ArticleBiophysical journal2002
Molecular dynamics simulation of site-directed spin labeling: experimental validation in muscle fibers.
Article in Biophysical journal, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 52 citations in OpenAlex.
- Article
- 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
- Article
- Article
- Molecular dynamics simulations and drug discovery.BMC biology · 2011Review
- EPR spectra and molecular dynamics agree that the nucleotide pocket of myosin V is closed and that it opens on binding actin.Journal of molecular biology · 2011Article
- Multiple conformations of the nucleotide site of Kinesin family motors in the triphosphate state.Journal of molecular biology · 2011Article
- Conformational analysis of a nitroxide side chain in an α-helix with density functional theory.The journal of physical chemistry. B · 2011Article
- Phosphorylation-induced structural changes in smooth muscle myosin regulatory light chain.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Actin-binding cleft closure in myosin II probed by site-directed spin labeling and pulsed EPR.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Interactions between branched DNAs and peptide inhibitors of DNA repair.Nucleic acids research · 2008Article
- Structure and dynamics of the force-generating domain of myosin probed by multifrequency electron paramagnetic resonance.Biophysical journal · 2008Article
- Simulation of nitroxide electron paramagnetic resonance spectra from brownian trajectories and molecular dynamics simulations.Biophysical journal · 2008Article
- Site-directed spin labeling studies on nucleic acid structure and dynamics.Progress in nucleic acid research and molecular biology · 2008Review
- Modeling a spin-labeled fusion peptide in a membrane: implications for the interpretation of EPR experiments.Biophysical journal · 2007Article
- Dynamics of the nitroxide side chain in spin-labeled proteins.The journal of physical chemistry. B · 2006Article
- Motional restrictions of membrane proteins: a site-directed spin labeling study.Biophysical journal · 2006Article
- A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations.Biophysical journal · 2006Article
- Force field impact and spin-probe modeling in molecular dynamics simulations of spin-labeled T4 lysozyme.Journal of molecular modeling · 2005Article
- Site-directed spin labeling reveals a conformational switch in the phosphorylation domain of smooth muscle myosin.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
Abstract
We have developed a computational molecular dynamics technique to simulate the motions of spin labels bound to the regulatory domain of scallop myosin. These calculations were then directly compared with site-directed spin labeling experimental results obtained by preparing seven single-cysteine mutants of the smooth muscle (chicken gizzard) myosin regulatory light chain and performing electron paramagnetic resonance experiments on these spin-labeled regulatory light chains in functional scallop muscle fibers. We determined molecular dynamics simulation conditions necessary for obtaining a convergent orientational trajectory of the spin label, and from these trajectories we then calculated correlation times, orientational distributions, and order parameters. Simulated order parameters closely match those determined experimentally, validating our molecular dynamics modeling technique, and demonstrating our ability to predict preferred sites for labeling by computer simulation. In several cases, more than one rotational mode was observed within the 14-ns trajectory, suggesting that the spin label samples several local energy minima. This study uses molecular dynamics simulations of an experimental system to explore and enhance the site-directed spin labeling technique.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.