Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix.

The Journal of Physical Chemistry. B
Deniz SezerBenoît Roux

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.

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Citations

Sep 4, 2009·Photosynthesis Research·Johann P Klare, Heinz-Jürgen Steinhoff
Jun 5, 2013·Progress in Nuclear Magnetic Resonance Spectroscopy·Gunnar Jeschke
Dec 21, 2010·The Journal of Physical Chemistry. B·Yury E ShapiroEva Meirovitch
Dec 18, 2010·The Journal of Physical Chemistry. B·Eva MeirovitchJack H Freed
Dec 18, 2010·The Journal of Physical Chemistry. B·Dora Toledo WarshaviakWayne L Hubbell
Mar 13, 2012·The Journal of Physical Chemistry. B·Jessica L SarverSunil Saxena
Jan 26, 2011·The Journal of Chemical Physics·Yun-Wei Chiang, Jack H Freed
Aug 22, 2008·The Journal of Chemical Physics·Albert C Pan, Benoît Roux
Apr 23, 2009·Protein Science : a Publication of the Protein Society·Mark R FleissnerWayne L Hubbell
Apr 14, 2016·Theoretical Chemistry Accounts·Maria Grazia ConcilioSelena G Burgess
Apr 1, 2016·Physical Chemistry Chemical Physics : PCCP·D AbdullinO Schiemann
Sep 8, 2015·Physical Chemistry Chemical Physics : PCCP·Sami Emre KüçükDeniz Sezer
Mar 8, 2016·Protein Science : a Publication of the Protein Society·Timothy F CunninghamSunil Saxena
Oct 15, 2014·Journal of Magnetic Resonance·Derek Marsh
Dec 1, 2010·Physical Chemistry Chemical Physics : PCCP·Yevhen PolyhachGunnar Jeschke
Nov 29, 2013·Physical Chemistry Chemical Physics : PCCP·Deniz Sezer
Feb 11, 2015·Physical Chemistry Chemical Physics : PCCP·Sami Emre KüçükDeniz Sezer
Sep 23, 2014·Biochemistry·Indra D SahuGary A Lorigan
Jul 30, 2009·Physical Chemistry Chemical Physics : PCCP·Deniz SezerThomas F Prisner
Aug 18, 2010·Physical Chemistry Chemical Physics : PCCP·Emiliano StendardoVincenzo Barone
Jun 22, 2011·Physical Chemistry Chemical Physics : PCCP·Deniz Sezer, Snorri Th Sigurdsson
Oct 12, 2012·Physical Chemistry Chemical Physics : PCCP·Sonja GrubišićVincenzo Barone
Oct 28, 2020·Physical Chemistry Chemical Physics : PCCP·Sebastian SpicherOlav Schiemann
Jan 23, 2021·PLoS Computational Biology·Giulio TeseiKresten Lindorff-Larsen
Aug 14, 2008·The Journal of Physical Chemistry. B·Deniz SezerBenoit Roux
May 27, 2010·Journal of the American Chemical Society·Loïc SalmonMartin Blackledge
Sep 25, 2009·The Journal of Physical Chemistry. B·Mirco ZerbettoEva Meirovitch
Jul 14, 2010·Progress in Nuclear Magnetic Resonance Spectroscopy·Eva MeirovitchJack H Freed

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