Parametrization, Molecular Dynamics Simulation, and Calculation of Electron Spin Resonance Spectra of a Nitroxide Spin Label on a Polyalanine α-Helix Export

@article{citeulike:4863579, abstract = {The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, is studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulate MTSSL attached to a polyalanine alpha-helix in explicit solvent to elucidate the factors affecting its conformational dynamics. Electron spin resonance spectra at 9 and 250 GHz are simulated in the time domain using the MD trajectories and including global rotational diffusion appropriate for the tumbling of T4 Lysozyme in solution. Analysis of the MD simulations reveals the presence of significant hydrophobic interactions of the spin label with the alanine side chains.}, author = {Sezer, Deniz and Freed, Jack H. and Roux, Benoit}, citeulike-article-id = {4863579}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/jp711375x}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/jp711375x}, day = {1}, doi = {10.1021/jp711375x}, journal = {The Journal of Physical Chemistry B}, keywords = {charmm, mtsl, parametrization}, month = {May}, number = {18}, pages = {5755--5767}, posted-at = {2009-06-16 01:03:55}, priority = {2}, title = {Parametrization, Molecular Dynamics Simulation, and Calculation of Electron Spin Resonance Spectra of a Nitroxide Spin Label on a Polyalanine α-Helix}, url = {http://dx.doi.org/10.1021/jp711375x}, volume = {112}, year = {2008} }

TY - JOUR ID - citeulike:4863579 L3 - citeulike-article-id:4863579 N2 - The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, is studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulate MTSSL attached to a polyalanine alpha-helix in explicit solvent to elucidate the factors affecting its conformational dynamics. Electron spin resonance spectra at 9 and 250 GHz are simulated in the time domain using the MD trajectories and including global rotational diffusion appropriate for the tumbling of T4 Lysozyme in solution. Analysis of the MD simulations reveals the presence of significant hydrophobic interactions of the spin label with the alanine side chains. IS - 18 JF - The Journal of Physical Chemistry B EP - 5767 TI - Parametrization, Molecular Dynamics Simulation, and Calculation of Electron Spin Resonance Spectra of a Nitroxide Spin Label on a Polyalanine α-Helix VL - 112 SP - 5755 KW - charmm KW - mtsl KW - parametrization AU - Sezer, Deniz AU - Freed, Jack AU - Roux, Benoit PY - 2008/05/01/ UR - http://dx.doi.org/10.1021/jp711375x ER -