Arrhenius curves of hydrogen transfers: tunnel effects, isotope effects and effects of pre-equilibria

Limbach, Hans−Heinrich; López, Juan Miguel; Kohen, Amnon

doi:10.1098/rstb.2006.1872

Cited by 140 publications

(173 citation statements)

References 56 publications

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“…Within an entirely different chemical environment, experimental rate constants related to multiple proton transfer reactions in condensed matter also show strong sub-Arrhenius behaviour [102][103][104]. Also, sub-Arrhenius behaviour has been revealed for rates of processes promoted by enzymatic catalysis [55,68,105].…”

Section: (B) Sub-arrhenius Casesmentioning

confidence: 94%

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

Aquilanti

Coutinho

Carvalho-Silva

2017

Phil. Trans. R. Soc. A.

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relaxing the thermodynamic equilibrium limit, either for a binomial distribution if d > 0 or for a negative binomial distribution if d < 0, formally corresponding to Fermionlike or Boson-like statistics, respectively. The current status of the phenomenology is illustrated emphasizing case studies; specifically (i) the super-Arrhenius kinetics, where transport phenomena accelerate processes as the temperature increases; (ii) the sub-Arrhenius kinetics, where quantum mechanical tunnelling propitiates low-temperature reactivity; (iii) the anti-Arrhenius kinetics, where processes with no energetic obstacles are rate-limited by molecular reorientation requirements. Particular attention is given for case (i) to the treatment of diffusion and viscosity, for case (ii) to formulation of a transition rate theory for chemical kinetics including quantum mechanical tunnelling, and for case (iii) to the stereodirectional specificity of the dynamics of reactions strongly hindered by the increase of temperature.This article is part of the themed issue 'Theoretical and computational studies of nonequilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

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Section: (B) Sub-arrhenius Casesmentioning

confidence: 94%

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

Aquilanti

Coutinho

Carvalho-Silva

2017

Phil. Trans. R. Soc. A.

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“…The second exponential function that contributes to k obs will derive from f i and represent the free energy change for conformational reequilibration, ΔG o c . The simplest case of a two-state equilibrium between active and inactive conformers, described first by Truhlar and Kohen (56) and developed further by Limbach et al (17), is given by:…”

Section: Discussionmentioning

confidence: 99%

“…In one instance, it was shown that convex Arrhenius curves can arise from a temperature-dependent equilibrium between two enzyme conformations with different kinetic properties (17). Alternatively, noting that the Arrhenius prefactor (cf.…”

mentioning

confidence: 99%

Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors

Nagel

Dong

Bahnson

et al. 2011

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

154

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A growing body of data supports a role for protein motion in enzyme catalysis. In particular, the ability of enzymes to sample catalytically relevant conformational substates has been invoked to model kinetic and spectroscopic data. However, direct experimental links between rapidly interconverting conformations and the chemical steps of catalysis remain rare. We report here on the kinetic analysis and characterization of the hydride transfer step catalyzed by a series of mutant thermophilic alcohol dehydrogenases (ht-ADH), presenting evidence for Arrhenius prefactor values that become enormously elevated above an expected value of approximately 10 13 s −1 when the enzyme operates below its optimal temperature range. Restoration of normal Arrhenius behavior in the ht-ADH reaction occurs at elevated temperatures. A simple model, in which reduced temperature alters the ability of the ht-ADH variants to sample the catalytically relevant region of conformational space, can reproduce the available data. These findings indicate an impaired landscape that has been generated by the combined condition of reduced temperature and mutation at a single, active-site hydrophobic side chain. The broader implication is that optimal enzyme function requires the maintenance of a relatively smooth landscape that minimizes low energy traps.A complete understanding of the origins of the remarkable rate acceleration and specificity achieved by enzymes remains elusive. Increasingly, studies on the fundamental basis for enzymatic catalysis have focused on the requirement for a range of protein motions in order to achieve efficient enzyme catalysis. Among these, evidence for a class of motion termed conformational sampling (or preorganization) has begun to accumulate recently (cf. refs. 1-4). The impact of such motions can be seen either in the formation of an enzyme-substrate complex or in its subsequent conversion to product.For example, a recent study of adenylate kinase implicates a temperature-dependent preequilibrium among conformers that are either "competent" or "incompetent" toward ligand binding (5). In the context of catalysis, studies of single-enzyme molecules indicate multiple, slowly interconverting conformers that lead to product with different rate constants (6-8). Extensive work on dihydrofolate reductase has shown the role of slow loop closures that occur along the reaction coordinate with the same (millsecond) time constants as catalysis (9, 10).Although computational studies also suggest a role for rapid conformational sampling in enzyme reactions (11, 12), demonstrating the direct link of these motions to catalysis is quite challenging. In this study, we use the thermophilic alcohol dehydrogenase from Bacillus stearothermophilus (ht-ADH) as a system to examine the presence of rapidly interconverting protein substates during catalysis. The ht-ADH catalyzes the transfer of a hydride equivalent from an alcohol donor to an NAD þ cofactor, and previous studies have shown that ht-ADH carries out its reaction via quantum t...

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“…(This has been used to directly fit thermophilic alcohol dehydrogenase data. 489 ) Various explanations are possible for the average energy of molecules that react increasing less rapidly than the average energy of all possible reactants; for example, there could be a pool of especially reactive states that does not broaden as temperature increases. Antoniou and Schwartz 119 have postulated that convex Arrhenius plots could arise from tunneling strongly coupled to a promoting vibration.…”

Section: Thermophilic Alcohol Dehydrogenasementioning

confidence: 99%

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

2006

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Arrhenius curves of hydrogen transfers: tunnel effects, isotope effects and effects of pre-equilibria

Cited by 140 publications

References 56 publications

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

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

Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

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