Parameter estimation for ligand binding systems kinetics applied to 1,25-dihydroxycholecalciferol

A mathematical analysis of the kinetics of the hormone-receptor interaction was applied to the 1,25-dihydroxycholecalciferol-intestinal receptor system. The exact analytical solution and the numerical integration of the kinetic equation were installed in a Statistical Analysis System (SAS) computer program to estimate the rate constants of the reaction. Estimates of the parameters obtained by these two methods are similar, demonstrating that the numerical integration can be combined with the nonlinear regression procedure for least-squares parameter fitting using a simple SAS program. This enables estimation of kinetics rate constants when the kinetic equation cannot be solved analytically. The ratio of the rate constants (ka/kd) found by the nonlinear procedure is close to the independently determined equilibrium (Scatchard) constant in the nonlinear analysis.     

SOME ENZYMIC ASPECTS OF THE PRODUCTION OF OXIDIZED OR REDUCED METABOLITES OF CATECHOLAMINES AND 5-HYDROXYTRYPTAMINE BY BRAIN TISSUES

The Michaelis constants of purified aldehyde dehydrogenase (aldehyde: NAD oxidoreductase, EC 1.2.1.3) and aldehyde reductases (alcohol: NADP oxidoreductase, EC 1.1.1.2) from pig brain have been obtained for a number of biologically important aldehydes. The aldehydes include 3,4-dihydroxyphenylacetaldehyde, D-3,4-dihydroxyphenylglycolaldehyde, and 5-hydroxyindoleacetaldehyde. The relative activities of the aldehyde-catabolizing enzymes in the soluble fractions of the cerebral cortex and caudate nucleus of pig brain have also been obtained. The values are used to show that the metabolic fates of the various aldehydes—and hence of the parent amines—may be explained in terms of the simple kinetics of these enzymes. It is also shown that the metabolic fates of the aldehydes may be influenced by their rates of synthesis. As the rate of aldehyde production increases the proportion of aldehyde reduced may be expected to increase at the expense of the proportion of aldehyde oxidized. It is further concluded from the kinetic constants that selective inhibition of aldehyde dehydrogenase may greatly affect the catabolism of dopamine and 5-hydroxytryptamine by altering the relevant aldehyde concentrations, while the catabolism of norepinephrine is little affected under these circumstances. Conversely, it is concluded that selective inhibition of the aldehyde reductases should scarcely affect the catabolism of dopamine and 5-hydroxytryptamine, but that the catabolism of norepinephrine should be markedly affected. The results also indicate that the concentrations of the various deaminated metabolites of the biogenic amines could be selectively controlled by modulation of the activity of the enzymes of aldehyde catabolism in brain.     

Fluidics-resolved estimation of protein adsorption kinetics in a biomicrofluidic system

Protein adsorption on surfaces is a complex phenomenon that is described by the balance of convective/diffusive transport of the protein species to the surface and its adsorption/desorption at the surface. The extent of binding depends on a variety of factors such as protein/surface interactions, availability of binding sites, localized concentrations of protein near biomaterial surfaces and flow characteristics of the protein in that region. Factors such as time-varying flows, complex device geometries, presence of multiple competitive species, or possible denaturing of proteins when they attach to the surface make it extremely difficult to quantitatively analyze protein interactions with surfaces. Adsorption/desorption rate constants are often inferred using simplistic models which neglect mass transport and have limited use across different microfluidic systems and flow protocols. In this work, we have developed and demonstrated a fluidics-resolved model that evaluates protein adsorption, accounting for both the fluidic transport and the biochemical kinetics in complex biomicrofluidic devices. The model is valid for both flow and static conditions. An automated procedure was also developed to extract the "intrinsic" mass-transport-independent adsorption kinetic rate constants from experimental data using a least squares optimization method. The automated data extraction methodology is applied to two proteins (alkaline phosphatase and glucose oxidase) that have been brought into contact with poly(etheretherketone) and Teflon capillaries. The applicability of the procedure in analyzing flow and adsorption in complex microfluidic structures is also demonstrated.     

Kinetic and structural features of betaine aldehyde dehydrogenases: Mechanistic and regulatory implications

The betaine aldehyde dehydrogenases (BADH; EC 1.2.1.8) are so-called because they catalyze the irreversible NAD(P)⁺-dependent oxidation of betaine aldehyde to glycine betaine, which may function as (i) a very efficient osmoprotectant accumulated by both prokaryotic and eukaryotic organisms to cope with osmotic stress, (ii) a metabolic intermediate in the catabolism of choline in some bacteria such as the pathogen Pseudomonas aeruginosa, or (iii) a methyl donor for methionine synthesis. BADH enzymes can also use as substrates aminoaldehydes and other quaternary ammonium and tertiary sulfonium compounds, thereby participating in polyamine catabolism and in the synthesis of γ-aminobutyrate, carnitine, and 3-dimethylsulfoniopropionate. This review deals with what is known about the kinetics and structural properties of these enzymes, stressing those properties that have only been found in them and not in other aldehyde dehydrogenases, and discussing their mechanistic and regulatory implications.     

Dynamic analysis of ABA accumulation in relation to the rate of ABA catabolism in maize tissues under water deficit

The plant hormone abscisic acid (ABA) accumulates in plant tissues which experience water deficit (stress ABA). This study analysed its accumulation as a function of both synthesis and catabolism in maize tissues. By following the disappearance of the stress ABA when ABA synthesis was blocked by nordihydroguaiaretic acid (NDGA), the rate of the catabolism of stress ABA was determined. When compared with the catabolic rate of baseline (non-stress) ABA, stress ABA showed a catabolic rate >11 times higher. With such an elevated catabolic rate, it is proposed that the xanthophyll precursor pool may not be able to sustain the ABA accumulation, and such a proposition has been substantiated by further experiments where fluridone is used to limit the availability of upstream ABA precursors. When fluridone was used, stress ABA accumulation could only be sustained for a few hours, i.e. approximately 5 h for leaf and 1 h for root tissues. In detached roots, stress ABA accumulation could not be sustained even if fluridone was not used, suggesting that stress ABA accumulation in root systems requires the continuous import of ABA precursors from the shoots. Such an assumption was substantiated by the observation that defoliation or shading significantly reduced ABA accumulation in intact roots. The present study suggests that ABA catabolism is rapid enough to play an important role in the regulation of ABA accumulation.     

The role of mRNA and protein stability in gene expression

How important is the stability of gene products in the process of gene expression? We use a dual-compartment mathematical model to demonstrate the effects that changing the rates of synthesis and degradation of hypothetical mRNAs and proteins would have on the final concentration of protein. The model predicts that the concentration of protein at steady state equals the product of the rate constants for synthesis of mRNA and protein (ks1 and ks2) divided by the product of the rate constants for degradation (kd1 and kd2) and that the rate at which protein concentration changes depends on the rate constants for degradation of both the mRNA and the protein. This permits great flexibility in controlling induction kinetics for particular gene products, since their synthesis, translation, and degradation may be regulated coordinately to permit induction to be stable or transient or to amplify the final yield of protein. We suggest single exons may encode structural features that cause both mRNAs and proteins to be labile, thereby ensuring that modal stabilities of highly regulated macromolecules are similar.     

Chymotrypsin-catalyzed peptide synthesis. Kinetic analysis of the kinetically controlled peptide-bond formation

The kinetics of peptide-bond formation catalyzed by delta-chymotrypsin has been studied for a number of peptide products of different length using fixed concentrations of the acyl component (Ac-Phe-OMe, Ac-Ala-Ala-Phe-OMe, or Ac-Ala-Ala-Tyr-OMe) and varying concentration of the amino component (H-Ala-NH2 or H-Ala-Ala-NH2). The time course of the reactions was followed by monitoring ester consumption and peptide product formation by analytical HPLC. On the basis of a plausible four-centre mechanistic model, the theoretical time course of these reactions was calculated using rate and equilibrium constants determined by separate kinetic experiments. The excellent agreement observed between the theoretical and the experimental time courses supports the proposed mechanism and provides evidence for the validity of the present kinetic approach. By focusing attention on the rate constants which are critical for efficient synthesis, this mechanistic information constitutes a valuable basis for the use of the enzymatic peptide synthesis in preparative applications.     

Protein turnover and amino acid transport kinetics in end-stage renal disease

Protein and amino acid metabolism is abnormal in end-stage renal disease (ESRD). Protein turnover is influenced by transmembrane amino acid transport. The effect of ESRD and hemodialysis (HD) on intracellular amino acid transport kinetics is unknown. We studied intracellular amino acid transport kinetics and protein turnover by use of stable isotopes of phenylalanine, leucine, lysine, alanine, and glutamine before and during HD in six ESRD patients. Data obtained from amino acid concentrations and enrichment in the artery, vein, and muscle compartments were used to calculate intracellular amino acid transport and muscle protein synthesis and catabolism. Fractional muscle protein synthesis (FSR) was estimated by the precursor product approach. Despite a significant decrease in the plasma concentrations of amino acids in the artery and vein during HD, the intracellular concentrations remained stable. Outward transport of the amino acids was significantly higher than the inward transport during HD. FSR increased during HD (0.0521 +/- 0.0043 vs. 0.0772 +/- 0.0055%/h, P < 0.01). Results derived from compartmental modeling indicated that both protein synthesis (118.3 +/- 20.6 vs. 146.5 +/- 20.6 nmol.min-1.100 ml leg-1, P < 0.01) and catabolism (119.8 +/- 18.0 vs. 174.0 +/- 14.2 nmol.min-1.100 ml leg-1, P < 0.01) increased during HD. However, the intradialytic increase in catabolism exceeded that of synthesis (57.8 +/- 13.8 vs. 28.0 +/- 8.5%, P < 0.05). Thus HD alters amino acid transport kinetics and increases protein turnover, with net increase in protein catabolism.     

General method of analysis of kinetic equations for multistep reversible mechanisms in the single-exponential regime: application to kinetics of open complex formation between Esigma70 RNA polymerase and lambdaP(R) promoter DNA

A novel analytical method based on the exact solution of equations of kinetics of unbranched first- and pseudofirst-order mechanisms is developed for application to the process of Esigma70 RNA polymerase (R)-lambdaPR promoter (P) open complex formation, which is described by the minimal three-step mechanism with two kinetically significant intermediates (I1, I2), [equation: see text], where the final product is an open complex RPo. The kinetics of reversible and irreversible association (pseudofirst order, [R] > [P]) to form long-lived complexes (RPo and I2) and the kinetics of dissociation of long-lived complexes both exhibit single exponential behavior. In this situation, the analytical method provides explicit expressions relating observed rate constants to the microscopic rate constants of mechanism steps without use of rapid equilibrium or steady-state approximations, and thereby provides a basis for interpreting the composite rate constants of association (ka), isomerization (ki), and dissociation (kd) obtained from experiment for this or any other sequential mechanism of any number of steps. In subsequent papers, we apply this formalism to analyze kinetic data obtained in the reversible and irreversible binding regimes of Esigma70 RNA polymerase (R)-lambdaP(R) promoter (P) open complex formation.     

The ligand affinity of proteins measured by isothermal denaturation kinetics

An isothermal denaturation kinetic method was developed for identifying potential ligands of proteins and measuring their affinity. The method is suitable for finding ligands specific toward proteins of unknown function and for large-scale drug screening. It consists of analyzing the kinetics of isothermal denaturation of the protein-with and without the presence of potential specific ligands-as measured by long-wavelength fluorescent dyes whose quantum yield increases when bound to hydrophobic regions exposed upon unfolding of the proteins. The experimental procedure was developed using thymidylate kinase and stromelysin as target proteins. The kinetics of thermal unfolding of both of these enzymes were consistent with a pathway of two consecutive first-order rate-limiting steps. Reflecting the stabilizing effect of protein/ligand complexes, the presence of specific ligands decreased the value of the rate constants of both steps in a dose-dependent manner. The dependence of the rate constants on ligand concentration obeyed a simple binding isotherm, the analysis of which yielded an accurate equilibrium constant for ligand binding. The method was validated by comparing its results with those obtained under the same conditions by steady-state fluorescence spectroscopy, circular dichroism, and uv spectrophotometry: The corresponding rate constants were comparable for each of the analytical detection methods.     

Steady-state kinetics of solitary batrachotoxin-treated sodium channels. Kinetics on a bounded continuum of polymer conformations.

The underlying principles of the kinetics and equilibrium of a solitary sodium channel in the steady state are examined. Both the open and closed kinetics are postulated to result from round-trip excursions from a transition region that separates the openable and closed forms. Exponential behavior of the kinetics can have origins different from small-molecule systems. These differences suggest that the probability density functions (PDFs) that describe the time dependences of the open and closed forms arise from a distribution of rate constants. The distribution is likely to arise from a thermal modulation of the channel structure, and this provides a physical basis for the following three-variable equation: [formula; see text] Here, A0 is a scaling term, k is the mean rate constant, and sigma quantifies the Gaussian spread for the contributions of a range of effective rate constants. The maximum contribution is made by k, with rates faster and slower contributing less. (When sigma, the standard deviation of the spread, goes to zero, then p(f) = A0 e-kt.) The equation is applied to the single-channel steady-state probability density functions for batrachotoxin-treated sodium channels (1986. Keller et al. J. Gen. Physiol. 88: 1-23). The following characteristics are found: (a) The data for both open and closed forms of the channel are fit well with the above equation, which represents a Gaussian distribution of first-order rate processes. (b) The simple relationship [formula; see text] holds for the mean effective rat constants. Or, equivalently stated, the values of P open calculated from the k values closely agree with the P open values found directly from the PDF data. (c) In agreement with the known behavior of voltage-dependent rate constants, the voltage dependences of the mean effective rate constants for the opening and closing of the channel are equal and opposite over the voltage range studied. That is, [formula; see text] "Bursts" are related to the well-known cage effect of solution chemistry.     

Protein synthesis as an early response to fertilization of the sea urchin egg: A model

We have developed a quantitative computer model which simulates the rise in protein synthesis resulting from the fertilization of the sea urchin egg. The model predicts the kinetics of incorporation of radioactively labeled amino acids into proteins for the experimental situation in which the amino acid pool is labeled prior to fertilization. The computer model is used to examine the impact of changes in the values of major parameters such as the time of initiation of protein synthesis, the rate at which mRNA is unmasked, the ribosome transit time, and the rate of depletion of the labeled amino acid pool on the kinetics of amino acid incorporation. When experimentally determined values for these parameters are used the model predicts kinetics which closely approximate the kinetics actually observed in newly fertilized eggs. We suggest that the rate at which mRNA is made available for translation and a change in the elongation rate following fertilization control the rise in protein synthesis, and that both of these processes are initiated within 0–2 min following the initial fertilization event.     

Effect of testosterone on purine nucleotide metabolism in rat liver.

In previous studies, we found that castration induced interesting morphological and biochemical changes in rat liver. For the present study, we have examined the effects of testosterone on the kinetics of purine nucleotide metabolism with the aim of determining the steps affected by testosterone deficiency. A biomathematical model of purine nucleotide metabolism was used to analyze the many reactions involved. The model simplifies purine nucleotide metabolism to four main steps: 1) de novo synthesis from PRPP to IMP; 2) the inosinic branch point from IMP to GMP or AMP; 3) catabolism of IMP, AMP and GMP to uric acid; 4) RNA and DNA formation from AMP and GMP. We evaluated rate constants from each step from variations in specific radioactivity of metabolites labelled with (14)C-formate, a precursor of de novo synthesis. The model was applied to the liver of normal and castrated rats before and after testosterone treatment. All four steps were slowed after castration, and were not completely restored by androgen administration. The model can give a clear representation of the kinetics of the reactions involved in the liver nucleotide metabolism investigated here, and we propose that a similar approach could be useful whenever a quantitative evaluation of the results obtained in vivo after administration of labelled precursors is required.     

The Catabolism of Tryptophan to Indole-3-Ethanol by Crithidia fasciculata and Phytomonas davidi1

Crithidia fasciculata and Phytomonas davidi catabolize tryptophan (TRP) to indole-3-ethanol, which was identified by both thin layer and gas chromatography. The catabolic pathway involved in this metabolic conversion is suggested to be similar to that proposed for other members of the family Trypanosomatidae. Although this catabolism occurs at both 25° and 37°C, the catabolic rate is greater at 37°C, a non-permissive growth temperature. Conditions that inhibit protein synthesis would appear to favor the catabolism of tryptophan to indole-3-ethanol. The possible importance of this catabolic pathway to these organisms is discussed.     

DISAPPEARANCE OF NEWLY SYNTHESIZED AND TOTAL DOPAMINE FROM THE STRIATUM OF THE RAT AFTER INHIBITION OF SYNTHESIS: EVIDENCE FOR A HOMOGENEOUS KINETIC COMPARTMENT

Abstract— The hypothesis that the biphasic disappearance of dopamine (DA) from the rat striatum following inhibition of synthesis with α-methyl-p-tyrosine (AMPT) represents catabolism from separate‘functional’and 'storage’compartments (Javoy & Glowinski , 1971) was tested by administering ³H-tyrosine i.v. 10 min before 400 mg per kg AMPT. The levels of newly synthesized ³H-DA and total DA were then determined at 5-min intervals. While both declined biphasically, the rate of decay of ³H-DA was significantly less than that predicted by the two-pool hypothesis. In fact, the patterns of change of ³H-DA and total DA were identical and the specific activity of DA did not vary following AMPT. To determine if an increase in DA synthesis and release would result in the preferential catabolism of newly synthesized ³H-DA, the experiment was repeated fol!owing treatment with 0.1 mg per kg haloperidol i.v. ³H-DA and total DA still exhibited identical biphasic declines and there was no change in the specific activity of DA after AMPT even though ³H-DA levels were increased three-fold by haloperidol. Thus (a) no evidence for the preferential catabolism of newly synthesized ³H-DA was obtained and (b) newly synthesized and total striatal DA behaved as if localized in a homogeneous kinetic compartment under all conditions employed. Rates of striatal DA metabolism were estimated in both experiments from changes in total DA after AMPT and by the formation of ³H-DA in the initial 10 min after ³H-tyrosine injection. Results of both approaches were consistent and indicated that the rates of striatal DA synthesis and catabolism may vary rapidly between approx. 20 and 90 nmol per g per h without violating single compartment kinetics. It is proposed that any labile pool contains no more than a few per cent of the DA in the striatum and the implications of this hypothesis are discussed.     

Investigation of transmitter-receptor interactions by analyzing postsynaptic membrane noise using stochastic kinetics

The stoichiometric and kinetic details of transmitter-receptor interaction (the number of conformations and the rate constants of conformation changes) in synaptic transmission have been investigated analyzing postsynaptic membrane noises by the aid of the fluctuation-dissipation theorem of stochastic chemical kinetics. The main assumptions are the following: (i) the transmitter-receptor interaction is modelled by a closed compartment system (a special complex chemical reaction) of unknown length,- (ii) the quantity of transmitter is maintained at a constant level,- (iii) the conductance is a linear function of the conformation quantity vector.- The main conclusion is: the conductance spectral density function is determined by three qualitatively different factors: (i) the length of the compartment system,- (ii) the precise form of the conductance-conformation quantity vector,-(iii) the matrix of the reaction rate constants.     

Thermodynamic and Kinetic Analyses of DNA Triplex Formation: Application of Filter-Binding Assay

Abstract

We have developed a simple and efficient method for studying equilibrium thermodynamics and kinetics of DNA triplex formation, which utilizes a filter-binding procedure. The application of this method to the triplex formation between a double-stranded homopurine-homopyrimidine and a single-stranded homopyrimidine oligonucleotides has demonstrated its ability in the quantitative estimation of equilibrium binding constants and rate constants under various conditions. Thus, this simple method can serve as a powerful tool for the systematic analysis of sequence and environmental effects on the equilibrium and kinetic quantities in the triplex formation.     

THE EFFECTS OF CARBON MONOXIDE INHIBITION ON ATP LEVEL AND THE RATE OF MITOSIS IN THE SEA URCHIN EGG

The requirements for ATP synthesis during the various phases of mitosis were investigated in the oxygen-requiring eggs of the sea urchin, Strongylocentrotus purpuratus. CO in the dark, a specific inhibitor of respiration, was used to inhibit ATP synthesis. The kinetics of respiratory inhibition were determined by analyzing ATP levels with the luciferin-luciferase assay. The kinetics of mitotic inhibition were determined by analysis of the rate of mitosis. It was found that CO inhibition resulted in a decrease in the normal ATP level. Coincident with this decrease was a decrease in the rate of mitosis which stops completely when the ATP drops below 50 per cent of the normal level. With the use of various degrees of CO inhibition, the rate of mitosis is shown to be related to the resultant ATP level. These results contradict the basic premise of the energy reservoir hypothesis, and also disagree with other reports that cells in mitosis are insensitive to inhibitors of energy metabolism. Data are presented which demonstrate that these conflicting reports result from insufficient inhibition of ATP synthesis. The above findings all indicate that mitosis depends on the continuous synthesis and utilization of ATP.     

Mitochondrial transport in proline catabolism in plants: the existence of two separate translocators in mitochondria isolated from durum wheat seedlings

Abiotic stresses, such as high salinity or drought, can cause proline accumulation in plants. Such an accumulation involves proline transport into mitochondria where proline catabolism occurs. By using durum wheat seedlings as a plant model system, we investigated how proline enters isolated coupled mitochondria. The occurrence of two separate translocators for proline, namely a carrier solely for proline and a proline/glutamate antiporter, is shown in a functional study in which we found the following: (1) Mitochondria undergo passive swelling in isotonic proline solutions in a stereospecific manner. (2) Externally added l-proline (Pro) generates a mitochondrial membrane potential (ΔΨ) with a rate depending on the transport of Pro across the mitochondrial inner membrane. (3) The dependence of the rate of generation of ΔΨ on increasing Pro concentrations exhibits hyperbolic kinetics. Proline transport is inhibited in a competitive manner by the non-penetrant thiol reagent mersalyl, but it is insensitive to the penetrant thiol reagent N-ethylmaleimide (NEM). (4) No accumulation of proline occurs inside the mitochondria as a result of the addition of proline externally, whereas the content of glutamate increases both in mitochondria and in the extramitochondrial phase. (5) Glutamate efflux from mitochondria occurs at a rate which depends on the mitochondrial transport, and it is inhibited in a non-competitive manner by NEM. The dependence of the rate of glutamate efflux on increasing proline concentration shows saturation kinetics. The physiological role of carrier-mediated transport in the regulation of proline catabolism, as well as the possible occurrence of a proline/glutamate shuttle in durum wheat seedlings mitochondria, are discussed.Catello Di Martino, Roberto Pizzuto these authors contributed equally to the paper     

Rate constants of agonist binding to muscarinic receptors in rat brain medulla. Evaluation by competition kinetics

The method of competition kinetics, which measures the binding kinetics of an unlabeled ligand through its effect on the binding kinetics of a labeled ligand, was employed to investigate the kinetics of muscarinic agonist binding to rat brain medulla pons homogenates. The agonists studied were acetylcholine, carbamylcholine, and oxotremorine, with N-methyl-4-[3H]piperidyl benzilate employed as the radiolabeled ligand. Our results suggested that the binding of muscarinic agonists to the high affinity sites is characterized by dissociation rate constants higher by 2 orders of magnitude than those of antagonists, with rather similar association rate constants. In contrast, the major differences between the kinetic binding parameters of agonists and antagonists to the low affinity agonist binding sites are in the association rate constants, which were 2-5 orders of magnitude lower for agonists. This demonstrates that there are basic differences in the interactions of agonists with the low and high affinity sites. Our findings also suggest that isomerization of the muscarinic receptors following ligand binding is significant in the case of antagonists, but not of agonists. Moreover, it is demonstrated that in the medulla pons preparation, agonist-induced interconversion between high and low affinity bindings sites does not occur to an appreciable extent.