Protein dynamics and enzyme catalysis: the ghost in the machine?

2012 ◽  
Vol 40 (3) ◽  
pp. 515-521 ◽  
Author(s):  
David R. Glowacki ◽  
Jeremy N. Harvey ◽  
Adrian J. Mulholland
Keyword(s):  
Protein Dynamics ◽  
Enzyme Catalysis ◽  
Isotope Effects ◽  
State Theory ◽  
Quantum Tunnelling ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Kinetic Isotope ◽  
Temperature Dependences ◽  
Multiple Conformations

One of the most controversial questions in enzymology today is whether protein dynamics are significant in enzyme catalysis. A particular issue in these debates is the unusual temperature-dependence of some kinetic isotope effects for enzyme-catalysed reactions. In the present paper, we review our recent model [Glowacki, Harvey and Mulholland (2012) Nat. Chem. 4, 169–176] that is capable of reproducing intriguing temperature-dependences of enzyme reactions involving significant quantum tunnelling. This model relies on treating multiple conformations of the enzyme–substrate complex. The results show that direct ‘driving’ motions of proteins are not necessary to explain experimental observations, and show that enzyme reactivity can be understood and accounted for in the framework of transition state theory.

scholarly journals Quantum tunneling observed without its characteristic large kinetic isotope effects

2015 ◽  
Vol 112 (24) ◽  
pp. 7438-7443 ◽  
Author(s):  
Tetsuya Hama ◽  
Hirokazu Ueta ◽  
Akira Kouchi ◽  
Naoki Watanabe
Keyword(s):  
Chemical Kinetics ◽  
Quantum Tunneling ◽  
Interstellar Dust ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
State Theory ◽  
Dust Particles ◽  
Interplanetary Dust Particles ◽  
Chemical Systems ◽  
Kinetic Isotope

Classical transition-state theory is fundamental to describing chemical kinetics; however, quantum tunneling is also important in explaining the unexpectedly large reaction efficiencies observed in many chemical systems. Tunneling is often indicated by anomalously large kinetic isotope effects (KIEs), because a particle’s ability to tunnel decreases significantly with its increasing mass. Here we experimentally demonstrate that cold hydrogen (H) and deuterium (D) atoms can add to solid benzene by tunneling; however, the observed H/D KIE was very small (1–1.5) despite the large intrinsic H/D KIE of tunneling (≳100). This strong reduction is due to the chemical kinetics being controlled not by tunneling but by the surface diffusion of the H/D atoms, a process not greatly affected by the isotope type. Because tunneling need not be accompanied by a large KIE in surface and interfacial chemical systems, it might be overlooked in other systems such as aerosols or enzymes. Our results suggest that surface tunneling reactions on interstellar dust may contribute to the deuteration of interstellar aromatic and aliphatic hydrocarbons, which could represent a major source of the deuterium enrichment observed in carbonaceous meteorites and interplanetary dust particles. These findings could improve our understanding of interstellar physicochemical processes, including those during the formation of the solar system.

scholarly journals Kinetic isotope effects of <sup>12</sup>CH<sub>3</sub>D  + OH and <sup>13</sup>CH<sub>3</sub>D  + OH from 278 to 313 K

2016 ◽  
Vol 16 (7) ◽  
pp. 4439-4449 ◽  
Author(s):  
L. M. T. Joelsson ◽  
J. A. Schmidt ◽  
E. J. K. Nilsson ◽  
T. Blunier ◽  
D. W. T. Griffith ◽  
...  
Keyword(s):  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
State Theory ◽  
Atmospheric Methane ◽  
Isotopic Signatures ◽  
Budget Analysis ◽  
Kinetic Isotope ◽  
Methane Budget ◽  
Source Signal ◽  
Clumped Isotope

Abstract. Methane is the second most important long-lived greenhouse gas and plays a central role in the chemistry of the Earth's atmosphere. Nonetheless there are significant uncertainties in its source budget. Analysis of the isotopic composition of atmospheric methane, including the doubly substituted species 13CH3D, offers new insight into the methane budget as the sources and sinks have distinct isotopic signatures. The most important sink of atmospheric methane is oxidation by OH in the troposphere, which accounts for around 84 % of all methane removal. Here we present experimentally derived methane + OH kinetic isotope effects and their temperature dependence over the range of 278 to 313 K for CH3D and 13CH3D; the latter is reported here for the first time. We find kCH4/kCH3D = 1.31 ± 0.01 and kCH4/k13CH3D = 1.34 ± 0.03 at room temperature, implying that the methane + OH kinetic isotope effect is multiplicative such that (kCH4/k13CH4)(kCH4/kCH3D) = kCH4/k13CH3D, within the experimental uncertainty, given the literature value of kCH4/k13CH4 = 1.0039 ± 0.0002. In addition, the kinetic isotope effects were characterized using transition state theory with tunneling corrections. Good agreement between the experimental, quantum chemical, and available literature values was obtained. Based on the results we conclude that the OH reaction (the main sink of methane) at steady state can produce an atmospheric clumped isotope signal (Δ(13CH3D) = ln([CH4][13CH3D]/[13CH4][CH3D])) of 0.02 ± 0.02. This implies that the bulk tropospheric Δ(13CH3D) reflects the source signal with relatively small adjustment due to the sink signal (i.e., mainly OH oxidation).

Restricted Intramolecular Energy Flow in Large Molecules. Heterogeneous and Enzyme Catalysis

1997 ◽  
Vol 62 (8) ◽  
pp. 1150-1158 ◽  
Author(s):  
Milan Šolc
Keyword(s):  
Energy Flow ◽  
Enzyme Catalysis ◽  
Reaction Rate ◽  
Vibrational Energy ◽  
Heavy Atom ◽  
Energy Localization ◽  
Large Molecules ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Intramolecular Energy Flow

The free intramolecular energy flow can be restricted by the presence of a heavy atom in the molecule. As a result of this restriction, adsorbed molecules bonded on the metal surface and/or substrate molecules in the enzyme-substrate complex with a metal atom near the binding site can have a higher vibrational energy than the surroundings. The reaction rate is then enhanced by this energy localization.

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