Biomedical subjects

M Cascante

Publications and source records attributed to M Cascante.

At least 73 records · Page 4Linked to original sources

PubMed1995

Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model validation and dynamic behavior.

In the first two papers of this series (immediately preceding, this issue), we characterized the steady-state properties of a model of a fermentation pathway in Saccharomyces cerevisiae in four experimental conditions. In each of these conditions, the pictures obtained by metabolic control analysis and biochemical systems theory were coincident, which illustrates the relatedness of the two approaches. In this paper we analyze the quality of this description by means of the tools available within biochemical systems theory, and we show that in some of the experimental conditions studied the system is poorly characterized. The most critical condition corresponds to the immobilization of the cells at pH 5.5, in which the kinetic characterization appears to be inaccurate. Furthermore, sensitivity analysis and the study of the local steady-state stability identify the most critical parameters. The results of these analyses are confirmed by the predictions of the dynamic response of the model using its S-system representation. This illustrates the utility of these tools and warns against using the steady-state characterization without testing its validity.

Fermentation↗

PubMed1995

Control in channelled pathways. A matrix method calculating the enzyme control coefficients.

The usual equations expressing the enzyme control coefficients (quantitative indicators of 'global' control properties of a pathway) via the elasticity coefficients (reflecting local kinetic properties of an enzyme reaction), cannot be applied to a variety of 'non-ideal' pathways, in particular to pathways with metabolic channelling. Here we show that the relationship between the control and elasticity coefficients can be obtained by considering such a metabolic pathway as a network of elemental chemical conversions (steps). To calculate the control coefficients of enzymes one should first determine the elasticity coefficients of such elemental steps and then take their appropriate combinations. Although the method is illustrated for a channelled pathway it can be used for any non-ideal pathway including those with high enzyme concentrations where the sequestration of metabolites by enzymes cannot be neglected.

Journal Article↗

PubMed1995

Coenzyme cycles and metabolic control analysis: the determination of the elasticity coefficients from the generalised connectivity theorem.

Metabolic control analysis allows one to express the elasticity coefficients (which describe the "local" kinetic features of enzymes) in terms of the control coefficients (quantitative indicators of the "global" control properties). However, when coenzymes (or metabolites linked by conservation constraints) are present in the pathway this procedure yields the "apparent" values of elasticity coefficients that correspond to the kinetic responses of the enzymes to such a simultaneous change of the coenzyme forms which leaves the total concentration of these forms unchanged (e.g., NAD+ + NADH in the glycolysis). We show that a generalised connectivity theorem (Kholodenko et al, Eur. J. Biochem. (1994) 225, 179-186) makes it possible to express the elasticity coefficients with respect to every coenzyme form separately. Such expressions include (i) the control coefficients and (ii) the responses to changes in the total concentrations of the coenzymes.

Coenzymes↗

PubMed1994

Structure identifiability in metabolic pathways: parameter estimation in models based on the power-law formalism.

An important step in understanding a metabolic pathway is to identify its structure, in terms of the flow of material and information. In pursuing this goal, the available information for a given system is usually obtained from experiments in vitro and comes from different sources. Frequently, the final set of regulatory signals acting in the system in vivo is unclear, and some kind of test is needed on the intact system. Besides defining an appropriate experimental approach, identification of the regulatory pattern needs a theoretical framework in which the different experimental measurements can be evaluated and a final picture can be agreed on. Mathematical approaches based on sensitivity coefficients provide a useful tool for addressing this problem. Within this framework, the appropriate parameters are related to both the structure of the reaction network and the signals that regulate the target system. Thus the identification of the regulatory structure can be related to the estimation of the appropriate set of parameters. In pursuing this goal, we will show the limitations of using steady-state measurements and the usefulness of using dynamic data. We suggest a way to test the regulatory pattern in a given metabolic pathway by combining both kinds of data, and we show, by using a reference system, the potential of the method suggested.

Metabolism↗

PubMed1994

Enzyme-enzyme interactions and metabolite channelling: alternative mechanisms and their evolutionary significance.

Metabolite channelling may result from different kinetic mechanisms in which enzyme-enzyme interactions occur, so that intermediates are not released into the bulk solution and cannot be used by enzymes outside the channel. From an evolutionary point of view, the emergence of such mechanisms may provide new functional possibilities for the system, which would result in a selective advantage. Hence, it would be useful to evaluate the objective advantages provided by the various options by considering different criteria for functional effectiveness. Following this strategy, the goal of this paper is to compare a model for a free-diffusion two-enzyme system with two different models with inclusion of enzyme-enzyme interactions. In addition, models with simultaneous free and interacting branches are also analysed, and their advantages or disadvantages are presented. Basic guidelines are suggested that help in predicting the occurrence of specific mechanisms in different circumstances, and provide theoretical evidence in support of the hypothesis that no single solution simultaneously optimizes all the possible desired properties of the system.

Biological Evolution↗

PubMed1993

Dramatic changes in control properties that accompany channelling and metabolite sequestration.

A simple summation theorem describes the control of fluxes in 'ideal' metabolic pathways. This paper shows how this theorem and the control properties of a pathway change when direct transfer of intermediates and/or sequestration of metabolites involved in moiety conservations (by enzymes present at high concentrations) take place. The derived generalized summation theorem quantifies the extent to which metabolite sequestration decreases and direct metabolite transfer can increase the control exerted by enzymes on the flux. The implications of metabolite channelling for the control of fluxes are discussed quantitatively.

Enzymes↗

PubMed1993

Metabolic pathway characterization from transient response data obtained in situ: parameter estimation in S-system models.

The actual values of internal metabolites and fluxes can be measured by a number of experimental techniques and they provide important information for evaluating the properties of a metabolic pathway in situ. In this paper we propose a strategy to properly exploit this information. The suggested approach permits estimation of a set of parameters on the whole system so that a useful model can be constructed and used to describe its components and systemic properties and to predict its behavior under new conditions. A simulated reference pathway is provided to validate this method and to show its utility in metabolic studies.

Animals↗

PubMed1993

Experimental strategy to study the pH dependence of the kinetic behavior of enzymes: practical application to chicken liver xanthine dehydrogenase.

An experimental strategy has been developed to analyze the pH dependence of kinetic parameters in two-substrate enzyme kinetics based upon model discrimination, parameter refinement, and optimal discrete design. The experimental protocol proposed includes obtaining reproducible experimental results in different sessions, replicates of each experimental determination, and rejection of outliers. This strategy leads to an empirical kinetic equation that fits the experimental results. As a practical application of this strategy we studied the pH dependence of kinetic parameters of chicken liver xanthine dehydrogenase. We obtained an empirical rate law from the determination of the initial rates at different substrate concentrations and pH. Finally, we have proposed a plausible kinetic mechanism that may explain the experimental findings. This model is not the only one leading to the empirical equation, but it is based on previous experimental findings (Bruguera, P., López-Cabrera, A., and Canela, E. I., 1988, Biochem. J. 249, 171-178).

Animals↗

PubMed1992

A model for adenosine transport and metabolism.

1. A model is presented for adenosine transport and metabolism in different steady states. The model considers steady-state equations for metabolic enzymes based on information from the literature on their kinetic behaviour. 2. Assuming that extracellular adenosine and inosine are translocated by three transporters, we have devised rate equations for these nucleoside transporters which are valid when both nucleosides are present. Since the Na(+)-independent transporter can either incorporate nucleosides into the cell or release them, various conditions have been simulated in which inosine was either incorporated or released. 3. Control analyses are reported which show that the fluxes towards intracellular adenine nucleosides are controlled by ecto-5'-nucleotidase in some circumstances and by the nucleoside transporters in others. The nucleoside transporter is responsible for five fluxes (two Na+ dependent adenosine transport mechanisms, a Na(+)-dependent inosine transport, a Na(+)-independent adenosine transport and a Na(+)-independent inosine influx or efflux) but the control is not always positive for all these fluxes. The control patterns of these five fluxes indicate that, in the presence of extracellular adenosine and inosine, the intracellular metabolism of adenine derivatives would be highly dependent on the extracellular and intracellular concentrations of both nucleosides, on the ectoenzymes (5'-nucleotidase and adenosine deaminase) and on the transporter. 4. Predictions of the model were examined. The results indicate that a change in one independent variable (extracellular AMP concentration) makes the system evolve towards a new steady state which is far from the initial one and has a different control pattern. In contrast, simulation of inhibition of the carriers produces only slight modification of the fluxes since the concentrations of the metabolites change to counteract the effect. Thus, for instance, a 50% inhibition of the three carriers does not affect the flux towards intracellular adenine nucleotides. Finally, our model has confirmed that the evolution of the concentration of extracellular adenosine, when an increase in extracellular AMP is produced, agrees with the behaviour expected for a neurohormone.

Adenosine↗

PubMed1992

The molybdoenzymes xanthine oxidase and aldehyde oxidase contain fast- and slow-DTNB reacting sulphydryl groups.

The reactivities with an excess of 5-5'-dithiobis (2-nitrobenzoic) acid (DTNB) of sulphydryl residues present in xanthine oxidase and aldehyde oxidase were studied and compared. The results show that two classes of sulphydryl groups with quite different reactivities exist in both enzymes either native or denatured. Some of the available sulphydryl residues thus react instantaneously with the DTNB, whereas the others react very slowly following pseudo-first-order kinetics. The number of sulphydryl residues of each class and the rate constant of slowly reacting groups are, respectively, 1.7 and 0.8 in native xanthine oxidase and 1.6 and 1.7 in native aldehyde oxidase. In denatured enzymes, the number of fast- and slow-reacting sulphydryl residues obtained are, respectively, 13.9 and 7.9 in xanthine oxidase and 5.7 and 5.4 in aldehyde oxidase. Analogously, the rate constant for the slowly reacting groups is similar for the two native enzymes, but in denatured aldehyde oxidase it is double that of denatured xanthine oxidase.

Aldehyde Oxidase↗

PubMed1991

Biochemical systems theory: increasing predictive power by using second-order derivatives measurements.

Models based on the power-law formalism provide a useful tool for analyzing metabolic systems. Within this methodology, the S-system variant furnishes the best strategy. In this paper we explore an extension of this formalism by considering second-order derivative terms of the Taylor series which the power-law is based upon. Results show that the S-system equations which include second-order Taylor coefficients give better accuracy in predicting the response of the system to a perturbation. Hence, models based on this new approach could provide a useful tool for quantitative purposes if one is able to measure the required derivatives experimentally. In particular we show the utility of this approach when it comes to discriminating between two mechanisms that are equivalent in the S-system a representation based on first-order coefficients. However, the loss of analytical tractability is a serious disadvantage for using this approach as a general tool for studying metabolic systems.

Kinetics↗

PubMed1991

Control analysis of transition times. Extension of analysis and matrix method.

The present theoretical basis of Control Analysis is extended with the definition of Transition Time Response Coefficients. Some new relationships between local and global coefficients defined in Control Analysis are presented. These relationships are in the form of matrix products constructed in a priori form. The use of these straightforward relationships is shown in an exemplary application corresponding to an experimental system consisting of the glycolytic degradation from glucose to glyceraldehyde-3-phosphate.

Animals↗

PubMed1991

An improved purification procedure for sulfite oxidase from bovine liver.

Sulfite oxidase (Sulfite:O2 oxidoreductase, EC 1.8.3.1) has been purified 2,440-fold from bovine liver. The procedure developed was used to isolate the enzyme from 1,000 g of liver and permitted the rapid isolation of enzyme with a very high specific activity (40,405 mU/mg). The enzyme preparations obtained have been characterized by electrophoretic and spectrophotometric analysis and the molecular mass and the Stokes radius of the enzyme have been determined.

Acetone↗

PubMed1990

Control analysis of systems having two steps catalyzed by the same protein molecule in unbranched chains.

The analysis of the control of a metabolic pathway having an enzyme catalyzing two different reactions (or a protein displaying two different activities) has been performed. For such systems although the summation theorems are valid, the flux and concentration connectivity theorems of the metabolic control analysis are not valid. Another general relationship of control analysis is shown to be more widely obeyed and holds in these systems. An exemplary case, where the enzyme catalyzes two irreversible reactions, demonstrates that the level of one internal intermediate is constant, i.e. it does not depend upon the independent variables of the system.

Catalysis↗

PubMed1990

Application of inverse regression for estimating molecular masses and Stokes radii of globular proteins by gel filtration chromatography.

The aim of this paper is to apply inverse regression as a method for treating experimental data obtained from gel filtration chromatography in order to obtain estimates of hydrodynamic parameters of globular proteins with true confidence intervals. The method is illustrated with the determination, using inverse regression, of molecular mass and Stokes radius for four test proteins (aldolase, chymotrypsinogen A, aldehyde oxidase and xanthine oxidase), from experimental data obtained with a Sephacryl S-300 column. A simple personal computer (PC) program written in standard basic, that is useful for this purpose, is included.

Acrylic Resins↗

PubMed1990

Occurrence and comparison of sulfite oxidase activity in mammalian tissues.

Tissue extracts from six mammalian species have been assayed for sulfite oxidase (sulfite: ferricytochrome c oxidoreductase, EC 1.8.3.1) activity with cytochrome c as electron acceptor. Our results show a large distribution of sulfite oxidase activity in mammalian tissues. Liver, kidney, and heart tissues exhibit high activities whereas brain, spleen, and testis show very low activities. No significant species dependence was observed for the activity of this enzyme.

Animals↗

PubMed1990

Purification of adenosine deaminase from chicken-egg yolk by affinity column chromatography.

Adenosine deaminase (adenosine aminohydrolase; E.C. 3.5.4.4) has been purified 4686-fold from egg yolk. The procedure developed was used to isolate the enzyme from eight chicken eggs. An easily prepared affinity column employing purine riboside was used as the final step in the purification. The method developed permits the rapid isolation and a high recovery of the protein. The specific activity of the enzyme preparation obtained is 81.4 mU/mg.

Adenosine Deaminase↗

PubMed1989

Use of implicit methods from general sensitivity theory to develop a systematic approach to metabolic control. I. Unbranched pathways.

It is shown that metabolic control theory (MCT), is its present form, is a particular case of general sensitivity theory, which studies the effects of parameter variations on the behavior of dynamic systems. It has been shown that metabolic control theory is obtained from this more general theory for the particular case of steady-state and linear relationships between velocities and enzyme concentrations. In such conditions the relationships between elasticities and flux control coefficients are easily obtained. These relationships are in the form of a matrix product constructed in a priori form. Relationships between combined response coefficients and concentration control coefficients are presented. The use of implicit methodology from general sensitivity theory provides a generalization of MCT, which is applied to unbranched pathways. For this particular case, provided the matrices have been properly constructed, the matrix of global properties (flux and concentration control coefficients) can be obtained by inversion of the matrix of local properties (elasticities). The theorems of MCT (concentration summation, flux summation, flux connectivity, and concentration connectivity) applicable for unbranched pathways are directly obtained by inspection of the matrix product. With these results, the present theoretical basis of MCT is extended with a more structured framework that allows a wider range of application. The results make clearer the relatedness of MCT to the more general approach provided by biochemical systems theory (BST).

Kinetics↗