A Structure-Based Simulation Approach for Electron Paramagnetic Resonance Spectra Using Molecular and Stochastic Dynamics Simulations

• Published in: Biophysical journal Vol. 91; no. 7; pp. 2647 - 2664
• Main Authors: Beier, Christian, Steinhoff, Heinz-Jürgen
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-10-2006; Biophysical Society
• Subjects: Algorithms; Bacteriorhodopsins - chemistry; Bacteriorhodopsins - genetics; Biophysics; Computer Simulation; Electron Spin Resonance Spectroscopy; Electrons; Models, Molecular; Molecules; Mutation; Octoxynol - chemistry; Proteins; Simulation; Spectroscopy, Imaging, Other Techniques; Spectrum analysis; Spin Labels; Stochastic Processes
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1529/biophysj.105.080051

Electron paramagnetic resonance (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 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 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 timescale MD at 300
K with explicit water. The following potential-dependent stochastic dynamics 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 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 bacteriorhodopsin with Triton X-100 are examined.