Literature DB >> 28613876

Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions.

Subhendu Roy1, Patrick Schopf2, Arieh Warshel1.   

Abstract

The origin of the non-Arrhenius behavior of the rate constant for hydride transfer enzymatic reactions has been a puzzling problem since its initial observation. This effect has been used originally to support the idea that enzymes work by dynamical effects and more recently to suggest an entropy funnel model. Our analysis, however, has advanced the idea that the reason for the non-Arrhenius trend reflects the temperature dependence of the rearrangements of the protein polar groups in response to the change in the charge distribution of the reacting system during the transition from the ground state (GS) to the transition state (TS). Here we examine the validity of our early proposal by simulating the catalytic reaction of alcohol dehydrogenase (ADH) and determine the microscopic origin of the entropic and enthalpic contributions to the activation barrier. The corresponding analysis establishes the origin of the non-Arrhenius behaviors and quantifies our original suggestion that the classical effect is due to the entropic contributions of the environment. We also find that the quantum effects reflect in part the temperature dependence of the donor-acceptor distance.

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Year:  2017        PMID: 28613876      PMCID: PMC8269111          DOI: 10.1021/acs.jpcb.7b03698

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  24 in total

1.  How important are entropic contributions to enzyme catalysis?

Authors:  J Villa; M Strajbl; T M Glennon; Y Y Sham; Z T Chu; A Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2000-10-24       Impact factor: 11.205

2.  What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?

Authors:  Pankaz K Sharma; Yun Xiang; Mitsunori Kato; Arieh Warshel
Journal:  Biochemistry       Date:  2005-08-30       Impact factor: 3.162

3.  Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase.

Authors:  Mingliang Wang; Zhenyu Lu; Weitao Yang
Journal:  J Chem Phys       Date:  2006-03-28       Impact factor: 3.488

4.  A hierarchy of timescales in protein dynamics is linked to enzyme catalysis.

Authors:  Katherine A Henzler-Wildman; Ming Lei; Vu Thai; S Jordan Kerns; Martin Karplus; Dorothee Kern
Journal:  Nature       Date:  2007-11-18       Impact factor: 49.962

5.  Efficient coupling of catalysis and dynamics in the E1 component of Escherichia coli pyruvate dehydrogenase multienzyme complex.

Authors:  Sachin Kale; Gözde Ulas; Jaeyoung Song; Gary W Brudvig; William Furey; Frank Jordan
Journal:  Proc Natl Acad Sci U S A       Date:  2008-01-23       Impact factor: 11.205

Review 6.  Dynamic personalities of proteins.

Authors:  Katherine Henzler-Wildman; Dorothee Kern
Journal:  Nature       Date:  2007-12-13       Impact factor: 49.962

7.  Proton-transport mechanisms in cytochrome c oxidase revealed by studies of kinetic isotope effects.

Authors:  Ann-Louise Johansson; Suman Chakrabarty; Catrine L Berthold; Martin Högbom; Arieh Warshel; Peter Brzezinski
Journal:  Biochim Biophys Acta       Date:  2011-04-02

8.  Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase.

Authors:  Hanbin Liu; Arieh Warshel
Journal:  J Phys Chem B       Date:  2007-06-16       Impact factor: 2.991

9.  Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase.

Authors:  Suwipa Saen-Oon; Mahmoud Ghanem; Vern L Schramm; Steven D Schwartz
Journal:  Biophys J       Date:  2008-01-30       Impact factor: 4.033

10.  Protein surface softness is the origin of enzyme cold-adaptation of trypsin.

Authors:  Geir Villy Isaksen; Johan Åqvist; Bjørn Olav Brandsdal
Journal:  PLoS Comput Biol       Date:  2014-08-28       Impact factor: 4.475

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  5 in total

1.  Glutamine Hydrolysis by Imidazole Glycerol Phosphate Synthase Displays Temperature Dependent Allosteric Activation.

Authors:  George P Lisi; Allen A Currier; J Patrick Loria
Journal:  Front Mol Biosci       Date:  2018-02-06

2.  Temperature Dependence of Rate Processes Beyond Arrhenius and Eyring: Activation and Transitivity.

Authors:  Valter H Carvalho-Silva; Nayara D Coutinho; Vincenzo Aquilanti
Journal:  Front Chem       Date:  2019-05-29       Impact factor: 5.221

3.  Conformational sampling and kinetics changes across a non-Arrhenius break point in the enzyme thermolysin.

Authors:  Ming Dong; Mackenzie L Lauro; Timothy J Koblish; Brian J Bahnson
Journal:  Struct Dyn       Date:  2020-02-14       Impact factor: 2.920

4.  Hidden Conformational States and Strange Temperature Optima in Enzyme Catalysis.

Authors:  Johan Åqvist; Jaka Sočan; Miha Purg
Journal:  Biochemistry       Date:  2020-09-25       Impact factor: 3.162

5.  Evolution of Optimized Hydride Transfer Reaction and Overall Enzyme Turnover in Human Dihydrofolate Reductase.

Authors:  Jiayue Li; Jennifer Lin; Amnon Kohen; Priyanka Singh; Kevin Francis; Christopher M Cheatum
Journal:  Biochemistry       Date:  2021-12-07       Impact factor: 3.162

  5 in total

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