Deviations from Michaelis-Menten kinetics. Computation of the probabilities of obtaining complex curves from simple kinetic schemes.

1. It is possible to calculate the intrinsic probability associated with any curve shape that is allowed for rational functions of given degree when the coefficients are independent or dependent random variables with known probability distributions. 2. Computations of such probabilities are described when the coefficients of the rational function are generated according to several probability distribution functions and in particular when rate constants are varied randomly for several simple model mechanisms. 3. It is concluded that each molecular mechanism is associated with a specific set of curve-shape probabilities, and this could be of value in discriminating between model mechanisms. 4. It is shown how a computer program can be used to estimate the probability of new complexities such as extra inflexions and turning points as the degree of rate equations increases. 5. The probability of 3 : 3 rate equations giving 2 : 2 curve shapes is discussed for unrestricted coefficients and also for the substrate-modifier mechanisms. 6. The probability associated with the numerical values of coefficients in rate equations is also calculated for this mechanism, and a possible method for determining the approximate magnitude of product-release steps is given. 7. The computer programs used in the computations have been deposited as Supplement SUP 50113 (21 pages) with the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem, J. (1978) 169, 5.     

Integrated steady state rate equations and the determination of individual rate constants.

Integrated steady state rate equations have been used to determine the kinetic constants (Vs, Ks, Vp, and Kp) and rate constants (k1, k2, k3, and k4) of the reversible enzyme mechanism: (see article). The fumarase reaction has been used as a model to illustrate the procedures for determining these constants. In contrast to initial velocity studies, the values of the constants have been obtained by examining the enzyme reaction in only one direction rather than in both forward and reverse directions. To accomplish this, a new procedure is described for fitting data to integrated rate equations which eliminates problems encountered when data are analyzed graphically. The advantages of examining on enzyme reaction in one direction with these new procedures allow this method to be extended to the examination of enzymes with simple mechanisms where initial velocities are difficult to measure because either the substrate or product is not readily available, or because the reaction is not readily reversible.     

Inversion of Markov processes to determine rate constants from single-channel data.

The determination of rate constants from single-channel data can be very difficult, in part because the single-channel lifetime distributions commonly analyzed by experimenters often have a complicated mathematical relation to the channel gating mechanism. The standard treatment of channel gating as a Markov process leads to the prediction that lifetime distributions are exponential functions. As the number of states of a channel gating scheme increases, the number of exponential terms in the lifetime distribution increases, and the weights and decay constants of the lifetime distributions become progressively more complicated functions of the underlying rate constants. In the present study a mathematical strategy for inverting these functions is introduced in order to determine rate constants from single-channel lifetime distributions. This inversion is easy for channel gating schemes with two or fewer states of a given conductance, so the present study focuses on schemes with more states. The procedure is to derive explicit equations relating the parameters of the lifetime distribution to the rate constants of the scheme. Such equations can be derived using the equality between symmetric functions of eigenvalues of a matrix and sums over principle minors, as well as expressions for the moments, derivatives, and weights of a lifetime distribution. The rate constants are then obtained as roots to this system of equations. For a gating scheme with three sequential closed states and a single gateway state, exact analytical expressions were found for each rate constant in terms of the parameters of the three-exponential closed-time distribution. For several other gating schemes, systems of equations were found that could be solved numerically to obtain the rate constants. Lifetime distributions were shown to specify a unique set of real rate constants in sequential gating schemes with up to five closed or five open states. For kinetic schemes with multiple gating pathways, the analysis of simulated data revealed multiple solutions. These multiple solutions could be distinguished by examining two-dimensional probability density functions. The utility of the methods introduced here are demonstrated by analyzing published data on nicotinic acetylcholine receptors, GABA(A) receptors, and NMDA receptors.     

The structure of steady-state enzyme kinetic equations: a graph-theoretical algorithm for obtaining conditions for reduction in degree by common-factor cancellation

Many enzyme kinetic steady-state equations are so complicated that analysis of their predictions, preferably by graph-theoretical methods, without deriving the equations is desirable. An example of such a method is given here. It is a graph-theoretical algorithm for determining non-trivial relations between the rate constants of a mechanism that cause the numerator and denominator of its rate expression have a common factor so permitting the degree of the expression to be reduced. An algorithm for writing the several different forms of the reduced rate equation is also given. The algorithm is applied to some standard simple enzymic mechanisms that give relatively complicated rate equations.In the case of a 2:2 equation, the sign of curvature in a double reciprocal plot depends on the sign of the expression in the common-factor condition.     

Enzyme deactivation

Enzyme deactivation kinetics is often first-order. Different examples of first-order deactivation kinetics exhibited by different enzymes under a wide variety of conditions are presented. Examples of both soluble and immobilized enzymes are presented. The influence of different parameters, chemical modification of specific residues, inhibitors, inactivators, protecting agents, induced conformational changes by external agents, enzyme concentration, and different substrates on the first-order inactivation kinetics of different enzymes is analyzed. The different examples presented from a variety of different areas provides a judicious framework and collection demonstrating the wide applicability of first-order deactivation kinetics. Examples of reversible first-order deactivation kinetics and deactivation-disguise kinetics are also presented.Different mechanisms are also presented to model complex enzyme deactivations. The non-series type mechanisms are emphasized and these involve the substrate and chemical modifiers. Substrate-dependent deactivation rate expressions that are of "separable" and "non-separable" type are presented. Rate expressions involving time-dependent rate constants along with their corresponding mechanisms are presented. Examples of enzymes that exhibit a deactivation-free grace period are also given. An interesting case of enzyme inactivation is the loss of activity in the presence of an auto-decaying reagent. The method is presented by which the intrinsic inactivation rate constants may be obtained. Examples of pH-dependent enzyme inactivation are presented that may be modelled by a five-step (or a simplified two-step) mechanism, and also by a single-step mechanism involving residual activity for the final state. Appropriate examples of enzyme inactivation are presented in each case to highlight the different mechanisms involved.     

A theoretical model of the competition between hydrolase and carboxylesterase in protection against organophosphorus poisoning

A system of coupled non-linear differential equations describing interactions between organophosphorus compounds (OPs), OP hydrolase, acetylcholinesterase (AChE), and carboxylesterase (CaE) in a single compartment was derived incorporating irreversible combination of OP with AChE, hydrolytic breakdown of OP, and irreversible combination of OP with CaE. The equations were then uncoupled, providing non-linear differential equations on AChE, CaE and OP concentrations. One steady state solution of the AChE equation provided theoretical expressions for the amounts of OP hydrolyzed, bound with CaE, and bound with AChE. Assuming that the LD50 of an OP reflects the dose that depletes AChE to a 'minimal essential' level and that a single compartment model is applicable in vivo, the steady state solution becomes an equation predicting the LD50 from rate constants, initial enzyme levels, and the allowable AChE depletion. Normalization by initial AChE concentration produced a dimensionless relationship describing an 'OP toxicity surface' that clearly demonstrates regions where hydrolysis and CaE offer protection against OP poisoning. The surface can be used to theoretically predict an LD50 given only kinetic rate constants and effective whole-body AChE and CaE levels. Predictions of LD50s of seven OPs in rats were compared with published data. The relationship was found to adequately predict published LD50s spanning 5 orders of magnitude. The OP toxicity surface relationship provides a conceptual tool for use in OP toxicity research but should be particularly useful in predicting the relative protective effects of catalytic and stoichiometric scavenger mechanisms for an OP.     

Electrophoretic control of reconstituted adenine nucleotide translocation

The initial velocity of adenine nucleotide exchange catalyzed by the reconstituted ADP-ATP carrier from beef heart mitochondria was measured under the influence of membrane potential and with different nucleotide distributions between the internal liposomal and the external buffer volume. Both Vmax and Km of adenine nucleotide uptake not only changed due to the applied potential but also depended on the respective nucleotide distribution. The rate equations for the ADP-ATP exchange under the various conditions were derived. These equations were simplified by assuming two alternative situations; either (a) af affinity type model, where the membrane potential influences only the affinity of the adenine nucleotide carrier toward ATP and ADP, or (b) a velocity type or distribution model, where the membrane potential modulates the rate constants of the ADP-ATP exchange. On the basis of several simplifications in the reconstituted system, the rate equations could be solved and the rate constants and dissociation constants of the exchange in the "energized" and in the "deenergized" state could be calculated. These values were used to derive prediction tables for normalized exchange rates under different nucleotide distributions, which were then compared with the experimental data. Only the exchange rates predicted by the velocity-type model agreed with the measured values. On the basis of this model a definite asymmetry caused by the membrane potential could be seen. Whereas this asymmetry is not very pronounced in the case of carrier-ADP complexes, about 40 times more ATP-loaded binding sites face the outside of the vesicles in the energized state.     

Equations of substrate-limited growth: the case for blackman kinetics

A simplified model of cell metabolism, consisting of a series of linked reversible enzymatic reactions dependent on the concentration of a single external substrate has been developed. The general mathematical solution for this system of reactions is presented. This general solution confirms the concept of a rate-limiting step, or “master reaction”, in biological systems as first proposed by Blackman. The maximum rate of such a process is determined by, and equal to, the maximum rate of the slowest forward reaction in the series. Of practical interest in modeling the growth rate of cells are three cases developed from the general model. The simplest special case results in the Monod equation when the maximum forward rate of one enzymatic reaction in the cell is much less than the maximum forward rate of any other enzymatic reactions. More realistic is the case where the maximum forward rates of more than one enzymatic reaction are slow. When two slow enzymatic reactions are separated from each other by any number of fast reactions that overall can be described by a large equilibrium constant, the Blackman form results: and A third case is that in which two slow enzymatic steps are separated by an equilibrium constant that is not large. Unlike the Monod and Blackman forms, which contain only two arbitrary constants, this model contains three arbitrary constants: The Monod and Blackman forms are special cases of this three constant form. In comparing equations with two arbitrary constants the Monod equation gave poorer fit of the data in most cases than the Blackman form. It is concluded that workers modeling the growth of microorganisms should give a t least as much consideration to the Blackman form as is given to the Monod equation.     

Determination of lectin-sugar dissociation constants by agarose affinity electrophoresis

Agarose crossed affinity electrophoresis (aff-EP) was employed for the determination of lectin-sugar dissociation constants (Ki). In the first dimension of the aff-EP increasing amounts of sugar (alpha-methyl-D-mannoside) were added to a given concentration of lectin (concanavalin A). Then the electrophoresis was run with alpha 1-acid glycoprotein, alpha 1-antitrypsin and alpha-fetoprotein as markers of lectin-sugar interactions. Mathematical equations for determination of the mechanisms and constants of lectin-sugar-glycoprotein interactions were developed. The mean value of the concanavalin A-alpha-methyl-D-mannoside dissociation constant calculated according to the introduced equations was 0.28 mM. In this system it was also possible to determine lectin-glycoprotein dissociation constants (K). The observed influence of the sugar on lectin-glycoprotein binding might be due to hydrophobic interactions since the addition of nonionic detergent caused reversal of this phenomenon.     

Some experiences in the estimation of parameters in non-linear differential equations

The author describes a procedure developed by himself and his colleagues for obtaining estimates of the parameters of rate equations, together with information about confidence regions for the estimates. The program has been used successfully for processing results from the chemical engineering industry, with highly non-linear model systems, particularly since temperature was a variable, and the "rate constants" were non-linear combinations of other constants. In biochemical situations, in which investigations are almost always at constant temperature, the non-linearity should not be so extreme, and the procedure may well be capable of dealing with more than 5 to 7 parameters for which it is recommended.     

Presteady-state kinetics and carrier-mediated transport: A theoretical analysis

Summary Kinetic studies of cotransport mechanisms have so far been limited to the conventional steady-state approach which does not allow in general to resolve either isomerization or ratelimiting steps and to determine the values of the individual rate constants for the elementary reactions involved along a given transport pathway. Such questions can only be answered using presteady-state or relaxation experiments which, for technical reasons, have not yet been introduced into the field of cotransport kinetics. However, since two recent reports seem compatible with the observation of such transient kinetics, it would appear that theoretical studies are needed to evaluate the validity of such claims and to critically evaluate the expectations from a presteady-state approach. We thus report such a study which was performed on a simple four-state mechanism of carrier-mediated transport. The time-dependent equation for zero-trans substrate uptake was thus derived and then extended to models withp intermediary steps. It is concluded that (p-1) exponential terms will describe the approach to the steady state but that such equations have low analytical value since the parameters of the flux equation cannot be expressed in terms of the individual rate constants of the elementary reactions for models withp>5. We thus propose realistic simplifications based on the time-scale separation hypothesis which allows replacement of the rate constants of the rapid steps by their equilibrium constants, thereby reducing the complexity of the kinetic system. Assuming that only one relaxation can be observed, this treatment generates approximate models for which analytical expressions can easily be derived and simulated through computer modeling. When performed on the four-state mechanism of carrier-mediated transport, the simulations demonstrate the validity of the approximate solutions derived according to this hypothesis. Moreover, our approach clearly shows that presteady-state kinetics, should they become applicable to (co)transport kinetics, could be invaluable in determining more precise transport mechanisms.     

Direct measurement of equilibrium constants for high-affinity hemoglobins

The biological functions of heme proteins are linked to their rate and affinity constants for ligand binding. Kinetic experiments are commonly used to measure equilibrium constants for traditional hemoglobins comprised of pentacoordinate ligand binding sites and simple bimolecular reaction schemes. However, kinetic methods do not always yield reliable equilibrium constants with more complex hemoglobins for which reaction mechanisms are not clearly understood. Furthermore, even where reaction mechanisms are clearly understood, it is very difficult to directly measure equilibrium constants for oxygen and carbon monoxide binding to high-affinity (K(D) < 1 micro M) hemoglobins. This work presents a method for direct measurement of equilibrium constants for high-affinity hemoglobins that utilizes a competition for ligands between the "target" protein and an array of "scavenger" hemoglobins with known affinities. This method is described for oxygen and carbon monoxide binding to two hexacoordinate hemoglobins: rice nonsymbiotic hemoglobin and Synechocystis hemoglobin. Our results demonstrate that although these proteins have different mechanisms for ligand binding, their affinities for oxygen and carbon monoxide are similar. Their large affinity constants for oxygen, 285 and approximately 100 micro M(-1) respectively, indicate that they are not capable of facilitating oxygen transport.     

Progress-curve equations for reversible enzyme-catalysed reactions inhibited by tight-binding inhibitors.

The rate equation for a tight-binding inhibitor of an enzyme-catalysed first-order reversible reaction was used to derive two integrated equations. One of them covers the situations in which competitive, uncompetitive or non-competitive inhibition occurs and the other refers to the special non-competitive case where the two inhibition constants are equal. For these equations, graphical and non-linear regression methods are proposed for distinguishing between types of inhibition and for calculating inhibition constants from progress-curve data. The application of the non-linear regression to the analysis of stimulated progress curves in the presence of a tight-binding inhibitor is also presented. The results obtained are valid for any type of 'dead-end'-complex-forming inhibitor and can be used to characterize an unknown inhibitor on the basis of progress curves.     

Determination of reaction rate constants in the mammillary system

It is shown that the individual rate constants can be determined for the composite chemical system: $$A + B_i \rightleftarrows C_i ; i = 1...N$$ with only measurements of the unbound species,A(t), required. The dissociation rate constants can be determined by direct analysis of a single steady state tracer study. The association constants then follow from the analysis of stable equilibrium determinations reported earlier (Hart, 1965). An approximate solution when tracer methods are in-applicable is also given.     

A general pre-steady-state solution to complex kinetic mechanisms

We have developed a general method for solving transient kinetic equations using Laplace transforms. Laplace transforms can be used to transform systems of differential equations that describe pre-steady-state kinetics to systems of linear algebraic equations. The general form of the pre-steady-state solution is (formula; see text) where I(t) is the time dependence of the physically observed property of the system, n is the number of intermediates, lambda i are the observed rate constants (reciprocals of the relaxation times), t is time, and Ii are the amplitude coefficients associated with each observed rate constant. We have written a program in compiled BASIC to run on a personal computer to evaluate Ii and lambda i. The program will evaluate the rate constants and coefficients of a mechanism with eight intermediates and seven relaxation times in 4 s on an 8-MHz PC-XT equipped with a math coprocessor. The most complex mechanism that we have solved, a mechanism containing 20 intermediates and 19 relaxation times, required approximately 5 min. We believe that this method will be useful to evaluate the differences in transient properties of complex biochemical mechanisms.     

Nonlinear "hydrophobicity-antiesterase activity" model for various types of organophosphorous compounds

The dependence of antiesteratic activity on the structure of insecticides (RO)2P(O)SCH(COOEt)SP(O)(OR)2 (I) and (RO)2P(O)SCH(COOEt)OP(S)(OR)2 (II) was examined. Nonlinear regression equations (parabolic and bilinear) "hydrophobicity-antiesteratic activity" were derived. Basing on the studies of the relationships between hydrophobicity and individual constants, the detailed mechanisms were proposed for the interaction of type (I) and (II) compounds with the esterase active centers. The mechanisms implicate different kinds of sorbtion for compounds of type I and II. Applicability of bilinear models, similar to that of Kubinyi type, for analyzing the structure-antienzyme activity dependences was demonstrated. Thus, several equations were obtained starting from the literature data on inhibition of esterases with diverse organophosphorus compounds.     

Global parameter optimization for cardiac potassium channel gating models.

Quantitative ion channel model evaluation requires the estimation of voltage dependent rate constants. We have tested whether a unique set of rate constants can be reliably extracted from nonstationary macroscopic voltage clamp potassium current data. For many models, the rate constants derived independently at different membrane potentials are not unique. Therefore, our approach has been to use the exponential voltage dependence predicted from reaction rate theory (Stevens, C. F. 1978. Biophys. J. 22:295-306; Eyring, H., S. H. Lin, and S. M. Lin. 1980. Basic Chemical Kinetics. Wiley and Sons, New York) to couple the rate constants derived at different membrane potentials. This constrained the solution set of rate constants to only those that also obeyed this additional set of equations, which was sufficient to obtain a unique solution. We have tested this approach with data obtained from macroscopic delayed rectifier potassium channel currents in voltage-clamped guinea pig ventricular myocyte membranes. This potassium channel has relatively simple kinetics without an inactivation process and provided a convenient system to determine a globally optimized set of voltage-dependent rate constants for a Markov kinetic model. The ability of the fitting algorithm to extract rate constants from the macroscopic current data was tested using "data" synthesized from known rate constants. The simulated data sets were analyzed with the global fitting procedure and the fitted rate constants were compared with the rate constants used to generate the data. Monte Carlo methods were used to examine the accuracy of the estimated kinetic parameters. This global fitting approach provided a useful and convenient method for reliably extracting Markov rate constants from macroscopic voltage clamp data over a broad range of membrane potentials. The limitations of the method and the dependence on initial guesses are described.     

General continuum analysis of transport through pores. II. Nonuniform pores.

A general continuum derivation of the nonelectrolyte (Js) and volume (Jv) flux through a pore whose cross section is a function of axial position (nonuniform) is given. In general, the flux equations cannot be reduced to the same form as for a uniform pore and it is not possible to characterize the pore kinetics by three constants as in the uniform pore case. However, it is shown that under certain conditions, the nonuniform pore equations can be approximated by the uniform pore form and can be characterized by three constants (omega, sigma, Lp). The only condition needed to reduce the Jv equation to the uniform form is that the solution be dilute. The deviation of the Js equation from the uniform form is characterized by an asymmetrical function of Jv whose maximum value is estimated. It is shown that the maximum posible fractional deviation of the Js equation from the uniform form is given by the parameter: 0:5sigmaJv/omegaRT. Since this parameter is less then 0.15 for most membrane studies, the nonuniform Js equation can usually be approximated by the uniform pore form. The general results are illustrated by explicit calculations on several models of nonuniform pores. It is shown, for example, that the "equivalent pore radius" defined in the usual way is a function of the experimental parameter that is measured and is not unique.     

Relations between biochemical thermodynamics and biochemical kinetics

The parameters in steady-state or rapid-equilibrium rate equations for enzyme-catalyzed reactions depend on the temperature, pH, and ionic strength, and may depend on the concentrations of specific species in the buffer. When the complete rate equation (i.e. the equation with parameters for the reverse reaction as well as the forward reaction) is determined, there are one or more Haldane relations between some of the kinetic parameters and the apparent equilibrium constant for the reaction that is catalyzed. When the apparent equilibrium constant can be calculated from the kinetic parameters, the equilibrium composition can be calculated. This is remarkable because the kinetic parameters all depend on the properties of the enzymatic site, but the apparent equilibrium constant and the equilibrium composition do not. The effects of ionic strength and pH on the unoccupied enzymatic site and the occupied enzymatic site have to cancel in the Haldane relation or in the calculation of the apparent equilibrium constant using the rate constants for the steps in the mechanism. Several simple enzymatic mechanisms and their complete rate equations are discussed.