A novel approach to the simulation of nitroxide spin label EPR spectra from a single truncated dynamical trajectory.
A simple effective method for calculation of EPR spectra from a single truncated dynamical trajectory of spin probe orientations is reported. It is shown that an accurate simulation can be achieved from the small initial fraction of a dynamical trajectory until the point when the autocorrelation function of re-orientational motion of spin label has relaxed. This substantially reduces the amount of time for spectra simulation compared to previous approaches, which require multiple full length trajectories (normally of several microseconds) to achieve the desired resolution of EPR spectra. Our method is applicable to trajectories generated from both Brownian dynamics and molecular dynamics (MD) calculations. Simulations of EPR spectra from Brownian dynamical trajectories under a variety of motional conditions including bi-modal dynamics with different hopping rates between the modes are compared to those performed by conventional method. Since the relatively short timescales of spin label motions are realistically accessible by modern MD computational methods, our approach, for the first time, opens the prospect of the simulation of EPR spectra entirely from MD trajectories of real proteins structures.
Oganesyan
V S
VS
CMSB, Centre for Metalloprotein Spectroscopy and Biology, Henry Wellcome Unit of Biological EPR, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, UK. v.oganesyan@uea.ac.uk
D003198:Computer Simulation; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D009589:Nitrogen Oxides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D013113:Spin Labels
D009589:Nitrogen Oxides; D011506:Proteins; D013113:Spin Labels