title: Calculating slow-motional electron paramagnetic resonance spectra from molecular dynamics using a diffusion operator approach.
abstract: A number of groups have utilized molecular dynamics (MD) to calculate slow-motional electron paramagnetic resonance (EPR) spectra of spin labels attached to biomolecules. Nearly all such calculations have been based on some variant of the trajectory method introduced by Robinson, Slutsky and Auteri (J. Chem. Phys. 1992,96, 2609-2616). Here we present an alternative approach that is specifically adapted to the diffusion operator-based stochastic Liouville equation (SLE) formalism that is also widely used to calculate slow-motional EPR line shapes. Specifically, the method utilizes MD trajectories to derive diffusion parameters such as the rotational diffusion tensor, diffusion tilt angles, and expansion coefficients of the orienting potential, which are then used as direct inputs to the SLE line shape program. This approach leads to a considerable improvement in computational efficiency over trajectory-based methods, particularly for high frequency, high field EPR. It also provides a basis for deconvoluting the effects of local spin label motion and overall motion of the labeled molecule or domain: once the local motion has been characterized by this approach, the label diffusion parameters may be used in conjunction with line shape analysis at lower EPR frequencies to characterize global motions. The method is validated by comparison of the MD predicted line shapes to experimental high frequency (250 GHz) EPR spectra.
authors.affiliation: Department of Chemistry and Chemical Biology, Northeastern University, Boston Massachusetts 02115, USA. D.Budil@neu.edu
authors.forename: David E
authors.initials: DE
authors.lastname: Budil
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: Sale
authors.forename: Khaled A
authors.initials: KA
authors.lastname: Khairy
authors.forename: Peter G
authors.initials: PG
authors.lastname: Fajer
mesh_terms: D003198:Computer Simulation; D004058:Diffusion; D004578:Electron Spin Resonance Spectroscopy / Q000295:instrumentation / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D013113:Spin Labels; D013816:Thermodynamics
chemical_list: D013113:Spin Labels