» Articles » PMID: 22354429

Good Vibrations in Enzyme-catalysed Reactions

Overview
Journal Nat Chem
Specialty Chemistry
Date 2012 Feb 23
PMID 22354429
Citations 109
Authors
Affiliations
Soon will be listed here.
Abstract

Fast motions (femtosecond to picosecond) and their potential involvement during enzyme-catalysed reactions have ignited considerable interest in recent years. Their influence on reaction chemistry has been inferred indirectly from studies of the anomalous temperature dependence of kinetic isotope effects and computational simulations. But can such motion reduce the width and height of energy barriers along the reaction coordinate, and contribute to quantum mechanical and/or classical nuclear-transfer chemistry? Here we discuss contemporary ideas for enzymatic reactions invoking a role for fast 'promoting' (or 'compressive') motions that, in principle, can aid hydrogen-transfer reactions. Of key importance is the direct demonstration of a role for compressive motions and the ability to understand in atomic detail the structural origin of these fast motions, but so far this has not been achieved. Here we discuss both indirect experimental evidence that supports a role for compressive motion and the additional insight gained from computational simulations.

Citing Articles

Decoupling of the onset of anharmonicity between a protein and its surface water around 200 K.

Zheng L, Zhou B, Wu B, Tan Y, Huang J, Tyagi M Elife. 2024; 13.

PMID: 39158544 PMC: 11333040. DOI: 10.7554/eLife.95665.


Temporal Resolution of Activity-Related Solvation Dynamics in the TIM Barrel Enzyme Murine Adenosine Deaminase.

Gao S, Wu X, Zhang W, Richardson T, Barrow S, Thompson-Kucera C ACS Catal. 2024; 14(7):4554-4567.

PMID: 39099600 PMC: 11296675. DOI: 10.1021/acscatal.3c02687.


Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity.

Karvelis E, Swanson C, Tidor B ACS Catal. 2024; 14(14):10491-10509.

PMID: 39050899 PMC: 11264209. DOI: 10.1021/acscatal.4c01446.


Study of the Effects of Remote Heavy Group Vibrations on the Temperature Dependence of Hydride Kinetic Isotope Effects of the NADH/NAD Model Reactions.

Singh G, Austin A, Bai M, Bradshaw J, Hammann B, Kabotso D ACS Omega. 2024; 9(18):20593-20600.

PMID: 38737086 PMC: 11080011. DOI: 10.1021/acsomega.4c02383.


Identification of the Thermal Activation Network in Human 15-Lipoxygenase-2: Divergence from Plant Orthologs and Its Relationship to Hydrogen Tunneling Activation Barriers.

Ohler A, Taylor P, Bledsoe J, Iavarone A, Gilbert N, Offenbacher A ACS Catal. 2024; 14(7):5444-5457.

PMID: 38601784 PMC: 11003420. DOI: 10.1021/acscatal.4c00439.


References
1.
Liu H, Warshel A . The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies. Biochemistry. 2007; 46(20):6011-25. DOI: 10.1021/bi700201w. View

2.
Pang J, Hay S, Scrutton N, Sutcliffe M . Deep tunneling dominates the biologically important hydride transfer reaction from NADH to FMN in morphinone reductase. J Am Chem Soc. 2008; 130(22):7092-7. DOI: 10.1021/ja800471f. View

3.
Nunez S, Antoniou D, Schramm V, Schwartz S . Promoting vibrations in human purine nucleoside phosphorylase. A molecular dynamics and hybrid quantum mechanical/molecular mechanical study. J Am Chem Soc. 2004; 126(48):15720-9. DOI: 10.1021/ja0457563. View

4.
Bandaria J, Dutta S, Nydegger M, Rock W, Kohen A, Cheatum C . Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase. Proc Natl Acad Sci U S A. 2010; 107(42):17974-9. PMC: 2964212. DOI: 10.1073/pnas.0912190107. View

5.
Meyer M, Tomchick D, Klinman J . Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (I553) in soybean lipoxygenase-1. Proc Natl Acad Sci U S A. 2008; 105(4):1146-51. PMC: 2234106. DOI: 10.1073/pnas.0710643105. View