Why Enzymes Are Proficient Catalysts: Beyond the Pauling Paradigm

Zhang, Xiyun; Houk, K. N.

doi:10.1002/chin.200529293

Cited by 33 publications

(90 citation statements)

References 1 publication

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“…The lowest reaction barrier is largely determined by the active-site electrostatic environment, which is constituted by the achieved transition-state configuration. Various theoretical models were proposed and a series of review articles were recently published [46,[50][51][52][53][54][55][56][57][58][59][60][61].…”

Section: Discussionmentioning

confidence: 99%

Femtochemistry in enzyme catalysis: DNA photolyase

Kao

Saxena

Wang

et al. 2007

Cell Biochem Biophys

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Photolyase uses light energy to split UV-induced cyclobutane pyrimidine dimers in damaged DNA. This photoenzyme encompasses a series of elementary dynamical processes during repair function from early photoinitiation by a photoantenna molecule to enhance repair efficiency, to in vitro photoreduction through aromatic residues to reconvert the cofactor to the active form, and to final photorepair to fix damaged DNA. The corresponding series of dynamics include resonance energy transfer, intraprotein electron transfer, and intermolecular electron transfer, bond breaking-making rearrangements and back electron return, respectively. We review here our recent direct studies of these dynamical processes in real time, which showed that all these elementary reactions in the enzyme occur within subnanosecond timescale. Active-site solvation was observed to play a critical role in the continuous modulation of catalytic reactions. As a model system for enzyme catalysis, we isolated the enzyme-substrate complex in the transition-state region and mapped out the entire evolution of unmasked catalytic reactions of DNA repair. These observed synergistic motions in the active site reveal a perfect correlation of structural integrity and dynamical locality to ensure maximum repair efficiency on the ultrafast time scale.

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Section: Discussionmentioning

confidence: 99%

Femtochemistry in enzyme catalysis: DNA photolyase

Kao

Saxena

Wang

et al. 2007

Cell Biochem Biophys

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“…We note that nucleophilic covalent catalysis is the most dominant form of covalent catalysis, with electrophilic second, and only a single entry in which homolytic methods are employed. It has been reported that partially covalent catalysis occurs in enzymes 29 and in MACiE we have chosen to classify such partial covalent/ionic bonds under proton shuttling or electrostatic stabilisation, as a consequence of the structure of MACiE annotations.…”

Section: Functions Performed By Amino Acid Residues During Catalysismentioning

confidence: 99%

Understanding the Functional Roles of Amino Acid Residues in Enzyme Catalysis

Holliday

Mitchell

Thornton

2009

Journal of Molecular Biology

135

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“…Enzymes can be viewed as cellular tools to control and regulate the concentrations of certain molecules. The enthalpic barrier generally reported in the literature varies from 15 to 40 kcal/mol for different proteins (25). In solid state physics, the magnetization of 50-100 nm sized grains may be reversed by overcoming an energy barrier (26,27).…”

Section: Figurementioning

confidence: 99%

A Kinetic Analysis of DNA Ejection from Tailed Phages Revealing the Prerequisite Activation Energy

Raspaud

Forth

São-José³

et al. 2007

Biophysical Journal

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All tailed bacteriophages follow the same general scheme of infection: they bind to their specific host receptor and then transfer their genome into the bacterium. DNA translocation is thought to be initiated by the strong pressure due to DNA packing inside the capsid. However, the exact mechanism by which each phage controls its DNA ejection remains unknown. Using light scattering, we analyzed the kinetics of in vitro DNA release from phages SPP1 and lambda (Siphoviridae family) and found a simple exponential decay. The ejection characteristic time was studied as a function of the temperature and found to follow an Arrhenius law, allowing us to determine the activation energy that governs DNA ejection. A value of 25-30 kcal/mol is obtained for SPP1 and lambda, comparable to the one measured in vitro for T5 (Siphoviridae) and in vivo for T7 (Podoviridae). This suggests similar mechanisms of DNA ejection control. In all tailed phages, the opening of the connector-tail channel is needed for DNA release and could constitute the limiting step. The common value of the activation energy likely reflects the existence for all phages of an optimum value, ensuring a compromise between efficient DNA delivery and high stability of the virus.

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Why Enzymes Are Proficient Catalysts: Beyond the Pauling Paradigm

Abstract: For Abstract see ChemInform Abstract in Full Text.

Cited by 33 publications

References 1 publication

Femtochemistry in enzyme catalysis: DNA photolyase

Femtochemistry in enzyme catalysis: DNA photolyase

Understanding the Functional Roles of Amino Acid Residues in Enzyme Catalysis

A Kinetic Analysis of DNA Ejection from Tailed Phages Revealing the Prerequisite Activation Energy

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