Literature DB >> 17581872

Coupling of hydrogenic tunneling to active-site motion in the hydrogen radical transfer catalyzed by a coenzyme B12-dependent mutase.

Agnieszka Dybala-Defratyka1, Piotr Paneth, Ruma Banerjee, Donald G Truhlar.   

Abstract

Hydrogen transfer reactions catalyzed by coenzyme B(12)-dependent methylmalonyl-CoA mutase have very large kinetic isotope effects, indicating that they proceed by a highly quantal tunneling mechanism. We explain the kinetic isotope effect by using a combined quantum mechanical/molecular mechanical potential and semiclassical quantum dynamics calculations. Multidimensional tunneling increases the magnitude of the calculated intrinsic hydrogen kinetic isotope effect by a factor of 3.6 from 14 to 51, in excellent agreement with experimental results. These calculations confirm that tunneling contributions can be large enough to explain even a kinetic isotope effect >50, not because the barrier is unusually thin but because corner-cutting tunneling decreases the distance over which the system tunnels without a comparable increase in either the effective potential barrier or the effective mass for tunneling.

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Year:  2007        PMID: 17581872      PMCID: PMC1904141          DOI: 10.1073/pnas.0702188104

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  27 in total

Review 1.  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

2.  Radical Shuttling in a Protein: Ribose Pseudorotation Controls Alkyl-Radical Transfer in the Coenzyme B(12) Dependent Enzyme Glutamate Mutase This work was supported by the Österreichische Akademie der Wissenschaften (APART fellowship 614), the Österreichische Fonds zur Förderung der wissenschaftlichen Forschung (FWF-project 11599), and the European Commission (TMR project number ERB 4061 PL 95-0307). Crystallographic data were collected at the EMBL-beamline BW7B at DESY in Hamburg, Germany. We thank the beamline scientists for their assistance, and Ingrid Dreveny, Günter Gartler, Gerwald Jogl, and Oliver Sauer for their help during data collection. This research emerged from a collaboration with Prof. W. Buckel (Marburg) who supplied us with clones of the glutamate mutase proteins.

Authors:  Karl Gruber; Riikka Reitzer; Christoph Kratky
Journal:  Angew Chem Int Ed Engl       Date:  2001-09-17       Impact factor: 15.336

Review 3.  Radical carbon skeleton rearrangements: catalysis by coenzyme B12-dependent mutases.

Authors:  Ruma Banerjee
Journal:  Chem Rev       Date:  2003-06       Impact factor: 60.622

Review 4.  The incorporation of quantum effects in enzyme kinetics modeling.

Authors:  Donald G Truhlar; Jiali Gao; Cristobal Alhambra; Mireia Garcia-Viloca; José Corchado; Maria Luz Sánchez; Jordi Villà
Journal:  Acc Chem Res       Date:  2002-06       Impact factor: 22.384

Review 5.  How enzymes work: analysis by modern rate theory and computer simulations.

Authors:  Mireia Garcia-Viloca; Jiali Gao; Martin Karplus; Donald G Truhlar
Journal:  Science       Date:  2004-01-09       Impact factor: 47.728

6.  Structure of the 5,6-dimethyl-benzimidazolylcobamide coenzyme.

Authors:  P G LENHERT; D C HODGKIN
Journal:  Nature       Date:  1961-12-09       Impact factor: 49.962

7.  How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex.

Authors:  J Masuda; N Shibata; Y Morimoto; T Toraya; N Yasuoka
Journal:  Structure       Date:  2000-07-15       Impact factor: 5.006

8.  5'-Deoxyadenosine contacts the substrate radical intermediate in the active site of ethanolamine ammonia-lyase: 2H and 13C electron nuclear double resonance studies.

Authors:  R LoBrutto; V Bandarian; O T Magnusson; X Chen; V L Schramm; G H Reed
Journal:  Biochemistry       Date:  2001-01-09       Impact factor: 3.162

9.  Thermodynamic and kinetic characterization of Co-C bond homolysis catalyzed by coenzyme B(12)-dependent methylmalonyl-CoA mutase.

Authors:  S Chowdhury; R Banerjee
Journal:  Biochemistry       Date:  2000-07-11       Impact factor: 3.162

10.  Theoretical evaluation of the hydrogen kinetic isotope effect on the first step of the methylmalonyl-CoA mutase reaction.

Authors:  A Dybala-Defratyka; P Paneth
Journal:  J Inorg Biochem       Date:  2001-10       Impact factor: 4.155

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  20 in total

1.  Taking Ockham's razor to enzyme dynamics and catalysis.

Authors:  David R Glowacki; Jeremy N Harvey; Adrian J Mulholland
Journal:  Nat Chem       Date:  2012-01-29       Impact factor: 24.427

2.  An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling.

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  J Phys Org Chem       Date:  2010-07       Impact factor: 2.391

3.  Cobalamin- and corrinoid-dependent enzymes.

Authors:  Rowena G Matthews
Journal:  Met Ions Life Sci       Date:  2009-01-30

4.  Theoretical studies on bimolecular reaction dynamics.

Authors:  David C Clary
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-14       Impact factor: 11.205

5.  The enzyme aromatic amine dehydrogenase induces a substrate conformation crucial for promoting vibration that significantly reduces the effective potential energy barrier to proton transfer.

Authors:  Linus O Johannissen; Nigel S Scrutton; Michael J Sutcliffe
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

Review 6.  Transition state theory for enzyme kinetics.

Authors:  Donald G Truhlar
Journal:  Arch Biochem Biophys       Date:  2015-05-23       Impact factor: 4.013

7.  The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm.

Authors:  Patrick Schopf; Matthew J L Mills; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-24       Impact factor: 11.205

8.  Two-dimensional infrared spectroscopy of azido-nicotinamide adenine dinucleotide in water.

Authors:  Samrat Dutta; William Rock; Richard J Cook; Amnon Kohen; Christopher M Cheatum
Journal:  J Chem Phys       Date:  2011-08-07       Impact factor: 3.488

9.  Hydrogen tunneling in adenosylcobalamin-dependent glutamate mutase: evidence from intrinsic kinetic isotope effects measured by intramolecular competition.

Authors:  Miri Yoon; Hangtian Song; Kristina Håkansson; E Neil G Marsh
Journal:  Biochemistry       Date:  2010-04-13       Impact factor: 3.162

Review 10.  At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  Proteins       Date:  2010-05-01
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