Dynamic aspect of kinetics of reaction catalyzed by lactate dehydrogenase

The influence of solvent viscosity on the kinetic parameters of the pyruvate reduction reaction catalyzed by lactate dehydrogenase has been investigated. The viscosity was adjusted by sucrose and glycerol solutions at concentrations from 0 to 44% and from 0 to 63%, respectively. The reaction rate decreased abruptly with an increase in viscosity. The study of different reaction stages (enzyme-substrate complex formation, catalysis, inhibitory complex decomposition, competitive inhibition by chlorine ions) revealed that the catalysis (and the related conformational changes) is the only stage (of the above mentioned) that depends markedly on the solvent viscosity. The reaction is insensitive to the changes in the dielectric properties of the solution induced by the addition of alcohols and dioxane. The observed power dependence of the rate constant on viscosity is explained in terms of Kramer's theory which considers the proton transition through the activation barrier to be a diffusion in the field of random forces. The influence of solvent viscosity on enzymic kinetics indicates a direct relation between solvent dynamics and relevant protein conformational movements.     

Toward an understanding of the role of dynamics on enzymatic catalysis in lactate dehydrogenase

The motions of key residues at the substrate binding site of lactate dehydrogenase (LDH) were probed on the 10 ns to 10 ms time scale using laser-induced temperature-jump relaxation spectroscopy employing both UV fluorescence and isotope-edited IR absorption spectroscopy as structural probes. The dynamics of the mobile loop, which closes over the active site and is important for catalysis and binding, were characterized by studies of the inhibitor oxamate binding to the LDH/NADH binary complex monitoring the changes in emission of bound NADH. The bound NAD-pyruvate adduct, whose pyruvate moiety likely interacts with the same residues that interact with pyruvate in its ternary complex with LDH, served as a probe for any relative motions of active site residues against the substrate. The frequencies of its C=O stretch and -COO(-) antisymmetric stretch shift substantially should any relative motion of the polar moieties at the active site (His-195, Asp-168, Arg-109, and Arg-171) occur. The dynamics associated with loop closure are observed to involve several steps with motions from 1 to 300 microms. Apart from the "melting" of a few residues on the protein's surface, no kinetics were observed on any time scale in experiments of the bound NAD-pyr adduct although the measurements were made with a high degree of accuracy, even for final temperatures close to the unfolding transition of the protein. This is contrary to simple physical considerations and models. These results show that, once a productive protein/substrate complex is formed, the binding pocket is very rigid with very little, if any, motion apart from the mobile loop. The results also show that loop opening involves concomitant movement of the substrate out of the binding pocket.     

Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase

We have studied the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) and the coenzyme nicotinamide adenine dinucleotide phosphate (NADPH); the substrate is 5-protonated 7,8-dihydrofolate, and the product is tetrahydrofolate. The potential energy surface is modeled by a combined quantum mechanical-molecular mechanical (QM/MM) method employing Austin model 1 (AM1) and a simple valence bond potential for 69 QM atoms and employing the CHARMM22 and TIP3P molecular mechanics force fields for the other 21 399 atoms; the QM and MM regions are joined by two boundary atoms treated by the generalized hybrid orbital (GHO) method. All simulations are carried out using periodic boundary conditions at neutral pH and 298 K. In stage 1, a reaction coordinate is defined as the difference between the breaking and forming bond distances to the hydride ion, and a quasithermodynamic free energy profile is calculated along this reaction coordinate. This calculation includes quantization effects on bound vibrations but not on the reaction coordinate, and it is used to locate the variational transition state that defines a transition state ensemble. Then, the key interactions at the reactant, variational transition state, and product are analyzed in terms of both bond distances and electrostatic energies. The results of both analyses support the conclusion derived from previous mutational studies that the M20 loop of DHFR makes an important contribution to the electrostatic stabilization of the hydride transfer transition state. Third, transmission coefficients (including recrossing factors and multidimensional tunneling) are calculated and averaged over the transition state ensemble. These averaged transmission coefficients, combined with the quasithermodynamic free energy profile determined in stage 1, allow us to calculate rate constants, phenomenological free energies of activation, and primary and secondary kinetic isotope effects. A primary kinetic isotope effect (KIE) of 2.8 has been obtained, in good agreement with the experimentally determined value of 3.0 and with the value 3.2 calculated previously. The primary KIE is mainly a consequence of the quantization of bound vibrations. In contrast, the secondary KIE, with a value of 1.13, is almost entirely due to dynamical effects on the reaction coordinate, especially tunneling.     

Ligand binding and protein dynamics in lactate dehydrogenase

Recent experimental studies suggest that lactate dehydrogenase (LDH) binds its substrate via the formation of a LDH/NADH.substrate encounter complex through a select-fit mechanism, whereby only a minority population of LDH/NADH is binding-competent. In this study, we perform molecular dynamics calculations to explore the variations in structure accessible to the binary complex with a focus on identifying structures that seem likely to be binding-competent and which are in accord with the known experimental characterization of forming binding-competent species. We find that LDH/NADH samples quite a range of protein conformations within our 2.148 ns calculations, some of which yield quite facile access of solvent to the active site. The results suggest that the mobile loop of LDH is perhaps just partially open in these conformations and that multiple open conformations, yielding multiple binding pathways, are likely. These open conformations do not require large-scale unfolding/melting of the binary complex. Rather, open versus closed conformations are due to subtle protein and water rearrangements. Nevertheless, the large heat capacity change observed between binding-competent and binding-incompetent can be explained by changes in solvation and an internal rearrangement of hydrogen bonds. We speculate that such a strategy for binding may be necessary to get a ligand efficiently to a binding pocket that is located fairly deep within the protein's interior.     

Asp338 controls hydride transfer in Escherichia coli IMP dehydrogenase

IMP dehydrogenase (IMPDH) catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD(+). This reaction involves the formation of a covalent adduct with an active site Cys. This intermediate, E-XMP, hydrolyzes to produce XMP. The mutation of Asp338 to Ala severely impairs the activity of Escherichia coli IMPDH, decreasing the value of k(cat) by 650-fold. No (D)V(m) or (D)V/K(m) isotope effects are observed when 2-(2)H-IMP is the substrate for wild-type IMPDH. Values of (D)V(m) = 2.6 and (D)V/K(m) (IMP) = 3.4 are observed for Asp338Ala. Moreover, while a burst of NADH production is observed for wild-type IMPDH, no burst is observed for Asp338Ala. These observations indicate that the mutation has decreased the rate of hydride transfer by at least 5 x 10(3)-fold. In contrast, k(cat) for the hydrolysis of 2-chloroinosine-5'-monophosphate is decreased by only 8-fold. In addition, the rate constant for inactivation by 6-chloropurine riboside 5'-monophosphate is increased by 3-fold. These observations suggest that the mutation has little effect on the nucleophilicity of the active site Cys residue. These results are consistent with a recent crystal structure that shows a hydrogen bonding network between Asp338, the 2'-OH of IMP, and the amide group of NAD(+) [Colby, T. D., Vanderveen, K., Strickler, M. D., Markham, G. D., and Goldstein, B. M. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 3531-3536].     

Potential of mean force calculation for the proton and hydride transfer reactions catalyzed by medium-chain acyl-CoA dehydrogenase: effect of mutations on enzyme catalysis

Potential of mean force calculations have been performed on the wild-type medium-chain acyl-CoA dehydrogenase (MCAD) and two of its mutant forms. Initial simulation and analysis of the active site of the enzyme reveal that an arginine residue (Arg256), conserved in the substrate-binding domain of this group of enzymes, exists in two alternate conformations, only one of which makes the enzyme active. This active conformation was used in subsequent computations of the enzymatic reactions. It is known that the catalytic alpha,beta-dehydrogenation of fatty acyl-CoAs consists of two C-H bond dissociation processes: a proton abstraction and a hydride transfer. Energy profiles of the two reaction steps in the wild-type MCAD demonstrate that the reaction proceeds by a stepwise mechanism with a transient species. The activation barriers of the two steps differ by only approximately 2 kcal/mol, indicating that both may contribute to the rate-limiting process. Thus this may be a stepwise dissociation mechanism whose relative barriers can be tuned by suitable alterations of the substrate and/or enzyme. Analysis of the structures along the reaction path reveals that Arg256 plays a key role in maintaining the reaction center hydrogen-bonding network involving the thioester carbonyl group, which stabilizes transition states as well as the intervening transient species. Mutation of this arginine residue to glutamine increases the activation barrier of the hydride transfer reaction by approximately 5 kcal/mol, and the present simulations predict a substantial loss of catalytic activity for this mutant. Structural analysis of this mutant reveals that the orientation of the thioester moiety of the substrate has been changed significantly as compared to that in the wild-type enzyme. In contrast, simulation of the active site of the Thr168Ala mutant shows no significant change in the relative orientation of the substrate and the cofactor in the active site; as a result, this mutation has very little effect on the overall reaction barrier, and this is consistent with the experimental data. This study demonstrates that significant insights into the catalytic mechanism can be obtained from simulation studies, and the results can be used to design novel mechanistic probes for the enzyme.     

The physiological role of the isoenzymes of lactate dehydrogenase in potatoes

Four of the five isoenzymes of lactate dehydrogenase present in potato tubers have been isolated and their kinetic properties examined. The pyruvate-reductase activity of isoenzyme-4 is greatly reduced at low pH, the affinity for both pyruvate and NADH is reduced and ATP has a stronger inhibitory effect. If the design properties of an enzyme dictate a high affinity for substrates, then the Km values for lactate, glyoxylate and NAD are consistent with an oxidative role for isoenzyme-4. The same considerations do not permit a conclusion about the physiological role of isoenzymes-1 to-3. However, an overview of the kinetic properties of these isoenzymes indicates that isoenzyme-1 is best adapted for the role of pyruvate reductase. Consideration of the relationships between kinetic constants and electrophoretic mobilities of the isoenzymes, leads us to predict that isoenzyme-5 is well adapted for a role in the oxidation of lactate or glyoxylate. The lactate dehydrogenase of potato leaves appears to consist prodominantly of an isoenzyme with the same mobility as isoenzyme-2 of the tubers and the two isoenzymes are probably identical. The kinetic properties of this isoenzyme are consistent with roles in either oxidation or reduction.Abbreviation Tris 2-amino-2-(hydroxymethyl)-1,3-propanediol     

Mechanism of lactic acid oxidation catalyzed by lactate dehydrogenase from the tail muscle of Homarus americanus.

The mechanism of lactic acid oxidation in the tail muscles of Homarus americanus was studied. In solutions of intermediate ionic strength (0.55) time-course progress curves for lactic acid oxidation as catalyzed by lactate dehydrogenase exhibited a lag period. Evidence is presented which indicates that the lactate dehydrogenase found in the tail muscles of the lobster exists in two distinct physical and kinetic forms. The equilibrium of these forms is dependent upon the ionic strength of the reaction mixture. In low ionic strength solutions, the enzyme exists as a tetrameric species with an apparent K_m for lactic acid of 1.1 m; in high ionic strength solutions, the enzyme exists as a dimer and the corresponding K_m is 0.028 m. At intermediate ionic strengths, an equilibrium between the two physical and kinetic species exists which is modulated by the NADH mole-fraction ($\text{[}\text{NADH}\text{]}\text{[}\text{NADH}\text{+}\text{NAD}{}^{\mathrm{+}}\text{]}$) and, in turn, this modulation results in sigmoidal time-course progress curves. The role of this enzyme is discussed as affected by in vivo ionic strength, temperature and levels of oxidized and reduced nicotine adenine dinucleotides.     

Solution conformation of lactate dehydrogenase as studied by saturation transfer ESR spectroscopy.

Several binary and ternary inhibitor and 'dead end' complexes of pig heart lactate dehydrogenase (L-lactate:NAD+ oxidoreductase, EC 1.1.1.27) were studied by saturation transfer ESR spectroscopy by means of an active NAD analog, spin-labeled at N6. The mobility of the spin-label depends on the nature of small molecules bound at the remote catalytic end of the coenzyme. The spin-label was found to serve as a reporter group monitoring the conformation of the peptide loop that is folded down over the active cleft in crystals of ternary complexes. The data suggest a fluctuation of the loop between open and closed forms in solution. The structure of the inhibitor molecules has been correlated with their ability to stabilize a more closed conformation of the loop.     

Phosphorylation of lactate dehydrogenase by ATP

Evidence is presented indicating that phosphorylation of porcine muscle lactate dehydrogenase by [gamma-32P] ATP occurs at carboxyl residues of the protein. The phosphoenzyme complex was moderately stable at pH 6.8 and 25 degrees C, with a half-life of 3.5 h. In the presence of NADH rapid dephosphorylation occurred. Formation of an abortive complex with NAD-pyruvate also caused hydrolysis of the phosphoenzyme. The phosphorylated lactate dehydrogenase was shown to serve as a phosphate donor for phosphorylation of ADP.     

A special role of phosphate in the stability of lactate dehydrogenase against destruction by a polyelectrolyte

It has been shown by X-ray structure analysis that proteins have specific anion-binding sites for sulfate, citrate, and phosphate ions; however, the functional role of these anions is not always clear. Thus, it is unknown which of two phosphate anions, mono- or divalent, determines the stability of cellular proteins under stress conditions. In the present work, the influence of phosphate, sulfate, and chloride on the stability of lactate dehydrogenase (LDH) in the presence of poly(styrenesulfonate) (PSS) has been investigated by the methods of steady-state kinetics and intrinsic protein fluorescence. The study is based on the analysis of differences between the influence of phosphate and sulfate ions on the process at two pH values, 6.2 and 7.0, at which the ratio of the concentrations of mono- and bivalent phosphate forms differs, whereas sulfate remains in the bivalent form. It was shown that the differences between the influence of phosphate and sulfate ions at pH 7.0 were greater; divalent phosphate ions much more effectively stabilized LDH against destruction by a polyelectrolyte compared with sulfate and monovalent phosphate. It was concluded that, of two anion-binding sites of the LDH molecule, the intersubunit center plays the most important role in its stabilization against destruction by polyelectrolyte, and, of two forms of phosphate anions, its bivalent form HPO ₄ ^?2 plays the stabilizing role.     

Stereochemistry of the hydrogen transfer to NADP catalyzed by D-galactose dehydrogenase from Pseudomonas fluorescens.

The stereochemistry of the hydrogen transfer to NADP catalyzed by D-galactose dehydrogenase (EC 1.1.1.48) from P. fluorescens was investigated. The label at C-1 of D-[1-³H] galactose was enzymatically transferred to NADP and the resulting [4-³H]NADPH was isolated and its stereo-chemistry at C-4 investigated. It was found that the label was exclusively located at the 4(S) position in NADPH which calls for classification as a B-enzyme. The correlation of this finding with tentative classification rules of NAD(P)-linked dehydrogenases in regard to their stereo-chemistry of hydrogen transfer to the coenzyme is discussed.     

Stereochemistry of the hydrogen transfer to NAD catalyzed by D-galactose dehydrogenase from Pseudomonas fluorescens.

The stereochemistry of the hydrogen transfer to NAD catalyzed by D-galactose dehydrogenase (E.C. 1.1.1.48) from P. fluorescens was investigated. The label at C-1 of D-[1--3H] galactose was enzymatically transferred to NAD and the resulting [4--3H]NADH was isolated and its stereochemistry at C-4 investigated. It was found that the label was exclusively located at the 4(S) position in NADH which calls for classification as a B-enzyme. This result was confirmed by an alternate approach in which [4--3H]NAD was reduced by D-galactose as catalyzed by D-galactose dehydrogenase. The sterochemistry at C-4 of the nicotinamide ring would then have to opposite to that in the first experiment. As expected, the label was now exclusively located in the 4(R) position, again confirming the B-calssification of the enzyme.