Molecular dynamics simulation and EPR spectroscopy of nitroxide side chains in bacteriorhodopsin

Heinz-Jürgen Steinhoff, Matthias Müller, Christian Beier and Matthias Pfeiffer

Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780 Bochum, Germany
Max-Planck-Institut für Biochemie, Am Klopferspitz 18 a, 82152 Martinsried, Germany

A novel approach for the simulation of electron paramagnetic resonance (EPR) spectra was used to combine molecular dynamics (MD) simulations with experimental data. Reorientational dynamics trajectories of a sequence of nitroxide side chains attached to cysteine substitution mutants of bacteriorhodopsin (BR) were calculated by means of MD simulations. EPR spectra calculated from these data were found to be in excellent agreement with the experimental spectra. Simulation of EPR difference spectra for two BR conformations reveal that experimentally detected changes of the nitroxide dynamics during the catalytic cycle of BR are consistent with a transient conformational change of helix F.