Double hydrogen tunneling revisited: The breakdown of experimental tunneling criteria

Tautermann, Christofer S.; Loferer, Markus J.; Voegele, Andreas F.; Liedl, Klaus R.

doi:10.1063/1.1753262

Cited by 54 publications

(45 citation statements)

References 67 publications

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“…16 has widely been accepted 17 as an indicator of quantum mechanical tunneling; however, the reliability of using this criterion has recently been questioned by Tautermann and coworkers. 18 Our results show that large A H /A D values can be obtained with a moderate amount of tunneling, since the tunneling transmission coefficients are about 3 for the ecDHFR catalyzed hydride transfer over the temperature range being investigated, and Table 1 shows that an even larger A H /A D ratio is obtained without considering tunneling contributions than when it is included, which is the typical situation for moderate tunneling. 15 An Arrhenius plot of the calculated KIE is shown in Figure 3, where the results for a gasphase hydrogen transfer reaction 19 with a similar magnitude of the KIE are included for comparison.…”

Section: Unlikementioning

confidence: 58%

Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase

et al. 2005

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The H/D primary kinetic isotope effect (KIE) for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) is calculated as a function of temperature employing ensemble-averaged variational transition-state theory with multidimensional tunneling. The calculated KIEs display only a small temperature dependence over the temperature range of 5 to 45 °C. We identify two key features that contribute to canceling most of the temperature dependence of the KIE that would be expected on the basis of simpler models. Related issues such as the isotope effects on Arrhenius preexponential factors, large differences between free energies of activation and Arrhenius activation energy, and fluctuations of effective barriers are also discussed. This paper presents a theoretical explanation of the unusual temperature dependence 1 of the kinetic isotope effect (KIE) for the hydride transfer chemical step of the reaction catalyzed by E. coli dihydrofolate reductase (ecDHFR). The explanation identifies two general features that may be important in interpreting enzymatic kinetic isotope effects more generally.Many enzyme reactions involve hydron transfer (transfer of H + , H − , or H • ). Such reactions have significant contributions from zero-point energy and tunneling; KIEs have been extensively used to study these effects. [1][2][3][4][5][6][7] Surprisingly, a number of enzymes have been found to display almost temperature-independent KIEs, 1-4 which are contrary to experience with small-molecule chemistry or simple tunneling models. Recent multidimensional tunneling calculations have been successfully used to study tunneling effects on enzymatic KIEs, but the most accurate methods have so far been applied only at a single temperature. 8 DHFR catalyzes the reduction of 7,8-dihydrofolate (DHF) to 5,6,7, with the key chemical step being the transfer of a hydride ion from the nicotinamide ring of the cofactor nicotinamide adinine dinucleotide phosphate (NADPH). At pH ≅ 7, product release is partly rate-limiting 9 and the H/D kinetic isotope effect is about 1.1-1.3, but the intrinsic KIE on the hydride transfer step is >3. 10 Furthermore, at 25 °C, the phenomenological free energy of activation derived from the rate constant 9 by using © 2005 American Chemical Society HHS Public Access Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript transition-state theory is 13.4 kcal/mol, 7 and the free energy of reaction calculated from the experimental equilibrium constant 9 is −4.4 kcal/mol. 7Here, we report a dynamical simulation of the ecDHFR system using a combined quantum mechanical and molecular mechanical (QM/MM) approach. As depicted in Figure 1, the reactive fragment that involves transferring a hydride ion from the C4 position of NADPH (the cofactor) to the C6 in N5-preprotonated DHF (the substrate) to form THF (the product) is treated quantum mechanically. The hydride transfer KIEs at 5 and 45 °C and 1 atm are calculated using ensemble-averaged variational transition-stat...

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Section: Unlikementioning

confidence: 58%

Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase

et al. 2005

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“…In systems where non-classical isotope effects have been suggested from temperature dependency or theoretical simulation, the experimental relationship between primary H/T and D/T KIEs has been shown to be very close to the semi-classical limit (Northrop 1991;Jonsson et al 1994;Bahnson et al 1997;Chin & Klinman 2000). Several recent gas-phase calculations for a small model reaction also resulted in a Swain-Schaad exponent that did not deviate significantly from its semi-classical value at ambient temperature (300-350 K; Kiefer & Hynes 2003Tautermann et al 2004;. Furthermore, even if the magnitude of the exponent (3.3) was altered for a full tunnelling model, it is not expected to change over the narrow temperature range under study and, hence, should not affect the trend manifested in the temperature dependence of the intrinsic isotope effects (Francisco et al 2002;Sikorski et al 2004).…”

Section: Methodsmentioning

confidence: 96%

The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase

Wang

Goodey

Benkovic

et al. 2006

Phil. Trans. R. Soc. B

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Residues M42 and G121 of Escherichia coli dihydrofolate reductase (ecDHFR) are on opposite sides of the catalytic centre (15 and 19 Å away from it, respectively). Theoretical studies have suggested that these distal residues might be part of a dynamics network coupled to the reaction catalysed at the active site. The ecDHFR mutant G121V has been extensively studied and appeared to have a significant effect on rate, but only a mild effect on the nature of H-transfer. The present work examines the effect of M42W on the physical nature of the catalysed hydride transfer step. Intrinsic kinetic isotope effects (KIEs), their temperature dependence and activation parameters were studied. The findings presented here are in accordance with the environmentally coupled hydrogen tunnelling. In contrast to the wild-type (WT), fluctuations of the donor-acceptor distance were required, leading to a significant temperature dependence of KIEs and deflated intercepts. A comparison of M42W and G121V to the WT enzyme revealed that the reduced rates, the inflated primary KIEs and their temperature dependences resulted from an imperfect potential surface prearrangement relative to the WT enzyme. Apparently, the coupling of the enzyme's dynamics to the reaction coordinate was altered by the mutation, supporting the models in which dynamics of the whole protein is coupled to its catalysed chemistry.

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“…16 By "quasiclassical" we mean "in the absence of tunneling". (As mentioned in section 1, this is sometimes 209 Although the secondary Swain-Schaad exponent has been widely used as an indicator of the degree of tunneling, the reliability of this simple tunneling criterion has recently been questioned, 253 and it has been tested in the absence of tunneling for a large variety of organic reactions based on realistic potential energy surfaces, 254 and subjected to additional generalization. 255 The most serious problem with using Swain-Schaad-type arguments to derive quasiclassical limits for the relationship of H/T to D/T KIEs is that such arguments are based on one-dimensional models of tunneling, but we have known for a long time that the effective potential for tunneling depends on the isotopic composition of the system.…”

Section: Previous Reviewsmentioning

confidence: 99%

“…Such a tunneling criterion has been questioned and tested recently. 253 More conservative criteria invoke tunneling when A H /A D < 0.5. 241 Some workers also use a criterion based on activation energy, namely E a (D) − E a (H) > 1.2 262 or 1.4 243 kcal/mol.…”

Section: Isotope Effects On Arrhenius Pre-exponential Factorsmentioning

confidence: 99%

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

2006

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Double hydrogen tunneling revisited: The breakdown of experimental tunneling criteria

Cited by 54 publications

References 67 publications

Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase

Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase

The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase

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

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