Literature DB >> 20457944

Elusive transition state of alcohol dehydrogenase unveiled.

Daniel Roston1, Amnon Kohen.   

Abstract

For several decades the hydride transfer catalyzed by alcohol dehydrogenase has been difficult to understand. Here we add to the large corpus of anomalous and paradoxical data collected for this reaction by measuring a normal (> 1) 2 degrees kinetic isotope effect (KIE) for the reduction of benzaldehyde. Because the relevant equilibrium effect is inverse (< 1), this KIE eludes the traditional interpretation of 2 degrees KIEs. It does, however, enable the development of a comprehensive model for the "tunneling ready state" (TRS) of the reaction that fits into the general scheme of Marcus-like models of hydrogen tunneling. The TRS is the ensemble of states along the intricate reorganization coordinate, where H tunneling between the donor and acceptor occurs (the crossing point in Marcus theory). It is comparable to the effective transition state implied by ensemble-averaged variational transition state theory. Properties of the TRS are approximated as an average of the individual properties of the donor and acceptor states. The model is consistent with experimental findings that previously appeared contradictory; specifically, it resolves the long-standing ambiguity regarding the location of the TRS (aldehyde-like vs. alcohol-like). The new picture of the TRS for this reaction identifies the principal components of the collective reaction coordinate and the average structure of the saddle point along that coordinate.

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Year:  2010        PMID: 20457944      PMCID: PMC2906880          DOI: 10.1073/pnas.1000931107

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


  26 in total

1.  Atomic description of an enzyme reaction dominated by proton tunneling.

Authors:  Laura Masgrau; Anna Roujeinikova; Linus O Johannissen; Parvinder Hothi; Jaswir Basran; Kara E Ranaghan; Adrian J Mulholland; Michael J Sutcliffe; Nigel S Scrutton; David Leys
Journal:  Science       Date:  2006-04-14       Impact factor: 47.728

2.  Linking protein structure and dynamics to catalysis: the role of hydrogen tunnelling.

Authors:  Judith P Klinman
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-08-29       Impact factor: 6.237

Review 3.  Electrostatic basis for enzyme catalysis.

Authors:  Arieh Warshel; Pankaz K Sharma; Mitsunori Kato; Yun Xiang; Hanbin Liu; Mats H M Olsson
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

4.  Estimation of rate and dissociation constants involving ternary complexes in reactions catalysed by yeast alcohol dehydrogenase.

Authors:  F M Dickinson; C J Dickenson
Journal:  Biochem J       Date:  1978-06-01       Impact factor: 3.857

5.  Experimental evidence for enzyme-enhanced coupled motion/quantum mechanical hydrogen tunneling by ketosteroid isomerase.

Authors:  Thomas C Wilde; Grzegorz Blotny; Ralph M Pollack
Journal:  J Am Chem Soc       Date:  2008-04-22       Impact factor: 15.419

6.  Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase.

Authors:  A Kohen; R Cannio; S Bartolucci; J P Klinman
Journal:  Nature       Date:  1999-06-03       Impact factor: 49.962

7.  Modeling temperature dependent kinetic isotope effects for hydrogen transfer in a series of soybean lipoxygenase mutants: The effect of anharmonicity upon transfer distance.

Authors:  Matthew P Meyer; Judith P Klinman
Journal:  Chem Phys       Date:  2005-12-07       Impact factor: 2.348

8.  Boundary conditions for the Swain-Schaad relationship as a criterion for hydrogen tunneling.

Authors:  Amnon Kohen; Jan H Jensen
Journal:  J Am Chem Soc       Date:  2002-04-17       Impact factor: 15.419

Review 9.  Hydrogen tunneling and protein motion in enzyme reactions.

Authors:  Sharon Hammes-Schiffer
Journal:  Acc Chem Res       Date:  2006-02       Impact factor: 22.384

10.  Activity of yeast alcohol dehydrogenases on benzyl alcohols and benzaldehydes: characterization of ADH1 from Saccharomyces carlsbergensis and transition state analysis.

Authors:  Suresh Pal; Doo-Hong Park; Bryce V Plapp
Journal:  Chem Biol Interact       Date:  2008-11-05       Impact factor: 5.192

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  37 in total

1.  Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes.

Authors:  Bryce V Plapp; S Ramaswamy
Journal:  Biochemistry       Date:  2012-05-01       Impact factor: 3.162

2.  A critical test of the "tunneling and coupled motion" concept in enzymatic alcohol oxidation.

Authors:  Daniel Roston; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2013-09-10       Impact factor: 15.419

3.  Triple isotopic labeling and kinetic isotope effects: exposing H-transfer steps in enzymatic systems.

Authors:  Arundhuti Sen; Atsushi Yahashiri; Amnon Kohen
Journal:  Biochemistry       Date:  2011-06-30       Impact factor: 3.162

4.  Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.

Authors:  Qi Guo; Lokesh Gakhar; Kyle Wickersham; Kevin Francis; Alexandra Vardi-Kilshtain; Dan T Major; Christopher M Cheatum; Amnon Kohen
Journal:  Biochemistry       Date:  2016-05-03       Impact factor: 3.162

5.  Femtosecond dynamics coupled to chemical barrier crossing in a Born-Oppenheimer enzyme.

Authors:  Rafael G Silva; Andrew S Murkin; Vern L Schramm
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-07       Impact factor: 11.205

6.  Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis.

Authors:  Karthik K Shanmuganatham; Rachel S Wallace; Ann Ting-I Lee; Bryce V Plapp
Journal:  Protein Sci       Date:  2018-01-25       Impact factor: 6.725

Review 7.  A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer.

Authors:  Archie C Reyes; Tina L Amyes; John P Richard
Journal:  Org Biomol Chem       Date:  2017-10-31       Impact factor: 3.876

8.  Stereospecific multiple isotopic labeling of benzyl alcohol.

Authors:  Daniel Roston; Amnon Kohen
Journal:  J Labelled Comp Radiopharm       Date:  2013-12-11       Impact factor: 1.921

9.  A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase.

Authors:  Zhen Wang; Thelma Abeysinghe; Janet S Finer-Moore; Robert M Stroud; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2012-10-15       Impact factor: 15.419

10.  QM/MM Analysis of Transition States and Transition State Analogues in Metalloenzymes.

Authors:  D Roston; Q Cui
Journal:  Methods Enzymol       Date:  2016-07-01       Impact factor: 1.600

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