SIMULATING ESR SPECTRA OF NITROXIDE SPIN LABELS FROM MD & STOCH TRAJECTORIES

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Simulating electron spin resonance spectra of nitroxide spin labels from motional models is necessary for the quantitative analysis of experimental spectra. We have developed a framework for modeling the spin label dynamics by using trajectories such as those from molecular dynamics (MD) simulations combined with stochastic treatment of the global protein tumbling. This was achieved in the time domain after two efficient numerical integrators were developed: One for the quantal dynamics of the spins and the other for the classical rotational diffusion. For the quantal dynamics, we propagated the relevant part of the spin density matrix in Hilbert space. For the diffusional tumbling, we worked with quaternions, which enabled the treatment of anisotropic diffusion in a potential expanded as a sum of spherical harmonics. Time-averaging arguments were invoked to bridge the gap between the smaller time step of the MD trajectories and the larger time steps appropriate for the rotational diffusion and/or quantal spin dynamics