Protein Dynamics and EPR-Spectroscopy: Comparison of Molecular Dynamic Simulations with Experiment.
Steinhoff HJ and Karim C
Electron paramagnetic resonance (EPR) experiments and molecular dynamics
simulations on the residual motion of hemoglobin bound spin labels provide
information about dynamical and rate processes in proteins. Rapid (ps time
range) reorientational fluctuations of the nitroxide ring of the spin labels
within a conformational substate can be experimentally characterized and
distinguished from low frequency (ns time range) transitions between the
conformational substates which are observed above 200K in solved samples.
A comparison of the experimentally determined magnitudes and frequencies
of the reorientational motions and the results of molecular dynamics simulations
for several nitroxide locations yields good agreement for the short time
dynamics. Evidence for relatively large scale motions involving rare jumps
are observed in the molecular dynamic trajectories. A simple approach using
Kramers'theory and a two state jump model permits to combine EPR results
and molecular dynamics simulations in the case of these rare events.