Analysis Of Metabolic Systems Research Articles

Report on The First Maga Circe Conference on Metabolic Systems Analysis

Report on The First Maga Circe Conference on Metabolic Systems Analysis

In silico analysis of lactic acid secretion metabolism through the top-down approach: Effect of grouping in enzyme kinetics

A top-down approach is known to be a useful and effective technique for the design and analysis of metabolic systems. In this study, we have constructed a grouped metabolic network forLactococcus lactis under aerobic conditions using grouped enzyme kinetics. To test the usefulness of grouping work, a non-grouped system and grouped systems were compared quantitatively with each other. Here, grouped systems were designed as two groups according to the extent of grouping. The overall simulated flux values in grouped and non-grouped models had pretty similar distribution trends, but the details on flux ratio at the pyruvate branch point showed a little difference. This result indicates that our grouping technique can be used as a good model for complicated metabolic networks, however, for detailed analysis of metabolic network, a more robust mechanism should be considered. In addition to the data for the pyruvate branch point analysis, some major flux control coefficients were obtained in this research.

A cybernetic modeling framework for analysis of metabolic systems

We present a cybernetic perspective of metabolic systems, designed to take full account of regulatory processes, which profoundly influence the course of metabolism through dependence not only on the organism's genomic constitution, but also on abiotic environmental influences. The cybernetic perspective relies on proposing “mechanisms” of choice behavior by which biological systems drive enzyme syntheses and allosteric processes for chemical reactions that promote perceived local or global cellular objectives. This article is an exposition of the framework, attempting to show how experimental data can be used to facilitate model identification. Such an approach is proposed with the view to exploit detailed cellular measurements such as metabolite and mRNA or enzyme levels. We present a modular approach that originates with the metabolic network to be modeled and systematically breaks it down into smaller regulatory units which can be modeled using previously established cybernetic competitions [Kompala, D. S., Ramkrishna, D., Jansen, N. B., & Tsao, G. T. (1986). Investigation of bacterial growth on mixed substrates: experimental evaluation of cybernetic models. Biotechnology and Bioengineering, 28, 1044–1055; Straight, J. V., & Ramkrishna, D. (1990). Regulation of complex growth dynamics—substitutable and complementary processes. Abstracts of the papers of The American Chemical Society, 200, 4-BIOT]. Experimental data can assist in rapid formulation of numerous specific combinatorial alternatives suggested by the metabolic network. Methods are discussed within this continuously evolving framework for the identification of cybernetic models from data with illustrative examples.

Proteomic basis for the possible use of lymphocytes for metabolic screenings.

The advent of proteomics has provided a tool for the concomitant identification and determination of a large series of proteins using two-dimensional gel electrophoresis with subsequent mass spectrometrical analysis. We tried an approach to analyse the high abundance enzyme proteome of a lymphocytic cell line. Immortalised lymphocytes were grown in RPMI 1640 in the presence of glutamine, harvested and the 100,000 x g supernatant of the homogenate was applied on two-dimensional gel electrophoresis with subsequent in-gel digestion of protein spots and MALDI-TOF (Matrix-associated laser desorption/ionization mass spectroscopy) analysis of resulting peptides using specific software. A series of 57 metabolic enzymes were identified including enzymes of carbohydrate, amino acid, purine and intermediary metabolism. We are presenting a tool for the analysis of metabolic systems including enzyme deficiencies at the protein level with the advantage of unambiguous identification of proteins and thus complementing enzyme activity determinations.

Use of network analysis of metabolic systems in bioengineering

Basic ideas and recent developments in network analysis of metabolic systems and various applications of this analysis in bioengineering are reviewed. Central concepts are the null-space to the stoichiometry matrix and the elementary flux modes. The applicability of elementary-modes analysis in biotechnology is illustrated by the synthesis of the cyclooctadepsipeptides PF1022 in the fungus Mycelia sterilia. Network analysis is also useful in metabolic flux analysis. In particular, a procedure for finding out which reaction rates can be uniquely calculated in underdetermined reaction networks is outlined. The concept of 'enzyme subsets' is explained and its use for analysing genetic regulation is demonstrated. In particular, the correlation between expression data concerning the diauxic shift in yeast and the enzyme subsets in yeast metabolism is discussed.

Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems

The elucidation of organism-scale metabolic networks necessitates the development of integrative methods to analyze and interpret the systemic properties of cellular metabolism. A shift in emphasis from single metabolic reactions to systemically defined pathways is one consequence of such an integrative analysis of metabolic systems. The constraints of systemic stoichiometry, and limited thermodynamics have led to the definition of the flux space within the context of convex analysis. The flux space of the metabolic system, containing all allowable flux distributions, is constrained to a convex polyhedral cone in a high-dimensional space. From metabolic pathway analysis, the edges of the high-dimensional flux cone are vectors that correspond to systemically defined "extreme pathways" spanning the capabilities of the system. The addition of maximum flux capacities of individual metabolic reactions serves to further constrain the flux space and has led to the development of flux balance analysis using linear optimization to calculate optimal flux distributions. Here we provide the precise theoretical connections between pathway analysis and flux balance analysis allowing for their combined application to study integrated metabolic function. Shifts in metabolic behavior are calculated using linear optimization and are then interpreted using the extreme pathways to demonstrate the concept of pathway utilization. Changes to the reaction network, such as the removal of a reaction, can lead to the generation of suboptimal phenotypes that can be directly attributed to the loss of pathway function and capabilities. Optimal growth phenotypes are calculated as a function of environmental variables, such as the availability of substrate and oxygen, leading to the definition of phenotypic phase planes. It is illustrated how optimality properties of the computed flux distributions can be interpreted in terms of the extreme pathways. Together these developments are applied to an example network and to core metabolism of Escherichia coli demonstrating the connections between the extreme pathways, optimal flux distributions, and phenotypic phase planes. The consequences of changing environmental and internal conditions of the network are examined for growth on glucose and succinate in the face of a variety of gene deletions. The convergence of the calculation of optimal phenotypes through linear programming and the definition of extreme pathways establishes a different perspective for the understanding of how a defined metabolic network is best used under different environmental and internal conditions or, in other words, a pathway basis for the interpretation of the metabolic reaction norm.

Estudo comparativo de métodos para a predição do consumo máximo de oxigênio e limiar anaeróbio em atletas

A aplicação de uma bateria de testes de avaliação da aptidão física em laboratório envolve uma série de equipamentos sofisticados, principalmente quando o objetivo é a determinação da potência aeróbia (consumo máximo de oxigênio e limiar anaeróbio). Os equipamentos para obtenção desses índices são de alto custo financeiro e requerem profissionais com bom conhecimento, técnico e científico, para seu manuseio, além da impossibilidade de sua utilização para aplicar testes em grande escala. A análise da distância percorrida para determinado tempo ou, ainda, o tempo gasto para percorrer uma metragem prefixada, têm sido muito utilizados com o objetivo de estimar, ou refletir, a aptidão aeróbia, tanto em crianças como em adultos. A proposta deste estudo foi a de analisar a correlação entre os valores de consumo máximo de oxigênio (VO2 máx) obtidos num teste de campo, no caso o teste de Cooper (TC), com os determinados através de método direto, em laboratório, além da tentativa de validar este teste de campo e outro, denominado teste de 4.000 metros, na predição do limiar anaeróbio (LA). Foram avaliados 63 jogadores de futebol de campo, com idade variando entre 15 e 20 anos; todos os atletas foram submetidos a três testes, sendo o primeiro realizado em laboratório e os dois subseqüentes em pista de atletismo, no prazo máximo de sete dias. No primeiro teste, realizado em esteira rolante, determinou-se o VO2 máx e o limiar anaeróbio ventilatório (LAV), com o uso de um sistema metabólico computadorizado; nos testes subseqüentes, realizados em campo, seguiu-se, respectivamente, o protocolo preconizado por Cooper (TC) e uma corrida de 4.000 metros, em que se determinou o tempo gasto para o percurso determinado. Foi calculado o coeficiente de correlação linear de Pearson (r) e obtiveram-se como resultados: • A velocidade do LA mostrou correlação direta significante (r = 0,60 para p < 0,05) com a velocidade média no TC; • A velocidade do LA mostrou correlação direta significante (r = 0,74 para p < 0,05) com a velocidade média no T 4.000; • O VO2 máx determinado pelo método direto não mostrou correlação significante com o VO2 máx determinado através do TC (r = 0,23 para p < 0,05). Os resultados sugerem a imprecisão do teste de Cooper na predição do VO2 máx para essa população e a possibilidade da utilização de testes de campo, por exemplo, os realizados no presente estudo, para a predição do limiar anaeróbio. O teste de 4.000 metros apresentou maior precisão do que o teste de Cooper no intuito de predizer a velocidade do limiar anaeróbio.

Control analysis of metabolic systems involving quasi-equilibrium reactions

Reactions for which the rates are extremely sensitive to changes in the concentrations of variable metabolite concentrations contribute little to the control of biochemical reaction networks. Yet they do interfere with the calculation of the system's behaviour, both in terms of numerical integration of the rate equations and in terms of the analysis of metabolic control. We here present a way to solve this problem systematically for systems with time hierarchies. We identify the fast reactions and fast metabolites, group them apart from the other (“slow”) reactions and metabolites, and then apply the appropriate quasi-equilibrium condition for the fast subsystem. This then makes it possible to eliminate the fast reactions and their elasticity coefficients from the calculations, allowing the calculation of the control coefficients of the slow reactions in terms of the elasticity coefficients of the slow reactions. As expected, the elasticity coefficients of the fast reactions drop out of the calculations, and they are irrelevant for control at the time resolution of the steady state of the slow reactions. The analysis, when applied iteratively, is expected to be particularly valuable for the control analysis of living cells, where a time hierarchy exists, the fastest being at the level of enzyme kinetics and the slowest at gene expression.

The Fusion of Control Analysis and Temporal Analysis of Metabolic Systems

Metabolic control analysis and the study of the transient response of metabolic systems had coincident births in 1973. They developed along parallel lines until in 1989/90 their complete fusion occurred. It was evident that the control of the transient response of metabolism could be described in terms of general control properties, such as the flux and concentration control coefficients and elasticities. Consequently, it is possible to define temporal control coefficients which relate to the lifetimes of individual metabolite pools or to the total system temporal response. These control coefficients are readily expressed in terms of the flux and concentration control coefficients. Therefore, to analyse the control of metabolism is also to analyse its temporal response.

Time-Dependent Control of Metabolic Systems by External Effectors

The expression of elasticity coefficients for time-dependent enzyme inhibition/activation by an external effector was initially derived. Only a limited number of restrictive assumptions were used, for example, the enzyme was considered to obey Michaelis-Menten kinetics and effectors were taken to be competitive. Then, a simple metabolic system under the control of a time-dependent effector (inhibitor or activator) was analysed and the expression of the control coefficients were obtained. In addition, two numerical examples were used to represent the control coefficients as functions of time and effector concentration. The results indicate that the control coefficients vary in a relatively limited range of values; however, for certain intervals of time and of effector concentration local minima or major modifications of the coefficients may be recorded. The physiological importance of non-steady state analysis of metabolic systems controlled by external effectors was also discussed. It was stressed that the non-steady state treatment may contribute to creating a more realistic image of the metabolic control processes.

Molecular Probes for Analysis of Metabolic Systems in Chloroplasts : -As a Trial for New Style Research,Plant Molecular Physiology-

Molecular Probes for Analysis of Metabolic Systems in Chloroplasts : -As a Trial for New Style Research,Plant Molecular Physiology-

Temporal analysis of metabolic systems and its application to metabolite channelling

When a metabolic system undergoes a transition between steady states, the lag or transition time of the system is determined by the aggregated lifetimes of the metabolite pools. This allows the transition time, and hence the temporal responsiveness of the system, to be estimated from a knowledge of the starting and finishing steady states and obviates the need for dynamic measurements. The analysis of temporal response in metabolic systems may be integrated with the general field of metabolic control analysis by the definition of a temporal control coefficient (Cei tau) in terms of flux and concentration control coefficients. The temporal control coefficient exhibits summation and other properties analogous to the flux and concentration control coefficients. For systems in which static metabolite channels exist, the major kinetic advantage of channelling is a reduction in pool sizes and, as a result, a more rapid system response reflected in a reduced transition time. The extent of the channelling advantage may therefore be assessed from a knowledge of the system transition time. This reveals that no channelling advantage is achieved at high enzyme concentrations (i.e., comparable to Km) or, in the case of 'leaky' channels, where rapid equilibrium kinetic mechanisms obtain. In the case of a perfect channel with no leakage and direct transfer of metabolite between adjacent enzyme active sites, the transition time is minimized and equal to the lifetime of the enzyme-substrate complex.

Integration of temporal analysis and control analysis of metabolic systems

A theory is developed that integrates approaches to the analysis of pathway transient response and metabolic control analysis. A Temporal Control Coefficient is defined that is a measure of the system's transient response to modulation of enzyme activity or concentration. The approach allows for the analysis of the establishment of a steady state from rest, of the system's 'agility' of response to minor perturbations of a pre-existing steady state and of the macroscopic transition between steady states. In the last-mentioned case it is shown that, like the transient time itself, the control of transient response retains the property of independence from the mechanism of the transition. In consequence, the Temporal Control Coefficient can be defined in terms of the control properties of the initial and final states alone without reference to the mechanism of transition. A summation property is shown to apply to the Temporal Control Coefficients in each case. Connectivity relationships between elasticities and Temporal Control Coefficients are also established.

Analysis of metabolic systems with complex slow and fast dynamics

Analysis of metabolic systems with complex slow and fast dynamics

Analysis of metabolic systems with complex slow and fast dynamics

We briefly review the results of other authors concerning the analysis of systems with time hierarchy, especially the Tikhonov theorem. A theorem, recently proved by the authors, making possible rigorous analysis of systems with complex fast dynamics is stated and discussed. A model example of a simple enzymatic reaction with product activation and slow (genetically driven) enzyme turnover is rigorously studied. It is shown that even in such a simple model there exist certain regions of parameters for which fast variables oscillate. Thus the classical Tikhonov theorem is not applicable here and we are forced to use another method--for example the author's presented theorem--or a purely numerical solution. These two methods are compared.

Thermodynamics of the control of metabolism

A theory is presented, describing the control analysis of metabolic systems in terms of Gibbs free energies, extending earlier work of Kacser and Burns (25), and Heinrich and Rapoport (29). It is shown that relationships exist between flux control coefficients (the degree to which enzymes control steady-state fluxes) and free-energy elasticity coefficients, defined as the fractional change in the rate of a reaction induced by a standard change in one free-energy difference, while all the other free-energy differences are kept constant. Application of this extended control analysis to some biochemical reactions, including proton translocation, demonstrates that 1. Problems arising in the control analysis because of conservation (sum concentration of substrate and product constant) can be circumvented. 2. Although free-energy elasticity coefficients are maximal when the reaction is close to equilibrium, they can also be significant when the reaction is not close to equilibrium. 3. Problems in the control analysis caused by compartmentation can be resolved by defining control parameters that refer to the organelle as a whole. 4. These latter control parameters obey the above-mentioned relationships.

Dynamics, regulation, block description and optimal performance of cellular metabolism in open conditions: Outline of a unifying concept

AbstractThe paper offers a survey of theoretical concepts for the analysis of metabolic systems in open connditions such as realized in cultures of microbial cells. The dynamics and regulation of metabolism within the cell is condensed into a block description of the system to which global performance and design criteria are applied.

Control of the Flux in the Arginine Pathway of Neurospora crassa: Effects of Co-ordinate Changes of Enzyme Concentration

The flux to arginine was determined in growing mycelium of Neurospora crassa carrying the aga mutation, by measuring the exponential growth rate and the arginine content of the free pool and that in protein. Derepression of the enzymes in the pathway by a factor of about three resulted in a 14% increase in the flux. Using a mutant (cpc-1), which affected the cross-pathway control, the pathway enzymes were found to have about threefold lower activities. This resulted in a 16% decrease in the measured flux. The effect of arginine acting as a feedback inhibitor of acetylglutamate kinase was estimated in an arg-12 mutant by varying the steady-state arginine concentration using histidine as a competitive inhibitor of the citrulline uptake. It is concluded that the feedback loop is mainly responsible for the small response of the flux to the large coordinate changes in the pathway enzymes. The results are discussed in terms of control analysis of metabolic systems.

Recent advances in molecular pathology isotopic analysis of metabolic systems: Part II

Recent advances in molecular pathology isotopic analysis of metabolic systems: Part II