Mechanistic study of protein phosphatase-1 (PP1), a catalytically promiscuous enzyme

The reaction catalyzed by the protein phosphatase-1 (PP1) has been examined by linear free energy relationships and kinetic isotope effects. With the substrate 4-nitrophenyl phosphate (4NPP), the reaction exhibits a bell-shaped pH-rate profile for kcat/KM indicative of catalysis by both acidic and basic residues, with kinetic pKa values of 6.0 and 7.2. The enzymatic hydrolysis of a series of aryl monoester substrates yields a Br?nsted beta(lg) of -0.32, considerably less negative than that of the uncatalyzed hydrolysis of monoester dianions (-1.23). Kinetic isotope effects in the leaving group with the substrate 4NPP are (18)(V/K) bridge = 1.0170 and (15)(V/K) = 1.0010, which, compared against other enzymatic KIEs with and without general acid catalysis, are consistent with a loose transition state with partial neutralization of the leaving group. PP1 also efficiently catalyzes the hydrolysis of 4-nitrophenyl methylphosphonate (4NPMP). The enzymatic hydrolysis of a series of aryl methylphosphonate substrates yields a Br?nsted beta(lg) of -0.30, smaller than the alkaline hydrolysis (-0.69) and similar to the beta(lg) measured for monoester substrates, indicative of similar transition states. The KIEs and the beta(lg) data point to a transition state for the alkaline hydrolysis of 4NPMP that is similar to that of diesters with the same leaving group. For the enzymatic reaction of 4NPMP, the KIEs are indicative of a transition state that is somewhat looser than the alkaline hydrolysis reaction and similar to the PP1-catalyzed monoester reaction. The data cumulatively point to enzymatic transition states for aryl phosphate monoester and aryl methylphosphonate hydrolysis reactions that are much more similar to one another than the nonenzymatic hydrolysis reactions of the two substrates.     

Nucleophilic participation in the transition state for human thymidine phosphorylase

Recombinant human thymidine phosphorylase catalyzes the reaction of arsenate with thymidine to form thymine and 2-deoxyribose 1-arsenate, which rapidly decomposes to 2-deoxyribose and inorganic arsenate. The transition-state structure of this reaction was determined using kinetic isotope effect analysis followed by computer modeling. Experimental kinetic isotope effects were determined at physiological pH and 37 degrees C. The extent of forward commitment to catalysis was determined by pulse-chase experiments to be 0.70%. The intrinsic kinetic isotope effects for [1'-(3)H]-, [2'R-(3)H]-, [2'S-(3)H]-, [4'-(3)H]-, [5'-(3)H]-, [1'-(14)C]-, and [1-(15)N]-thymidines were determined to be 0.989 +/- 0.002, 0.974 +/- 0.002, 1.036 +/- 0.002, 1.020 +/- 0.003, 1.061 +/- 0.003, 1.139 +/- 0.005, and 1.022 +/- 0.005, respectively. A computer-generated model, based on density functional electronic structure calculations, was fit to the experimental isotope effect. The structure of the transition state confirms that human thymidine phosphorylase proceeds through an S(N)2-like transition state with bond orders of 0.50 to the thymine leaving group and 0.33 to the attacking oxygen nucleophile. The reaction differs from the dissociative transition states previously reported for N-ribosyl transferases and is the first demonstration of a nucleophilic transition state for an N-ribosyl transferase. The large primary (14)C isotope effect of 1.139 can occur only in nucleophilic displacements and is the largest (14)C primary isotope effect reported for an enzymatic reaction. A transition state structure with substantial bond order to the attacking nucleophile and leaving group is confirmed by the slightly inverse 1'-(3)H isotope effect, demonstrating that the transition state is compressed by the impinging steric bulk of the nucleophile and leaving group.     

The Kinetic Isotope Effect as a Probe of Spin Crossover in the CH Activation of Methane by the FeO+ Cation

Two‐state reactivity (TSR) is often used to explain the reaction of transition‐metal–oxo reagents in the bare form or in the complex form. The evidence of the TSR model typically comes from quantum‐mechanical calculations for energy profiles with a spin crossover in the rate‐limiting step. To prove the TSR concept, kinetic profiles for C? H activation by the FeO⁺ cation were explored. A direct dynamics approach was used to generate potential energy surfaces of the sextet and quartet H‐transfers and rate constants and kinetic isotope effects (KIEs) were calculated using variational transition‐state theory including multidimensional tunneling. The minimum energy crossing point with very large spin–orbit coupling matrix element was very close to the intrinsic reaction paths of both sextet and quartet H‐transfers. Excellent agreement with experiments were obtained when the sextet reactant and quartet transition state were used with a spin crossover, which strongly support the TSR model.     

Rate constants and isotope effects for the reaction of H-atom abstraction from RH substrates by PINO radicals

The kinetics of the reactions of hydrogen atom abstraction from the C–H bonds of substrates of different structures by phthalimide-N-oxyl radicals is studied. The rate constants of this reaction are measured and the kinetic isotope effects are determined. It is shown that in addition to the thermodynamic factor, Coulomb forces and donor–acceptor interactions affect the reaction between phthalimide-N-oxyl radicals and substrate molecules, altering the shape of the transition state. This favors the tunneling of hydrogen atoms and leads to a substantial reduction in the activation energy of the process.     

Kinetics and mechanism of the aminolysis of aryl phenyl chlorothiophosphates with anilines

Kinetic studies of the reactions of aryl phenyl chlorothiophosphates (1) and aryl 4-chlorophenyl chlorothiophosphates (2) with substituted anilines in acetonitrile at 55.0 degrees C are reported. The negative values of the cross-interaction constant rhoXY (rhoXY = -0.22 and -0.50 for 1 and 2, respectively) between substituents in the nucleophile (X) and substrate (Y) indicate that the reactions proceed by concerted SN2 mechanism. The primary kinetic isotope effects (kH/kD = 1.11-1.13 and 1.10-1.46 for 1 and 2, respectively) involving deuterated aniline nucleophiles are obtained. Front- and back-side nucleophilic attack on the substrates is proposed mainly on the basis of the primary kinetic isotope effects. A hydrogen-bonded, four-center-type transition state is suggested for a front-side attack, while the trigonal bipyramidal pentacoordinate transition state is suggested for a back-side attack. The MO theoretical calculations of the model reactions of dimethyl chlorothiophosphate (1') and dimethyl chlorophosphate (3') with ammonia are carried out. Considering the specific solvation effect, the front-side nucleophilic attack can occur competitively with the back-side attack in the reaction of 1'.     

Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS

Protein farnesyltransferase (FTase) catalyzes farnesylation of a variety of peptide substrates. (3)H α-secondary kinetic isotope effect (α-SKIE) measurements of two peptide substrates, CVIM and CVLS, are significantly different and have been proposed to reflect a rate-limiting S(N)2-like transition state with dissociative characteristics for CVIM, while, due to the absence of an isotope effect, CVLS was proposed to have a rate-limiting peptide conformational change. Potential of mean force quantum mechanical/molecular mechanical studies coupled with umbrella sampling techniques were performed to further probe this mechanistic dichotomy. We observe the experimentally proposed transition state (TS) for CVIM but find that CVLS has a symmetric S(N)2 TS, which is also consistent with the absence of a (3)H α-SKIE. These calculations demonstrate facile substrate-dependent alterations in the transition state structure catalyzed by FTase.     

Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State

The origin of substrate preference in promiscuous enzymes was investigated by enzyme isotope labelling of the alcohol dehydrogenase from Geobacillus stearothermophilus (BsADH). At physiological temperature, protein dynamic coupling to the reaction coordinate was insignificant. However, the extent of dynamic coupling was highly substrate‐dependent at lower temperatures. For benzyl alcohol, an enzyme isotope effect larger than unity was observed, whereas the enzyme isotope effect was close to unity for isopropanol. Frequency motion analysis on the transition states revealed that residues surrounding the active site undergo substantial displacement during catalysis for sterically bulky alcohols. BsADH prefers smaller substrates, which cause less protein friction along the reaction coordinate and reduced frequencies of dynamic recrossing. This hypothesis allows a prediction of the trend of enzyme isotope effects for a wide variety of substrates.     

A theoretical analysis of rate constants and kinetic isotope effects corresponding to different reactant valleys in lactate dehydrogenase

In some enzymatic systems large conformational changes are coupled to the chemical step, in such a way that dispersion of rate constants can be observed in single-molecule experiments, each corresponding to the reaction from a different reactant valley. Under this perspective here we present a computational study of pyruvate to lactate transformation catalyzed by lactate dehydrogenase. The reaction consists of a hydride transfer and a proton transfer that seem to take place concertedly. The degree of asynchronicity and the energy barrier depend on the particular starting reactant valley. In order to estimate rate constants we used a free energy perturbation technique adapted to follow the intrinsic reaction coordinate for several possible reaction paths. Tunneling effects are also obtained with a slightly modified version of the ensemble-averaged variational transition state theory with multidimensional tunneling contributions. According to our results the closure of the active site by means of a flexible loop can lead to the formation of different reactant complexes displaying different features in the disposition of some key residues (such as Arg109), interactions with the substrate and number of water molecules in the active site. The chemical step of the reaction takes place with a different reaction rate from each of these complexes. Finally, primary kinetic isotope effects for replacement of the transferring hydrogen of the cofactor with a deuteride are in good agreement with experimental observations, thus validating our methodology.     

The Kinetic Isotope Effect as a Probe of Spin Crossover in the C?H Activation of Methane by the FeO+ Cation

Two‐state reactivity (TSR) is often used to explain the reaction of transition‐metal–oxo reagents in the bare form or in the complex form. The evidence of the TSR model typically comes from quantum‐mechanical calculations for energy profiles with a spin crossover in the rate‐limiting step. To prove the TSR concept, kinetic profiles for C H activation by the FeO⁺ cation were explored. A direct dynamics approach was used to generate potential energy surfaces of the sextet and quartet H‐transfers and rate constants and kinetic isotope effects (KIEs) were calculated using variational transition‐state theory including multidimensional tunneling. The minimum energy crossing point with very large spin–orbit coupling matrix element was very close to the intrinsic reaction paths of both sextet and quartet H‐transfers. Excellent agreement with experiments were obtained when the sextet reactant and quartet transition state were used with a spin crossover, which strongly support the TSR model.     

Accumulation of tetrahedral intermediates in cholinesterase catalysis: a secondary isotope effect study

In a previous communication, kinetic β-deuterium secondary isotope effects were reported that support a mechanism for substrate-activated turnover of acetylthiocholine by human butyrylcholinesterase (BuChE) wherein the accumulating reactant state is a tetrahedral intermediate ( Tormos , J. R. ; et al. J. Am. Chem. Soc. 2005 , 127 , 14538 - 14539 ). In this contribution additional isotope effect experiments are described with acetyl-labeled acetylthiocholines (CL(3)COSCH(2)CH(2)N(+)Me(3); L = H or D) that also support accumulation of the tetrahedral intermediate in Drosophila melanogaster acetylcholinesterase (DmAChE) catalysis. In contrast to the aforementioned BuChE-catalyzed reaction, for this reaction the dependence of initial rates on substrate concentration is marked by pronounced substrate inhibition at high substrate concentrations. Moreover, kinetic β-deuterium secondary isotope effects for turnover of acetylthiocholine depended on substrate concentration, and gave the following: (D3)k(cat)/K(m) = 0.95 ± 0.03, (D3)k(cat) = 1.12 ± 0.02 and (D3)βk(cat) = 0.97 ± 0.04. The inverse isotope effect on k(cat)/K(m) is consistent with conversion of the sp(2)-hybridized substrate carbonyl in the E + A reactant state into a quasi-tetrahedral transition state in the acylation stage of catalysis, whereas the markedly normal isotope effect on k(cat) is consistent with hybridization change from sp(3) toward sp(2) as the reactant state for deacylation is converted into the subsequent transition state. Transition states for Drosophila melanogaster AChE-catalyzed hydrolysis of acetylthiocholine were further characterized by measuring solvent isotope effects and determining proton inventories. These experiments indicated that the transition state for rate-determining decomposition of the tetrahedral intermediate is stabilized by multiple protonic interactions. Finally, a simple model is proposed for the contribution that tetrahedral intermediate stabilization provides to the catalytic power of acetylcholinesterase.     

Measurement of the alpha-secondary kinetic isotope effect for the reaction catalyzed by mammalian protein farnesyltransferase

Protein farnesytransferase (FTase) catalyzes the transfer of a 15-carbon prenyl group from farnesyl diphosphate (FPP) to the cysteine residue of target proteins and is a member of the newest class of zinc metalloenzymes that catalyze sulfur alkylation. Common substrates of FTase include oncogenic Ras proteins, and therefore inhibitors are under development for the treatment of various cancers. An increased understanding of the salient features of the chemical transition state of FTase may aid in the design of potent inhibitors and enhance our understanding of the mechanism of this class of zinc enzymes. To investigate the transition state of FTase we have used transient kinetics to measure the alpha-secondary 3H kinetic isotope effect at the sensitive C1 position of FPP. The isotope effect for the FTase single turnover reaction using a peptide substrate that is farnesylated rapidly is near unity, indicating that a conformational change, rather than farnesylation, is the rate-limiting step. To look at the chemical step, the kinetic isotope effect was measured as 1.154 +/- 0.006 for a peptide that is farnesylated slowly, and these data suggest that FTase proceeds via a concerted mechanism with dissociative character.     

The effect of solvent on the structure of the transition state for the S(N)2 reaction between cyanide ion and ethyl chloride in DMSO and THF probed with six different kinetic isotope effects

The secondary alpha- and beta-deuterium, the alpha-carbon, the nucleophile carbon, the nucleophile nitrogen, and the chlorine leaving group kinetic isotope effects for the S(N)2 reaction between cyanide ion and ethyl chloride were determined in the very slightly polar solvent THF at 30 degrees C. A comparison of these KIEs with those reported earlier for the same reaction in the polar solvent DMSO shows that the transition state in THF is only slightly tighter with very slightly shorter NC-C(alpha) and C(alpha)-Cl bonds. This minor change in transition state structure does not account for the different transition structures that were earlier suggested by interpreting the experimental KIEs and the gas-phase calculations, respectively. It therefore seems unlikely that the different transition states suggested by the two methods are due to the lack of appropriate solvent modeling in the theoretical calculations. Previously it was predicted that the transition state of S(N)2 reactions where the nucleophile and the leaving group have the same charge would be unaffected by a change in solvent. The experimental KIEs support this view.     

Dynamic effects on the periselectivity, rate, isotope effects, and mechanism of cycloadditions of ketenes with cyclopentadiene

The cycloadditions of cyclopentadiene with diphenylketene and dichloroketene are studied by a combination of kinetic and product studies, kinetic isotope effects, standard theoretical calculations, and trajectory calculations. In contrast to recent reports, the reaction of cyclopentadiene with diphenylketene affords both [4 + 2] and [2 + 2] cycloadducts directly. This is surprising, since there is only one low-energy transition structure for adduct formation in mPW1K calculations, but quasiclassical trajectories started from this single transition structure afford both [4 + 2] and [2 + 2] products. The dichloroketene reaction is finely balanced between [4 + 2] and [2 + 2] cycloaddition modes in mPW1K calculations, as the minimum-energy path (MEP) leads to different products depending on the basis set. The MEP is misleading in predicting a single product, as trajectory studies for the dichloroketene reaction predict that both [4 + 2] and [2 + 2] products should be formed. The periselectivity does not reflect transition state orbital interactions. The (13)C isotope effects for the dichloroketene reaction are well-predicted from the mPW1K/6-31+G** transition structure. However, the isotope effects for the diphenylketene reaction are not predictable from the cycloaddition transition structure and transition state theory. The isotope effects also appear inconsistent with kinetic observations, but the trajectory studies evince that nonstatistical recrossing can reconcile the apparently contradictory observations. B3LYP calculations predict a shallow intermediate on the energy surface, but trajectory studies suggest that the differing B3LYP and mPW1K surfaces do not result in qualitatively differing mechanisms. Overall, an understanding of the products, rates, selectivities, isotope effects, and mechanism in these reactions requires the explicit consideration of dynamic trajectories.     

Intrinsic primary and secondary hydrogen kinetic isotope effects for alanine racemase from global analysis of progress curves

The pyridoxal phosphate dependent alanine racemase catalyzes the interconversion of L- and D-alanine. The latter is an essential component of peptidoglycan in cell walls of Gram-negative and -positive bacteria, making alanine racemase an attractive target for antibacterials. Global analysis of protiated and deuterated progress curves simultaneously enables determination of intrinsic kinetic and equilibrium isotope effects for alanine racemase. The intrinsic primary kinetic isotope effects for Calpha hydron abstraction are 1.57 +/- 0.05 in the D --> L direction and 1.66 +/- 0.09 in the L --> D direction. Secondary kinetic isotope effects were found for the external aldimine formation steps in both the L --> D (1.13 +/- 0.05, forward; 0.90 +/- 0.03, reverse) and D --> L (1.13 +/- 0.06, forward; 0.89 +/- 0.03, reverse) directions. The secondary equilibrium isotope effects calculated from these are 1.26 +/- 0.07 and 1.27 +/- 0.07 for the L --> D and D --> L directions, respectively. These equilibrium isotope effects imply substantial ground-state destabilization of the C-H bond via hyperconjugation with the conjugated Schiff base/pyridine ring pi system. The magnitudes of the intrinsic primary kinetic isotope effects, the lower boundary on the energy of the quinonoid intermediate, and the protonation states of the active site catalytic acids/bases (K39-epsilonNH2 and Y265-OH) suggest that the pKa of the substrate Calpha-H bond in the external aldimine lies between those of the two catalytic bases, such that the proton abstraction transition state is early in the D --> L direction and late in the L --> D direction.     

Calculations of substituent and solvent effects on the kinetic isotope effects of Menshutkin reactions

Nitrogen, deuterium, halogen, and carbon kinetic isotope effects have been modeled for the Menshutkin reaction between methyl halides and substituted N,N-dimethylaniline at the HF/6-31G(d) level of theory augmented by the C-PCM continuum solvent model for several solvents. Systematic changes in geometries of the transition states and Gibbs free energies of activation have been found with phenyl ring substituents, solvent, and the leaving group. Kinetic isotope effects also change systematically; however, these changes are predicted to be small, inside the usual precision of the experimental measurements. On the contrary, no correlation has been found between the kinetic isotope effects and the Hammett constants for para substituents. Thus opposite to previous assumptions, our results indicate that kinetic isotope effects on the Menshutkin reaction cannot be used to predict the position of the transition state on the reaction coordinate.     

Kinetic isotope effects of L-Dopa decarboxylase

A mixed centroid path integral and free energy perturbation method (PI-FEP/UM) has been used to investigate the primary carbon and secondary hydrogen kinetic isotope effects (KIEs) in the amino acid decarboxylation of L-Dopa catalyzed by the enzyme L-Dopa decarboxylase (DDC) along with the corresponding uncatalyzed reaction in water. DDC is a pyridoxal 5'-phosphate (PLP) dependent enzyme. The cofactor undergoes an internal proton transfer between the zwitterionic protonated Schiff base configuration and the neutral hydroxyimine tautomer. It was found that the cofactor PLP makes significant contributions to lowering the decarboxylation barrier, while the enzyme active site provides further stabilization of the transition state. Interestingly, the O-protonated configuration is preferred both in the Michaelis complex and at the decarboxylation transition state. The computed kinetic isotope effects (KIE) on the carboxylate C-13 are consistent with that observed on decarboxylation reactions of other PLP-dependent enzymes, whereas the KIEs on the α carbon and secondary proton, which can easily be validated experimentally, may be used as a possible identification for the active form of the PLP tautomer in the active site of DDC.     

Solvent effect on concertedness of the transition state in the hydrolysis of p-nitrophenyl acetate

[reaction: see text]. The reaction pathway for the alkaline hydrolysis of p-nitrophenyl acetate is investigated using density functional theory. It is shown that solvent plays an indispensable role in shaping the concerted transition state. The concertedness of this transition state is supported by good agreement with the measured kinetic isotope effects.     

Combined QM/MM study of the mechanism and kinetic isotope effect of the nucleophilic substitution reaction in haloalkane dehalogenase

Combined QM/MM molecular dynamics simulations have been carried out for the dehalogenation reaction of the nucleophilic displacement of dichloroethane catalyzed by haloalkane dehalogenase. The computed chlorine kinetic isotope effects and free energies of activation in the wild-type and the Phe172Trp mutant enzyme are found to be consistent with experiment. In comparison with the uncatalyzed model reaction in water, the enzyme lowers the activation barrier by about 16 kcal/mol. The enormous enzymatic action was attributed to a combination of contributions from a change in the solvation effect and transition state stabilization. The unique features of tryptophan's ability to interact favorably with hydrophobic substrates and to form hydrogen bonds to the leaving group chloride ion at the transition state enable both factors to make significant contributions to the barrier lowering mechanism in the enzyme. This is in contrast to the reference reaction in water, in which hydrogen bonding interactions are weakened at the transition state because of dispersed charge distribution at the transition state relative to that in the reactant and product states.     

Transition states for glucopyranose interconversion

Glucose is a central molecule in biology and chemistry, and the anomerization reaction has been studied for more than 150 years. Transition-state structure is the last impediment to an in-depth understanding of its solution chemistry. We have measured kinetic isotope effects on the rate constants for approach of alpha-glucopyranose to its equilibrium with beta-glucopyranose, and these were converted into unidirectional kinetic isotope effects using equilibrium isotope effects. Saturation transfer 13C NMR spectroscopy has yielded the relative free energies of the transition states for the ring-opening and ring-closing reactions, and both transition states contribute to the experimental kinetic isotope effects. Both transition states of the anomerization process have been modeled with high-level computational theory with constraints from the primary, secondary, and solvent kinetic isotope effects. We have found the transition states for anomerization, and we have also concluded that it is forbidden for the water molecule to form a hydrogen bond bridge to both OH1 and O5 of glucose simultaneously in either transition state.     

Determining the transition-state structure for different SN2 reactions using experimental nucleophile carbon and secondary alpha-deuterium kinetic isotope effects and theory

Nucleophile (11)C/ (14)C [ k (11)/ k (14)] and secondary alpha-deuterium [( k H/ k D) alpha] kinetic isotope effects (KIEs) were measured for the S N2 reactions between tetrabutylammonium cyanide and ethyl iodide, bromide, chloride, and tosylate in anhydrous DMSO at 20 degrees C to determine whether these isotope effects can be used to determine the structure of S N2 transition states. Interpreting the experimental KIEs in the usual fashion (i.e., that a smaller nucleophile KIE indicates the Nu-C alpha transition state bond is shorter and a smaller ( k H/ k D) alpha is found when the Nu-LG distance in the transition state is shorter) suggests that the transition state is tighter with a slightly shorter NC-C alpha bond and a much shorter C alpha-LG bond when the substrate has a poorer halogen leaving group. Theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion. The results show that the experimental nucleophile (11)C/ (14)C KIEs can be used to determine transition-state structure in different reactions and that the usual method of interpreting these KIEs is correct. The magnitude of the experimental secondary alpha-deuterium KIE is related to the nucleophile-leaving group distance in the S N2 transition state ( R TS) for reactions with a halogen leaving group. Unfortunately, the calculated and experimental ( k H/ k D) alpha's change oppositely with leaving group ability. However, the calculated ( k H/ k D) alpha's duplicate both the trend in the KIE with leaving group ability and the magnitude of the ( k H/ k D) alpha's for the ethyl halide reactions when different scale factors are used for the high and the low energy vibrations. This suggests it is critical that different scaling factors for the low and high energy vibrations be used if one wishes to duplicate experimental ( k H/ k D) alpha's. Finally, neither the experimental nor the theoretical secondary alpha-deuterium KIEs for the ethyl tosylate reaction fit the trend found for the reactions with a halogen leaving group. This presumably is found because of the bulky (sterically hindered) leaving group in the tosylate reaction. From every prospective, the tosylate reaction is too different from the halogen reactions to be compared.