PMID: 11916410Mar 28, 2002Paper

Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase

Journal of the American Chemical Society
Stavros CaratzoulasSteven D Schwartz

Abstract

In this article we present computational studies of horse liver alcohol dehydrogenase (HLADH). The computations identify a rate-promoting vibration that is symmetrically coupled to the reaction coordinate. In HLADH a bulky amino acid (Val203) is positioned at the face of the nicotinamide adenine dinucleotide (NAD(+)) cofactor distal to alcohol substrate to restrict the separation of reactants and control the stereochemistry. Molecular dynamics simulations were performed on the dimeric HLADH, including the NAD cofactor, the substrate, and the crystallographic waters, for three different configurations, reactants, products, and transition state. From the spectral density for the substrate-NAD relative motion, and that for the NAD-Val203 relative motion, we find that the two motions are in resonance. By computing the associated spectrum, we find that the reaction coordinate is coupled with the substrate-NAD motion, and from the fact that the coupling vanishes at or near the transition state (demonstrated by the disappearance of strong features in the spectral density), we conclude that the substrate-NAD motion plays the role of a promoting vibration symmetrically coupled to the reaction coordinate.

References

Mar 10, 1989·Science·Y ChaJ P Klinman
Aug 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·W Bialek, J N Onuchic
Apr 15, 1997·Proceedings of the National Academy of Sciences of the United States of America·I DaizadehA A Stuchebrukhov
Nov 14, 1997·Proceedings of the National Academy of Sciences of the United States of America·D Antoniou, S D Schwartz
Dec 16, 1997·Proceedings of the National Academy of Sciences of the United States of America·B J BahnsonJ P Klinman
Jun 24, 1998·Proceedings of the National Academy of Sciences of the United States of America·P ZávodszkyG A Petsko
Sep 25, 1998·The Journal of Biological Chemistry·W W ClelandJ A Gerlt
Mar 13, 1999·Biochemistry·J BasranN S Scrutton
Jun 1, 2000·Biochemistry·T C Bruice, S J Benkovic

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Citations

Sep 4, 2008·Photosynthesis Research·Sam Hay, Nigel S Scrutton
Jul 20, 2010·Interdisciplinary Sciences, Computational Life Sciences·Kara E Ranaghan, Adrian J Mulholland
Dec 24, 2013·Chemical Reviews·Joshua P Layfield, Sharon Hammes-Schiffer
Mar 28, 2009·Journal of the American Chemical Society·Karunesh Arora, Charles L Brooks Iii
Jul 23, 2009·Journal of the American Chemical Society·Jigar N BandariaAmnon Kohen
Nov 7, 2009·Journal of the American Chemical Society·Christopher R PudneyNigel S Scrutton
Oct 28, 2011·The Journal of Physical Chemistry. B·Dimitri Antoniou, Steven D Schwartz
Nov 17, 2009·The Journal of Physical Chemistry. B·Arvind Ramanathan, Pratul K Agarwal
Feb 23, 2012·Nature Chemistry·Sam Hay, Nigel S Scrutton
Jun 27, 2002·European Journal of Biochemistry·Dimitri AntoniouSteven D Schwartz
Jun 27, 2002·European Journal of Biochemistry·Michael J Knapp, Judith P Klinman
Nov 9, 2011·Proceedings of the National Academy of Sciences of the United States of America·Rafael G SilvaVern L Schramm
Jul 29, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·J R E T Pineda, S D Schwartz
Jul 29, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Michael J SutcliffeNigel S Scrutton
Jun 8, 2006·Annual Review of Biochemistry·Sharon Hammes-Schiffer, Stephen J Benkovic
Nov 17, 2011·PLoS Biology·Arvind Ramanathan, Pratul K Agarwal
Sep 28, 2004·The Journal of Chemical Physics·Dimitri AntoniouSteven D Schwartz
Dec 14, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jia Luo, Thomas C Bruice
Aug 28, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jia Luo, Thomas C Bruice
Jun 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Zhao-Xun LiangJudith P Klinman
Jul 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Sara L Quaytman, Steven D Schwartz
May 21, 2003·Proceedings of the National Academy of Sciences of the United States of America·Thomas H RodCharles L Brooks
Jul 15, 2015·FEBS Letters·Vickery L Arcus, Christopher R Pudney
Mar 8, 2016·Journal of Chemical Theory and Computation·Matthew J Varga, Steven D Schwartz
Jun 22, 2016·The Journal of Physical Chemistry Letters·Michael W Dzierlenga, Steven D Schwartz
Jul 6, 2004·Archives of Biochemistry and Biophysics·Laura MasgrauNigel S Scrutton
Apr 4, 2015·Physical Chemistry Chemical Physics : PCCP·Linus O JohannissenNigel S Scrutton
Oct 19, 2006·Physical Chemistry Chemical Physics : PCCP·Michael J Sutcliffe, Nigel S Scrutton
Jun 23, 2010·Physical Chemistry Chemical Physics : PCCP·Daniel MurdockPatrick H Vaccaro
Jul 23, 2003·Nature Structural Biology·Elizabeth D GetzoffUlrich K Genick
Apr 25, 2019·Chembiochem : a European Journal of Chemical Biology·Alan F ScottRudolf K Allemann
Apr 22, 2020·Annual Review of Physical Chemistry·Christopher M Cheatum
Oct 26, 2005·The Biochemical Journal·Richard S SwanwickRudolf K Allemann
Dec 23, 2017·Protein Science : a Publication of the Protein Society·Karthik K ShanmuganathamBryce V Plapp

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