PMID: 9164461Mar 1, 1997Paper

A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin

Nature Structural Biology
D VitkupM Karplus

Abstract

The distribution of carbon monoxide after photodissociation in the myoglobin haem pocket has been investigated using molecular dynamics simulations at 300 K. The results show that both intermediates (one close to the haem iron and one further away) observed in recent low temperature X-ray studies of photodissociated CO have a high probability of occurrence, even at ambient temperatures. The fact that the O of CO is oriented toward the haem iron in the closer intermediate provides an explanation for the slow rate of CO geminate rebinding. A refinement against X-ray data generated from the molecular dynamics simulations indicates that the CO has a broader distribution in the haem pocket than is apparent from the experimental electron density. This effect is likely to be general for systems containing highly mobile groups.

References

Oct 1, 1976·Proceedings of the National Academy of Sciences of the United States of America·J P CollmanK S Suslick
Nov 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·P A AnfinrudR M Hochstrasser
Jan 1, 1989·Proteins·R J Loncharich, B R Brooks
May 9, 1987·Biophysical Chemistry·A AnsariT B Sauke
Nov 5, 1986·Journal of Molecular Biology·J KuriyanG A Petsko
Jun 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·J O AlbenK T Yue
Oct 27, 1994·Nature·I SchlichtingR M Sweet
Dec 15, 1993·Structure·M Levitt, B H Park
Jan 1, 1993·Annual Review of Biophysics and Biomolecular Structure·J Hajdu
Oct 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·P J Steinbach, B R Brooks
Jul 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·H HartmannF Parak
Jan 23, 1987·Science·A T BrüngerM Karplus

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Citations

Feb 9, 2002·Proteins·Dennis VitkupGregory A Petsko
Mar 16, 2002·Chemical Record : an Official Publication of the Chemical Society of Japan ... [et Al.]·Y Mizutani, T Kitagawa
May 7, 1998·Computers & Chemistry·W Nowak
Jul 20, 2002·Biophysical Chemistry·Markus MeuwlyMartin Karplus
Dec 15, 2000·Current Opinion in Structural Biology·I Schlichting, K Chu
Nov 5, 1997·Current Opinion in Structural Biology·K Moffat, Z Ren
Dec 7, 2006·Physical Chemistry Chemical Physics : PCCP·Damián E BikielDarío A Estrin
Feb 11, 2009·Proceedings of the National Academy of Sciences of the United States of America·Ayana TomitaShin-Ichi Adachi
May 10, 2013·The Journal of Chemical Physics·Andrey KrokhotinXubiao Peng
May 9, 2012·The Journal of Chemical Physics·Takayuki TsudukiTakahisa Yamato
Oct 19, 2004·Proceedings of the National Academy of Sciences of the United States of America·Gerhard HummerPhilip A Anfinrud
Apr 7, 2004·Proceedings of the National Academy of Sciences of the United States of America·David R Nutt, Markus Meuwly
May 1, 2007·Biophysical Journal·Massimiliano AnselmiAlfredo Di Nola
Nov 29, 2007·Proteins·Matteo CeccarelliPaolo Ruggerone
Sep 29, 2004·Journal of Structural Biology·Friedrich SchottePhilip A Anfinrud
Mar 15, 2013·Biochimica Et Biophysica Acta·Ursula LieblMarten H Vos
Sep 8, 2016·Proceedings of the National Academy of Sciences of the United States of America·Levin U L Brinkmann, Jochen S Hub
Jan 23, 2017·The Journal of Chemical Physics·Ernest Awoonor-Williams, Christopher N Rowley
Mar 21, 2000·Nature·A OstermannG U Nienhaus
Mar 1, 1997·Nature Structural Biology·M LimP A Anfinrud
Feb 13, 2013·Chemistry : a European Journal·Karin NienhausG Ulrich Nienhaus
May 13, 2008·Journal of Computational Chemistry·Carmen HerrmannMarkus Reiher
Feb 19, 2010·Acta Crystallographica. Section A, Foundations of Crystallography·Ayana TomitaShin-ichi Adachi
Sep 12, 2015·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Michał MajMinhaeng Cho
Apr 21, 2005·Journal of the American Chemical Society·Seongheun Kim, Manho Lim
Dec 31, 2009·Journal of the American Chemical Society·Luca MaraglianoEric Vanden-Eijnden
Dec 8, 2004·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·David R Nutt, Markus Meuwly
Nov 18, 2015·Journal of Chemical Theory and Computation·David De SanchoRobert B Best
May 17, 2012·The Journal of Physical Chemistry. B·Seongheun KimManho Lim
Jul 21, 2006·The Journal of Physical Chemistry. B·David R NuttMarkus Meuwly
Dec 4, 2003·Journal of the American Chemical Society·Constantinos KoutsoupakisConstantinos Varotsis

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