Literature DB >> 21831831

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions.

Andrew J Adamczyk1, Jie Cao, Shina C L Kamerlin, Arieh Warshel.   

Abstract

The proposal that enzymatic catalysis is due to conformational fluctuations has been previously promoted by means of indirect considerations. However, recent works have focused on cases where the relevant motions have components toward distinct conformational regions, whose population could be manipulated by mutations. In particular, a recent work has claimed to provide direct experimental evidence for a dynamical contribution to catalysis in dihydrofolate reductase, where blocking a relevant conformational coordinate was related to the suppression of the motion toward the occluded conformation. The present work utilizes computer simulations to elucidate the true molecular basis for the experimentally observed effect. We start by reproducing the trend in the measured change in catalysis upon mutations (which was assumed to arise as a result of a "dynamical knockout" caused by the mutations). This analysis is performed by calculating the change in the corresponding activation barriers without the need to invoke dynamical effects. We then generate the catalytic landscape of the enzyme and demonstrate that motions in the conformational space do not help drive catalysis. We also discuss the role of flexibility and conformational dynamics in catalysis, once again demonstrating that their role is negligible and that the largest contribution to catalysis arises from electrostatic preorganization. Finally, we point out that the changes in the reaction potential surface modify the reorganization free energy (which includes entropic effects), and such changes in the surface also alter the corresponding motion. However, this motion is never the reason for catalysis, but rather simply a reflection of the shape of the reaction potential surface.

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Year:  2011        PMID: 21831831      PMCID: PMC3161549          DOI: 10.1073/pnas.1111252108

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


  28 in total

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5.  A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis.

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Review 7.  At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Authors:  Shina C L Kamerlin; Arieh Warshel
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Authors:  Michael S Marlow; Jakob Dogan; Kendra K Frederick; Kathleen G Valentine; A Joshua Wand
Journal:  Nat Chem Biol       Date:  2010-04-11       Impact factor: 15.040

10.  Hidden alternative structures of proline isomerase essential for catalysis.

Authors:  James S Fraser; Michael W Clarkson; Sheena C Degnan; Renske Erion; Dorothee Kern; Tom Alber
Journal:  Nature       Date:  2009-12-03       Impact factor: 49.962

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  75 in total

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3.  Evidence that a 'dynamic knockout' in Escherichia coli dihydrofolate reductase does not affect the chemical step of catalysis.

Authors:  E Joel Loveridge; Enas M Behiry; Jiannan Guo; Rudolf K Allemann
Journal:  Nat Chem       Date:  2012-03-11       Impact factor: 24.427

4.  Resolving the complex role of enzyme conformational dynamics in catalytic function.

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Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-26       Impact factor: 11.205

5.  Visualizing networks of mobility in proteins.

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Journal:  Nat Methods       Date:  2013-09       Impact factor: 28.547

Review 6.  Computer aided enzyme design and catalytic concepts.

Authors:  Maria P Frushicheva; Matthew J L Mills; Patrick Schopf; Manoj K Singh; Ram B Prasad; Arieh Warshel
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7.  Cation trafficking propels RNA hydrolysis.

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Journal:  Nat Struct Mol Biol       Date:  2018-08-03       Impact factor: 15.369

Review 8.  Multiple intermediates, diverse conformations, and cooperative conformational changes underlie the catalytic hydride transfer reaction of dihydrofolate reductase.

Authors:  Karunesh Arora; Charles L Brooks
Journal:  Top Curr Chem       Date:  2013

9.  Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis.

Authors:  Garima Jindal; Arieh Warshel
Journal:  Proteins       Date:  2017-09-30

Review 10.  Relationship of femtosecond-picosecond dynamics to enzyme-catalyzed H-transfer.

Authors:  Christopher M Cheatum; Amnon Kohen
Journal:  Top Curr Chem       Date:  2013
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