Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations.
Multifrequency electron spin resonance (ESR) spectra provide a wealth of structural and dynamic information about the local environment of the spin label and, indirectly, about the spin-labeled protein. Relating the features of the observed spectra to the underlying molecular motions and interactions is, however, challenging. To make progress toward a rigorous interpretation of ESR spectra, we perform extensive molecular dynamics (MD) simulations of fully solvated T4 Lysozyme, labeled with the spin label MTSSL at positions 72 and 131. These two sites have been the object of numerous experimental studies and are generally considered as prototypical solvent-exposed sites on the surfaces of alpha-helices. To extend the time window afforded by the MD simulations, stochastic Markov models reflecting the dynamics of the spin label side chains in terms of their rotameric states are constructed from the trajectories. The calculated multifrequency ESR spectra are in very good agreement with experiment for three different magnetic field strengths without adjusting any parameters. During the trajectories, the spin labels interconvert among a fairly large number of conformations and display a propensity to form interactions with protein residues other than their nearest neighbors along the helix. The detailed picture of the spin label emerging from the MD simulations provides useful insight into the molecular origins of the available spectroscopic and crystallographic data.
Sezer
Deniz
D
Department of Physics, Cornell University, Ithaca, New York 14853, USA.
Freed
Jack H
JH
Roux
Benoît
B
D017122:Bacteriophage T4 / Q000201:enzymology; D003198:Computer Simulation; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D008390:Markov Chains; D008956:Models, Chemical; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry*; D011487:Protein Conformation; D013113:Spin Labels; D013269:Stochastic Processes; D013816:Thermodynamics
D013113:Spin Labels; D009113:Muramidase