Simulation of nitroxide electron paramagnetic resonance spectra from brownian trajectories and molecular dynamics simulations.
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.
DeSensi
Susan C
SC
Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, USA.
Rangel
David P
DP
Beth
Albert H
AH
Lybrand
Terry P
TP
Hustedt
Eric J
EJ
D003198:Computer Simulation; D004058:Diffusion; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry* / Q000648:ultrastructure*; D009569:Nitric Oxide / Q000737:chemistry; D020030:Nitric Oxide Donors / Q000737:chemistry*; D011487:Protein Conformation; D013113:Spin Labels
D020030:Nitric Oxide Donors; D013113:Spin Labels; D009569:Nitric Oxide; D009113:Muramidase