ArticleBiophysical journal2006
A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Review
- Resolving distance variations by single-molecule FRET and EPR spectroscopy using rotamer libraries.Biophysical journal · 2021Article
- DEER and RIDME Measurements of the Nitroxide-Spin Labelled Copper-Bound Amine Oxidase Homodimer from Arthrobacter Globiformis.Applied magnetic resonance · 2021Article
- 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
- Probing the Secondary Structure of Membrane Peptides Using (2)H-Labeled d(10)-Leucine via Site-Directed Spin-Labeling and Electron Spin Echo Envelope Modulation Spectroscopy.The journal of physical chemistry. B · 2016Article
- Nanometer-scale water- and proton-diffusion heterogeneities across water channels in polymer electrolyte membranes.Angewandte Chemie (International ed. in English) · 2015Article
- Probing columnar discotic liquid crystals by EPR spectroscopy with a rigid-core nitroxide spin probe.Angewandte Chemie (International ed. in English) · 2013Article
- Article
- Determining α-helical and β-sheet secondary structures via pulsed electron spin resonance spectroscopy.Biochemistry · 2012Article
- Enhancement of electron spin echo envelope modulation spectroscopic methods to investigate the secondary structure of membrane proteins.The journal of physical chemistry. B · 2012Article
- 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
- Simulation vs. reality: a comparison of in silico distance predictions with DEER and FRET measurements.PloS one · 2012Article
- Monomeric and dimeric conformation of the vinculin tail five-helix bundle in solution studied by EPR spectroscopy.Biophysical journal · 2011Article
- Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR.RNA (New York, N.Y.) · 2011Article
- Molecular details of Bax activation, oligomerization, and membrane insertion.The Journal of biological chemistry · 2010Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Electron paramagnetic resonance (EPR) spectroscopy using site-directed spin-labeling is an appropriate technique to analyze the structure and dynamics of flexible protein regions as well as protein-protein interactions under native conditions. The analysis of a set of protein mutants with consecutive spin-label positions leads to the identification of secondary and tertiary structure elements. In the first place, continuous-wave EPR spectra reflect the motional freedom of the spin-label specifically linked to a desired site within the protein. EPR spectra calculations based on molecular dynamics (MD) and stochastic dynamics simulations facilitate verification or refinement of predicted computer-aided models of local protein conformations. The presented spectra simulation algorithm implies a specialized in vacuo MD simulation at 600 K with additional restrictions to sample the entire accessible space of the bound spin-label without large temporal effort. It is shown that the distribution of spin-label orientations obtained from such MD simulations at 600 K agrees well with the extrapolated motion behavior during a long timescale MD at 300 K with explicit water. The following potential-dependent stochastic dynamics simulation combines the MD data about the site-specific orientation probabilities of the spin-label with a realistic rotational diffusion coefficient yielding a set of trajectories, each more than 700 ns long, essential to calculate the EPR spectrum. Analyses of a structural model of the loop between helices E and F of bacteriorhodopsin are illustrated to demonstrate the applicability and potentials of the reported simulation approach. Furthermore, effects on the motional freedom of bound spin-labels induced by solubilization of bacteriorhodopsin with Triton X-100 are examined.
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