Literature DB >> 14663649

Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymes.

Mats H M Olsson1, Per E M Siegbahn, Arieh Warshel.   

Abstract

The role of nuclear quantum mechanical effects in enzyme catalysis has recently attracted significant interest both from theoretical and experimental points of view. From a theoretical point of view, it is undoubtedly a challenge to try to account for the observed tunneling in the protein by microscopic simulations without adjustable parameters. One of the most spectacular examples of nuclear quantum mechanical effects is the reaction of lipoxygenase, which is characterized by a very large kinetic isotope effect and, thus, provides an excellent benchmark for simulation approaches. In the present study, we report a microscopic simulation of the large kinetic isotope effect in soybean lipoxygenase and its temperature dependence. This is, to the best of our knowledge, the first time that a very large nuclear quantum mechanical contribution to the activation free energy of a hydrogen atom transfer reaction and its temperature dependence have been evaluated by microscopic simulation. The simulation reproduces quite well the experimental kinetic information and the corresponding difference between the classical and quantum mechanical activation free energies for the H and D transfer reactions.

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Year:  2003        PMID: 14663649     DOI: 10.1007/s00775-003-0503-2

Source DB:  PubMed          Journal:  J Biol Inorg Chem        ISSN: 0949-8257            Impact factor:   3.358


  10 in total

Review 1.  Lipoxygenases: occurrence, functions, catalysis, and acquisition of substrate.

Authors:  A R Brash
Journal:  J Biol Chem       Date:  1999-08-20       Impact factor: 5.157

2.  Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction.

Authors:  I Feierberg; V Luzhkov; J Aqvist
Journal:  J Biol Chem       Date:  2000-07-28       Impact factor: 5.157

Review 3.  Quantum mechanical methods for enzyme kinetics.

Authors:  Jiali Gao; Donald G Truhlar
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

Review 4.  Dynamics of biochemical and biophysical reactions: insight from computer simulations.

Authors:  A Warshel; W W Parson
Journal:  Q Rev Biophys       Date:  2001-11       Impact factor: 5.318

5.  Temperature-dependent isotope effects in soybean lipoxygenase-1: correlating hydrogen tunneling with protein dynamics.

Authors:  Michael J Knapp; Keith Rickert; Judith P Klinman
Journal:  J Am Chem Soc       Date:  2002-04-17       Impact factor: 15.419

Review 6.  The structure and function of lipoxygenase.

Authors:  M J Nelson; S P Seitz
Journal:  Curr Opin Struct Biol       Date:  1994-12       Impact factor: 6.809

7.  Hydride transfer in liver alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion.

Authors:  S R Billeter; S P Webb; P K Agarwal; T Iordanov; S Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2001-11-14       Impact factor: 15.419

8.  Density-functional investigation on the mechanism of H-atom abstraction by lipoxygenase.

Authors:  Nicolai Lehnert; Edward I Solomon
Journal:  J Biol Inorg Chem       Date:  2002-11-14       Impact factor: 3.358

9.  A crosslinked cofactor in lysyl oxidase: redox function for amino acid side chains.

Authors:  S X Wang; M Mure; K F Medzihradszky; A L Burlingame; D E Brown; D M Dooley; A J Smith; H M Kagan; J P Klinman
Journal:  Science       Date:  1996-08-23       Impact factor: 47.728

10.  The first experimental test of the hypothesis that enzymes have evolved to enhance hydrogen tunneling.

Authors:  Kenneth M Doll; Bruce R Bender; Richard G Finke
Journal:  J Am Chem Soc       Date:  2003-09-10       Impact factor: 15.419

  10 in total
  10 in total

1.  Arrhenius curves of hydrogen transfers: tunnel effects, isotope effects and effects of pre-equilibria.

Authors:  Hans-Heinrich Limbach; Juan Miguel Lopez; Amnon Kohen
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-08-29       Impact factor: 6.237

Review 2.  Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions.

Authors:  Jingzhi Pu; Jiali Gao; Donald G Truhlar
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

3.  Theoretical Studies of Proton-Coupled Electron Transfer: Models and Concepts Relevant to Bioenergetics.

Authors:  Sharon Hammes-Schiffer; Elizabeth Hatcher; Hiroshi Ishikita; Jonathan H Skone; Alexander V Soudackov
Journal:  Coord Chem Rev       Date:  2008-02-01       Impact factor: 22.315

Review 4.  Hydrogen tunneling in enzymes and biomimetic models.

Authors:  Joshua P Layfield; Sharon Hammes-Schiffer
Journal:  Chem Rev       Date:  2013-12-20       Impact factor: 60.622

5.  Impact of distal mutation on hydrogen transfer interface and substrate conformation in soybean lipoxygenase.

Authors:  Sarah J Edwards; Alexander V Soudackov; Sharon Hammes-Schiffer
Journal:  J Phys Chem B       Date:  2010-05-20       Impact factor: 2.991

6.  Analysis of Hydrogen Tunneling in an Enzyme Active Site using von Neumann Measurements.

Authors:  Isaiah Sumner; Srinivasan S Iyengar
Journal:  J Chem Theory Comput       Date:  2010       Impact factor: 6.006

7.  Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations.

Authors:  Pengfei Li; Alexander V Soudackov; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2018-02-19       Impact factor: 15.419

8.  Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events.

Authors:  Prasad Phatak; Isaiah Sumner; Srinivasan S Iyengar
Journal:  J Phys Chem B       Date:  2012-08-17       Impact factor: 2.991

Review 9.  Proton-coupled electron transfer in solution, proteins, and electrochemistry.

Authors:  Sharon Hammes-Schiffer; Alexander V Soudackov
Journal:  J Phys Chem B       Date:  2008-10-09       Impact factor: 2.991

Review 10.  Applications of density functional theory to iron-containing molecules of bioinorganic interest.

Authors:  Hajime Hirao; Nandun Thellamurege; Xi Zhang
Journal:  Front Chem       Date:  2014-04-29       Impact factor: 5.221

  10 in total

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