Subunit coupling and kinetic co-operativity of polymeric enzymes. Amplification, attenuation and inversion effects

The principles of structural kinetics, as applied to dimeric enzymes, allow us to understand how the strength of subunit coupling controls both substrate-binding co-operativity, under equilibrium conditions, and kinetic co-operativity, under steady state conditions. When subunits are loosely coupled, positive substrate-binding co-operativity may result in either an inhibition by excess substrate or a positive kinetic co-operativity. Alternatively, negative substrate-binding co-operativity is of necessity accompanied by negative kinetic co-operativity. Whereas the extent of negative kinetic co-operativity is attenuated with respect to the corresponding substrate-binding co-operativity, the positive kinetic co-operativity is amplified with respect to that of the substrate-binding co-operativity. Strong kinetic co-operativity cannot be generated by a loose coupling of subunits. If subunit is propagated to the other, the dimeric enzyme may display apparently surprising co-operativity effects. If the strain of the active sites generated by subunit coupling is relieved in the non-liganded and fully-liganded states, both substrate-binding co-operativity and kinetic co-operativity cannot be negative. If the strain of the active sites however, is not relieved in these states, negative substrate-binding co-operativity is accompanied by either a positive or a negative co-operativity. The possible occurrence of a reversal of kinetic co-operativity, with respect to substrate-binding co-operativity, is the direct consequence of quaternary constraints in the dimeric enzyme. Moreover, tight coupling between subunits may generate a positive kinetic co-operativity which is not associated with any substrate-binding co-operativity. In other words a dimeric enzyme may well bind the substrate in a non co-operative fashion and display a positive kinetic co-operativity generated by the strain of the active sites.     

Enzyme mechanisms from molecular modeling and isotope effects

The application of kinetic isotope effects and molecular modeling to characterize three enzyme-catalyzed reactions is presented; the mechanism of the chloroacid dehalogenase catalyzed reaction is approached using chlorine kinetic isotope effects and solvent kinetic isotope effects. The pre-steady-state phase of the reaction catalyzed by methylmalonyl-CoA mutase is approached by different QM/MM schemes and the results are validated by comparison with the experimental value of the deuterium kinetic isotope effect. Finally, a procedure for improving QM/MM calculations is illustrated by analysis of the trihydroxynaphthalene reductase-catalyzed reaction.     

Pseudo-Second-Order Kinetic Model for Biosorption of Methylene Blue onto Tamarind Fruit Shell: Comparison of Linear and Nonlinear Methods

In this study, the sorption of methylene blue, a basic dye, onto tamarind fruit shell was studied by performing batch kinetic sorption experiments. The equilibrium kinetic data were analyzed using the pseudo-second-order kinetic model. A comparison between linear least squares method and nonlinear regression method of estimating the kinetic parameters was examined. Four pseudo-second-order kinetic linear equations were discussed. The coefficient of determination (r ²), and the chi-square (χ²) test were employed as error analysis methods to determine the best-fitting equation. Kinetic parameters obtained from four kinetic linear equations using the linear method differed but they were the same when nonlinear method was used. Present investigation showed that by linear method a Type 1 expression very well represent the kinetic uptake of methylene blue onto tamarind fruit shell. Linear method was found to check only the hypothesis instead of verifying the kinetic model. Nonlinear regression method was found to be the more appropriate method to determine the rate kinetic parameters.     

The enzymatic mechanism of glucuronidation catalyzed by two purified rat liver steroid UDP-glucuronosyltransferases

A kinetic analysis of two homogeneous rat liver steroid (3 alpha-hydroxysteroid and 17 beta-hydroxysteroid) UDP-glucuronosyltransferases was conducted using bisubstrate kinetic analysis, product inhibition studies, and dead-end competitive inhibition studies. Double reciprocal plots of initial velocity versus substrate concentration, using bisubstrate kinetic analysis, gave a sequential mechanism. Product inhibition studies were compatible with either a rapid equilibrium, random-order kinetic mechanism or an ordered Theorell-Chance mechanism. Results of dead-end competitive inhibition studies excluded an ordered Theorell-Chance mechanism. The cumulative results are consistent with a rapid equilibrium random-order sequential kinetic mechanism for the glucuronidation of testosterone by purified 17 beta-hydroxysteroid UDP-glucuronosyltransferase and of androsterone by purified 3 alpha-hydroxysteroid UDP-glucuronosyltransferase.     

Pig heart lipoamide dehydrogenase: solvent equilibrium and kinetic isotope effects.

Lipoamide dehydrogenase is a flavoprotein which catalyzes the reversible oxidation of dihydrolipoamide, Lip(SH)2, by NAD+. The ping-pong kinetic mechanism involves stable oxidized and two-electron-reduced forms. We have investigated the rate-limiting nature of proton transfer steps in both the forward and reverse reactions catalyzed by the pig heart enzyme by using a combination of alternate substrates and solvent kinetic isotope effect studies. With NAD+ as the variable substrate, and at a fixed, saturating concentration of either Lip(SH)2 or DTT, inverse solvent kinetic isotope effects of 0.68 +/- 0.05 and 0.71 +/- 0.05, respectively, were observed on V/K. Solvent kinetic isotope effects on V of 0.91 +/- 0.07 and 0.69 +/- 0.02 were determined when Lip(SH)2 or DTT, respectively, was used as reductant. When Lip(SH)2 or DTT was used as the variable substrate, at a fixed concentration of NAD+, solvent kinetic isotope effects of 0.74 +/- 0.06 and 0.51 +/- 0.04, respectively, were observed on V/K for these substrates. Plots of the kinetic parameters versus mole fraction D2O (proton inventories) were linear in all cases. Solvent kinetic isotope effect measurements performed in the reverse direction using NADH as the variable substrate showed equivalent, normal solvent kinetic isotope effects on V/KNADH when oxidized lipoamide, lipoic acid, or DTT were present at fixed, saturating concentrations. Solvent kinetic isotope effects on V were equal to 1.5-2.1. When solvent kinetic isotope effect measurements were performed using the disulfide substrates lipoamide, lipoic acid, or DTT as the variable substrates, normal kinetic isotope effects on V/K of 1.3-1.7 were observed.(ABSTRACT TRUNCATED AT 250 WORDS)     

The place of inactivated actin and its kinetic predecessor in actin folding-unfolding

The kinetics of actin unfolding induced by guanidine hydrochloride of different concentrations was studied. The parametric representation of the kinetic dependencies of tryptophan fluorescence intensity changes recorded at two wavelengths allowed us to detect and characterize a new essentially unfolded kinetic intermediate. Its characteristics suggested that this intermediate state is a premolten globule. It was shown that the equilibrium transition between inactivated and completely unfolded states is also a two-step process and proceeds via an essentially unfolded kinetic intermediate. The new kinetic pathway of actin unfolding--refolding was proposed. According to it, the founded essentially unfolded kinetic state is the on-pathway intermediate, while inactivated actin is the off-pathway misfolded state stabilized by aggregation of partially folded macromolecules of protein.     

Reduced kinetic models of facilitative transport

In spite of the highly complex structural dynamics of globular proteins, the processes mediated by them can usually be described in terms of relatively simple kinetic diagrams. How do complex proteins, characterized by undergoing transitions among a possibly very large number of intermediate states, exhibit functional properties that can be interpreted in terms of kinetic diagrams consisting of only a small number of states? One possible way of explaining this apparent contradiction is that, under some conditions, a reduction of the actual complete kinetic diagram that describes all of the macromolecular states and transitions takes place. In this work, we contribute with a formal basis to this interpretation, by generalizing the procedure of diagram reduction to the case of multicyclic kinetic diagrams. As an example, we apply the procedure to a complex kinetic model of facilitative transport. We develop Monte Carlo simulations to obtain the kinetic parameters of the complex model and we compare them with the ones analytically obtained from the reduced model. We confirm that, under some conditions, the kinetic behavior of the complex transporter is indistinguishable from the one of a four-state simple carrier model, derived from the former by diagram reduction. Besides introducing some novel methodological aspects, this work further contributes to the idea that, under many physiological and experimental conditions, a reduction occurs of the complete kinetic diagram that describes the dynamics of a globular protein.     

嗜酸氧化亚铁硫杆菌生长动力学方程的应用

基于Monod模型推导出了A．f的生长动力学方程模型,采用Gauss-Newton算法确定了在不同初始条件下细菌生长的动力学参数,即最大比生长速率‰、Monod常数K及R0。通过在不同初始条件下细菌生长特性的研究,得到了相应初始生长条件下以限制性底物亚铁离子浓度为表征的生长动力学方程,理论上揭示了动力学参数变化对细菌生长的影响规律,其中生长动力学方程的数值模拟与实验数据相吻合。     

Kinetic modeling of ATP synthesis by ATP synthase and its mechanistic implications

Based on the torsional mechanism of ATP synthesis by ATP synthase, a kinetic scheme has been developed in this work. The scheme considers adenine nucleotide transport, binding of substrates ADP and P(i), unbinding of product ATP, and ATP synthesis. This kinetic scheme has been analyzed mathematically, and a kinetic model has been obtained to explain the experimentally observed hyperbolic Michaellian dependence of the rate of ATP synthesis on the ADP concentration by ATP synthase under physiological steady-state operating conditions. The principal results of the kinetic model have been compared with the experimental data and an estimate of the enzymological kinetic parameters V(max), K(M), and K(I) has been determined. Mechanistic implications arising from further analysis of the kinetic model have been discussed. These biological implications provide deep insight into the sequence of events leading to ATP synthesis.     

Rapid determination of kinetic constants by competitive spectrophotometry

The use of competitive spectrophotometry to measure kinetic constants for enzyme-catalyzed reactions is described. The equation for the progress curve characterizing the kinetic behavior of an enzyme acting simultaneously on two alternative substrates is derived. By the addition of a competition term to the integrated Michaelis-Menten equation, the kinetic constants of an alternative substrate can be evaluated by measuring the competition with a substrate of known kinetic constants in a single experiment. Studies are presented involving the enzymes leucine aminopeptidase (LAP) and carboxypeptidase A (CPA). The results obtained with LAP and CPA showed that the kinetic constants determined using competitive spectrophotometry were in agreement with values cited in the literature or with values determined by single substrate enzyme kinetics.     

Kinetics of the trypsinogen activation by enterokinase and trypsin

A global kinetic analysis of the mechanisms of the trypsinogen activation by enterokinase and trypsin is presented. The kinetic equations of both the transient-phase and the steady-state of these mechanisms are presented. In addition, we here derive the corresponding kinetic equations for the case in which the condition of rapid equilibrium prevails and we propose a kinetic data analysis. The significance of this approach to the treatment of other zymogen activation processes is discussed.     

Kinetic chain lengths in highly cross-linked networks formed by the photoinitiated polymerization of divinyl monomers: a gel permeation chromatography investigation

Highly cross-linked networks formed by the photoinitiated polymerization of multifunctional monomers are finding application in the field of biomaterials because of their chemical versatility, reaction control, and ability to polymerize under physiological conditions. Typically, degradation is introduced into these networks via the cross-links and leads to the release of nondegradable but water-soluble kinetic chains formed during the chain polymerization process. In this study, gel permeation chromatography (GPC) was used to characterize kinetic chain length distributions in highly cross-linked systems that are being developed for orthopedic applications. By polymerizing divinyl monomers to various conversions and subsequently degrading them, we investigated the aspects of network structural evolution related to kinetic chain formation. In general, the average kinetic chain length increased with conversion until the onset of autodeceleration, when the kinetic chains decreased in length as the propagation reaction became diffusion-controlled. The distribution of kinetic chains also changed when different initiation conditions (i.e., initiator concentration and incident light intensity) were used, and a decrease in the kinetic chain lengths was observed at higher initiation rates. Finally, kinetic chain lengths were examined as a function of depth in thick samples polymerized with different light intensities and with a photobleaching initiator. Light attenuation through the sample led to different initiation rates as a function of depth and, consequently, spatial heterogeneity in the network structure as measured by the distributions of kinetic chains.     

Water dispersion kinetics during starch gelatinization

The kinetics of water dispersion during the gelatinization of dilute suspensions of maize starch was studied by analyzing changes in electrical conductance data recorded continuously with time. Several analytical methods were compared for the preliminary study of the activation energy of gelatinization. The probable mechanism of the process was investigated by a number of homogeneous and heterogeneous reaction kinetic models. A modified composite methodology coupled with a reduced-plot method was employed to fit the kinetic data. Two simultaneous elementary reactions, expressed by an autocatalytic kinetic model and a 3D moving phase-boundary rate model, predicted the overall kinetic behavior with appreciable success.     

Steady-state kinetics of coupled two-enzyme reactor with recycling of poly(ethylene glycol)-bound NAD

The kinetic properties of a continuous enzyme reactor containing rabbit muscle lactate dehydrogenase, horse liver alcohol dehydrogenase and poly(ethylene glycol)-bound NAD (PEG-NAD) were investigated experimentally and theoretically. The enzymes and PEG-NAD were retained in the reactor with an ultrafiltration membrane, and the substrates (pyruvate and ethanol) were fed continuously. The reactions of the dehydrogenases were coupled by the recycling of the cofactor. The steady-state concentration of L-lactate, one of the products, was measured under different experimental conditions and compared with the corresponding theoretical value. The theoretical value was calculated based on a simplified ordered bi-bi mechanism for the individual enzyme reactions, of which kinetic constants were determined by independent kinetic studies. Differences were found between the kinetic constants of the enzymes for NAD(H) and PEG-NAD(H). The steady-state values obtained by continuous operation were lower than those calculated, possibly due to the simplification made for the kinetic model; but there was general agreement between them in the dependence on the experimental conditions. The steady-state behavior of the enzyme reactor was explained semi-quantitatively by the simple kinetic model.     

Application of a graphic method for analyzing the kinetics of multienzyme reactions

A new graphic method is proposed to solve kinetic equations for polyenzymic reactions. Each graph apex is corresponded by the transmitting function deduced from kinetic equations by means of Laplas transformation. Application of this procedure allows to simplify the solution of kinetic equations and its analysis. The procedure suggested makes it possible to use the methods of automatic control when solving theoretical problems of enzymology.     

Autocatalytic oscillations in the early phase of the photoreduced methyl viologen-initiated fast kinetic reaction of hydrogenase

The kinetic characteristics of the hydrogen uptake reaction of hydrogenase, obtained by conventional activity measurements, led to the proposal of an autocatalytic reaction step in the hydrogenase cycle or during the activation process. The autocatalytic behavior of an enzyme reaction may result in oscillating concentrations of enzyme intermediates and/or products contributing to the autocatalytic step. This behavior has been investigated in the early phase of the hydrogenase-methyl viologen reaction. To measure fast hydrogenase kinetics, flash-reduced methyl viologen has been used as a light-induced trigger in transient kinetic phenomena associated with intermolecular electron transfer to hydrogenase. Here we report fast kinetic measurements of the hydrogenase-methyl viologen reaction by use of the excimer laser flash-reduced redox dye. The results are evaluated on the assumption of an autocatalytic reaction in the hydrogenase kinetic cycle. The kinetic constants of the autocatalytic reaction, i.e. the methyl viologen binding to and release from hydrogenase, were determined, and limits of the kinetic constants relating to the intramolecular (intraenzyme) reactions were set.     

Human erythrocyte glutathione reductase: chemical mechanism and structure of the transition state for hydride transfer

Kinetic parameters and primary deuterium kinetic isotope effects for NADH and five pyridine nucleotide substrates have been determined at pH 8.1 for human erythrocyte glutathione reductase. DV/KNADH and DV are equal to 1.4 and are pH independent below pH 8.1, but DV decreases to 1.0 at high pH as a group exhibiting a pK of 8.6 is deprotonated. This result suggests that as His-467' is deprotonated, the rate of the isotopically insensitive oxidative half-reaction is specifically decreased and becomes rate-limiting. For all substrates, equivalent V and V/K primary deuterium kinetic isotope effects are observed at pH values below 8.1. The primary deuterium kinetic isotope effect on V, but not V/K, is sensitive to solvent isotopic composition. The primary tritium kinetic isotope effects agree well with the corresponding value calculated from the primary deuterium kinetic isotope effects by using the Swain-Schaad relationship. This suggests that the primary deuterium kinetic isotope effects observed in these steady-state experiments are the intrinsic primary deuterium kinetic isotope effects for hydride transfer. The magnitude of the primary deuterium kinetic isotope effect is dependent on the redox potential of the pyridine nucleotide substrate used, varying from approximately 1.4 for NADH and -320 mV reductants to 2.7 for thioNADH to 4.2-4.8 for 3-acetylpyridine adenine dinucleotide (3APADH). The alpha-secondary tritium kinetic isotope effects also increase as the redox potential of the pyridine nucleotide substrate becomes more positive. Together, these data indicate that the transition state for hydride transfer is very early for NADH and becomes later for thioNADH and 3APADH, as predicted by Hammond's postulate.(ABSTRACT TRUNCATED AT 250 WORDS)     

A fluorescence stopped-flow study on troponin labeled with N-ethyl maleimide and N-(p-(2-benzimidazolyl)phenyl) maleimide

The kinetics of the conformational change of the troponin-C (TN-C) subunit in N-(p-(2-benzimidazolyl)phenyl) maleimide (BIPM)-N-ethyl maleimide (NEM)-labeled troponin induced by calcium binding or removal were studied with the fluorescence stopped-flow method. The kinetic process of the conformational change was biphasic, the rate constants of the two phases were determined as a function of the free calcium ion concentration of the protein solution. The kinetic behaviour of the conformational change of TN-C in BIPM-NEM-labeled troponin was explained by a simple molecular kinetic mechanism: (Formula: see text) This molecular kinetic mechanism is different from that of the isolated TN-C which we found in the previous work (1). That is, formation of a complex of TN-C with troponin-I (TN-I) and troponin-T (TN-T) modifies the molecular kinetic mechanism of the conformational change of TN-C.     

Kinetic behaviour of free lipase and mica-based immobilized lipase catalyzing the synthesis of sugar esters

The utilization of natural mica as a biocatalyst support in kinetic investigations is first described in this study. The formation of lactose caprate from lactose sugar and capric acid, using free lipase (free-CRL) and lipase immobilized on nanoporous mica (NER-CRL) as a biocatalyst, was evaluated through a kinetic study. The apparent kinetic parameters, K(m) and V(max), were determined by means of the Michaelis-Menten kinetic model. The Ping-Pong Bi-Bi mechanism with single substrate inhibition was adopted as it best explains the experimental findings. The kinetic results show lower K(m) values with NER-CRL than with free-CRL, indicating the higher affinity of NER-CRL towards both substrates at the maximum reaction velocity (V(max,app)>V(max)). The kinetic parameters deduced from this model were used to simulate reaction rate data which were in close agreement with the experimental values.