A rapid equilibrium random sequential bi-bi mechanism for human placental glutathione S-transferase

Double-reciprocal plots of initial-rate data for the conjugation of 1-chloro-2,4-dinitrobenzene (CDNB) and GSH by human placental GSH S-transferase pi were linear for both substrates. Computer modelling of the initial-rate data using nonlinear least-squares regression analysis favoured a rapid equilibrium random sequential bi-bi mechanism, over a steady-state random sequential mechanism or a steady-state or rapid equilibrium ordered mechanism. KGSH was calculated as 0.125 +/- 0.006 mM, KCDNB was 0.87 +/- 0.07 mM and alpha was 2.1 +/- 0.3 for the rapid equilibrium random model. The product, S-(2,4-dinitrophenyl)glutathione, was a competitive inhibitor with respect to GSH, and a mixed-type inhibitor toward CDNB (KP = 18 +/- 3 microM). The observed pattern of inhibition is consistent with a rapid equilibrium random mechanism, with a dead-end enzyme.CDNB.product complex, but inconsistent with the inhibition patterns of other bireactant mechanisms. Since rat liver GSH S-transferase 3-3 acts via a steady-state random sequential mechanism [1], while human placental GSH S-transferase and perhaps also rat liver GSH S-transferase 1-1 [2] exhibit rapid equilibrium random mechanisms, we conclude that the kinetic mechanism of the GSH S-transferases is isoenzyme-dependent.     

Kinetic formulations for the reduction of ketomalonate by lactate dehydrogenase

Initial rate kinetic studies of lactate dehydrogenase with ketomalonate and NADH as substrates suggest that this enzymatic system is adapted to a rapid equilibrium ordered bi-bi ternary complex mechanism. The application of the reaction product inhibition method reveals the existence of the enzyme-NADH-hydroxymalonate and enzyme-NAD(+)-ketomalonate abortive complexes. This kinetic behaviour is confirmed by the differential inhibition induced by several alternate products on the pyruvate-lactate dehydrogenase-NADH and ketomalonate-lactate dehydrogenase-NADH systems.     

Kinetic Formulations for the Reduction of Ketomalonate by Lactate Dehydrogenase

Abstract

Initial rate kinetic studies of lactate dehydrogenase with ketomalonate and NADH as substrates suggest that this enzymatic system is adapted to a rapid equilibrium ordered bi-bi ternary complex mechanism. The application of the reaction product inhibition method reveals the existence of the enzyme-NADH-hydroxy-malonate and enzyme-NAD⁺-ketomalonate abortive complexes. This kinetic behaviour is confirmed by the differential inhibition induced by several alternate products on the pyruvate-lactate dehydrogenase-NADH and ketomalonate-lactate dehydrogenase-NADH systems.     

Analysis of Ter-Ter enzyme kinetic mechanisms by computer simulation of isotope exchange at chemical equilibrium: development and application of ISOTER, a personal-computer-based program

A convenient, personal-computer-based program has been developed that allows simulation of isotopic exchange kinetics at chemical equilibrium catalyzed by a three reactant-three product (TerTer) enzyme system: A + B + C integral of P + Q + R. This program, ISOTER, utilizes a rapid algebraic method to calculate the exchange rate between any reactant-product pair as a function of the substrate concentration and avoids altogether the necessity of deriving an explicit (but cumbersome and impractical) equation for exchange rate. ISOTER was used to generate model saturation patterns for 16 different TerTer kinetic mechanisms, varying different combinations of reactant-product pairs in constant ratio at equilibrium: [all substrates], [A, P], [B, Q], and [C, R], while holding the nonvaried components constant. These model studies indicate that virtually every one of these mechanisms can be distinguished from the others. In addition, ISOTER has been used to fit multiple sets of experimental data for Escherichia coli glutamine synthetase, which produced a set of rate constants consistent with the previously proposed "preferred order random" kinetic mechanism.     

Kinetics and mechanism of methylene blue sorption onto palm kernel fibre

The kinetics and mechanism of the sorptive removal of methylene blue dye from aqueous solution using palm kernel fibre as adsorbent have been investigated. Batch kinetic experiments were performed and system variables investigated includes pH and initial dye concentration. The kinetic data were fitted to the pseudo-first, pseudo-second, intraparticle diffusion and mass transfer models. The pseudo-first order reaction kinetics fitted to the experimental data only in the first 5 min of sorption and then deviated, while the pseudo-second order kinetic model was found to fit the experimental data for the entire sorption period with high coefficient of determination. Equations were developed using the pseudo-second order model, which predicts the amounts of methylene blue at any contact time and initial concentration within the given range. This suggests that the sorption of methylene blue onto palm kernel fibre follows a chemical activation mechanism. A mathematical relationship was also drawn between the equilibrium sorption capacity and the change in pH (ΔH⁺) at the end of the kinetic experiments with varying initial dye concentration, supporting the fact that chemical reaction (ion exchange) occurred and is important in the rate determining step. Mass transfer was found to be favoured at high concentrations while intraparticle diffusion was favoured at low concentrations.     

A pH switch affects the steady-state kinetic mechanism of pyranose 2-oxidase from Trametes ochracea

The flavin-dependent pyranose 2-oxidase catalyzes the oxidation of d-glucose and other pyranoses at the C2 atom to yield 2-keto-sugars and hydrogen peroxide. Here, the steady-state kinetic mechanism of the enzyme from Trametes ochracea was investigated as a function of pH. Our findings show that the enzyme follows a bi-bi ping-pong kinetic mechanism at pH values <7.0, and a bi-bi ordered mechanism at pH values >7.0. Thus, at low pH the reactivity of the reduced enzyme with oxygen is controlled a by a conformational change of the enzyme that is associated with the release of the 2-keto-sugar from the active site of the enzyme. In contrast, at high pH the reduced enzyme-product complex permits the reaction of oxygen with the flavin. The study also illustrates that caution should be exerted in extrapolating the conclusions drawn on steady-state kinetic mechanisms established at a single pH value to other pH’s in flavoprotein oxidases.     

Kinetic study of the enzymatic cycling reaction conducted with 3alpha-hydroxysteroid dehydrogenase in the presence of excessive thio-NAD(+) and NADH

We have established a simple kinetic model applicable to the enzyme cycling reaction for the determination of 3alpha-hydroxysteroids. This reaction was conducted under the reversible catalytic function of a single 3alpha-hydroxysteroid dehydrogenase (3alpha-HSD) with nucleotide cofactors, thio-NAD(+) (one of the NAD(+) analogues) for the oxidation of 3alpha-hydroxysteroids and NADH for the reduction of 3-oxosteroids. This model was constructed based on the reaction mechanism of 3alpha-HSD, following an ordered bi-bi mechanism with cofactor binding first, under the assumption that the respective enzyme-cofactor complexes were distributed according to the initial ratio of thio-NAD(+) to NADH by the rapid equilibrium of both enzyme-cofactor complexes. The cycling rate in the new kinetic model could be expressed with the dissociation constants of enzyme-cofactor complexes and the initial concentrations of cofactors and enzyme. The cycling rate was verified by a comparison with the experimental data using 3alpha-HSD from Pseudomonas sp. B-0831. The results showed that the experimental data corresponded well with the results obtained from the kinetic model.     

Investigations of reaction kinetics for immobilized enzymes--identification of parameters in the presence of diffusion limitation

A method is proposed for identification of kinetic parameters when diffusion of substrates is limiting in reactions catalyzed by immobilized enzymes. This method overcomes conventional sequential procedures, which assume immobilization does not affect the conformation of the enzyme and, thus, consider intrinsic and inherent kinetics to be the same. The coupled equations describing intraparticle mass transport are solved simultaneously using numerical methods and are used for direct estimation of kinetic parameters by fitting modeling results to time-course measurements in a stirred tank reactor. While most traditional procedures were based on Michaelis-Menten kinetics, the method presented here is applicable to more complex kinetic mechanisms involving multiple state variables, such as ping-pong bi-bi. The method is applied to the kinetic resolution of (R/S)-1-methoxy-2-propanol with vinyl acetate catalyzed by Candida antarctica lipase B. A mathematical model is developed consisting of irreversible ping-pong bi-bi kinetics, including competitive inhibition of both enantiomers. The kinetic model, which fits to experimental data over a wide range of both substrates (5-95%) and temperatures (5-56 degrees C), is used for simulations to study typical behavior of immobilized enzyme systems.     

Full model for reversible kinetics of lipase-catalyzed sugar-ester synthesis in 2-methyl 2-butanol

A kinetic model derived from the ping-pong bi-bi reversible mechanism is proposed to described the acylation of glucose by lauric acid in 2-methyl 2-butanol mediated by Candida antarctica lipase at 60 degrees C. The model accounts for the effect of all four compounds in the reaction mixture, namely lauric acid, glucose, water, and lauroyl glucose ester. A supersaturated glucose solution was used to avoid limitations by glucose dissolution rate. Experiments with varied initial water content were performed to determine the effect of water on the initial reaction rate. The full time course of ester formation is described by five parameters: (a) three parameters evaluated from initial rate measurements; (b) the equilibrium constant, independently evaluated; and (c) one extra parameter fitted to the progress curve of ester formation. This reduced form of a full reversible kinetic model based on the ping-pong bi-bi mechanism is able to describe the complete course of lauroyl glucose ester synthesis. The proposed model provides a good fit for the experimental results.     

Reaction mechanism of non-allosteric phosphofructokinase.

The reaction mechanism of the non-allosteric phosphofructokinase from Lactobacillus plantarum was investigated by initial-rate bisubstrate kinetics and product inhibition kinetics adn by the measurement of equilibrium isotope exchange in the presence of various substrate and product concentrations. The reaction mechanism is clearly sequential. The product inhibition and equilibrium isotope-exchange patterns are consistent with an ordered bi-bi reaction sequence with fructose 6-phosphate as the leading substrate and ADP as the first product released from the enzyme.     

Characterization of the Kinetics of Cardiac Cytosolic Malate Dehydrogenase and Comparative Analysis of Cytosolic and Mitochondrial Isoforms

Because the mitochondrial inner membrane is impermeable to pyridine nucleotides, transport of reducing equivalents between the mitochondrial matrix and the cytoplasm relies on shuttle mechanisms, including the malate-aspartate shuttle and the glycerol-3-phosphate shuttle. These shuttles are needed for reducing equivalents generated by metabolic reactions in the cytosol to be oxidized via aerobic metabolism. Two isoenzymes of malate dehydrogenase (MDH) operate as components of the malate-aspartate shuttle, in which a reducing equivalent is transported via malate, which when oxidized to oxaloacetate, transfers an electron pair to reduce NAD to NADH. Several competing mechanisms have been proposed for the MDH-catalyzed reaction. This study aims to identify the pH-dependent kinetic mechanism for cytoplasmic MDH (cMDH) catalyzed oxidation/reduction of MAL/OAA. Experiments were conducted assaying the forward and reverse directions with products initially present, varying pH between 6.5 and 9.0. By fitting time-course data to various mechanisms, it is determined that an ordered bi-bi mechanism with coenzyme binding first followed by the binding of substrate is able to explain the kinetic data. The proposed mechanism is similar to, but not identical to, the mechanism recently determined for the mitochondrial isoform, mMDH. cMDH and mMDH mechanisms are also shown to both be reduced versions of a common, more complex mechanism that can explain the kinetic data for both isoforms. Comparing the simulated activity (ratio of initial velocity to the enzyme concentration) under physiological conditions, the mitochondrial MDH (mMDH) activity is predicted to be higher than cMDH activity under mitochondrial matrix conditions while the cMDH activity is higher than mMDH activity under cytoplasmic conditions, suggesting that the functions of the isoforms are kinetically tuned to their individual physiological roles.     

Hexavalent chromium removal from aqueous solutions by a novel powder prepared from Colocasia esculenta leaves

In this study, batch removal of hexavalent chromium from aqueous solutions by powdered Colocasia esculenta leaves was investigated. Batch experiments were conducted to study the effects of adsorption of Cr(VI) at different pH values, initial concentrations, agitation speeds, temperatures, and contact times. The biosorbent was characterized by scanning electron microscopy, energy-dispersive X-ray spectroscopy, and Fourier transform infrared spectrometer analysis. The biosorptive capacity of the adsorbent was dependent on the pH of the chromium solution in which maximum removal was observed at pH 2. The adsorption equilibrium data were evaluated for various adsorption isotherm models, kinetic models, and thermodynamics. The equilibrium data fitted well with Freundlich and Halsey models. The adsorption capacity calculated was 47.62 mg/g at pH 2. The adsorption kinetic data were best described by pseudo-second-order kinetic model. Thus, Colocasia esculenta leaves can be considered as one of the efficient and cheap biosorbents for hexavalent chromium removal from aqueous solutions.     

Steady-state kinetics of skeletal muscle myosin light chain kinase indicate a strong down regulation by products

The kinetic behaviour of myosin light chain kinase isolated from skeletal muscle was studied under steady-state conditions using highly purified phosphorylatable light chains 2 (LC2). Forward reaction, product inhibition, and reverse reaction data indicate a sequential mechanism which can be interpreted best by a rapid-equilibrium random bi-bi reaction model. The forward reaction parameters are KATP = 150 microM, KLC2 = 5.3 microM, and Ki LC2 = 7.6 microM. The enzyme forms a dead-end complex with ADP and light chain 2; Kd, ADP of this complex is 50 microM. The forward reaction is also strongly inhibited by the phosphorylated light chain 2, Ki, LC2P is 1.5 microM. An equilibrium constant Keq of about 70 can be calculated from the kinetic parameters which agrees with the directly measured value of about 60. The role of the two inhibitory mechanisms in the regulation of the enzyme and of the high energy of the light chain phosphate bond as deducible from Keq are discussed.     

Kinetics of the lipase-catalyzed synthesis of glucose esters in acetone

A simple kinetic model derived from a ping-pong bi-bi mechanism is proposed to describe the lipase-catalyzed esterification of glucose with fatty acids. The mathematical expressions derived from this model have been tested using several sets of data obtained from reactions carried out under different reaction conditions. The predicted values provide very good fits of the experimental data for temperatures from 30 to 60 degrees C, enzyme loadings from 90 to 180 mg, and fatty acid concentrations from 0.33M to 1M. Experiments conducted at different temperatures permit one to estimate an activation energy of approximately 12 kcal/mol for the rate-limiting step of the reaction (formation of the acyl-enzyme complex). The model also considers the kinetics of inactivation of the biocatalyst during the reaction.     

On the difficulties of fitting the double Michaelis-Menten equation to kinetic data

The double Michaelis-Menten equation describes the reaction kinetics of two independent, saturable uptake mechanisms. The use of this equation to describe drug uptake has been reported several times in the literature, and several methods have been published to fit the equation to data. So far, however, confidence intervals on the fitted kinetic parameters have not been provided. We present a grid-search method for fitting the double Michaelis-Menten equation to kinetic uptake data, and a Monte-Carlo procedure for estimating confidence intervals on the fitted parameters. We show that the fitting problem is extremely ill-conditioned, and that very accurate data are required before any confidence can be placed in the fitted parameters.     

Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models

The size and complexity of cellular systems make building predictive models an extremely difficult task. In principle dynamical time-course data can be used to elucidate the structure of the underlying molecular mechanisms, but a central and recurring problem is that many and very different models can be fitted to experimental data, especially when the latter are limited and subject to noise. Even given a model, estimating its parameters remains challenging in real-world systems. Here we present a comprehensive analysis of 180 systems biology models, which allows us to classify the parameters with respect to their contribution to the overall dynamical behaviour of the different systems. Our results reveal candidate elements of control in biochemical pathways that differentially contribute to dynamics. We introduce sensitivity profiles that concisely characterize parameter sensitivity and demonstrate how this can be connected to variability in data. Systematically linking data and model sloppiness allows us to extract features of dynamical systems that determine how well parameters can be estimated from time-course measurements, and associates the extent of data required for parameter inference with the model structure, and also with the global dynamical state of the system. The comprehensive analysis of so many systems biology models reaffirms the inability to estimate precisely most model or kinetic parameters as a generic feature of dynamical systems, and provides safe guidelines for performing better inferences and model predictions in the context of reverse engineering of mathematical models for biological systems.     

6His-Eco29kI methyltransferase methylation site and kinetic mechanism characterization

A new type II 6His-Eco29kI DNA methyltransferase was tested for methylation site (CC(Me)GCGG) and catalytic reaction optimal conditions. With high substrate concentrations, an inhibitory effect of DNA, but not AdoMet, on its activity was observed. Isotope partitioning and substrate preincubation assays showed that the enzyme-AdoMet complex is catalytically active. Considering effect of different concentrations of DNA and AdoMet on initial velocity, ping-pong mechanisms were ruled out. According to data obtained, the enzyme appears to work by preferred ordered bi-bi mechanism with AdoMet as leading substrate.     

Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway

In systems biology uncertainty about biological processes translates into alternative mathematical model candidates. Here, the goal is to generate, fit and discriminate several candidate models that represent different hypotheses for feedback mechanisms responsible for downregulating the response of the Sho1 branch of the yeast high osmolarity glycerol (HOG) signaling pathway after initial stimulation. Implementing and testing these candidate models by hand is a tedious and error-prone task. Therefore, we automatically generated a set of candidate models of the Sho1 branch with the tool modelMaGe. These candidate models are automatically documented, can readily be simulated and fitted automatically to data. A ranking of the models with respect to parsimonious data representation is provided, enabling discrimination between candidate models and the biological hypotheses underlying them. We conclude that a previously published model fitted spurious effects in the data. Moreover, the discrimination analysis suggests that the reported data does not support the conclusion that a desensitization mechanism leads to the rapid attenuation of Hog1 signaling in the Sho1 branch of the HOG pathway. The data rather supports a model where an integrator feedback shuts down the pathway. This conclusion is also supported by dedicated experiments that can exclusively be predicted by those models including an integrator feedback.modelMaGe is an open source project and is distributed under the Gnu General Public License (GPL) and is available from http://modelmage.org.     

Substrate specificity and stereoselectivity of horse liver alcohol dehydrogenase. Kinetic evaluation of binding and activation parameters controlling the catalytic cycles of unbranched, acyclic secondary alcohols and ketones as substrates of the native and active-site-specific Co(II)-substituted enzyme

1. The steady-state parameters kcat and Km and the rate constants of hydride transfer for the substrates isopropanol/acetone; (S)-2-butanol, (R)-2-butanol/2-butanone; (S)-2-pentanol, (R)-2-pentanol/2-pentanone; 3-pentanol/3-pentanone; (S)-2-octanol and (R)-2-octanol have been determined for the native Zn(II)-containing horse-liver alcohol dehydrogenase (LADH) and the specific active-site-substituted Co(II)LADH. 2. A combined evaluation of steady-state kinetic data and rate constants obtained from stopped-flow measurements, allowed the determination of all rate constants of the following ordered bi-bi mechanism: E in equilibrium E.NAD in equilibrium E.NAD.R1R2 CHOH in equilibrium E.NADH.R1R2CO in equilibrium E.NADH in equilibrium E. 3. On the basis of the different substrate specificities of LADH and yeast alcohol dehydrogenase (YADH), a procedure has been developed to evaluate the enantiomeric product composition of ketone reductions. 2-Butanone and 2-pentanone reductions revealed (S)-2-butanol (86%) and (S)-2-pentanol (95%) as the major products. 4. The observed enantioselectivity implies the existence of two productive ternary complexes; E.NADH.(pro-S) 2-butanone and E.NADH.(pro-R) 2-butanone. All rate constants describing the kinetic pathways of the system (S)-2-butanol, (R)-2-butanol/2-butanone have been determined. These data have been used to estimate the expected enantiomer product composition of 2-butanone reductions using apparent kcat/Km values for the two different ternary-complex configurations of 2-butanone. Additionally, these data have been used for computer simulations of the corresponding reaction cycles. Calculated, simulated and experimental data were found to be in good agreement. Thus, the system (S)-2-butanol, (R)-2-butanol/2-butanone is the first example of a LADH-catalyzed reaction for which the stereochemical course could be described in terms of rate constants of the underlying mechanism. 5. The effects of Co(II) substitution on the different steps of the kinetic pathway have been investigated. The free energy of activation is higher for alcohol oxidation and lower for ketone reduction when catalyzed by Co(II)LADH in comparison to Zn(II)LADH. However, the free energies of binding are affected by metal substitution in such a way that the enantioselectivity of ketone reduction is not significantly changed by the substitution of Co(II) for Zn(II). 6. Evaluation of the data shows that substrate specificity and stereoselectivity result from combination of the free energies of binding and activation, with differences in binding energies as the dominating factors. In this regard, the interactions of substrate molecules with the protein moiety are dominant over the interactions with the catalytic metal ion.