Ergodicity breaking of iron displacement in heme proteins

Soft Matter
Salman Seyedi, Dmitry V Matyushov

Abstract

We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by the softening of the force constant for atomic/molecular displacements by electrostatic and van der Waals forces from the protein-water thermal bath. Displacement softening passes through a nonergodic dynamical transition when the relaxation time of the force-force correlation function enters, with increasing temperature, the instrumental observation window. Two crossover temperatures are identified. The lower crossover, presently connected to the glass transition, is related to the dynamical unfreezing of rotations of water molecules within nanodomains polarized by charged surface residues of the protein. The higher crossover temperature, usually assigned to the dynamical transition, marks the onset of water translations. All crossovers are ergodicity breaking transitions depending on the corresponding observation windows. Allowing stretched exponential relaxation of the protein-water thermal bath significantly improves the theory-experiment agreement when applied to solid protein samples studied by Mössbauer spectroscopy.

References

Dec 13, 1991·Science·H FrauenfelderP G Wolynes
Jan 1, 1988·Annual Review of Biophysics and Biophysical Chemistry·H FrauenfelderR D Young
Jan 1, 1984·Progress in Biophysics and Molecular Biology·A Cooper
Sep 17, 1996·Proceedings of the National Academy of Sciences of the United States of America·M Gerstein, C Chothia
Apr 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·D I SvergunG Zaccai
Dec 7, 2000·Biophysical Journal·V A MakarovB M Pettitt
Apr 17, 2002·Physical Review Letters·M Tarek, D J Tobias
Jun 13, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·K AchterholdF G Parak
Jul 19, 2002·Biophysical Journal·Alessandro PaciaroniGiuseppe Onori
Nov 22, 2002·Proceedings of the National Academy of Sciences of the United States of America·P W FenimoreF G Parak
Mar 8, 2003·Quarterly Reviews of Biophysics·Frank GabelGiuseppe Zaccai
Mar 15, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Torsten Becker, Jeremy C Smith
Apr 15, 2004·Chemical Reviews·Samir Kumar Pal, Ahmed H Zewail
Aug 13, 2004·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Bertil Halle
Sep 4, 2004·Biophysical Journal·Torsten BeckerJeremy C Smith
Sep 28, 2004·Proceedings of the National Academy of Sciences of the United States of America·P W FenimoreR D Young
Aug 2, 2005·Biophysical Journal·Mingyang Lu, Jianpeng Ma
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Mar 29, 2006·Proceedings of the National Academy of Sciences of the United States of America·Naoko Nakagawa, Michel Peyrard
Oct 20, 2006·Biochimica Et Biophysica Acta·Arieh WarshelWilliam W Parson
Feb 27, 2007·Journal of the American Chemical Society·Tanping LiSherwin J Singer
May 15, 2007·Biophysical Journal·Kumiko Hayashi, Mitsunori Takano
Jun 15, 2007·The Journal of Physical Chemistry. B·Francesco PizzituttiPeter J Rossky
Jun 27, 2007·The Journal of Physical Chemistry. B·Paul AbbyadSteven G Boxer
Nov 21, 2007·Nature·Katherine A Henzler-WildmanDorothee Kern
May 27, 2008·The Journal of Chemical Physics·S KhodadadiA P Sokolov
Oct 7, 2008·Biophysical Journal·Bogdan M LeuJ Timothy Sage
Mar 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Hans FrauenfelderRobert D Young
May 26, 2009·The Journal of Physical Chemistry. B·Bertil Halle, Lennart Nilsson
Jul 7, 2009·Biochimica Et Biophysica Acta·Wolfgang Doster
Oct 6, 2009·The Journal of Physical Chemistry. B·Naoki ShinyashikiSimone Capaccioli
Apr 8, 2010·Biophysical Journal·S KhodadadiA P Sokolov
Jun 1, 2010·The Journal of Physical Chemistry. B·Stefania PerticaroliAssunta Morresi
Oct 26, 2010·Physical Chemistry Chemical Physics : PCCP·David N Lebard, Dmitry V Matyushov
May 27, 2011·The Journal of Physical Chemistry. B·Salvatore MagazùAntonio Benedetto
Aug 27, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Dmitry V Matyushov, Alexander Y Morozov
Nov 24, 2011·Physical Review Letters·Liang HongJeremy C Smith
Aug 7, 2012·The Journal of Physical Chemistry. B·Daniel R Martin, Dmitry V Matyushov
Nov 7, 2012·The Journal of Chemical Physics·Daniel R Martin, Dmitry V Matyushov
Nov 17, 2012·Angewandte Chemie·Kathleen WoodFrans A A Mulder

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Citations

Jul 8, 2020·The Journal of Physical Chemistry Letters·Daniel R Martin, Dmitry V Matyushov
Dec 6, 2018·The Journal of Physical Chemistry. B·Dmitry V Matyushov, Marshall D Newton
Apr 20, 2018·The Journal of Physical Chemistry Letters·Salman Seyedi, Dmitry V Matyushov

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Methods Mentioned

BETA
X-ray
neutron scattering
neutron
NMR

Software Mentioned

NAMD

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