Chemical mechanism of lysophosphatidylcholine: lysophosphatidylcholine acyltransferase from rabbit lung. pH-dependence of kinetic parameters.

Lysophosphatidylcholine: lysophosphatidylcholine acyltransferase is an enzyme that catalyses two reactions: hydrolysis of lysophosphatidylcholine and transacylation between two molecules of lysophosphatidylcholine to give disaturated phosphatidylcholine. Following the kinetic model previously proposed for this enzyme [Martín, Pérez-Gil, Acebal & Arche (1990) Biochem. J. 266, 47-53], the values of essential pK values in free enzyme and substrate-enzyme complexes have now been determined. The chemical mechanism of catalysis was dependent on the deprotonation of a histidine residue with pK about 5.7. This result was supported by the perturbation of pK values by addition of organic solvent. Very high and exothermic enthalpy of ionization was measured, indicating that a conformational re-arrangement in the enzyme accompanies the ionization of the essential histidine residue. These results, as well as the results from previous studies, enabled the proposal of a chemical mechanism for the enzymic reactions catalysed by lysophosphatidylcholine: lysophosphatidylcholine acyltransferase from rabbit lung.     

Introducing total substrates simplifies theoretical analysis at non-negligible enzyme concentrations: pseudo first-order kinetics and the loss of zero-order ultrasensitivity

The Briggs–Haldane standard quasi-steady state approximation and the resulting rate expressions for enzyme driven biochemical reactions provide crucial theoretical insight compared to the full set of equations describing the reactions, mainly because it reduces the number of variables and equations. When the enzyme is in excess of the substrate, a significant amount of substrate can be bound in intermediate complexes, so-called substrate sequestration. The standard quasi-steady state approximation is known to fail under such conditions, a main reason being that it neglects these intermediate complexes. Introducing total substrates, i.e., the sums of substrates and intermediate complexes, provides a similar reduction of the number of variables to consider but without neglecting the contribution from intermediate complexes. The present theoretical study illustrates the usefulness of such simplifications for the understanding of biochemical reaction schemes. We show how introducing the total substrates allows a simple analytical treatment of the relevance of significant enzyme concentrations for pseudo first-order kinetics and reconciles two proposed criteria for the validity of the pseudo first-order approximation. In addition, we show how the loss of zero-order ultrasensitivity in covalent modification cycles can be analyzed, in particular that approaches such as metabolic control analysis are immediately applicable to scenarios described by the total substrates with enzyme concentrations higher than or comparable to the substrate concentrations. A simple criterion which excludes the possibility of zero-order ultrasensitivity is presented.     

Biotinylation, a post-translational modification controlled by the rate of protein-protein association

Biotin protein ligases catalyze specific covalent linkage of the coenzyme biotin to biotin-dependent carboxylases. The reaction proceeds in two steps, including synthesis of an adenylated intermediate followed by biotin transfer to the carboxylase substrate. In this work specificity in the transfer reaction was investigated using single turnover stopped-flow and quench-flow assays. Cognate and noncognate reactions were measured using the enzymes and minimal biotin acceptor substrates from Escherichia coli, Pyrococcus horikoshii, and Homo sapiens. The kinetic analysis demonstrates that for all enzyme-substrate pairs the bimolecular rate of association of enzyme with substrate limits post-translational biotinylation. In addition, in noncognate reactions the three enzymes displayed a range of selectivities. These results highlight the importance of protein-protein binding kinetics for specific biotin addition to carboxylases and provide one mechanism for determining biotin distribution in metabolism.     

Plasma membrane and soluble lysophospholipases of Acanthamoeba castellanii

The soil amoeba Acanthamoeba castellanii contains two lysophospholipases, one soluble and one associated with the plasma membrane. The soluble lysophospholipase shows classical reaction kinetics at substrate concentrations below the apparent critical micelle concentration of lysophosphatidylcholine (about 39 μm). The reaction rate is constant at higher concentrations of substrate as expected for an enzyme that cannot hydrolyze micellar lysophosphatidylcholine. The reaction kinetics are more complex for the plasma membrane-bound enzyme showing two transitions at about 100 and 560 μm. Several possible interpretations of these data are discussed.     

Mathematical modelling of dynamics and control in metabolic networks. V. Static bifurcations in single biochemical control loops

Here we expand an earlier study of feedback activation in simple linear reaction sequences by searching the parameter space of biologically realistic rate laws for multiple stable steady states. The impetus for this work is to seek the origin of decision making strategies at the metabolic level, with particular emphasis on the switching between the operating conditions needed to meet changing substrate availability and organism requirements. The control loop considered herein is a linear reaction chain in which the end product of the reaction sequence feedback activates the first reaction in the sequence to produce feedback control. It has been found that the criteria for the existence of multiple steady state solutions in such loops involve only the kinetics of the regulatory enzyme controlling the first reaction and that of end product removal. The effects of these kinetics are examined here using two representative models for the regulatory enzyme: the lumped controller, based on Hill-type kinetics, and the symmetry model. The behavior of these two models is qualitatively similar, and both show the characteristics needed for switching between low and high substrate utilization. The removal rate is assumed to be of the Michaelis-Menten type. Judicious scaling of the governing equations permits separation of genetically determined kinetic parameters from concentration dependent ones. This allows us to conclude that, for a fixed set of kinetic parameters, the steady state flux through the loop can be switched between stable steady states by merely varying metabolite or enzyme concentrations. In particular, when the initial substrate exceeds a certain critical level, the loop can be "switched on" (by a discontinuous increase in the flux through the chain), and similarly, when it falls below a critical level, the pathway is shut down. Similar effects can be realized by varying the ratios of enzyme concentrations. It is proposed that by identifying these critical points one can gain significant insight into the objectives of decision making at the metabolic level.     

1,4-Diamino-2-butyne as the mechanism-based pea diamine oxidase inhibitor.

1,4-Diamino-2-butyne is a mechanism-based inhibitor of diamine oxidase (EC 1.4.3.6) from pea cotyledons. It shows saturation kinetics Km = 1 mM like a substrate, but its interaction leads to time-dependent loss of enzyme activity which is not restored by gel filtration. The substrate 1,4-diaminobutane and the competitive inhibitor 1,4-diamino-2-butanone protect the enzyme against inactivation. Changes in the enzyme electronic spectra with 1,4-diamino-2-butyne were found. The mechanism of the interaction involves an intermediate aminoallenic compound, which is formed with covalent bound pyrrole in the reaction of the nucleophile with the enzyme. The presence of a pyrrole in the inactivated enzyme was confirmed by reaction with Ehrlich's reagent. The kinetic data obtained in this study indicate that 1,4-diamino-2-butyne is a mechanism-based inactivator with number of turnovers, r = 17 and characteristic constants K' = 0.32 mM and k(in) = 4.89 min-1.     

Kinetic competence of enzymic intermediates: fact or fiction?

A number of enzymatic reactions involve intermediates that are not normally released during the reaction. Whether such an intermediate when added to the enzyme reacts as fast or faster than the normal substrates, and thus is "kinetically competent", depends on the degree to which the equilibrium constant for forming the intermediate from the substrates is different on the enzyme surface and in solution, as well as on the relative affinities of the enzyme for substrate and intermediate. Similar values for these equilibrium constants require that the intermediate react slowly, while a far more favorable value for intermediate formation on the enzyme allows the intermediate to react at up to the diffusion-limiting rate. When one intermediate is formed from two substrates, it may react much more rapidly than when two intermediates are formed from two substrates, or one from one. Comparison of the kinetics of the putative intermediate(s) and the substrate(s) can reveal a great deal about the mechanism of the catalytic reaction and the kinetic barrier that normally keeps the intermediate(s) on the enzyme.     

Studies on lysophospholipases. VI. The action of two purified lysophospholipases from beef liver on membrane-bound lysophosphatidylcholine.

The action of two lysophospholipases purified from beef liver on lysophosphatidylcholine in microsomal membranes has been studied. Enzyme I, which has been shown to be localized in the soluble fraction of the beef liver cell, has a higher specific activity on microsomal lysophosphatidylcholine than Enzyme II, which originates from the microsomal cell fraction. This trend is also observed with phosphatidylcholine liposomes and single bilayer vesicles in which lysophosphatidylcholine has been incorporated. At low mol fractions of lysophosphatidylcholine in liposomes, the maximum enzymatic rate is proportional to this mol fraction. Similar results are obtained with mixed micelles of lysophosphatidylcholine and Triton X-100. The results are explained in terms of a model in which the two-dimensional substrate density in the membrane surface controls the rate of enzyme action.     

Use of a silicic acid microcolumn to assay acyl-CoA: lysophosphatidylcholine acyltransferase

A simple and rapid method for assaying acyl-CoA:lysophosphatidylcholine acyltransferase is described. This method is based on silicic acid microcolumn chromatography using labelled lysophosphatidylcholine (lysoPC) as substrate. The reaction was stopped by conventional Folch extraction. The chloroform extract (2 ml) was deposited on the silica gel and pushed through with air, and then elution was performed with methanol/water (50:50, v/v). Under these conditions, only the labelled phosphatidylcholine (PC) synthesized was retained on the gel, and this was then removed from the column and counted immediately. This method gave enzyme activities comparable to those obtained with the TLC method, and has proved to be reproducible. The new method, however, is both faster and safer than the classical TLC method.     

Michaelis-Menten kinetics under spatially constrained conditions: application to mibefradil pharmacokinetics

Two different approaches were used to study the kinetics of the enzymatic reaction under heterogeneous conditions to interpret the unusual nonlinear pharmacokinetics of mibefradil. Firstly, a detailed model based on the kinetic differential equations is proposed to study the enzymatic reaction under spatial constraints and in vivo conditions. Secondly, Monte Carlo simulations of the enzyme reaction in a two-dimensional square lattice, placing special emphasis on the input and output of the substrate were applied to mimic in vivo conditions. Both the mathematical model and the Monte Carlo simulations for the enzymatic reaction reproduced the classical Michaelis-Menten (MM) kinetics in homogeneous media and unusual kinetics in fractal media. Based on these findings, a time-dependent version of the classic MM equation was developed for the rate of change of the substrate concentration in disordered media and was successfully used to describe the experimental plasma concentration-time data of mibefradil and derive estimates for the model parameters. The unusual nonlinear pharmacokinetics of mibefradil originates from the heterogeneous conditions in the reaction space of the enzymatic reaction. The modified MM equation can describe the pharmacokinetics of mibefradil as it is able to capture the heterogeneity of the enzymatic reaction in disordered media.     

A simple computer program with statistical tests for the analysis of enzyme kinetics.

A simple computer program that calculates the kinetic parameters of enzyme reactions is described. Parameters are determined by nonlinear, least-squares regression using either Marquardt-Levenberg or Gauss-Newton algorithms to find the minimum sum of squares. Three types of enzyme reactions can be analyzed: single substrate reactions (Michaelis-Menten and sigmoidal kinetics), enzyme activation at a fixed substrate value or enzyme inhibition at a fixed substrate value. The user can monitor goodness of fit through nonparametric statistical tests (performed automatically by the computer) and through visual examination of the pattern of residuals. The program is unique in providing equations for activator and inhibition analysis as well as in enabling the user to fix some of the parameters before regression analysis. The simplicity of the program makes it extremely useful for quickly determining kinetic parameters during the data-gathering process.     

Fluoride inhibition of inorganic pyrophosphatase. IV. Evidence for metal participation in the active center and a four-site model of metal effect on catalysis.

Atomic spectroscopy of native yeast inorganic pyrophosphatase (pyrophosphate phosphohydrolase, EC 3.6.1.1) after gel filtration showed that it only binds activating Mg2% in an easily dissociable manner. Formation of a covalent intermediate between the enzyme and an entire substrate molecular in the presence of fluoride, however, dramatically strengthened the binding of two Mg2+ per subunit and eliminated at neutral pH the effect of added metals on protein fluorescence but not on the absorption spectrum, suggesting that different mental binding sites influence the two spectra. This conclusion was confirmed by spectra studied on native enzyme. A third, low-affinity site for Mg2+ was found on the enzyme pH greater than 8. A model of enzyme-substrate-metal interactions was proposed, according to which the fluorescence-controlling site belongs to the active center and substrate can only be bound to it as a 1 : 1 complex with metals.     

Kinetics of a model of autocatalysis, coupling of a reaction in which the enzyme acts on one of its substrates.

A global kinetic analysis is presented of a model of an enzyme autocatalytic process, to which a reaction is coupled, in which the enzyme acts upon one of its substrates. The kinetic equations of both the transient phase and the steady state are derived for this mechanism. In addition, we determine the corresponding kinetic equations for several particular cases which are characterized by certain relations between the rate constants. Finally, a kinetic data analysis is proposed for one of these particular cases. It can easily be extended to any of the other cases.     

Substrate selectivity of lysophosphatidylcholine: lysophosphatidylcholine acyltransferase from rabbit lung

The influence of both polar group and acyl chain of lysophospholipids on the lysophosphatidylcholine: lysophosphatidylcholine acyltransferase from rabbit lung was studied. Both, transacylase and hydrolase activities of this enzyme, utilize selectively 1-[1-14C]palmitoyl-sn-glycero-3-phosphocholine when compared with 1-[9,10-3H2]palmitoyl-sn-glycero-3-phosphoethanolamine. Transacylase activity is more selective for lysophosphatidylcholine as acyl acceptor than as acyl donor. The amount of dipalmitoylphosphatidylcholine/min/mg protein synthesized from mixed lysophosphatidylcholine/lysophosphatidylethanolamine micelles does not change with increasing molar percentages of lysophosphatidylethanolamine in the mixture and is similar to that formed with pure lysophosphatidylcholine micelles. Transacylation reaction takes place preferentially with long and saturated acyl chains whereas hydrolysis reaction does more efficiently with longer acyl chains, independently of their insaturation degree.     

The steady-state kinetics of isotope exchange for one substrate–one product enzymic reactions

Steady-state kinetic equations for isotope exchange are derived for a number of one substrate-one product enzymic mechanisms in which two molecules of substrate or product can be combined with an enzyme molecule at the one time (e.g. allosteric mechanisms). The usual assumption, that the radioactive material is distributed among the substrate and product components according to a first-order law, is not valid. One can recognize whether isotope-exchange kinetics of an enzyme reaction follows first-order behaviour by using various initial concentrations of the labelled substance added to a mixture.     

An analysis of the reaction kinetics of the hexahaem nitrite reductase of the anaerobic rumen bacterium Wolinella succinogenes.

The reduction kinetics of both the resting and redox-cycled forms of the nitrite reductase from the anaerobic rumen bacterium Wolinella succinogenes were studied by stopped-flow reaction techniques. Single-turnover reduction of the enzyme by dithionite occurs in two kinetic phases for both forms of the enzyme. When the resting form of the enzyme is subjected to a single-turnover reduction by dithionite, the slower of the two kinetic phases exhibits a hyperbolic dependence of the rate constant on the square root of the reductant concentration, the limiting value of which (approximately 4 s-1) is assigned to a slow internal electron-transfer process. In contrast, when the redox-cycled form of the enzyme is reduced by dithionite in a single-turnover experiment, both kinetic phases exhibit linear dependences of the rate on the square root of dithionite concentration, with associated rate constants of 150 M-1/2.s-1 and 6 M-1/2.s-1. Computer simulations of both the reduction processes shows that no unique set of rate constants can account for the kinetics of both forms, although the kinetics of the redox-cycled species is consistent with a much enhanced rate of internal electron transfer. Under turnover conditions the time course for reduction of the enzyme, in the presence of millimolar levels of nitrite and 100 mM-dithionite, is extremely complex. A working model for the mechanism of the turnover activity of the enzyme is proposed which very closely describes the reaction kinetics over a wide range of substrate concentrations, as shown by computer simulation. The similarity in the action of the nitrite reductase enzyme and mammalian cytochrome c oxidase is commented upon.     

A kinetic analysis of enzyme inactivation as applied to the covalent modification of Na+ + K+ -ATPase and Ca2+ -ATPase

A kinetic analysis of enzyme inactivation due to the covalent binding of chemically modified ligands is presented. Reaction schemes similar to the Michaelis-Menten scheme have been studied as well as schemes with two states of the enzyme or two binding sites. The resulting kinetic equations lead to time courses of inactivation which can be represented by two exponential functions at least in a quasi-steady state approximation. These curves are frequently encountered in inactivation experiments. Since rapid methods for model selection and parameter estimation are desirable, but not available, a technique for a preliminary analysis of the experimental data is presented. A mere glance at the time courses shows what reaction schemes are inapplicable. For each family of inactivation curves, the construction of a line of intersections is proposed. This line contains essential kinetic information and can further be utilized for a rough parameter estimation. The technique is illustrated for three sets of experimental data where Na+ + K+ -ATPase and Ca2+ -ATPase have been inactivated by ATP-analogs.