ArticleJournal of the American Chemical Society2009
Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations.
Article in Journal of the American Chemical Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- EPR spectroscopy 80 years after its discovery.Science advances · 2026Review
- An Expanded Markov State Model-Transition Path Theory Framework for Ion Conduction Reactive Pathways through Membrane Channels.The journal of physical chemistry letters · 2026Article
- 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
- Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries.Biophysical journal · 2021Article
- A Global Minimization Toolkit for Batch-Fitting and χBiophysical journal · 2020Article
- Microsecond dynamics in proteins by two-dimensional ESR: Predictions.The Journal of chemical physics · 2020Article
- Modeling of motional EPR spectra using hindered Brownian rotational diffusion and the stochastic Liouville equation.The Journal of chemical physics · 2020Article
- Structural and dynamic origins of ESR lineshapes in spin-labeled GB1 domain: the insights from spin dynamics simulations based on long MD trajectories.Scientific reports · 2020Article
- Trajectory-Based Simulation of EPR Spectra: Models of Rotational Motion for Spin Labels on Proteins.The journal of physical chemistry. B · 2019Article
- Lipid Configurations from Molecular Dynamics Simulations.Biophysical journal · 2018Article
- Focus: Two-dimensional electron-electron double resonance and molecular motions: The challenge of higher frequencies.The Journal of chemical physics · 2015Article
- CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.Advances in protein chemistry and structural biology · 2014Review
- A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme.Chembiochem : a European journal of chemical biology · 2013Article
- Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy.The journal of physical chemistry. B · 2013Article
- Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme.The journal of physical chemistry. B · 2013Article
- Mapping molecular flexibility of proteins with site-directed spin labeling: a case study of myoglobin.Biochemistry · 2012Article
- Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations.The journal of physical chemistry. B · 2012Article
- Simulating the dynamics and orientations of spin-labeled side chains in a protein-DNA complex.The journal of physical chemistry. B · 2012Article
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3 authors.
Funding
Abstract
Multifrequency electron spin resonance (ESR) spectra provide a wealth of structural and dynamic information about the local environment of the spin label and, indirectly, about the spin-labeled protein. Relating the features of the observed spectra to the underlying molecular motions and interactions is, however, challenging. To make progress toward a rigorous interpretation of ESR spectra, we perform extensive molecular dynamics (MD) simulations of fully solvated T4 Lysozyme, labeled with the spin label MTSSL at positions 72 and 131. These two sites have been the object of numerous experimental studies and are generally considered as prototypical solvent-exposed sites on the surfaces of alpha-helices. To extend the time window afforded by the MD simulations, stochastic Markov models reflecting the dynamics of the spin label side chains in terms of their rotameric states are constructed from the trajectories. The calculated multifrequency ESR spectra are in very good agreement with experiment for three different magnetic field strengths without adjusting any parameters. During the trajectories, the spin labels interconvert among a fairly large number of conformations and display a propensity to form interactions with protein residues other than their nearest neighbors along the helix. The detailed picture of the spin label emerging from the MD simulations provides useful insight into the molecular origins of the available spectroscopic and crystallographic data.
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