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

The heterodimeric primase from the euryarchaeon Pyrococcus abyssi: a multifunctional enzyme for initiation and repair?

We report on the characterization of the DNA primase complex of the hyperthermophilic archaeon Pyrococcus abyssi (Pab). The Pab DNA primase complex is composed of the proteins Pabp41 and Pabp46, which show sequence similarities to the p49 and p58 subunits, respectively, of the eukaryotic polymerase alpha-primase complex. Both subunits were expressed, purified, and characterized. The Pabp41 subunit alone had no RNA synthesis activity but could synthesize long (up to 3 kb) DNA strands. Addition of the Pabp46 subunit increased the rate of DNA synthesis but decreased the length of the DNA fragments synthesized and conferred RNA synthesis capability. Moreover, in our experimental conditions, Pab DNA primase had comparable affinities for ribonucleotides and deoxyribonucleotides, and its activity was dependent on the presence of Mg2+ and Mn2+. Interestingly, Pab DNA primase also displayed DNA polymerase, gap-filling, and strand-displacement activities. Genetic analyses undertaken in Haloferax volcanii suggested that the eukaryotic-type heterodimeric primase is essential for survival in archaeal cells. Our results are in favor of a multifunctional archaeal primase involved in priming and repair.

A method of graphically analyzing substrate-inhibition kinetics

A model of substrate inhibition for enzyme catalysis was extended to describe the kinetics of photosynthetic production of ethylene by a recombinant cyanobacterium, which exhibits light-inhibition behavior similar to the substrate-inhibition behavior in enzyme reactions. To check the validity of the model against the experimental data, the model equation, which contains three kinetic parameters, was transformed so that a linear plot of the data could be made. The plot yielded reasonable linearity, and the parameter values could be estimated from the plot. The linear-plot approach was then applied to other inhibition kinetics including substrate inhibition of enzyme reactions and inhibitory growth of bacteria, whose analyses would otherwise require nonlinear least-squares fits or data measured in constrained ranges. Plots for three totally different systems all showed reasonable linearity, which enabled visual validation of the assumed kinetics. Parameter values evaluated from the plots were compared with results of nonlinear least-squares fits. A normalized linear plot for all the results discussed in this work is also presented, where dimensionless rates as a function of dimensionless concentration lie in a straight line. The linear-plot approach is expected to be complementary to nonlinear least-squares fits and other currently used methods in analyses of substrate-inhibition kinetics. Copyright 1999 John Wiley & Sons, Inc.

Testing and characterizing enzymes and membrane-bound carrier proteins acting on amphipathic ligands in the presence of bilayer membrane material and soluble binding protein. Application to the uptake of oleate into isolated cells

1. A multiphasic modelling approach [Heirwegh, Meuwissen, Vermeir & De Smedt (1988) Biochem. J. 254, 101-108] is applied to systems containing poorly water-soluble amphipathic reactants, membrane material, soluble binding protein and acceptor protein (enzyme or membrane-bound carrier protein). 2. The field of application is constrained by the assumptions (i) that the amount of acceptor-bound substrate is small compared with the total amount and (ii) that all preceding chemical reactions and steps of mass transport are rapid compared with the chemical change monitored. 3. Initial-rate formulae for systems in which an acceptor interacts with unbound or protein-bound ligand are given. The saturation curves are near-hyperbolic or sigmoidal, depending both (i) on the form of ligand (unbound or protein-bound) acted upon by the acceptor and (ii) on whether the assays are performed at constant concentration of soluble binding protein Cp or at constant substrate/binding-site molar ratio RS. 4. Several diagnostic features permit unequivocal distinction between acceptor action on unbound or protein-bound substrate. In the former case, saturation curves, run at the same constant concentration of one of several binding proteins of increasing binding affinity, will show progressively increasing inhibition, the shape changing from near-hyperbolic at Km' less than K1' to sigmoidal at Km' greater than K1'.Km' is the effective Michaelis constant of the acceptor and K1' the effective dissociation constant of the binding sites of the soluble protein (for the sites with the higher binding affinity, if several classes of binding site are present on the protein). Alternatively, the maximum velocity obtained at constant RS less than or equal to 1 should increase hyperbolically with RS/(1-RS) for a binding protein with a single class of binding site. The formula that applies when the binding protein contains two classes of independent binding site is also available. When the acceptor acts on protein-bound ligand, the maximum velocity obtained at constant binding-protein concentration, Cp, increases hyperbolically with Cp. 5. Application of these and additional criteria to initial-rate data on the uptake of oleate into isolated cells supports a mechanism of carrier-mediated uptake of the unbound ligand and allows one to clarify some observations that hitherto had been poorly explained. 6. The influence of soluble binding protein on the reaction and substrate specificities of ligand/acceptor interaction is also discussed. 7. In its present state, data treatment for 'double binding-protein systems' generally requires separate determination of the binding parameters of the soluble binding protein.(ABSTRACT TRUNCATED AT 400 WORDS)

Analysis of membrane-bound acceptors. A correction function for non-specific accumulation of poorly water-soluble hydrophobic or amphipathic ligands based on the ligand partition concept

Non-specific ligand accumulation into membrane material, which may contribute considerably to the experimental signal obtained in binding studies with labelled amphipathic and hydrophobic ligands, may be accounted for by linear partition of the ligands into the membrane phase. For application to binding data obtained at a single membrane-lipid concentration, a fitting procedure is proposed which allows one to correct for non-specific ligand partition. If the assumption is met that the amount of acceptor-bound ligand is small compared to the total amount present in the system, one can validly interpret the data in terms of total ligand concentrations. The apparent dissociation constants Kd(app) thus obtained should be corrected for the often large effects of the size of the partition compartment(s), by performing assays at several membrane-lipid concentrations. The importance of the latter correction is stressed and an approach for obtaining the characteristic effective dissociation constants Kd' is indicated. The procedure also yields estimates of the ligand/membrane partition coefficients.

The effects of systematic errors on the analysis of irreversible enzyme inhibition progress curves

The effects of errors in Km and Vmax. on the determination of the kinetic constants for the irreversible inhibition of acetylcholinesterase were determined. The results show that small errors in the values of Km and Vmax. give rise to large errors in the fitted parameters k2 and Kd. The problem may be minimized for multiple progress curves by selecting an appropriate number and distribution of inhibitor concentrations.

Nonlinear pharmacokinetics and interconversion of prednisolone and prednisone in rats

The pharmacokinetics of prednisolone and prednisone were examined in 32 rats at four intravenous doses (5, 10, 25, and 50 mg/kg). Each rat was given one dose of either intravenous prednisolone or prednisone, and plasma concentrations of both compounds were measured by HPLC. Mammillary moment analysis showed the apparent clearance and volume of distribution of prednisolone and the apparent clearance of prednisone to be dose-dependent. Further diagnostic analysis using a linear interconversion model revealed modest interconversion between the two steroids and at least two saturable clearance processes: the conversion of prednisolone to prednisone and the irreversible elimination of prednisone. A comprehensive model which incorporates the nonlinear clearances of prednisolone and prednisone plus the additional feature of nonlinear tissue distribution of prednisolone was then constructed. Four differential equations describing the rate of change of each steroid in each compartment were used to numerically fit by nonlinear least squares analysis all plasma concentration-time profiles simultaneously. The final estimates from the full model only partly agreed with the results from the two moment analyses but confirmed the general structure of the model. The nonlinear tissue distribution of prednisolone was reinforced by assay of muscle tissue. This study demonstrates the utility of the model-building process where simpler models yield insights into more elaborate schemes with complex nonlinear features.

The effect of hyperthermia in combination with melphalan on drug-sensitive and drug-resistant CHO cells in vitro

The effect of temperature on the cytotoxicity of melphalan in a pleiotropic drug-resistant mutant CHO cell line (CHR C5) and in its drug-sensitive parent (Aux B1) was studied in vitro using a clonogenic assay. The cytotoxicity of melphalan was significantly enhanced at elevated but non-lethal temperatures (39-41 degrees C) and hyperthermia potentiated the effect of melphalan in the lethal temperature range (43-44 degrees C) in both cell lines. The effect of temperature on membrane permeability to melphalan was studied to determine whether the increase in cytotoxicity was associated with increased intracellular drug levels. The uptake of 14C-labelled melphalan during 5 min increased with increasing temperature. Drug efflux, however, also increased at elevated temperatures. Intracellular drug levels at equilibrium were increased at elevated temperatures but the magnitude of this effect was small in comparison with the much larger increases in cytotoxicity.

Linear regression analysis for enzyme kinetic studies in toxicant interactions

A new method based on linear regression of per cent modulation in enzyme activity over substrate concentration is proposed to give an interpretative base to the influence of more than one modulator/inhibitor/toxicant, a situation commonly met with in toxicological studies-toxicant interactions. Advantages of this method over the classical kinetic methods are discussed in detail using brain Mg2+ ATPase activity of the fish Tilapia mossambica under in vitro regimes of hexachlorocyclohexane and malathion.

The effect of hyperthermia on the uptake and cytotoxicity of melphalan in Chinese hamster ovary cells

The effect of temperature on the cytotoxicity of melphalan in CHO cells was studied in an in vitro clonogenic assay. The cytotoxicity of melphalan was significantly increased at elevated temperatures with a 4 fold increase in cytotoxicity at 42 degrees C compared to 37 degrees C. The effect of temperature on membrane permeability to melphalan was studied to determine whether the increase in cytotoxicity was due to increased intracellular drug levels. Melphalan influx and efflux rates both increase with increasing temperature. There is, however, a small net increase in steady state intracellular drug levels with increasing temperature with a 20% increase in intracellular drug levels at 42 degrees C compared to 37 degrees C. The increase in drug uptake observed in insufficient to explain the much greater increase in cytotoxicity with increasing temperature.