance histograms is complex and highly coupled. Here, a novel restrained-ensemble molecular dynamics simulation method is developed to incorporate the information from multiple ESR/DEER distance histograms simultaneously. Illustrative tests on three coupled spin-labels inserted in T4 lysozyme show that the method efficiently imposes the experimental distance distribution in this system. Different rotameric states of the χ1 and χ2 dihedrals in the spin-labels are also explored by restrained ensemble simulations. Using this method, it is hoped that experimental restraints from ESR/DEER experiments can be used to refine structural properties of biological systems.
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