Simulation of nitroxide electron paramagnetic resonance spectra from brownian trajectories and molecular dynamics simulations.

DeSensi SC, Rangel DP, Beth AH, Lybrand TP, Hustedt EJ
Biophys J. 2008 94 (10): 3798-809

PMID: 18234808 · PMCID: PMC2367180 · DOI:10.1529/biophysj.107.125419

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.

MeSH Terms (10)

Computer Simulation Diffusion Electron Spin Resonance Spectroscopy Models, Chemical Models, Molecular Muramidase Nitric Oxide Nitric Oxide Donors Protein Conformation Spin Labels

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