Molecular dynamics and ESR spectra of a nitroxide spin label at solvent-exposed surface sites in proteins
Using atomistic molecular dynamics (MD) simulations in the interpretation of multifrequency electron spin resonance (ESR) spectra is desirable but challenging. In this thesis, some of the conceptual and computational tools that are required to rigorously pursue this task are developed and applied. First, an efficient numerical scheme for simulating ESR spectra in the time domain is established, followed by an exact and efficient integrator for an anisotropic, restricted, rotational Brownian diffusion. These two integrators provide a flexible structure that can easily incorporate additional dynamics coming from MD trajectories or other stochastic models of motion. Second, force field parameters for nitroxide spin labels are developed and critically evaluated against ab initio calculations. Third, the spin label MTSSL, most widely used in studies of proteins, is simulated on a solvated poly-alanine alpha helix, to gain insight into its conformational dynamics at solvent exposed helix sites in proteins. Fourth, a systematic framework for constructing discrete-state Markov jump models of the internal spin label dynamics from many, relatively short MD trajectories is developed in the context of MTSSL on the poly-alanine helix. Finally, MTSSL is simulated at several solvent-exposed sites on the protein T4 Lysozyme. The simulations reveal extensive interactions of the spin label with the local protein environment, which significantly affect the ordering and dynamics of the spin label. Spectra at three different magnetic field strengths, calculated from the MD trajectories, show remarkable agreement with experiment.
dissertation or thesis