SPECTROSCOPY, IMAGING, OTHER TECHNIQUES |
A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations
Christian Beier 1 and Heinz-Juergen Steinhoff 1*
1 Universitaet Osnabrueck
* To whom correspondence should be addressed. E-mail: hsteinho{at}uos.de.
Submitted on December 21, 2005
Revised on February 15, 2006
Accepted on 27 June 2006
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Abstract |
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EPR spectroscopy using site-directed spin labeling is an appropriate technique to analyze the structure and dynamics of flexible protein regions as well as protein-protein interactions under native conditions. The analysis of a set of protein mutants with consecutive spin label positions leads to the identification of secondary and tertiary structure elements. In the first place continuous wave (cw) EPR spectra reflect the motional freedom of the spin label specifically linked to a desired site within the protein. EPR spectra calculations based on molecular dynamics (MD) and stochastic dynamics (SD) simulations facilitate verification or refinement of predicted computer aided models of local protein conformations. The presented spectra simulation algorithm implies a specialized in vacuo MD simulation at 600 K with additional restrictions to sample the entire accessible space of the bound spin label without large temporal effort. It is shown that the distribution of spin label orientations obtained from such MD simulations at 600 K agrees well with the extrapolated motion behavior during a long time scale MD at 300 K with explicit water. A following potential-dependent SD simulation combines the MD data about the site-specific orientation probabilities of the spin label with a realistic rotational diffusion coefficient yielding a set of trajectories, each more than 700 ns long, essential to calculate the EPR spectrum. Analyses of a structural model of the loop between helices E and F of bacteriorhodopsin are illustrated in order to demonstrate the applicability and potentials of the reported simulation approach. Furthermore, effects on the motional freedom of bound spin labels induced by solubilization of BR with Triton X-100 are examined.
Key Words:
EPR spectroscopy, bacteriorhodopsin, long time scale molecular dynamics, membrane protein solubilization, side-chain mobility, site-directed spin labeling
