Literature DB >> 23746260

Hydrogen tunneling links protein dynamics to enzyme catalysis.

Judith P Klinman1, Amnon Kohen.   

Abstract

The relationship between protein dynamics and function is a subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Here, we show how the quantum mechanical hydrogen tunneling associated with enzymatic C-H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. A possible extension of this view to methyl transfer and other catalyzed reactions is also presented. The impact of understanding these dynamics on the conceptual framework for enzyme activity, inhibitor/drug design, and biomimetic catalyst design is likely to be substantial.

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Year:  2013        PMID: 23746260      PMCID: PMC4066974          DOI: 10.1146/annurev-biochem-051710-133623

Source DB:  PubMed          Journal:  Annu Rev Biochem        ISSN: 0066-4154            Impact factor:   23.643


  121 in total

1.  Pressure effects on enzyme-catalyzed quantum tunneling events arise from protein-specific structural and dynamic changes.

Authors:  Sam Hay; Linus O Johannissen; Parvinder Hothi; Michael J Sutcliffe; Nigel S Scrutton
Journal:  J Am Chem Soc       Date:  2012-06-05       Impact factor: 15.419

2.  Enzymatic methyl transfer: role of an active site residue in generating active site compaction that correlates with catalytic efficiency.

Authors:  Jianyu Zhang; Judith P Klinman
Journal:  J Am Chem Soc       Date:  2011-10-10       Impact factor: 15.419

3.  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

4.  Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase.

Authors:  Lin Wang; Nina M Goodey; Stephen J Benkovic; Amnon Kohen
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-10       Impact factor: 11.205

5.  Probes of hydrogen tunneling with horse liver alcohol dehydrogenase at subzero temperatures.

Authors:  S Tsai ; J P Klinman
Journal:  Biochemistry       Date:  2001-02-20       Impact factor: 3.162

6.  The use of isotope effects to determine transition-state structure for enzymic reactions.

Authors:  W W Cleland
Journal:  Methods Enzymol       Date:  1982       Impact factor: 1.600

7.  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

8.  Examination of enzymatic H-tunneling through kinetics and dynamics.

Authors:  Jigar N Bandaria; Christopher M Cheatum; Amnon Kohen
Journal:  J Am Chem Soc       Date:  2009-07-29       Impact factor: 15.419

9.  Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry.

Authors:  Joan J Englander; Charyl Del Mar; Will Li; S Walter Englander; Jack S Kim; David D Stranz; Yoshitomo Hamuro; Virgil L Woods
Journal:  Proc Natl Acad Sci U S A       Date:  2003-05-28       Impact factor: 11.205

10.  Evidence that both protium and deuterium undergo significant tunneling in the reaction catalyzed by bovine serum amine oxidase.

Authors:  K L Grant; J P Klinman
Journal:  Biochemistry       Date:  1989-08-08       Impact factor: 3.162

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  114 in total

1.  Protein-like proton exchange in a synthetic host cavity.

Authors:  William M Hart-Cooper; Carmelo Sgarlata; Charles L Perrin; F Dean Toste; Robert G Bergman; Kenneth N Raymond
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-30       Impact factor: 11.205

2.  Mechanism of Flavoprotein l-6-Hydroxynicotine Oxidase: pH and Solvent Isotope Effects and Identification of Key Active Site Residues.

Authors:  Paul F Fitzpatrick; Fatemeh Chadegani; Shengnan Zhang; Vi Dougherty
Journal:  Biochemistry       Date:  2017-01-26       Impact factor: 3.162

3.  A Biophysical Perspective on Enzyme Catalysis.

Authors:  Pratul K Agarwal
Journal:  Biochemistry       Date:  2018-12-18       Impact factor: 3.162

4.  Moving Through Barriers in Science and Life.

Authors:  Judith P Klinman
Journal:  Annu Rev Biochem       Date:  2019-06-20       Impact factor: 23.643

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

Authors:  Subhendu Roy; Patrick Schopf; Arieh Warshel
Journal:  J Phys Chem B       Date:  2017-07-05       Impact factor: 2.991

6.  Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase.

Authors:  Jiayue Li; Gabriel Fortunato; Jennifer Lin; Pratul K Agarwal; Amnon Kohen; Priyanka Singh; Christopher M Cheatum
Journal:  Biochemistry       Date:  2019-08-30       Impact factor: 3.162

7.  Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site.

Authors:  Lu Wang; Stephen D Fried; Steven G Boxer; Thomas E Markland
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-12       Impact factor: 11.205

8.  Kinetics of low-temperature transitions and a reaction rate theory from non-equilibrium distributions.

Authors:  Vincenzo Aquilanti; Nayara Dantas Coutinho; Valter Henrique Carvalho-Silva
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2017-04-28       Impact factor: 4.226

9.  Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.

Authors:  Shenshen Hu; Adam R Offenbacher; Erin M Thompson; Christine L Gee; Jarett Wilcoxen; Cody A M Carr; Daniil M Prigozhin; Vanessa Yang; Tom Alber; R David Britt; James S Fraser; Judith P Klinman
Journal:  J Am Chem Soc       Date:  2019-01-15       Impact factor: 15.419

10.  Cation trafficking propels RNA hydrolysis.

Authors:  Nadine L Samara; Wei Yang
Journal:  Nat Struct Mol Biol       Date:  2018-08-03       Impact factor: 15.369

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