Metal Complexation in Xylem Fluid : II. THEORETICAL EQUILIBRIUM MODEL AND COMPUTATIONAL COMPUTER PROGRAM

Theoretical considerations of metal complex formation in aqueous solutions were used to develop a computer program (CHELATE) to calculate all equilibrium species (free metal ions, metal complexes, etc.) in any user-defined system, such as xylem fluid. Mass-balance equations were established to describe each free metal ion and each free ligand concentration as a function of solution pH, total metal or total ligand, hydrogen-association constants, and the stability constants of known metal complexes. A default data base can be altered by the user to define any desired system covered by the stored equilibrium data. The program can currently handle nine metal ions, 35 ligands, and 500 complex species. The validity of the program was confirmed by using experimental test systems in which free-metal ion activity measurements were made with ion-selective electrodes.     

CHELATOR: an improved method for computing metal ion concentrations in physiological solutions.

An algorithm is presented for the calculation of metal ion concentrations from given total metal concentrations (and vice versa) in physiological media containing metal-chelating compounds. In such media, conditions differ from those used for stability constant determination of metal-chelator equilibria; therefore calculated metal ion concentrations are incorrect. We recompute stability constants to reflect the effects of ionic strength and temperature of physiological solutions. Twelve different equilibria can be considered per metal-chelator pair. The computer program also calculates the contribution of ionized species of metals, chelator, complexes and pH buffers to ionic strength. Measurements with a Ca-selective electrode and with fura-2 show that calculated ionic Ca2+ concentrations are correct from 10 nM up to the millimolar range. The importance of the correct calculation of metal ion concentrations in physiological experiments is demonstrated by data, and derived kinetic parameters, on Na+/Ca2+ exchange and the ATP-dependent Ca2+ pump of enterocyte plasma membrane vesicles. The program is written in Turbo Pascal and will run on IBM-compatible computers. It is menu-driven and supports the use of a Microsoft mouse.     

Monotonicity of interleukin-1 receptor-ligand binding with respect to antagonist in the presence of decoy receptor

We consider the interaction between interleukin-1 IL-1, its receptor IL-1RI, the receptor antagonist IL-1Ra and a decoy receptor (or trap) that binds both with the ligand and the antagonist. We study how the interaction between IL-1Ra and the decoy receptor influences the effect of either reagent on reducing the equilibrium concentration of the receptor-ligand complex. We obtain that, given a certain relationship among the equilibrium constants and the total concentrations of solutes, IL-1Ra can reverse the effect of the decoy receptor of decreasing the equilibrium concentration of the receptor-ligand complex. This finding derives from a mathematical result applicable to any reversible chemical reaction system comprising four species arranged in a square such that each species binds its two immediate neighbors. The result gives the monotonicity of the equilibrium concentrations of the complex species as functions of the total concentrations of the simple species.     

Analytical determination of apparent stability constants using a copper ion selective electrode

Copper(II) complexes of di-, tri- and tetra peptides with previously published protonation constants were re-investigated using pH and copper ion selective electrode (ISE) potentiometry in conjunction with a modified version of HYPERQUAD computer program. The purpose was to demonstrate the suitability of the ISE approach for the determination of apparent stability constants for copper(II) complexes with ligands for which proton stability constants were not available. The interactions of Cu²⁺ with oligopeptides were also analysed using surface enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-ToF-MS). The results provide an insight into the metal complex species formed, their apparent stabilities under selected conditions and the effect of the relative positions of certain amino acids within the peptide sequence.     

Speciation studies of aluminium(III)–acetate complexes under physiological conditions

Abstract

The aluminium complexes of acetic acid (ACT) have been studied using Potentiometric titrations under physiological conditions of temperature (37°C) and ionic strength (0.15 dm^?3 dm^?3 NaCI) and at different ligand to metal ratios. The variations of pH were measured with the help of a glass electrode calibrated daily in hydrogen ion concentrations. Results obtained within the pH range of 2.6–4.2 were analysed to determine stability constants using the SUPERQUAD program. Different complex combinations were considered during the calculation procedure, and evidence was found for ML₂ mononuclear species beside binuclear hydroxo-complexes M₂L(OH)₂ and M₂L(OH)₃ and metal ion hydroxides. Speciation calculations based on the corresponding constants were then used to simulate species distributions.     

Determination of free Ca ion concentrations with an ion-selective electrode in the presence of chelating agents in comparison with calculated values.

Experimentally determined free Ca ion concentrations, measured with a Ca-selective electrode, were compared with values calculated with a computer program utilizing stability constants of the chelating agents: NTA, EDTA, and EGTA used to set the free ion concentration in the range of 10^?3 to 10^?6m. In the presence of 0.1 m KCl, 2 mm MgCl₂, 20 mm Hepes (pH 7.4), 2 mm ATP, 0.1 mm CaCl₂ (total concentration), and various ligand concentrations the measured free Ca²⁺ levels were found to be approximately six to seven times greater than the computer-derived values. Apparent stability constants for Ca-ATP, Ca-EDTA, and Ca-EGTA were determined under these experimental conditions.     

The calibration and use of a calcium ion-specific electrode for kinetic studies of mitochondrial calcium transport.

A calcium ion-specific electrode has been used to study calcium transport by isolated,hepatic mitochondria. The methodology used requires only a sensitive pH meter operated in the millivolt mode with the electrode. Free calcium ion concentrations may be followed continuously. Using incubation conditions which cause release of intramitochondrial calcium, the calcium electrode system may also be used to determine total. intramitochondrial calcium. Techniques for the calibration of the electrode response are discussed. Free calcium ion concentrations have been calculated from total calcium concentrations and the association constants for the binding species present in the assay medium. The observation that the electrode response is linear to submicromolar concentrations allows calculation of a linear least-squares fit of millivolt reading to computed free calcium ion concentration. A computer program written in BASIC for these computations is included in Appendix material. The half-maximal rate constant for mitochondrial calcium uptake has been found to occur at a free calcium ion concentration of 6.5 μm. The interaction or Hill coefficient for the process is 2.3, indicating positive cooperativity.     

Speciation of ternary complexes of lead(II), cadmium(II) and mercury(II) with L-dopa and phenanthroline in propanediol-water mixtures

Abstract

The formation constants of ternary complexes of title systems have been determined pH-metrically in biologically relevant conditions at an ionic strength of 0.16 mol dm^-3 and 303 K. The overall stability constants have been evaluated using MINIQUAD75 computer program. The complexation equilibria have been derived on the basis of species distribution diagram. In the present study L-Dopa and 1, 10-phenanthroline are found to be compatible ligands, proving greater stability of ternary complexes as compared to binary ones. The trend in variation of stability constants with change in dielectric constant of medium is explained on the basis of electrostatic and non-electrostatic forces. Distributions of the species with pH at different compositions of propanediol-water mixtures are also presented. The factors responsible for the compatibility of both the ligands have also been discussed.     

Quantifying the inactivation rate constants for the molecular species comprising the catalytic cycle of Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase

When an unstable enzyme is incubated with its substrate(s), catalysis may cease before chemical equilibrium is attained. The residual substrate concentrations depend on their initial concentrations, the initial enzymic activity, and the inactivation rate constants for each molecular species that comprise the catalytic cycle. The underlying theory has been elaborated previously for single-substrate reactions and here it is extended to bi-substrate reactions. The theory is illustrated by application to glucose 6-phosphate dehydrogenase, which is unstable when exposed to a low concentration of sodium dodecyl sulphate. It is shown that the ternary complex containing both substrates is resistant to inactivation while each of the remaining complexes undergoes first-order decay. Rate constants for the inactivation of each complex are calculated.     

Effect of anionic micelles on speciation of L-glutamine in presence/absence of metals

Abstract

Protonation equilibria of L-glutamine and speciation of its complexes with Co(II), Ni(II) and Cu(II) have been studied in 0–2.5% w/v SLS–water media using pH-metric method. The protonation constants and binary stability constants have been calculated with the computer program MINIQUAD75. Selection of the best fit chemical models is based on standard deviation in stability constants and residual analysis using crystallographic R-factor and sum of squares of residuals in all mass-balance equations. The trend in the variation of stability constants of the complexes with mole fraction of the medium is attributed to the compartmentalisation of complexation equilibria. Distribution of species and effect of influential parameters on chemical speciation have also been presented.     

Quantifying the inactivation rate constants for the molecular species comprising the catalytic cycle of Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase

When an unstable enzyme is incubated with its substrate(s), catalysis may cease before chemical equilibrium is attained. The residual substrate concentrations depend on their initial concentrations, the initial enzymic activity, and the inactivation rate constants for each molecular species that comprise the catalytic cycle. The underlying theory has been elaborated previously for single-substrate reactions and here it is extended to bi-substrate reactions. The theory is illustrated by application to glucose 6-phosphate dehydrogenase, which is unstable when exposed to a low concentration of sodium dodecyl sulphate. It is shown that the ternary complex containing both substrates is resistant to inactivation while each of the remaining complexes undergoes first-order decay. Rate constants for the inactivation of each complex are calculated.     

Microcomputer simulation of steady-state enzyme kinetics for educational purposes

A BASIC program to assist the instruction of steady-state enzymekinetics has been developed for the IBM PC microcomputer. Itspurpose is to simulate laboratory experiments in order to minimizethe time required to obtain kinetic data from which studentsdeduce kinetic mechanisms and determine kinetic constants ofenzyme-catalyzed reactions. The program randomly selects a kineticscheme from various sequential, ping pong, and iso reactionsequences as well as values for the kinetic constants. The schemeand kinetic constants are unknown to the student at this time;the only thing he or she knows is the stoichiometry of the catalyzedreaction which can have two or three substrates and products.The student is prompted to enter values for concentrations ofsubstrates and products; several different concentrations foreach substrate and product can be entered in a single experiment.The program then calculates, displays and prints (if desired)the corresponding initial steadystate velocities. The studentcan perform as many experiments as desired until enough informationis obtained to determine the kinetic mechanism and to calculatevalues for the kinetic constants. Received on March 10, 1986; accepted on May 6, 1986     

Metal binding to ligands: cadmium complexes with glutathione revisited

We studied the interaction of gamma-L-glutamyl-L-cysteinyl-glycine (glutathione, GSH) with cadmium ions (Cd(2+)) by first performing classical potentiometric pH titration measurements and then turning to additional spectroscopic methods. To estimate the residual concentrations of free cadmium, we studied the competition of glutathione with a Cd(2+)-sensitive dye, either an absorbing dye (murexide) or a fluorescent one (FluoZin-1), and consistent results were obtained with the two dyes. In KCl-containing Tes, Mops, or Tris buffer at pH 7.0 to 7.1 and 37 degrees C (and at a total Cd(2+) concentration of 0.01 mM), results suggest that free cadmium concentration is halved when the concentration of glutathione is approximately 0.05 mM; this mainly reflects the combined apparent dissociation constant for the Cd(glutathione) 1:1 complex under these conditions. To identify the other complexes formed, we used far-UV spectroscopy of the ligand-to-metal charge transfer absorption bands. The Cd(glutathione)(2) 1:2 complex predominated over the 1:1 complex only at high millimolar concentrations of total glutathione and not at low submillimolar concentrations of total glutathione. The apparent conditional constants derived from these spectroscopy results made it possible to discriminate between sets of absolute constants that would otherwise have simulated the pH titration data similarly well in this complicated system. Related experiments showed that although the Cl(-) ions in our media competed (modestly) with glutathione for binding to Cd(2+), the buffers we had chosen did not bind Cd(2+) significantly under our conditions. Our experiments also revealed that Cd(2+) may be adsorbed onto quartz or glass vessel walls, reducing the accuracy of theoretical predictions of the concentrations of species in solution. Lastly, the experiments confirmed the rapid kinetics of formation and dissociation of the UV-absorbing Cd(glutathione)(2) 1:2 complexes. The methods described here may be useful for biochemists needing to determine conditional binding constants for charge transfer metal-ligand complexes under their own conditions.     

Bound and determined: a computer program for making buffers of defined ion concentrations.

A computer program that allows the preparation of buffers containing known concentrations of metal-ligand complexes at defined pH values and temperatures is described. Ligands are defined as compounds that bind metals and may include AMP, ADP, ATP, GMP, GDP, GTP, EGTA, EDTA, BAPTA, phosphate, sulfate, chloride, monocarboxylic acids, dicarboxylic acids, organophosphates, and/or citric acid. Metals may include sodium, potassium, magnesium, calcium, and/or manganese. The program uses association constants corrected for temperature and ionic strength so that solutions between 0 and 40 degrees C and between pH values of 4 and 10 can be defined. The program can perform the following: (i) calculate the concentration of all metal-ligand complexes when total metal and total ligand concentrations are known, (ii) calculate the concentration of metal ion required to make a solution of known free metal ion concentration when total ligand concentrations are known, (iii) calculate the concentration of ligand required to make a solution of known free metal ion concentration when total metal concentrations are known, and (iv) calculate the total concentrations of metal and ligand required to make a buffer of known metal-ligand concentration. Options i-iii are useful for making buffers of defined free metal ion concentrations; option iv is useful for making buffers of defined metal-nucleotide concentrations.     

Investigation of a Monte Carlo model for chemical reactions

Monte Carlo computer simulations are in use at a number of laboratories for calculating time-dependent yields, which can be compared with experiments in the radiolysis of water. We report here on calculations to investigate the validity and consistency of the procedures used for simulating chemical reactions in our code, RADLYS. Model calculations were performed of the rate constants themselves. The rates thus determined showed an expected rapid decline over the first few hundred ps and a very gradual decline thereafter out to the termination of the calculations at 4.5 ns. Results are reported for different initial concentrations and numbers of reactive species. Generally, the calculated rate constants are smallest when the initial concentrations of the reactants are largest. It is found that inhomogeneities that quickly develop in the initial random spatial distribution of reactants persist in time as a result of subsequent chemical reactions, and thus conditions may poorly approximate those assumed from diffusion theory. We also investigated the reaction of a single species of one type placed among a large number of randomly distributed species of another type with which it could react. The distribution of survival times of the single species was calculated by using three different combinations of the diffusion constants for the two species, as is sometimes discussed in diffusion theory. The three methods gave virtually identical results. Received: 6 May 1998 / Accepted in revised form: 5 July 1998     

Global Kinetic Explorer: A new computer program for dynamic simulation and fitting of kinetic data

We describe a new dynamic kinetic simulation program that allows multiple data sets to be fit simultaneously to a single model based on numerical integration of the rate equations describing the reaction mechanism. Unlike other programs that allow fitting based on numerical integration of rate equations, in the dynamic simulation rate constants, output factors, and starting concentrations of reactants can be scrolled while observing the change in the shape of the simulated reaction curves. Fast dynamic simulation facilitates the exploration of initial parameters that serve as the starting point for nonlinear regression in fitting data and facilitates exploration of the relationships between individual constants and observable reactions. The exploration of parameter space by dynamic simulation provides a powerful tool for learning kinetics and for evaluating the extent to which parameters are constrained by the data. This feature is critical to avoid overly complex models that are not supported by the data.     

Substitutions of prolines examine their role in kinetic trap formation of the caspase recruitment domain (CARD) of RICK

Caspase recruitment domains (CARDs) are small helical protein domains that adopt the Greek key fold. For the two CARDs studied to date, RICK-CARD and caspase-1-CARD (CP1-CARD), the proteins unfold by an apparent two-state process at equilibrium. However, the folding kinetics are complex for both proteins and may contain kinetically trapped species on the folding pathway. In the case of RICK-CARD, the time constants of the slow refolding phases are consistent with proline isomerism. RICK-CARD contains three prolines, P47 in turn 3, and P85 and P87. The latter two prolines constitute a nonconserved PxP motif in helix 6. To examine the role of the prolines in the complex folding kinetics of RICK-CARD, we generated seven proline-to-alanine mutants, including three single mutants, three double mutants, and one triple mutant. We examined the spectroscopic properties, equilibrium folding, binding to CP1-CARD, and folding kinetics. The results show that P85 is critical for maintaining the function of the protein and that all mutations decrease the stability. Results from single mixing and sequential mixing stopped-flow studies strongly suggest the presence of parallel folding pathways consisting of at least two unfolded populations. The mutations affect the distribution of the two unfolded species, thereby affecting the population that folds through each channel. The two conformations also are present in the triple mutant, demonstrating that interconversion between them is not due to prolyl isomerism. Overall, the data show that the complex folding pathway, especially formation of kinetically trapped species, is not due to prolyl isomerism.     

Chemical speciation of 2,3-dihydroxybenzoic acid complexes with some biologically essential metal ions in 1, 2-propanediol–water mixtures

Abstract

Chemical speciation of Co(II), Ni(II), Cu(II) and Zn(II) complexes of 2,3-dihydroxybenzoic acid in 0.0-60.0% v/v 1, 2-propanediol-water mixtures maintaining an ionic strength of 0.16 mol dm^-3 at 303±0.1 K has been studied pH metrically. The predominant complexes formed are ML, ML₂ and ML₂H₂ for Co(II), Ni(II) and Zn(II) and ML, ML₂, ML₂H and ML₂H₂ for Cu(II). Models containing different numbers of species were refined by using the computer program MINIQUAD75. Selection of the best fit chemical models was based on statistical parameters and residual analysis. The trend in variation of complex stability constants with dielectric constant of the medium is explained on the basis of electrostatic and non-electrostatic forces. Distributions of species, formation equilibria and effect of influential parameters on the stability constants have been presented. The possible structures of the various species are elucidated on the basis of the analysis of the pH-metric data.     

Complexation studies on inositol-phosphates. II. Alkali-metal complexes of D-myo-inositol 1,2,6 trisphosphate

The complexation properties of the D-myo-inositol 1,2,6 trisphosphate (Ins(1,2,6)P3) towards Li+, Na+, K+, Rb+, and Cs+ cations were studied at 25 degrees C in a 0.1 M tetra-n-butylammonium bromide medium. For all cations, mononuclear and protonated species were found. For smaller cations (Li+, Na+, and K+) a dinuclear complex was also put into evidence. The main characteristic of the complexes is its high stability; and of the ligand, its nonselectivity. The Ins(1,2,6)P3-K system was ascertained using Sammartano's method which additionally enabled the influence of various K+ concentrations on the protonations constants to be considered.     

Speciation studies of Co(II), Ni(II) and Cu(II) complexes of L-valine in acetonitrile–water mixtures

Abstract

Chemical speciation of binary complexes of Co(II), Ni(II) and Cu(II) with L-valine in 0.0-60.0% v/v acetonitrile-water mixtures was studied pH-metrically at an ionic strength of 0.16 mol L^-1 at 303.0 K. The existence of different binary complexes was established from the modelling studies, using the computer program MINIQUAD75. The appropriateness of the model was ascertained by studying the effect of errors in concentrations of the reagents. The trend in variation of stability constants with change in the permittivity of the medium is explained on the basis of electrostatic and non-electrostatic forces. The species distribution diagrams and the plausible equilibria for the formation of the species are also presented.