BIOPHYSICAL THEORY AND MODELING |
Simulation of nitroxide EPR spectra from Brownian trajectories and molecular dynamics simulations
Susan C DeSensi 1, David P Rangel 2, Albert H Beth 3, Terry P Lybrand 3 and Eric J Hustedt 3*
1 Boston University
2 University of Washington
3 Vanderbilt University
* To whom correspondence should be addressed. E-mail: eric.hustedt{at}vanderbilt.edu.
Submitted on November 7, 2007
Revised on December 11, 2007
Accepted on 27 December 2007
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Abstract |
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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.
Key Words:
electron paramagnetic resonance, molecular dynamics, monte carlo, site-directed spin labeling, spectral simulation
