title: Prediction of nitroxide spin label EPR spectra from MD trajectories: application to myoglobin.
abstract: We report the prediction of motional EPR spectra of the metalloprotein sperm whale myoglobin spin labelled with nitroxide directly from Molecular Dynamics (MD) simulations at the atomistic scale. We show that an accurate simulation of EPR spectra can be achieved from a single MD trajectory which is in excellent agreement with experiment. Simulations have been carried out using a general method reported previously by us for the simulation of EPR spectra form single dynamical trajectories. Our calculations demonstrate the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions around dihedral states, of slow conformational flips among different rotameric states and of the slow rotational diffusion of the protein itself. The MD-EPR methodology reported does not require any additional stochastic modelling using adjustable parameters and opens, for the first time, the prospect of the simulation of EPR spectra entirely from single MD trajectories. Such a technique not only simplifies the interpretation and analysis of EPR spectra but also opens the possibility, for example, of "computer engineering" of spin-labelled proteins with the desired properties prior to actual EPR experiment.
authors.affiliation: School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK.
authors.forename: Egidijus
authors.initials: E
authors.lastname: Kuprusevicius
authors.forename: Gaye
authors.initials: G
authors.lastname: White
authors.forename: Vasily S
authors.initials: VS
authors.lastname: Oganesyan
mesh_terms: D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D056004:Molecular Dynamics Simulation; D009211:Myoglobin / Q000737:chemistry*; D013113:Spin Labels
chemical_list: D009211:Myoglobin; D013113:Spin Labels