Abstract
This chapter describes the basic principles of Metabolic Control Analysis (MCA) which is a quantitative methodology to evaluate the importance and relative contribution of individual metabolic steps in the overall functioning of a particular system. The control on the flux through a metabolic pathway or subsystem can be quantified by the control coefficients of the individual enzymes or components which reflects the extent to which the component is rate-limiting. The perturbation of an individual step is measured by its elasticity coefficient. The effect of perturbation of a single step on the entire pathway or subsystemis, in turn, measured by the response coefficient. Differential control analysis can be used to compare flux through a single metabolic pathway in a pathogen with the same pathway in its host to identify uniquely vulnerable steps with the greatest potential for specifically inhibiting flux through the pathogen metabolic pathway. The utility of this methodology is illustrated with the glycolysis in Trypanosomes and with oncogenic signaling.
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References
Westerhoff HV, Palsson BO (2004) The evolution of molecular biology into systems biology. Nat Biotechnol 22: 1249–1252
Bakker BM, Assmus HE, Bruggeman F, Haanstra JR, Klipp E, Westerhoff H (2002) Network-based selectivity of antiparasitic inhibitors. Mol Biol Rep 29: 1–5
Alberghina L, Westerhoff HV (2005) Systems Biology. Definitions and Perspectives, Springer, Berlin, Germany
Olivier BG, Snoep JL (2004) Web-based kinetic modelling using JWS Online. Bioinformatics 20: 2143–2144
Westerhoff HV (2001) The silicon cell, not dead but live! Metab Eng 3: 207–210
Snoep JL (2005) The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level. Curr Opin Biotechnol 16: 336–343
Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Dam K, Westerhoff HV et al (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 267: 5313–5329
Tyson JJ, Chen K, Novak B (2001) Network dynamics and cell physiology. Nat Rev Mol Cell Biol 2: 908–916
Teusink B, Walsh MC, van Dam K, Westerhoff HV (1998) The danger of metabolic pathways with turbo design. Trends Biochem Sci 23: 162–169
Bakker BM, Mensonides FI, Teusink B, van Hoek P, Michels PA, Westerhoff HV (2000) Compartmentation protects trypanosomes from the dangerous design of glycolysis. Proc Natl Acad Sci USA 97: 2087–2092
Shulman RG, Rothman DL (2005) Metabolomics by in vivo NMR. John Wiley & Sons, Hoboken, NJ, USA
Bruggeman FJ, Boogerd FC, Westerhoff HV (2005) The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica. Febs J 272: 1965–1985
Kacser H, Burns JA (1973) The control of flux. Symp Soc Exp Biol 27: 65–104
Heinrich R, Rapoport TA (1974) A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur J Biochem 42: 89–95
Westerhoff HV, Van Dam K (1987) Thermodynamics and Control of Biological Free-Energy Transduction. Elsevier, Amsterdam, The Netherlands
Fell DA (1992) Metabolic control analysis: a survey of its theoretical and experimental development. Biochem J 286: 313–330
Fell DA (1997) Understanding the control of metabolism. Portland Press, London, UK
Heinrich R, Schuster S (1996) The regulation of cellular systems. Chapman & Hall, New York, USA
Kholodenko BN, Westerhoff HV (1993) Metabolic channelling and control of the flux. FEBS Lett 320: 71–74
Groen AK, Wanders RJ, Westerhoff HV, van der Meer R, Tager JM (1982) Quantification of the contribution of various steps to the control of mitochondrial respiration. J Biol Chem 257: 2754–2757
Bakker BM, Michels PA, Opperdoes FR, Westerhoff HV (1999) What controls glycolysis in bloodstream form Trypanosoma brucei? J Biol Chem 274: 14551–14559
Hornberg JJ, Bruggeman FJ, Binder B, Geest CR, Bij de Vaate AJM, Lankelma J, Heinrich R, Westerhoff HV (2005) Principles behind the multifarious control of signal transduction: ERK phosphorylation and kinase/phosphatase control. FEBS J 272: 244–258
Lee E, Salic A, Kruger R, Heinrich R, Kirschner MW (2003) The roles of APC and axin derived from experimental and theoretical analysis of the Wnt pathway. PLoS Biology 1: e10
Ihekwaba AE, Broomhead DS, Grimley RL, Benson N, Kell DB (2004) Sensitivity analysis of parameters controlling oscillatory signalling in the NF-kB pathway: the roles of IKK and IkBa. Syst Biol 1: 93–103
Hornberg JJ, Binder B, Bruggeman FJ, Schoeberl B, Heinrich R, Westerhoff HV (2005) Control of MAPK signalling: from complexity to what really matters. Oncogene 24: 5533–5542
Peletier MA, Westerhoff HV, Kholodenko BN (2003) Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law. J Theor Biol 225: 477–487
Schuster S, Kahn D, Westerhoff HV (1993) Modular analysis of the control of complex metabolic pathways. Biophys Chem 48: 1–17
Kahn D, Westerhoff HV (1991) Control theory of regulatory cascades. J Theor Biol 153: 255–285
Westerhoff HV, Koster JG, Van Workum M, Rudd KE (1989) On the control of gene expression. In: A Cornish-Bowden, ML Cardenas (eds): Control ofmetabolic processes. Plenum Press, New York, USA. pp. 399–413
Bruggeman F, Westerhoff H, Hoek J, Kholodenko B (2002) Modular response analysis of cellular regulatory networks. J Theor Biol 218: 507
Kholodenko BN (1988) How do external parameters control fluxes and concentrations of metabolites? An additional relationship in the theory of metabolic control. FEBS Lett 232: 383–386
Bakker BM, Westerhoff HV, Opperdoes FR, Michels PA (2000) Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs. Mol Biochem Parasitol 106: 1–10
Rigoulet M, Averet N, Mazat JP, Guerin B, Cohadon F (1988) Redistribution of the flux-control coefficients in mitochondrial oxidative phosphorylations in the course of brain edema. Biochim Biophys Acta 932: 116–123
Mazat JP, Rossignol R, Malgat M, Rocher C, Faustin B, Letellier T (2001) What do mitochondrial diseases teach us about normal mitochondrial functions that we already knew: threshold expression of mitochondrial defects. Biochim Biophys Acta 1504: 20–30
Verlinde CL, Hannaert V, Blonski C, Willson M, Perie JJ, Fothergill-Gilmore LA, Opperdoes FR, Gelb MH, Hol WG, Michels PA (2001) Glycolysis as a target for the design of new anti-trypanosome drugs. Drug Resist Updat 4: 50–65
Eisenthal R, Cornish-Bowden A (1998) Prospects for antiparasitic drugs. The case of Trypanosoma brucei, the causative agent of African sleeping sickness. J Biol Chem 273: 5500–5505
Bakker BM, Michels PA, Opperdoes FR, Westerhoff HV (1997) Glycolysis in bloodstream from Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes. J Biol Chem 272: 3207–3215
Bakker BM, Walsh MC, ter Kuile BH, Mensonides FI, Michels PA, Opperdoes FR, Westerhoff HV (1999) Contribution of glucose transport to the control of the glycolytic flux in Trypanosoma brucei. Proc Natl Acad Sci USA 96: 10098–10103
Albert MA, Haanstra JR, Hannaert V, Van Roy J, Opperdoes FR, Bakker BM, Michels PA (2005) Experimental and in silico analyses of glycolytic flux control in bloodstream from Trypanosoma brucei. J Biol Chem 280: 28306–28315
Mulquiney PJ, Kuchel PW (1999) Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: equations and parameter refinement. Biochem J 342 Pt 3: 581–596
Joshi A, Palsson BO (1989) Metabolic dynamics in the human red cell. Part I-A comprehensive kinetic model. J Theor Biol 141: 515–528
Schuster R, Holzhutter HG (1995) Use of mathematical models for predicting the metabolic effect of large-scale enzyme activity alterations. Application to enzyme deficiencies of red blood cells. Eur J Biochem 229: 403–418
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR (2004) A census of human cancer genes. Nat Rev Cancer 4: 177–183
Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100: 57–70
Vogelstein B, Kinzler KW (2004) Cancer genes and the pathways they control. Nat Med 10: 789–799
Gatenby RA, Maini PK (2003) Mathematical oncology: cancer summed up. Nature 421: 321
Kitano H (2003) Cancer robustness: tumour tactics. Nature 426: 125
Butcher EC, Berg EL, Kunkel EJ (2004) Systems biology in drug discovery. Nat Biotechnol 22: 1253–1259
Christopher R, Dhiman A, Fox J, Gendelman R, Haberitcher T, Kagle D, Spizz G, Khalil IG, Hill C (2004) Data-driven computer simulation of human cancer cell. Ann NY Acad Sci 1020: 132–153
Khalil IG, Hill C (2005) Systems biology for cancer. Curr Opin Oncol 17: 44–48
Hornberg JJ, Bruggeman FJ, Westerhoff HV, Lankelma J (2006) Cancer: A Systems Biology Disease. Biosystems 83: 81–90
Alberghina L, Chiaradonna F, Vanoni M (2004) Systems biology and the molecular circuits of cancer. Chembiochem 5: 1322–1333
DeVita VT, Hellman S, Rosenberg SA (2001) Cancer: Principles & Practice of Oncology. 6th edition. Lippincott Williams & Wilkins, Philidelphia, PA, USA
Krause DS, Van Etten RA (2005) Tyrosine kinases as targets for cancer therapy. N Engl J Med 353: 172–187
Mendelsohn J, Baselga J (2000) The EGF receptor family as targets for cancer therapy. Oncogene 19: 6550–6565
Sebolt-Leopold JS, Herrera R (2004) Targeting the mitogen-activated protein kinase cascade to treat cancer. Nat Rev Cancer 4: 937–947
Shawver LK, Slamon D, Ullrich A (2002) Smart drugs: tyrosine kinase inhibitors in cancer therapy. Cancer Cell 1: 117–123
Schoeberl B, Eichler-Jonsson C, Gilles ED, Muller G (2002) Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol 20: 370–375
Chiaradonna F, Magnani C, Sacco E, Manzoni R, Alberghina L, Vanoni M (2005) Acquired glucose sensitivity of k-ras transformed fibroblasts. Biochem Soc Trans 33: 297–299
Cascante M, Boros LG, Comin-Anduix B, de Atauri P, Centelles JJ, Lee PW (2002) Metabolic control analysis in drug discovery and disease. Nat Biotechnol 20: 243–249
Comin-Anduix B, Boren J, Martinez S, Moro C, Centelles JJ, Trebukhina R, Petushok N, Lee WN, Boros LG, Cascante M (2001) The effect of thiamine supplementation on tumour proliferation. A metabolic control analysis study. Eur J Biochem 268: 4177–4182
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Hornberg, J.J., Bruggeman, F.J., Bakker, B.M., Westerhoff, H.V. (2007). Metabolic control analysis to identify optimal drug targets. In: Boshoff, H.I., Barry, C.E. (eds) Systems Biological Approaches in Infectious Diseases. Progress in Drug Research, vol 64. Birkhäuser Basel. https://doi.org/10.1007/978-3-7643-7567-6_7
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DOI: https://doi.org/10.1007/978-3-7643-7567-6_7
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