Mechanisms and Free Energies of Enzymatic Reactions

Gao, Jiali; Ma, Shuhua; Major, Dan Thomas; Nam, Kwangho; Pu, Jingzhi; Truhlar, Donald G.

doi:10.1002/chin.200644270

Cited by 25 publications

(32 citation statements)

References 233 publications

(402 reference statements)

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“…The PMF was obtained from a series of 35 umbrella sampling simulations for the reaction in water and 17 in the enzyme (4). Periodic boundary conditions were used along with the particle mesh-Ewald method (38) for the uncatalyzed reaction in a box of Ϸ30 ϫ 30 ϫ 30 Å 3 .…”

Section: Methodsmentioning

confidence: 99%

“…An intriguing, yet unanswered, question is whether enzymes have evolved to enhance tunneling to accelerate the reaction rate because quantum effects on rate acceleration are much smaller than hydrogen bonding and electrostatic stabilization of the transition state (1,4,5). Nevertheless, a small factor of two in rate enhancement can have important physiological impacts.…”

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confidence: 99%

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Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Major

Héroux

Orville

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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The proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution.PI-FEP/UM simulations ͉ enzyme catalysis ͉ kinetic isotope effects ͉ X-ray structure A lthough the dominant factor in enzyme catalysis is the lowering of the quasiclassical free energy barrier of the enzymatic reaction in comparison with the uncatalyzed process (1-3), quantum mechanical tunneling has been recognized to also play a role in enzymatic hydrogen transfer reactions (2, 3). An intriguing, yet unanswered, question is whether enzymes have evolved to enhance tunneling to accelerate the reaction rate because quantum effects on rate acceleration are much smaller than hydrogen bonding and electrostatic stabilization of the transition state (1, 4, 5). Nevertheless, a small factor of two in rate enhancement can have important physiological impacts. Although it appears straightforward to address this question by comparing the enzymatic and the uncatalyzed reaction in solution, the difficulty is to design a model system that mimics exactly the same enzymatic reaction and mechanism. The present study examines the structure of nitroalkane oxidase (NAO) complex with nitroethane and kinetic isotope effects at the primary and secondary sites for the enzymatic and the uncatalyzed reaction. The computational findings are consistent with experimental data, suggesting that there is a differential tunneling effect for the proton transfer reaction in NAO and in water. Analysis of tunneling paths reveals that the enzyme reduces both the free energy of activation and the width of the effective potential, resulting in enhanced proton tunneling in the active site.The flavoenzyme NAO catalyzes the conversion of nitroalkanes to nitrite and aldehydes or ketones (Fig. S1) (6). The ␣-proton abstraction of the small substrate nitroethane by Asp-402 is rate-limiting, which is accelerated by a factor of 10 9 over the uncatalyzed reaction between n...

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Major

Héroux

Orville

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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“…Under some conditions, such as high temperature, extremes of pH or mechanical forces, protein will unfold into random coil that loses biochemical function (Selkoe 2003). Since folding and unfolding are essential to life, literatures on the study of these processes are very rich (Gao and Truhlar 2002;Gao et al 2006;Freddolino et al 2010;Yang et al 2010;Alhambra et al 2000;Duan et al 2010;Shank et al 2010). And it has been greatly advanced in recent years by the development of fast time-resolved techniques.…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein

Zhao

Cheng

2011

Amino Acids

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Steered molecular dynamics simulations are performed to explore the unfolding and refolding processes of CLN025, a 10-residue beta-hairpin. In unfolding process, when CLN025 is pulled along the termini, the forceextension curve goes back and forth between negative and positive values not long after the beginning of simulation. That is so different from what happens in other peptides, where force is positive most of the time. The abnormal phenomenon indicates that electrostatic interaction between the charged termini plays an important role in the stability of the beta-hairpin. In the refolding process, the collapse to beta-hairpin-like conformations is very fast, within only 3.6 ns, which is driven by hydrophobic interactions at the termini, as the hydrophobic cluster involves aromatic rings of Tyr1, Tyr2, Trp9, and Tyr10. Our simulations improve the understanding on the structure and function of this type of miniprotein and will be helpful to further investigate the unfolding and refolding of more complex proteins.

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“…However, a connection between promoting motions and potential energy barrier modulation has never been demonstrated directly, and recent work has shown that the temperature dependence of kinetic isotope effects can be accounted for by conformational effects for a number of enzymes (5). Whereas some authors postulate dynamics as a key driving force in catalysis (1)(2)(3)(4), others have performed analyses showing activation free-energy reduction, which is an equilibrium property, to be the source of catalysis (6)(7)(8)(9)(10)(11)(12)(13)(14). Enzyme reactions, and particularly their dynamics, present formidable challenges for study, and progress requires a combination of theoretical, experimental, and computational approaches (5,(15)(16)(17)(18) (20).…”

mentioning

confidence: 99%

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

Luk

Ruiz‐Pernía

Dawson

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

127

262

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Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy ( 15 N, 13 C, 2 H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy enzyme reflects differences in environmental coupling to the hydride transfer step. Importantly, the barrier and contribution of quantum tunneling are not affected, indicating no significant role for "promoting motions" in driving tunneling or modulating the barrier. The chemical step is slower in the heavy enzyme because protein motions coupled to the reaction coordinate are slower. The fact that the heavy enzyme is only slightly less active than its light counterpart shows that protein dynamics have a small, but measurable, effect on the chemical reaction rate.kinetics | computational chemistry | biological chemistry | biophysics | quantum biology

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Mechanisms and Free Energies of Enzymatic Reactions

Abstract: ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Cited by 25 publications

References 233 publications

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction

Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

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