ArticleBiophysical journal2008
Simulation of nitroxide electron paramagnetic resonance spectra from brownian trajectories and molecular dynamics simulations.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Rapid Analysis of DEER Signals Including Short Distances.The journal of physical chemistry letters · 2025Article
- Monitoring Protein-Protein Interactions in the Cyanobacterial Circadian Clock in Real Time via Electron Paramagnetic Resonance Spectroscopy.Biochemistry · 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
- Direct Prediction of EPR Spectra from Lipid Bilayers: Understanding Structure and Dynamics in Biological Membranes.Chemphyschem : a European journal of chemical physics and physical chemistry · 2018Article
- Full Atom Simulations of Spin Label Conformations.Methods in enzymology · 2015Article
- Automated structure refinement for a protein heterodimer complex using limited EPR spectroscopic data and a rigid-body docking algorithm: a three-dimensional model for an ankyrin-CDB3 complex.The journal of physical chemistry. B · 2014Article
- Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.Journal of chemical theory and computation · 2012Article
- Direct simulation of magnetic resonance relaxation rates and line shapes from molecular trajectories.The journal of physical chemistry. B · 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
- MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL.Applied magnetic resonance · 2012Article
- Distance measurements on a dual-labeled TOAC AChR M2δ peptide in mechanically aligned DMPC bilayers via dipolar broadening CW-EPR spectroscopy.The journal of physical chemistry. B · 2012Article
- Conformational changes in BAK, a pore-forming proapoptotic Bcl-2 family member, upon membrane insertion and direct evidence for the existence of BH3-BH3 contact interface in BAK homo-oligomers.The Journal of biological chemistry · 2010Article
- Probing the effect of transport inhibitors on the conformation of the mitochondrial citrate transport protein via a site-directed spin labeling approach.Journal of bioenergetics and biomembranes · 2010Article
- Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins.European biophysics journal : EBJ · 2010Article
- Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins.Progress in nuclear magnetic resonance spectroscopy · 2009Article
- Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations.Journal of the American Chemical Society · 2009Article
- Simulation of nitroxide electron paramagnetic resonance spectra from brownian trajectories and molecular dynamics simulations.Biophysical journal · 2008Article
- Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix.The journal of physical chemistry. B · 2008Article
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5 authors.
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Abstract
A simulated continuous wave electron paramagnetic resonance spectrum of a nitroxide spin label can be obtained from the Fourier transform of a free induction decay. It has been previously shown that the free induction decay can be calculated by solving the time-dependent stochastic Liouville equation for a set of Brownian trajectories defining the rotational dynamics of the label. In this work, a quaternion-based Monte Carlo algorithm has been developed to generate Brownian trajectories describing the global rotational diffusion of a spin-labeled protein. Also, molecular dynamics simulations of two spin-labeled mutants of T4 lysozyme, T4L F153R1, and T4L K65R1 have been used to generate trajectories describing the internal dynamics of the protein and the local dynamics of the spin-label side chain. Trajectories from the molecular dynamics simulations combined with trajectories describing the global rotational diffusion of the protein are used to account for all of the dynamics of a spin-labeled protein. Spectra calculated from these combined trajectories correspond well to the experimental spectra for the buried site T4L F153R1 and the helix surface site T4L K65R1. This work provides a framework to further explore the modeling of the dynamics of the spin-label side chain in the wide variety of labeling environments encountered in site-directed spin labeling studies.
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