Molecular dynamics simulation of site-directed spin labeling: Experimental validation in muscle fibers

Leslie E.W. LaConte, Vincent Voelz, Wendy Nelson, Michael Enz, David D. Thomas

Research output: Contribution to journalArticlepeer-review

34 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1854-1866
Number of pages13
JournalBiophysical journal
Volume83
Issue number4
DOIs
StatePublished - Oct 1 2002

Bibliographical note

Funding Information:
This work was supported by grants from the National Institutes of Health Grant AR32961-16, the Muscular Dystrophy Association, and the Minnesota Supercomputer Institute (to D.D.T.). L.E.W.L. was supported by a National Institutes of Health training grant and by a Doctoral Dissertation Fellowship from the University of Minnesota Graduate School.

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