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IEE Proceedings - Systems Biology

Volume 153, Issue 5, September 2006

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Volume 153, Issue 5

September 2006

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  • 12th BTK Meeting: ‘Systems Biology: redefining BioThermoKinetics’

    • Editorial: 12th BTK Meeting: ‘Systems Biology: redefining BioThermoKinetics’
      Summation theorems for flux and concentration control coefficients of dynamic systems
      • Author(s): R. Conradie ; H.V. Westerhoff ; J.M. Rohwer ; J.-H.S. Hofmeyr ; J.L. Snoep
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 314 –317
      • DOI:  10.1049/ip-syb:20060024
      • Type: Article
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      • p. 314 –317 (4)
        Metabolic control analysis (MCA) was developed to quantify how system variables are affected by parameter variations in a system. In addition, MCA can express the global properties of a system in terms of the individual catalytic steps, using connectivity and summation theorems to link the control coefficients to the elasticity coefficients. MCA was originally developed for steady-state analysis and not all summation theorems have been derived for dynamic systems. A method to determine time-dependent flux and concentration control coefficients for dynamic systems by expressing the time domain as a function of percentage progression through any arbitrary fixed interval of time is reported. Time-dependent flux and concentration control coefficients of dynamic systems, provided that they are evaluated in this novel way, obey the same summation theorems as steady-state flux and concentration control coefficients, respectively.
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      Time-dependent hierarchical regulation analysis: deciphering cellular adaptation
      • Author(s): F.J. Bruggeman ; J. de Haan ; H. Hardin ; J. Bouwman ; S. Rossell ; K. van Eunen ; B.M. Bakker ; H.V. Westerhoff
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 318 –322
      • DOI:  10.1049/ip-syb:20060027
      • Type: Article
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      • p. 318 –322 (5)
        Cells adapt to changes in their environment by the concerted action of many different regulatory mechanisms. Examples of such mechanisms are feedback inhibition by intermediates of metabolism, covalent modification of enzymes and changes in the abundance of mRNAs and proteins. These mechanisms act in parallel at different levels in the cellular hierarchy while regulating a single process. Existing hierarchical regulation analysis determines the relative importance of these mechanisms when the cell regulates a transition from one steady-state to another. Here, the analysis is extended to the regulation of time-dependent phenomena, for which two methods are introduced and illustrated with a kinetic model incorporating transcription and translation of metabolic enzymes.
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      Metabolic control analysis for large changes: extension to variable elasticity coefficients
      • Author(s): L. Acerenza  and  F. Ortega
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 323 –326
      • DOI:  10.1049/ip-syb:20060004
      • Type: Article
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      • p. 323 –326 (4)
        Modular approaches are powerful systems biology strategies to deal with complexity. They consist in lumping conceptually all that is irrelevant to the problem under study, leaving explicit the portions of interest. Modular (or top-down) metabolic control analysis is a theoretical and experimental approach to study the sensitivity properties of complex metabolic systems. Initially, it was conceived for infinitesimal changes but, recently, it started to be developed for large metabolic changes. A central result of this approach is that the systemic properties, represented by control coefficients, can be expressed as a function of the properties of isolated modules, the elasticity coefficients. Here we extend the theory for large changes to the case that the elasticity coefficients depend on the extent of the change. The novel theory is used to analyse experimental data related to the control of glycolytic flux in Escherichia coli. Our analysis shows that the pattern of control for large changes is quantitatively and qualitatively different from the one obtained applying the infinitesimal treatment.
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      Conditions for effective allosteric feedforward and feedback in metabolic pathways
      • Author(s): J.-H.S. Hofmeyr ; J.M. Rohwer ; J.L. Snoep
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 327 –331
      • DOI:  10.1049/ip-syb:20060019
      • Type: Article
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      • p. 327 –331 (5)
        Whether an allosteric feedback or feedforward modifier actually has an effect on the steady-state properties of a metabolic pathway depends not only on the allosteric modifier effect itself, but also on the control properties of the affected allosteric enzyme in the pathway of which it is part. Different modification mechanisms are analysed: mixed inhibition, allosteric inhibition and activation of the reversible Monod–Wyman–Changeux and reversible Hill models. In conclusion, it is shown that, whereas a modifier effect on substrate and product binding (specific effects) can be an effective negative feedback mechanism, it is much less effective as a positive feedforward mechanism. The prediction is that catalytic effects that change the apparent limiting velocity would be more effective in feedforward activation.
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      How to keep glycolytic metabolite concentrations constant when ATP/ADP and NADH/NAD+ change
      • Author(s): P. Liguzinski  and  B. Korzeniewski
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 332 –334
      • DOI:  10.1049/ip-syb:20060005
      • Type: Article
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      • p. 332 –334 (3)
        Glycolytic flux may increase over 100 times in skeletal muscle during rest-to-work transition, whereas glycolytic metabolite concentrations remain relatively constant. This constancy cannot be explained by an identical direct activation of all glycolytic enzymes because the concentrations of ATP, ADP, AMP, Pi, NADH and NAD+, modulators of the activity of different glycolytic enzymes, change. It is demonstrated in the present in silico study that a perfect homeostasis of glycolytic metabolite concentrations can be achieved if glycolysis is divided into appropriate blocks of enzymes that are directly activated to a different extent in order to compensate the effect of the modulators.
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      Comparing the regulatory behaviour of two cooperative, reversible enzyme mechanisms
      Evaluation of a simplified generic bi-substrate rate equation for computational systems biology
      • Author(s): J.M. Rohwer ; A.J. Hanekom ; C. Crous ; J.L. Snoep ; J.-H.S. Hofmeyr
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 338 –341
      • DOI:  10.1049/ip-syb:20060026
      • Type: Article
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      • p. 338 –341 (4)
        The evaluation of a generic simplified bi-substrate enzyme kinetic equation, whose derivation is based on the assumption of equilibrium binding of substrates and products in random order, is described. This equation is much simpler than the mechanistic (ordered and ping-pong) models, in that it contains fewer parameters (that is, no Ki values for the substrates and products). The generic equation fits data from both the ordered and the ping-pong models well over a wide range of substrate and product concentrations. In the cases where the fit is not perfect, an improved fit can be obtained by considering the rate equation for only a single set of product concentrations. Due to its relative simplicity in comparison to the mechanistic models, this equation will be useful for modelling bi-substrate reactions in computational systems biology.
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      Experimental evidence for allosteric modifier saturation as predicted by the bi-substrate Hill equation
      • Author(s): A.J. Hanekom ; J.-H.S. Hofmeyr ; J.L. Snoep ; J.M. Rohwer
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 342 –345
      • DOI:  10.1049/ip-syb:20060029
      • Type: Article
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      • p. 342 –345 (4)
        The cooperative enzyme reaction rates predicted by the bi-substrate Hill equation and the bi-substrate Monod-Wyman-Changeux (MWC) equation when allosterically inhibited are compared in silico. Theoretically, the Hill equation predicts that when the maximum inhibitory effect at a certain substrate condition has been reached, an increase in allosteric inhibitor concentration will have no effect on reaction rate, that is the Hill equation shows allosteric inhibitor saturation. This saturating inhibitory effect is not present in the MWC equation. Experimental in vitro data for pyruvate kinase, a bi-substrate cooperative enzyme that is allosterically inhibited, are presented. This enzyme also shows inhibitor saturation, and therefore serves as experimental evidence that the bi-substrate Hill equation predicts more realistic allosteric inhibitor behaviour than the bi-substrate MWC equation.
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      Control analysis of the importance of phosphoglycerate enolase for metabolic fluxes in Lactococcus lactis subsp. lactis IL1403
      • Author(s): B. Koebmann ; C. Solem ; P.R. Jensen
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 346 –349
      • DOI:  10.1049/ip-syb:20060022
      • Type: Article
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      • p. 346 –349 (4)
        The glycolytic enzyme phosphoglycerate enolase (PGE) catalyses the step from 2-phosphoglycerate to phosphoenolpyruvate in glycolysis. A control analysis of PGE on growth, glycolytic flux and product formation in Lactococcus lactis subsp. lactis IL1403 is presented. A library of strains with a modulated expression of PGE from 36 to 232% relative to wildtype level was constructed. Selected strains were studied with respect to growth, glycolytic flux and product formation in a chemically defined medium. On the basis of these data, flux control coefficients of PGE on the respective fluxes were calculated. At wildtype level, PGE was found to have no significant flux control on growth, glycolytic flux or product formation, but at 36% of PGE activity relative to wildtype, the flux control on the growth rate was estimated to be CPGEJµ≃0.7, on the glycolytic flux CPGEJg≃0.8, on lactate formation CPGEJlactate≃1.3, on formate formation CPGEJformate≃0.5 and on acetate formation CPGEJacetate≃0.25. These flux control coefficients show that the metabolism of L. lactis subsp. lactis IL1403 becomes slightly more mixed acid at reduced PGE activities. Estimation of the relative turnover of PGE indicates that excess capacity of PGE in L. lactis IL1403 may be as low as twofold.
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      Contribution of ATP synthase to stimulation of respiration by Ca2+ in heart mitochondria
      • Author(s): R. Baniene ; Z. Nauciene ; S. Maslauskaite ; G. Baliutyte ; V. Mildazienė
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 350 –353
      • DOI:  10.1049/ip-syb:20060009
      • Type: Article
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      • p. 350 –353 (4)
        A variety of experimental conditions were applied with the aim to estimate the correlation between the contribution of ATP synthase to the respiratory flux control and the calcium-induced activation of succinate oxidation in heart mitochondria isolated from rat, rabbit and guinea pig. The sensitivity of respiration in heart mitochondria to the decrease in temperature from 37°C to 28°C decreases in the order rabbit>guinea pig>rat. Ca2+ effect on succinate oxidation rate in state 3 respiration was species- and temperature-dependent and ranged from 0 (rat, 37°C) to +44% (rabbit, 28°C). For mitochondria from all experimental animals, the increase of Ca2+ in physiological range of concentration did not change state 2 respiration rate, and the stimulatory effect of Ca2+ on state 3 respiration was more pronounced at 28°C than at 37°C. The respiratory subsystem was sensitive to Ca2+ ions only in rabbit heart mitochondria. A high positive correlation between Ca2+ ability to stimulate succinate oxidation in state 3 and the control exerted by ATP synthase over the respiratory flux provides argument confirming stimulation of ATP synthase by Ca2+ ions.
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      Evolutionary changes of metabolic networks and their biosynthetic capacities
      • Author(s): O. Ebenhöh ; T. Handorf ; D. Kahn
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 354 –358
      • DOI:  10.1049/ip-syb:20060014
      • Type: Article
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      • p. 354 –358 (5)
        The metabolic networks of different species show a large variety in their structural design. In this work, the evolution of functional properties of metabolism in relation with metabolic network structure is investigated. The metabolism of ancestral species is inferred from the metabolism of contemporary species using a Bayesian network model for metabolism evolution. Subsequently, these networks are analysed with the recently developed method of network expansion. This method allows for a structural analysis of metabolic networks as well as a quantification of network functions in terms of their synthesising capacities when they are provided with certain external resources. The evolutionary dynamics of one particular network function: the metabolic expansion of glucose is investigated.
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      Hierarchy of metabolic compounds based on their synthesising capacity
      • Author(s): T. Handorf ; O. Ebenhöh ; D. Kahn ; R. Heinrich
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 359 –363
      • DOI:  10.1049/ip-syb:20060021
      • Type: Article
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      • p. 359 –363 (5)
        The concept of scopes is applied to analyse large metabolic networks. Scopes are defined as sets of metabolites that can be synthesised by a metabolic network when it is provided with given seeds (Sets of initial metabolic compounds). Thus, scopes represent synthesising capacities of the seeds in the network. A hierarchy is discussed in the sense that compounds, which are part of the scope of another compound, possess scopes themselves that are subsets of the former scope. This hierarchy is analysed by means of a directed acyclic graph. Using a simple chemical model, it is found that this hierarchy contains specific structures that can, to a large extent, be explained by the chemical composition of the participating compounds. In this way, it represents a new kind of map of metabolic networks, arranging the metabolic compounds according to their chemical capacity.
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      Expansion of signal transduction networks
      • Author(s): B. Binder ; O. Ebenhöh ; K. Hashimoto ; R. Heinrich
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 364 –368
      • DOI:  10.1049/ip-syb:20060030
      • Type: Article
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      • p. 364 –368 (5)
        Signal transduction networks of different cell types show a large variety in their structural design. In this paper, basic structural properties of signal transduction networks are investigated. For this, such networks with the recently developed method of network expansion are analysed. This method allows for a structural analysis of networks by calculating signal expansion profiles when provided with certain compounds, for example growth factors, inactive kinases and so on (seed compounds), to initiate such an expansion. The presented results may put forth valuable hints on the evolution of signalling networks.
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      Pathway classification of TCA cycle
      • Author(s): S. Pérès ; M. Beurton-Aimar ; J.P. Mazat
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 369 –371
      • DOI:  10.1049/ip-syb:20060013
      • Type: Article
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      • p. 369 –371 (3)
        The structural analysis of large metabolic networks exhibits a combinatorial explosion of elementary modes. A new method of classification has been developed [called aggregation around common motif (ACoM)], which groups elementary modes into classes with similar substructures. This method is applied to the tricarboxylic acid cycle and metabolite carriers. The analysis of this network evidences a great number of elementary flux modes (204) despite the low number of reactions (23). The ACoM is used to class these elementary modes in a low number of sets (8) with biological meanings.
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      Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism
      • Author(s): J. Ohta
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 372 –374
      • DOI:  10.1049/ip-syb:20060018
      • Type: Article
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      • p. 372 –374 (3)
        An approach for analysis of biological networks is proposed. In this approach, named the connectivity matrix (CM) method, all the connectivities of interest are expressed in a matrix. Then, a variety of analyses are performed on GNU Octave or Matlab. Each node in the network is expressed as a row vector or numeral that carries information defining or characterising the node itself. Information about connectivity itself is also expressed as a row vector or numeral. Thus, connection of node n1 to node n2 through edge e is expressed as [n1, n2, e], a row vector formed by the combination of three row vectors or numerals, where n1, n2 and e indicate two different nodes and one connectivity, respectively. All the connectivities in any given network are expressed as a matrix, CM, each row of which corresponds to one connectivity. Using this CM method, inter-metabolite atom-level connectivity is investigated in a model metabolic network composed of the reactions for glycolysis, oxidative decarboxylation of pyruvate, citric acid cycle, pentose phosphate pathway and gluconeogenesis.
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      ScrumPy: metabolic modelling with Python
      • Author(s): M.G. Poolman
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 375 –378
      • DOI:  10.1049/ip-syb:20060010
      • Type: Article
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      • p. 375 –378 (4)
        ScrumPy is a software package used for the definition and analysis of metabolic models. It is written using the Python programming language that is also used as a user interface. ScrumPy has features for both kinetic and structural modelling, but the emphasis is on structural modelling and those features of most relevance to analysis of large (genome-scale) models. The aim is at describing ScrumPy's functionality to readers with some knowledge of metabolic modelling, but implementation, programming and other computational details are omitted. ScrumPy is released under the Gnu Public Licence, and available for download from http://mudshark.brookes.ac.uk/ScrumPy.
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      Challenges to be faced in the reconstruction of metabolic networks from public databases
      • Author(s): M.G. Poolman ; B.K. Bonde ; A. Gevorgyan ; H.H. Patel ; D.A. Fell
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 379 –384
      • DOI:  10.1049/ip-syb:20060012
      • Type: Article
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      • p. 379 –384 (6)
        In the post-genomic era, the biochemical information for individual compounds, enzymes, reactions to be found within named organisms has become readily available. The well-known KEGG and BioCyc databases provide a comprehensive catalogue for this information and have thereby substantially aided the scientific community. Using these databases, the complement of enzymes present in a given organism can be determined and, in principle, used to reconstruct the metabolic network. However, such reconstructed networks contain numerous properties contradicting biological expectation. The metabolic networks for a number of organisms are reconstructed from KEGG and BioCyc databases, and features of these networks are related to properties of their originating database.
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      Software tools that facilitate kinetic modelling with large data sets: an example using growth modelling in sugarcane
      • Author(s): L. Uys ; J.-H.S. Hofmeyr ; J.L. Snoep ; J.M. Rohwer
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 385 –389
      • DOI:  10.1049/ip-syb:20060050
      • Type: Article
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      • p. 385 –389 (5)
        A solution to manage cumbersome data sets associated with large modelling projects is described. A kinetic model of sucrose accumulation in sugarcane is used to predict changes in sucrose metabolism with sugarcane internode maturity. This results in large amounts of output data to be analysed. Growth is simulated by reassigning maximal activity values, specific to each internode of the sugarcane plant, to parameter attributes of a model object. From a programming perspective, only one model definition file is required for the simulation software used; however, the amount of input data increases with each extra internode that is modelled, and likewise the amount of output data that is generated also increases. To store, manipulate and analyse these data, the modelling was performed from within a spreadsheet. This was made possible by the scripting language Python and the modelling software PySCeS through an embedded Python interpreter available in the Gnumeric spreadsheet program.
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      Molecular modelling of KATP channel blockers-ADP/ATP carrier interactions
      • Author(s): A. Ziemys ; A. Toleikis ; D.M. Kopustinskiene
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 390 –393
      • DOI:  10.1049/ip-syb:20060007
      • Type: Article
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      • p. 390 –393 (4)
        The modelling of molecule–molecule interactions has been widely accepted as a tool for drug discovery and development studies. However, this powerful technique is unappreciated in physiological and biochemical studies, where it could be extremely useful for understanding the mechanisms of action of various compounds in cases when experimental data are controversial due to complexity of the investigated systems. In this study, based on the biochemical data suggesting involvement of mitochondrial ADP/ATP carrier in K+ and H+ transport to mitochondrial matrix molecular modelling is applied to elucidate the possible interactions between the ADP/ATP carrier and its putative ligands – KATP channel blockers glybenclamide, tolbutamide and 5-hydroxydecanoate. Results revealed that KATP channel blockers could bind to the specific location proximal to H1, H4, H5 and H6 transmembrane helices within the cavity of the ADP/ATP carrier. Analysis of the predicted binding site suggests that KATP channel blockers could interfere with both the ADP/ATP translocation and possible cation flux through the ADP/ATP carrier, and supports the hypothesis that the ADP/ATP carrier is a target of KATP channel modulators.
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      Brownian dynamic model of the glycine receptor chloride channel: effect of the position of charged amino acids on ion membrane currents
      • Author(s): S.E. Boronovsky ; I.P. Seraya ; Ya.R. Nartsissov
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 394 –397
      • DOI:  10.1049/ip-syb:20060008
      • Type: Article
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      • p. 394 –397 (4)
        Glycine is the major inhibitory neurotransmitter in the brainstem and spinal cord, where it participates in a variety of motor and sensory functions. It activates a special type of ligand-gated membrane receptor, which provides for Cl− ion conductance of the neuronal membrane. Computer simulations of a single-channel current through this receptor have been carried out on the basis of Brownian (Langevin) dynamics. The dependence of the currents on pore diameter and the location of the charged amino acid residues have been obtained. It has been shown that the presence and the symmetry of the filter-forming residues determined not only the ion-selectivity of the channel but also increased transmembrane anion current.
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      Is there an optimal ribosome concentration for maximal protein production?
      Organisation of B-cell receptors on the cell membrane
      • Author(s): D. Iber  and  T. Gruhn
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 401 –404
      • DOI:  10.1049/ip-syb:20060015
      • Type: Article
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      • p. 401 –404 (4)
        B-cell receptors (BCRs) have been reported to organise into oligomeric clusters on the B-cell surface, and mutations, that are likely to interfere with such clustering, result in B-cell unresponsiveness. This has led to the suggestion that pre-formed BCR clusters may be crucial for B-cell signalling. However, neither the size nor the fraction of BCRs organised in such clusters have yet been determined in experiments. Hence, the authors use a statistical approach to predict the membrane organisation of BCRs, based on available experimental data. For physiological parameters, most BCRs will organise into supramolecular polymers that comprise about five receptors where the non-covalent interactions are mediated by the IgH transmembrane helix. A reduction in the density of IgM to 2–5% of the normal density, a characteristic of anergic MD4 B cells, strongly reduces IgM polymerisation, and it is suggested that impaired BCR clustering may be responsible for the unresponsiveness of anergic B cells.
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      Computational model of excitable cell indicates ATP free energy dynamics in response to calcium oscillations are undampened by cytosolic ATP buffers
      • Author(s): R.G.P.M. van Stiphout ; N.A.W. van Riel ; P.J. Verhoog ; P.A.J. Hilbers ; K. Nicolay ; J.A.L. Jeneson
      • Source: IEE Proceedings - Systems Biology, Volume 153, Issue 5, p. 405 –408
      • DOI:  10.1049/ip-syb:20060017
      • Type: Article
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      • p. 405 –408 (4)
        Mitochondria in excitable cells are recurrently exposed to pulsatile calcium gradients that activate cell function. Rapid calcium uptake by the mitochondria has previously been shown to cause uncoupling of oxidative phosphorylation. To test (i) if periodic nerve firing may cause oscillation of the cytosolic thermodynamic potential of ATP hydrolysis and (ii) if cytosolic adenylate (AK) and creatine kinase (CK) ATP buffering reactions dampen such oscillations, a lumped kinetic model of an excitable cell capturing major aspects of the physiology has been developed. Activation of ATP metabolism by low-frequency calcium pulses caused large oscillation of the cytosolic, but not mitochondrial ATP/ADP, ratio. This outcome was independent of net ATP synthesis or hydrolysis during mitochondrial calcium uptake. The AK/CK ATP buffering reactions dampened the amplitude and rate of cytosolic ATP/ADP changes on a timescale of seconds, but not milliseconds. These model predictions suggest that alternative sources of capacitance in neurons and striated muscles should be considered to protect ATP-free energy-driven cell functions.
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