Origin of apparent swain–schaad deviations in criteria for tunneling

Huskey, W. Phillip

doi:10.1002/poc.610040607

Cited by 39 publications

(60 citation statements)

References 25 publications

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“…With tunneling included at the SCT-CVT level, the RGM broke down, 71 The calculated KIEs and SSEs presented in this section suggest that although hydride tunneling is important for the kinetic isotope effects in horse LADH, the effect of tunneling on the absolute rate constant is small (about 2 at 300 K); the qualitative behavior is very similar although not identical to those found in ref 21. Moreover, although tunneling has a substantial effect on the values of SSEs, other factors such as the variations in the position of transition state upon isotope substitution also have a significant influence.…”

Section: Iii2 Kinetics Isotope Effects In Ladh Effect Of Tunnelingsupporting

confidence: 49%

“…The effect of mixing primary and secondary isotopes 26,71 (i.e., using protonium at the primary position in measuring secondary H/T kinetic effect, but deuterium when considering the secondary D/T kinetic effect) is rather small at the TST and CVT levels for both the primary and secondary kinetic isotope effects (Table 1); i.e., the rule of the geometric mean (RGM) 72 is a good approximation in LADH without tunneling. With tunneling included at the SCT-CVT level, the RGM broke down, 71 The calculated KIEs and SSEs presented in this section suggest that although hydride tunneling is important for the kinetic isotope effects in horse LADH, the effect of tunneling on the absolute rate constant is small (about 2 at 300 K); the qualitative behavior is very similar although not identical to those found in ref 21.…”

Section: Iii2 Kinetics Isotope Effects In Ladh Effect Of Tunnelingmentioning

confidence: 99%

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A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH)

2002

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The proton and hydride transfers in horse liver alcohol dehydrogenase (LADH) were studied with a potential surface obtained by use of the self-consistent-charge-density-functional-tight-binding (SCC-DFTB) QM/ MM method implemented in the CHARMM program; a correction for solvent shielding was introduced by use of a continuum model. The proton transfers were found to proceed in a virtually concerted fashion before the hydride transfer. The calculations also showed that a radical mechanism, suggested as a possibility in the literature for the H transfer between the substrate and NAD + , is very unlikely. The energetics of the reaction and pK a 's of residues involved in catalysis indicate that the chemical steps of LADH, as characterized by the calculated value of k cat , are slow for a pH below 5.5, and the hydride transfer is hardly affected for pH between 5.5 and 8.1. These results are compared with the experimentally measured pH dependence of k cat for LADH, although a quantitative comparison is difficult because the chemical steps are only partially ratelimiting in the experiments. A perturbation analysis of the QM/MM energies suggest that a number of charged residues close to the active site (i.e., Asp 49, Glu 68, and Arg 369), as well as the phosphate groups of NAD + , make important contributions to the energetics of the proton and hydride transfer reactions; mutation experiments to test these predictions would be of interest. Ser 48 interacts with the substrate via a short hydrogen bond, which leads to an inverse solvent isotope effect, in accord with experiment. The overall calculated barrier and endothermicity and the effect of the double mutation (F93W,V203A) on the hydride transfer are in qualitative agreement with measurements; i.e., the hydride transfer barrier is higher in the mutant, presumably due mainly to the fact that the average distance between the donor and acceptor is larger. In accord with the study of Alhambra et al. (Alhambra, C.; Corchado, J. C.; Sánchez, M. L.; Gao, J.; Truhlar, D. G. J. Am. Chem. Soc. 2000, 122, 8197.), hydride tunneling was shown to be very important for the calculated magnitude of kinetic isotope effects and the Swain-Schaad exponents, although the absolute contribution of tunneling to the rate constant is calculated to be small (a factor of 2) at room temperature. It was shown that the secondary Swain-Schaad exponent can be affected by the variation in the position of the transition state upon secondary isotopic substitution. The exponent, therefore, does not necessarily reflect the magnitude of tunneling; i.e., one has to be cautious in using the secondary Swain-Schaad exponent to estimate the magnitude of tunneling. Equilibrium effects of protein "dynamics" on the hydride transfer in LADH were studied by potential of mean force calculations at different temperatures. To obtain a clearer description of the origin of the calculated variation, an analysis was made with the QM and MM atoms maintained at different temperatures by use of Nosé-Hoover thermostats. It was...

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Section: Iii2 Kinetics Isotope Effects In Ladh Effect Of Tunnelingsupporting

confidence: 49%

Section: Iii2 Kinetics Isotope Effects In Ladh Effect Of Tunnelingmentioning

confidence: 99%

A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH)

2002

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“…Finally, in accordance with the ensemble-averaged variational transition state theory (VTST) results from Truhlar, Gao, and co-workers (24,25), the model supports the recently articulated hypothesis that the inflated mSSEs reported for many ADHs since 1989 result from deflated 2°D/T KIEs because of the shorter donor-acceptor distance (DAD) required for D transfer (1,34). The present model mirrors some of the previous empirical calculations on ADH and other systems (16,17,22,23,35) but provides a more comprehensive molecular and electronic interpretation. The interpretation of experiment by this method agrees well with the results from QM/MM simulations (24,25) that also led to deviations from semiclassical 2°mSSEs in the forward direction.…”

supporting

confidence: 48%

“…These data completed the set of 2°KIEs available for this enzyme and allowed us to develop an empirical model that is consistent with all the data. This model shed light on the nature of the phenomenon described in the past as H tunneling and 1°-2°coupled motion (12,(15)(16)(17)(18). The picture of the reaction emphasizes the dual importance of a short DAD as well as degenerate donor and acceptor wells at the TRS.…”

Section: Discussionmentioning

confidence: 99%

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Elusive transition state of alcohol dehydrogenase unveiled

Roston

Kohen

2010

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

154

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For several decades the hydride transfer catalyzed by alcohol dehydrogenase has been difficult to understand. Here we add to the large corpus of anomalous and paradoxical data collected for this reaction by measuring a normal (>1) 2°kinetic isotope effect (KIE) for the reduction of benzaldehyde. Because the relevant equilibrium effect is inverse (<1), this KIE eludes the traditional interpretation of 2°KIEs. It does, however, enable the development of a comprehensive model for the "tunneling ready state" (TRS) of the reaction that fits into the general scheme of Marcus-like models of hydrogen tunneling. The TRS is the ensemble of states along the intricate reorganization coordinate, where H tunneling between the donor and acceptor occurs (the crossing point in Marcus theory). It is comparable to the effective transition state implied by ensemble-averaged variational transition state theory. Properties of the TRS are approximated as an average of the individual properties of the donor and acceptor states. The model is consistent with experimental findings that previously appeared contradictory; specifically, it resolves the long-standing ambiguity regarding the location of the TRS (aldehyde-like vs. alcohol-like). The new picture of the TRS for this reaction identifies the principal components of the collective reaction coordinate and the average structure of the saddle point along that coordinate.hydrogen tunneling | enzyme kinetic | secondary isotope effect | Swain-Schaad E nzymes enhance the rates of chemical reactions by many orders of magnitude, and extensive studies have uncovered many aspects of how they do so. The prevailing theory that enzymes stabilize the transition state (TS) relative to the reactants explains many phenomena, and a great deal of contemporary research focuses on how enzymes stabilize the TS. An unfortunate hindrance to developing an understanding of how enzymes stabilize the TS lies in the enigmatic nature of the TS. Many enzymatic hydrogen (proton, hydrogen, or hydride) transfers, for example, occur by quantum mechanical tunneling, where a particle passes through an energy barrier because of its wave properties (1-6).Yeast alcohol dehydrogenase (yADH) serves as an excellent model system for enzyme-catalyzed H transfer because unlike many other enzymes, the chemical step, oxidation of a primary alcohol to an aldehyde by NAD þ , is rate-limiting with aromatic substrates (7). Furthermore, the thermodynamics of the reaction allow for examination of both the forward (alcohol to aldehyde) and reverse (aldehyde to alcohol) reactions under similar conditions (8). This type of nicotinamide-dependent redox reaction appears ubiquitously in biology, and a detailed picture of the TS of such reactions may facilitate many medical and industrial applications.Intriguingly, decades of experiments on the reaction catalyzed by yADH have returned what appear to be contradictory results, some suggesting an early TS, whereas others point to a late TS (7-10). In pioneering studies, Klinman measured linear fr...

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Isotope Methods in Catalysis – Biological

Schowen

2002

Encyclopedia of Catalysis

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Isotopic methods in the study of biocatalysis are chiefly used to characterize the mechanisms by which enzymes catalyze their target reactions. The techniques in use include tracer methods, by which the positions of individual atoms in a starting molecule are traced in downstream intermediates or products; exchange methods, in which isotopic mixing between distinct pools such as the solvent and enzyme‐bound intermediates is measured in order to test mechanistic hypotheses; and kinetic isotope effects, in which the relative rates of reaction of different isotopes of the same element are measured to identify rate‐limiting steps and determine transition‐state structures and other mechanistic information. Tracer and exchange methods are illustrated but, not being subject to easy generalization, are not treated in detail. The bulk of the article is devoted to kinetic isotope effects in the study of biocatalysts.

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Origin of apparent swain–schaad deviations in criteria for tunneling

Cited by 39 publications

References 25 publications

A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH)

A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH)

Elusive transition state of alcohol dehydrogenase unveiled

Isotope Methods in Catalysis – Biological

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