Importance of barrier shape in enzyme-catalyzed reactions. Vibrationally assisted hydrogen tunneling in tryptophan tryptophylquinone-dependent amine dehydrogenases

Atomic level insight into the oxidative half-reaction of aromatic amine dehydrogenase

The quinoprotein aromatic amine dehydrogenase (AADH) uses a covalently bound tryptophan tryptophylquinone (TTQ) cofactor to oxidatively deaminate primary aromatic amines. Recent crystal structures have provided insight into the reductive half-reaction. In contrast, no atomic details are available for the oxidative half-reaction. The TTQ O7 hydroxyl group is protonated during reduction, but it is unclear how this proton can be removed during the oxidative half-reaction. Furthermore, compared with the electron transfer from the N-quinol form, electron transfer from the non-physiological O-quinol form to azurin is significantly slower. Here we report crystal structures of the O-quinol, N-quinol, and N-semiquinone forms of AADH. A comparison of oxidized and substrate reduced AADH species reveals changes in the TTQ-containing subunit, extending from residues in the immediate vicinity of the N-quinol to the putative azurin docking site, suggesting a mechanism whereby TTQ redox state influences interprotein electron transfer. In contrast, chemical reduction of the TTQ center has no significant effect on protein conformation. Furthermore, structural reorganization upon substrate reduction places a water molecule near TTQ O7 where it can act as proton acceptor. The structure of the N-semiquinone, however, is essentially similar to oxidized AADH. Surprisingly, in the presence of substrate a covalent N-semiquinone substrate adduct is observed. To our knowledge this is the first detailed insight into a complex, branching mechanism of quinone oxidation where significant structural reorganization upon reduction of the quinone center directly influences formation of the electron transfer complex and nature of the electron transfer process.

Atomic Description of an Enzyme Reaction Dominated by Proton Tunneling

We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for tryptamine oxidation by aromatic amine dehydrogenase. Combining experiment and computer simulation, we show proton transfer occurs predominantly to oxygen O2 of Asp(128)beta in a reaction dominated by tunneling over approximately 0.6 angstroms. The role of long-range coupled motions in promoting tunneling is controversial. We show that, in this enzyme system, tunneling is promoted by a short-range motion modulating proton-acceptor distance and no long-range coupled motion is required.

Coupling of protein motions and hydrogen transfer during catalysis by Escherichia coli dihydrofolate reductase

The enzyme DHFR (dihydrofolate reductase) catalyses hydride transfer from NADPH to, and protonation of, dihydrofolate. The physical basis of the hydride transfer step catalysed by DHFR from Escherichia coli has been studied through the measurement of the temperature dependence of the reaction rates and the kinetic isotope effects. Single turnover experiments at pH 7.0 revealed a strong dependence of the reaction rates on temperature. The observed relatively large difference in the activation energies for hydrogen and deuterium transfer led to a temperature dependence of the primary kinetic isotope effects from 3.0+/-0.2 at 5 degrees C to 2.2+/-0.2 at 40 degrees C and an inverse ratio of the pre-exponential factors of 0.108+/-0.04. These results are consistent with theoretical models for hydrogen transfer that include contributions from quantum mechanical tunnelling coupled with protein motions that actively modulate the tunnelling distance. Previous work had suggested a coupling of a remote residue,Gly121, with the kinetic events at the active site. However, pre-steady-state experiments at pH 7.0 with the mutant G121V-DHFR, in which Gly121 was replaced with valine, revealed that the chemical mechanism of DHFR catalysis was robust to this replacement. The reduced catalytic efficiency of G121V-DHFR was mainly a consequence of the significantly reduced pre-exponential factors, indicating the requirement for significant molecular reorganization during G121V-DHFR catalysis. In contrast, steady-state measurements at pH 9.5, where hydride transfer is rate limiting, revealed temperature-independent kinetic isotope effects between 15 and 35 degrees C and a ratio of the pre-exponential factors above the semi-classical limit, suggesting a rigid active site configuration from which hydrogen tunnelling occurs. The mechanism by which hydrogen tunnelling in DHFR is coupled with the environment appears therefore to be sensitive to pH.

Quantum mechanical hydrogen tunneling in bacterial copper amine oxidase reaction

A key step decisively affecting the catalytic efficiency of copper amine oxidase is stereospecific abstraction of substrate alpha-proton by a conserved Asp residue. We analyzed this step by pre-steady-state kinetics using a bacterial enzyme and stereospecifically deuterium-labeled substrates, 2-phenylethylamine and tyramine. A small and temperature-dependent kinetic isotope effect (KIE) was observed with 2-phenylethylamine, whereas a large and temperature-independent KIE was observed with tyramine in the alpha-proton abstraction step, showing that this step is driven by quantum mechanical hydrogen tunneling rather than the classical transition-state mechanism. Furthermore, an Arrhenius-type preexponential factor ratio approaching a transition-state value was obtained in the reaction of a mutant enzyme lacking the critical Asp. These results provide strong evidence for enzyme-enhanced hydrogen tunneling. X-ray crystallographic structures of the reaction intermediates revealed a small difference in the binding mode of distal parts of substrates, which would modulate hydrogen tunneling proceeding through either active or passive dynamics.

The role of tunneling in enzyme catalysis of C-H activation

Recent data from studies of enzyme catalyzed hydrogen transfer reactions implicate a new theoretical context in which to understand C-H activation. This is much closer to the Marcus theory of electron transfer, in that environmental factors influence the probability of effective wave function overlap from donor to acceptor atoms. The larger size of hydrogen and the availability of three isotopes (H, D and T) introduce a dimension to the kinetic analysis that is not available for electron transfer. This concerns the role of gating between donor and acceptor atoms, in particular whether the system in question is able to tune distance between reactants to achieve maximal tunneling efficiency. Analysis of enzyme systems is providing increasing evidence of a role for active site residues in optimizing the inter-nuclear distance for nuclear tunneling. The ease with which this optimization can be perturbed, through site-specific mutagenesis or an alteration in reaction conditions, is also readily apparent from an analysis of the changes in the temperature dependence of hydrogen isotope effects.

Computational studies of enzyme mechanism: linking theory with experiment in the analysis of enzymic H-tunnelling

Hydrogen transfer--an essential component of most biological reactions--is a quantum problem. A crucial question of great current interest is how enzymes modulate the quantum dynamics of hydrogen transfer to achieve their outstanding catalytic properties. That tunnelling occurs is now widely accepted, with the conceptual frameworks incorporating protein motion into the enzymic H-tunnelling process. Computational simulation can be used to help elucidate how enzymes work and facilitate H-tunnelling at the atomic level. We review the strength of a multidisciplinary approach--combining computational simulations with enzyme kinetics and structural biology--in revealing tunnelling mechanisms in enzymes. We focus on two paradigm systems--aromatic amine dehydrogenase, in which H-tunnelling is facilitated by fast (sub-picosecond) short range motions, and dihydrofolate reductase, in which a network of long-range coupled motions drives the tunnelling event.

Tryptophan tryptophylquinone cofactor biogenesis in the aromatic amine dehydrogenase of Alcaligenes faecalis

The heterologous expression of tryptophan trytophylquinone (TTQ)-dependent aromatic amine dehydrogenase (AADH) has been achieved in Paracoccus denitrificans. The aauBEDA genes and orf-2 from the aromatic amine utilization (aau) gene cluster of Alcaligenes faecalis were placed under the regulatory control of the mauF promoter from P. denitrificans and introduced into P. denitrificans using a broad-host-range vector. The physical, spectroscopic and kinetic properties of the recombinant AADH were indistinguishable from those of the native enzyme isolated from A. faecalis. TTQ biogenesis in recombinant AADH is functional despite the lack of analogues in the cloned aau gene cluster for mauF, mauG, mauL, mauM and mauN that are found in the methylamine utilization (mau) gene cluster of a number of methylotrophic organisms. Steady-state reaction profiles for recombinant AADH as a function of substrate concentration differed between 'fast' (tryptamine) and 'slow' (benzylamine) substrates, owing to a lack of inhibition by benzylamine at high substrate concentrations. A deflated and temperature-dependent kinetic isotope effect indicated that C-H/C-D bond breakage is only partially rate-limiting in steady-state reactions with benzylamine. Stopped-flow studies of the reductive half-reaction of recombinant AADH with benzylamine demonstrated that the KIE is elevated over the value observed in steady-state turnover and is independent of temperature, consistent with (a) previously reported studies with native AADH and (b) breakage of the substrate C-H bond by quantum mechanical tunnelling. The limiting rate constant (k(lim)) for TTQ reduction is controlled by a single ionization with pK(a) value of 6.0, with maximum activity realized in the alkaline region. Two kinetically influential ionizations were identified in plots of k(lim)/K(d) of pK(a) values 7.1 and 9.3, again with the maximum value realized in the alkaline region. The potential origin of these kinetically influential ionizations is discussed.

Quantum-instanton evaluation of the kinetic isotope effects

A general quantum-mechanical method for computing kinetic isotope effects is presented. The method is based on the quantum-instanton approximation for the rate constant and on the path-integral Metropolis-Monte Carlo evaluation of the Boltzmann operator matrix elements. It computes the kinetic isotope effect directly, using a thermodynamic integration with respect to the mass of the isotope, thus avoiding the more computationally expensive process of computing the individual rate constants. The method should be more accurate than variational transition-state theories or the semiclassical instanton method since it does not assume a single tunneling path and does not use a semiclassical approximation of the Boltzmann operator. While the general Monte Carlo implementation makes the method accessible to systems with a large number of atoms, we present numerical results for the Eckart barrier and for the collinear and full three-dimensional isotope variants of the hydrogen exchange reaction H + H2 --> H2 + H. In all seven test cases, for temperatures between 250 and 600 K, the error of the quantum instanton approximation for the kinetic isotope effects is less than approximately 10%.

Implementation of the bisection sampling method in path integral simulations

A bisection sampling method is implemented in the framework of a quantized classical path algorithm to include nuclear quantum effects in path integral simulations. The present study examines the convergence of these calculations on two model systems with respect to the number of beads used in the polymer chain and the number of configurations both in free-particle sampling and in classical configuration sampling. The results will be useful for future studies of kinetic isotope effects in enzymatic reactions.

Structure and mechanism of tryptophylquinone enzymes

Tryptophylquinone cofactors are formed by posttranslational modifications that result in the incorporation of two oxygens into a tryptophan side chain, and the covalent cross-linking of that side chain to another amino acid residue. Tryptophylquinone enzymes catalyze the oxidative deamination of primary amines, and utilize other redox proteins as electron acceptors. Mechanistic and structural studies of these enzymes are providing insight into how these enzymes utilize these highly reactive protein-derived quinones in a controlled manner to facilitate biologically important catalytic and electron transfer reactions.

Hydrogen tunneling in quinoproteins

It is now widely accepted that substrate C-H bond breakage by quinoprotein enzymes occurs by quantum mechanical tunneling. This paradigm shift in the conceptual framework for these reactions away from semi-classical transition state theory (i.e., including zero-point energy but with no tunneling correction) has been driven over recent years by experimental studies of the temperature dependence of kinetic isotope effects for these reactions in the TTQ-dependent enzymes methylamine dehydrogenase and aromatic amine dehydrogenase, which produced observations also inconsistent with the simple Bell correction model of tunneling. However, these data-specifically, the strong temperature dependence of reaction rates and the variable temperature dependence of kinetic isotope effects-are consistent with other tunneling models (denoted full tunneling models) in which protein and/or substrate fluctuations generate a configuration compatible with tunneling. These models accommodate substrate/protein (environment) fluctuations required to attain a configuration with degenerate quantum states and, when necessary, motion required to increase the probability of tunneling in these states. Furthermore, tunneling mechanisms in quinoproteins are supported by computational studies employing variational transition state theory with multidimensional tunneling corrections; these studies are also discussed in this review. Potential pitfalls in analyzing the temperature dependence of kinetic isotope effects as probes of tunneling are also discussed with reference to PQQ-dependent methanol dehydrogenase.

Thermal-activated protein mobility and its correlation with catalysis in thermophilic alcohol dehydrogenase

Temperature-dependent hydrogen-deuterium (H/D) exchange of the thermophilic alcohol dehydrogenase (htADH) has been studied by using liquid chromatography-coupled mass spectrometry. Analysis of the changes in H/D exchange patterns for the protein-derived peptides suggests that some regions of htADH are in a rigid conformational substate at reduced temperatures with limited cooperative protein motion. The enzyme undergoes two discrete transitions at approximately 30 and 45 degrees C to attain a more dynamic conformational substate. Four of the five peptides exhibiting the transition above 40 degrees C are in direct contact with the cofactor, and the NAD(+)-binding affinity is also altered in this temperature range, implicating a change in the mobility of the cofactor-binding domain >45 degrees C. By contrast, the five peptides exhibiting the transition at 30 degrees C reside in the substrate-binding domain. This transition coincides with a change in the activation energy of k(cat) for hydride transfer, leading to a linear correlation between k(cat) and the weighted average exchange rate constant k(HX(WA)) for the five peptides. These observations indicate a direct coupling between hydride transfer and protein mobility in htADH, and that an increased mobility is at least partially responsible for the reduced E(act) at high temperature. The data provide support for the hypothesis that protein dynamics play a key role in controlling hydrogen tunneling at enzyme active sites.

Rate-promoting vibrations and coupled hydrogen–electron transfer reactions in the condensed phase: A model for enzymatic catalysis

A model is presented for coupled hydrogen-electron transfer reactions in condensed phase in the presence of a rate promoting vibration. Large kinetic isotope effects (KIEs) are found when the hydrogen is substituted with deuterium. While these KIEs are essentially temperature independent, reaction rates do exhibit temperature dependence. These findings agree with recent experimental data for various enzyme-catalyzed reactions, such as the amine dehydrogenases and soybean lipoxygenase. Consistent with earlier results, turning off the promoting vibration results in an increased KIE. Increasing the barrier height increases the KIE, while increasing the rate of electron transfer decreases it. These results are discussed in light of other views of vibrationally enhanced tunneling in enzymes.

Rate of Enolate Formation Is Not Very Sensitive to the Hydrogen Bonding Ability of Donors to Carboxyl Oxygen Lone Pair Acceptors; A Ramification of the Principle of Non-Perfect Synchronization for General-Base-Catalyzed Enolate Formation

Two series of structures (1 and 2) possessing intramolecular hydrogen bonds to the lone-pair electrons of carbonyl oxygens have been examined to reveal the influence of the pK(a) of the hydrogen-bond donor on the rate of general-base-catalyzed enolate formation. The geometry of the hydrogen bonds is well accepted to be appropriate for intramolecular hydrogen-bond formation. Yet, as revealed by Brønsted plots, both series show very little dependence of the rate of enolate formation on the hydrogen-bond donor ability. The intramolecular hydrogen bonds give rate enhancements only on the order of 10-100-fold, and corrected Brønsted alpha-values are slightly below 0.1. The results can be understood by interpreting them in light of the Principle of Non-Perfect Synchronization. The results are consistent with the proton transfer occurring through an asynchronous transition state with the developing negative charge localized on carbon. We postulate that catalysts of enolate formation will be most effective if the binding groups are focused on stabilizing negative charge that is forming on the enolate carbon rather than on the enolate oxygen.

H-tunneling in the multiple H-transfers of the catalytic cycle of morphinone reductase and in the reductive half-reaction of the homologous pentaerythritol tetranitrate reductase

The mechanism of flavin reduction in morphinone reductase (MR) and pentaerythritol tetranitrate (PETN) reductase, and flavin oxidation in MR, has been studied by stopped-flow and steady-state kinetic methods. The temperature dependence of the primary kinetic isotope effect for flavin reduction in MR and PETN reductase by nicotinamide coenzyme indicates that quantum mechanical tunneling plays a major role in hydride transfer. In PETN reductase, the kinetic isotope effect (KIE) is essentially independent of temperature in the experimentally accessible range, contrasting with strongly temperature-dependent reaction rates, consistent with a tunneling mechanism from the vibrational ground state of the reactive C-H/D bond. In MR, both the reaction rates and the KIE are dependent on temperature, and analysis using the Eyring equation suggests that hydride transfer has a major tunneling component, which, unlike PETN reductase, is gated by thermally induced vibrations in the protein. The oxidative half-reaction of MR is fully rate-limiting in steady-state turnover with the substrate 2-cyclohexenone and NADH at saturating concentrations. The KIE for hydride transfer from reduced flavin to the alpha/beta unsaturated bond of 2-cyclohexenone is independent of temperature, contrasting with strongly temperature-dependent reaction rates, again consistent with ground-state tunneling. A large solvent isotope effect (SIE) accompanies the oxidative half-reaction, which is also independent of temperature in the experimentally accessible range. Double isotope effects indicate that hydride transfer from the flavin N5 atom to 2-cyclohexenone, and the protonation of 2-cyclohexenone, are concerted and both the temperature-independent KIE and SIE suggest that this reaction also proceeds by ground-state quantum tunneling. Our results demonstrate the importance of quantum tunneling in the reduction of flavins by nicotinamide coenzymes. This is the first observation of (i) three H-nuclei in an enzymic reaction being transferred by tunneling and (ii) the utilization of both passive and active dynamics within the same native enzyme.

The first experimental test of the hypothesis that enzymes have evolved to enhance hydrogen tunneling

The literature hypothesis that "the optimization of enzyme catalysis may entail the evolutionary implementation of chemical strategies that increase the probability of quantum-mechanical tunneling" is experimentally tested herein for the first time. The system employed is the key to being able to provide this first experimental test of the "enhanced hydrogen tunneling" hypothesis, one that requires a comparison of the three criteria diagnostic of tunneling (vide infra) for the same, or nearly the same, reaction with and without the enzyme. Specifically, studied herein are the adenosylcobalamin (AdoCbl, also known as coenzyme B(12))-dependent diol dehydratase model reactions of (i). H(D)(*) atom abstraction from ethylene glycol-d(0) and ethylene glycol-d(4) solvent by 5'-deoxyadenosyl radical (Ado(*)) and (ii.) the same H(*) abstraction reactions by the 8-methoxy-5'-deoxyadenosyl radical (8-MeOAdo(*)). The Ado(*) and 8-MeOAdo(*) radicals are generated by Co-C thermolysis of their respective precursors, AdoCbl and 8-MeOAdoCbl. Deuterium kinetic isotope effects (KIEs) of the H(*)(D(*)) abstraction reactions from ethylene glycol have been measured over a temperature range of 80-120 degrees C: KIE = 12.4 +/- 1.1 at 80 degrees C for Ado(*) and KIE = 12.5 +/- 0.9 at 80 degrees C for 8-MeOAdo(*) (values ca. 2-fold that of the predicted maximum primary times secondary ground-state zero-point energy (GS-ZPE) KIE of 6.4 at 80 degrees C). From the temperature dependence of the KIEs, zero-point activation energy differences ([E(D) - E(H)]) of 3.0 +/- 0.3 kcal mol(-)(1) for Ado(*) and 2.1 +/- 0.6 kcal mol(-)(1) for 8-MeOAdo(*) have been obtained, both of which are significantly larger than the nontunneling, zero-point energy only maximum of 1.2 kcal mol(-)(1). Pre-exponential factor ratios (A(H)/A(D)) of 0.16 +/- 0.07 for Ado(*) and 0.5 +/- 0.4 for 8-MeOAdo(*) are observed, both of which are significantly less than the 0.7 minimum for nontunneling behavior. The data provide strong evidence for the expected quantum mechanical tunneling in the Ado(*) and 8-MeOAdo(*)-mediated H(*) abstraction reactions from ethylene glycol. More importantly, a comparison of these enzyme-free tunneling data to the same KIE, (E(D) - E(H)) and A(H)/A(D) data for a closely related, Ado(*)-mediated H(*) abstraction reaction from a primary CH(3)- group in AdoCbl-dependent methylmalonyl-CoA mutase shows the enzymic and enzyme-free data sets are identical within experimental error. The Occam's Razor conclusion is that at least this adenosylcobalamin-dependent enzyme has not evolved to enhance quantum mechanical tunneling, at least within the present error bars. Instead, this B(12)-dependent enzyme simply exploits the identical level of quantum mechanical tunneling that is available in the enzyme-free, solution-based H(*) abstraction reaction. The results also require a similar, if not identical, barrier width and height within experimental error for the H(*) abstraction both within, and outside of, the enzyme.

A compelling experimental test of the hypothesis that enzymes have evolved to enhance quantum mechanical tunneling in hydrogen transfer reactions: the beta-neopentylcobalamin system combined with prior adocobalamin data

An intriguing but controversial hypothesis has appeared that "The optimization of enzyme catalysis may entail the evolutionary implementation of chemical strategies that increase the probability of tunneling and thereby accelerate the reaction rate" (Kohen, A.; Klinman, J. P. Acc. Chem. Res. 1998, 31, 397). Restated, enzymes may have evolved to enhance quantum mechanical tunneling by coupling to protein low nu modes that squeeze the reacting centers together in, for example, their H(*) atom abstraction reactions. Such a putative "protein squeezing" mechanism would enhance hydrogen quantum mechanical tunneling by reducing the barrier width. An alternative hypothesis is that enzymes do not enhance tunneling, but simply exploit the same amount of tunneling present in their enzyme-free solution reactions, if those reactions occur. A third, conceivable hypothesis is that enzymes might even inadvertently decrease the amount of tunneling as an undesired result of increasing the barrier width while reducing the barrier height. Testing these hypotheses experimentally requires the extremely rare event of being able to measure the amount of tunneling both in the enzyme system and in a very similar if not identical reaction in enzyme-free solution. This has been accomplished experimentally in only one prior case, our recent study of AdoCbl (coenzyme B(12)) and 8-Meo-AdoCbl undergoing enzyme-like H(*) abstraction reactions (Doll, K. M.; Bender, B. R.; Finke, R. G. to J. Am. Chem. Soc. 2003, in press). The data there reveal no change in the level of tunneling within or outside of the enzyme in comparison to the best literature data for an AdoCbl-dependent enzyme, methylmalonyl-CoA mutase. However, that first system suffers from two limitations: the measurement of the KIE (kinetic isotope effect) data in a nonenzymic 80-110 degrees C temperature range; and lower precision data than desired due to the HPLC-MS method required for one of the KIE analyses. These limitations have now been overcome by the synthesis, then thermolysis and KIE study vs temperature of the H(*) abstraction reaction of beta-neopentylcobalamin (beta-NpCbl) in ethylene glycol-d(0) and ethylene glycol-d(4). This is the first experimental test of Klinman's hypothesis using KIE data obtained at enzyme-relevant temperatures. The key data obtained are as follows: deuterium KIEs of 23.1 +/- 3.0 at 40 degrees C to 39.0 +/- 2.3 at 10 degrees C; an activation energy difference E(D) - E(H) of 3.1 +/- 0.3 kcal mol(-)(1); and a pre-exponential factor ratio A(H)/A(D) of 0.14 +/- 0.07. Moreover, our now three sets of data (NpCbl; AdoCbl; 8-MeOAdoCbl) are shown to lie on the same ln KIE vs 1/T linear plot yielding a set of enzyme-temperature-relevant, high-precision KIE, E(D) - E(H), and A(H)/A(D) data over a relatively large, 110 degrees C temperature range. Significantly, the enzyme-free solution KIE, E(D) - E(H), and A(H)/A(D) are identical within experimental error to those for methylmalonyl-CoA mutase. This finding leads to the conclusion that there is no enzymic enhancement of the tunneling in at least this B(12)-dependent enzyme. This B(12) enzyme does, however, exploit the same (unchanged) level of tunneling measured for the nonenzymic, Ado(*) solution H(*) abstraction reaction. A discussion is presented of the still open question of if this first experimental finding, of "no enzymic enhancement of tunneling" in one B(12)-dependent enzymic system, is likely to prove more general or not.

A new conceptual framework for enzyme catalysis. Hydrogen tunnelling coupled to enzyme dynamics in flavoprotein and quinoprotein enzymes

Recent years have witnessed high levels of activity in identifying enzyme systems that catalyse H-transfer by quantum tunneling. Rather than being restricted to a small number of specific enzymes as perceived initially, it has now become an accepted mechanism for H-transfer in a growing number of enzymes. Furthermore, H-tunneling is driven by the thermally induced dynamics of the enzyme. In some of those enzymes that break stable C-H bonds the reaction proceeds purely by quantum tunneling, without the need to partially ascend the barrier. Enzymes studied that fall into this category include the flavoprotein and quinoprotein amine dehydrogenases, which have proved to be excellent model systems. These enzymes have enabled us to study the relationship between barrier shape and reaction kinetics. This has involved studies with "slow" and "fast" substrates and enzymes impaired by mutagenesis. A number of key questions now remain, including the nature of the coupling between protein dynamics and quantum tunneling. The wide-ranging implications of quantum tunneling introduce a paradigm shift in the conceptual framework for enzyme catalysis, inhibition and design.

Barrier passage and protein dynamics in enzymatically catalyzed reactions

This review describes studies of particular enzymatically catalyzed reactions to investigate the possibility that catalysis is mediated by protein dynamics. That is, evolution has crafted the protein backbone of the enzyme to direct vibrations in such a fashion to speed reaction. The review presents the theoretical approach we have used to investigate this problem, but it is designed for the nonspecialist. The results show that in alcohol dehydrogenase, dynamic protein motion is in fact strongly coupled to chemical reaction in such a way as to promote catalysis. This result is in concert with both experimental data and interpretations for this and other enzyme systems studied in the laboratories of the two other investigators who have published reviews in this issue.

Optimizing the Michaelis complex of trimethylamine dehydrogenase: identification of interactions that perturb the ionization of substrate and facilitate catalysis with trimethylamine base

Recent evidence from isotope studies supports the view that catalysis by trimethylamine dehydrogenase (TMADH) proceeds from a Michaelis complex involving trimethylamine base and not, as thought previously, trimethylammonium cation. In native TMADH reduction of the flavin by substrate (perdeuterated trimethylamine) is influenced by two ionizations in the Michaelis complex with pK(a) values of 6.5 and 8.4; maximal activity is realized in the alkaline region. The latter ionization has been attributed to residue His-172 and, more recently, the former to the ionization of substrate itself. In the Michaelis complex, the ionization of substrate (pK(a) approximately 6.5 for perdeuterated substrate) is perturbed by approximately -3.3 to -3.6 pH units compared with that of free trimethylamine (pK(a) = 9.8) and free perdeuterated trimethylamine (pK(a) = 10.1), respectively, thus stabilizing trimethylamine base by approximately 2 kJ mol(-1). We show, by targeted mutagenesis and stopped-flow studies that this reduction of the pK(a) is a consequence of electronic interaction with residues Tyr-60 and His-172, thus these two residues are key for optimizing catalysis in the physiological pH range. We also show that residue Tyr-174, the remaining ionizable group in the active site that we have not targeted previously by mutagenesis, is not implicated in the pH dependence of flavin reduction. Formation of a Michaelis complex with trimethylamine base is consistent with a mechanism of amine oxidation that we advanced in our previous computational and kinetic studies which involves nucleophilic attack by the substrate nitrogen atom on the electrophilic C4a atom of the flavin isoalloxazine ring. Stabilization of trimethylamine base in the Michaelis complex over that in free solution is key to optimizing catalysis at physiological pH in TMADH, and may be of general importance in the mechanism of other amine dehydrogenases that require the unprotonated form of the substrate for catalysis.

Deuterium isotope effects during carbon-hydrogen bond cleavage by trimethylamine dehydrogenase. Implications for mechanism and vibrationally assisted hydrogen tunneling in wild-type and mutant enzymes

His-172 and Tyr-169 are components of a triad in the active site of trimethylamine dehydrogenase (TMADH) comprising Asp-267, His-172, and Tyr-169. Stopped-flow kinetic studies with trimethylamine as substrate have indicated that mutation of His-172 to Gln reduces the limiting rate constant for flavin reduction approximately 10-fold (Basran, J., Sutcliffe, M. J., Hille, R., and Scrutton, N. S. (1999) Biochem. J. 341, 307-314). A kinetic isotope effect (KIE = k(H)/k(D)) accompanies flavin reduction by H172Q TMADH, the magnitude of which varies significantly with solution pH. With trimethylamine, flavin reduction by H172Q TMADH is controlled by a single macroscopic ionization (pK(a) = 6.8 +/- 0.1). This ionization is perturbed (pK(a) = 7.4 +/- 0.1) in reactions with perdeuterated trimethylamine and is responsible for the apparent variation in the KIE with solution pH. At pH 9.5, where the functional group controlling flavin reduction is fully ionized, the KIE is independent of temperature in the range 277-297 K, consistent with vibrationally assisted hydrogen tunneling during breakage of the substrate C-H bond. Y169F TMADH is approximately 4-fold more compromised than H172Q TMADH for hydrogen transfer, which occurs non-classically. Studies with Y169F TMADH suggest partial thermal excitation of substrate prior to hydrogen tunneling by a vibrationally assisted mechanism. Our studies illustrate the varied effects of compromising mutations on tunneling regimes in enzyme molecules.