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Volumn 101, Issue 1, 2010, Pages 67-77

Modelling the optimal timing in metabolic pathway activation-Use of Pontryagin's Maximum Principle and role of the Golden section

Author keywords

Dynamic optimization; Golden section; Just in time expression; Modelling of metabolic pathways; Pontryagin's Maximum Principle

Indexed keywords

ENZYME ACTIVITY; GENE EXPRESSION; METABOLISM; NUMERICAL MODEL; OPTIMIZATION; SUBSTRATE;

EID: 77953609496     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2010.04.007     Document Type: Article
Times cited : (47)

References (53)
  • 1
    • 33751072633 scopus 로고    scopus 로고
    • Biological network design strategies: discovery through dynamic optimization
    • Adiwijaya B.S., Barton P.I., Tidor B. Biological network design strategies: discovery through dynamic optimization. Mol. Biosys. 2006, 2(12):650-659.
    • (2006) Mol. Biosys. , vol.2 , Issue.12 , pp. 650-659
    • Adiwijaya, B.S.1    Barton, P.I.2    Tidor, B.3
  • 3
    • 34547887655 scopus 로고    scopus 로고
    • Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
    • Beg Q.K., Vazquez A., Ernst J., de Menezes M.A., Bar-Joseph Z., Barabasi A.L., Oltvai Z.N. Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(31):12663-12668.
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , Issue.31 , pp. 12663-12668
    • Beg, Q.K.1    Vazquez, A.2    Ernst, J.3    de Menezes, M.A.4    Bar-Joseph, Z.5    Barabasi, A.L.6    Oltvai, Z.N.7
  • 4
    • 0009769960 scopus 로고
    • Time-optimal control for a growth-model
    • Bley T., Bogner H. Time-optimal control for a growth-model. Studia Biophys. 1981, 83(3):217-224.
    • (1981) Studia Biophys. , vol.83 , Issue.3 , pp. 217-224
    • Bley, T.1    Bogner, H.2
  • 6
    • 0036848010 scopus 로고    scopus 로고
    • Sequential activation of signaling pathways during innate immune responses in Drosophila
    • Boutros M., Agaisse H., Perrimon N. Sequential activation of signaling pathways during innate immune responses in Drosophila. Develop. Cell 2002, 3(5):711-722.
    • (2002) Develop. Cell , vol.3 , Issue.5 , pp. 711-722
    • Boutros, M.1    Agaisse, H.2    Perrimon, N.3
  • 7
    • 0026050621 scopus 로고
    • Total cell protein concentration as an evolutionary constraint on the metabolic control distribution in cells
    • Brown G.C. Total cell protein concentration as an evolutionary constraint on the metabolic control distribution in cells. J. Theor. Biol. 1991, 153(2):195-203.
    • (1991) J. Theor. Biol. , vol.153 , Issue.2 , pp. 195-203
    • Brown, G.C.1
  • 9
    • 55749116150 scopus 로고    scopus 로고
    • Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network
    • Chechik G., Oh E., Rando O., Weissman J., Regev A., Koller D. Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nat. Biotechnol. 2008, 26(11):1251-1259.
    • (2008) Nat. Biotechnol. , vol.26 , Issue.11 , pp. 1251-1259
    • Chechik, G.1    Oh, E.2    Rando, O.3    Weissman, J.4    Regev, A.5    Koller, D.6
  • 12
    • 45849120994 scopus 로고    scopus 로고
    • Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways
    • Chin C.S., Chubukov V., Jolly E.R., DeRisi J., Li H. Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways. Plos Biol. 2008, 6(6):1343-1356.
    • (2008) Plos Biol. , vol.6 , Issue.6 , pp. 1343-1356
    • Chin, C.S.1    Chubukov, V.2    Jolly, E.R.3    DeRisi, J.4    Li, H.5
  • 14
    • 23144432213 scopus 로고    scopus 로고
    • Optimality and evolutionary tuning of the expression level of a protein
    • Dekel E., Alon U. Optimality and evolutionary tuning of the expression level of a protein. Nature 2005, 436(7050):588-592.
    • (2005) Nature , vol.436 , Issue.7050 , pp. 588-592
    • Dekel, E.1    Alon, U.2
  • 15
    • 0021327427 scopus 로고
    • The kinetics of consecutive enzyme reactions. The design of coupled assays and the temporal response of pathways
    • Easterby J.S. The kinetics of consecutive enzyme reactions. The design of coupled assays and the temporal response of pathways. Biochem. J. 1984, 219(3):843-844.
    • (1984) Biochem. J. , vol.219 , Issue.3 , pp. 843-844
    • Easterby, J.S.1
  • 16
    • 0037342134 scopus 로고    scopus 로고
    • Stoichiometric design of metabolic networks: Multifunctionality, clusters, optimization, weak and strong robustness
    • Ebenhöh O., Heinrich R. Stoichiometric design of metabolic networks: Multifunctionality, clusters, optimization, weak and strong robustness. Bull. Math. Biol. 2003, 65(2):323-357.
    • (2003) Bull. Math. Biol. , vol.65 , Issue.2 , pp. 323-357
    • Ebenhöh, O.1    Heinrich, R.2
  • 19
    • 0025778726 scopus 로고
    • Is metabolic channelling the complicated solution to the easy problem of reducing transient times?
    • Heinrich R., Schuster S. Is metabolic channelling the complicated solution to the easy problem of reducing transient times?. J. Theor. Biol. 1991, 152(1):57-61.
    • (1991) J. Theor. Biol. , vol.152 , Issue.1 , pp. 57-61
    • Heinrich, R.1    Schuster, S.2
  • 21
    • 0025923478 scopus 로고
    • Mathematical analysis of enzymic reaction systems using optimization principles
    • Heinrich R., Schuster S., Holzhütter H.G. Mathematical analysis of enzymic reaction systems using optimization principles. Eur. J. Biochem. 1991, 201(1):1-21.
    • (1991) Eur. J. Biochem. , vol.201 , Issue.1 , pp. 1-21
    • Heinrich, R.1    Schuster, S.2    Holzhütter, H.G.3
  • 22
    • 0034733820 scopus 로고    scopus 로고
    • Regulating the cellular economy of supply and demand
    • Hofmeyr J.H.S., Cornish-Bowden A. Regulating the cellular economy of supply and demand. FEBS Lett. 2000, 476(1-2):47-51.
    • (2000) FEBS Lett. , vol.476 , Issue.1-2 , pp. 47-51
    • Hofmeyr, J.H.S.1    Cornish-Bowden, A.2
  • 24
    • 45749147804 scopus 로고    scopus 로고
    • Optimal control applied to a thoraco-abdominal CPR model
    • Jung E., Lenhart S., Protopopescu V., Babbs C. Optimal control applied to a thoraco-abdominal CPR model. Math. Med. Biol. 2008, 25(2):157-170.
    • (2008) Math. Med. Biol. , vol.25 , Issue.2 , pp. 157-170
    • Jung, E.1    Lenhart, S.2    Protopopescu, V.3    Babbs, C.4
  • 25
    • 0021277007 scopus 로고
    • Evolution of catalytic proteins. On the origin of enzyme species by means of natural selection
    • Kacser H., Beeby R. Evolution of catalytic proteins. On the origin of enzyme species by means of natural selection. J. Mol. Evol. 1984, 20(1):38-51.
    • (1984) J. Mol. Evol. , vol.20 , Issue.1 , pp. 38-51
    • Kacser, H.1    Beeby, R.2
  • 26
    • 0035875010 scopus 로고    scopus 로고
    • Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria
    • Kalir S., McClure J., Pabbaraju K., Southward C., Ronen M., Leibler S., Surette M.G., Alon U. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 2001, 292(5524):2080-2083.
    • (2001) Science , vol.292 , Issue.5524 , pp. 2080-2083
    • Kalir, S.1    McClure, J.2    Pabbaraju, K.3    Southward, C.4    Ronen, M.5    Leibler, S.6    Surette, M.G.7    Alon, U.8
  • 27
    • 2642585068 scopus 로고    scopus 로고
    • On the mystery of the golden angle in phyllotaxis
    • King S., Beck F., Lüttge U. On the mystery of the golden angle in phyllotaxis. Plant Cell Environ. 2004, 27(6):685-695.
    • (2004) Plant Cell Environ. , vol.27 , Issue.6 , pp. 685-695
    • King, S.1    Beck, F.2    Lüttge, U.3
  • 28
    • 85194580390 scopus 로고    scopus 로고
    • Reprogramming of metabolic systems by altering gene expression, Animating the cellular map
    • Stellenbosch University Press, Stellenbosch
    • Klipp E., Holzhütter H.G., Heinrich R. Reprogramming of metabolic systems by altering gene expression, Animating the cellular map. Proceedings of the 9th BioThermoKinetics Meeting 2000, 165-172. Stellenbosch University Press, Stellenbosch.
    • (2000) Proceedings of the 9th BioThermoKinetics Meeting , pp. 165-172
    • Klipp, E.1    Holzhütter, H.G.2    Heinrich, R.3
  • 29
    • 0036441029 scopus 로고    scopus 로고
    • Prediction of temporal gene expression. Metabolic optimization by re-distribution of enzyme activities
    • Klipp E., Heinrich R., Holzhütter H.G. Prediction of temporal gene expression. Metabolic optimization by re-distribution of enzyme activities. Eur. J. Biochem. 2002, 269(22):5406-5413.
    • (2002) Eur. J. Biochem. , vol.269 , Issue.22 , pp. 5406-5413
    • Klipp, E.1    Heinrich, R.2    Holzhütter, H.G.3
  • 31
    • 28844472123 scopus 로고    scopus 로고
    • Golden section in the structure of metals
    • Kraposhin V. Golden section in the structure of metals. Met. Sci. Heat Treat. 2005, 47(7):351-358.
    • (2005) Met. Sci. Heat Treat. , vol.47 , Issue.7 , pp. 351-358
    • Kraposhin, V.1
  • 32
    • 31344470684 scopus 로고    scopus 로고
    • The ideal free distribution and bacterial growth on two substrates
    • Krivan V. The ideal free distribution and bacterial growth on two substrates. Theor. Popul. Biol. 2006, 69(2):181-191.
    • (2006) Theor. Popul. Biol. , vol.69 , Issue.2 , pp. 181-191
    • Krivan, V.1
  • 33
    • 57649244968 scopus 로고    scopus 로고
    • Pontryagin's maximum principle in optimal control problems of orientation of a spacecraft
    • Levskii M. Pontryagin's maximum principle in optimal control problems of orientation of a spacecraft. J. Comput. Syst. Sci. Int. 2008, 47(6):974-986.
    • (2008) J. Comput. Syst. Sci. Int. , vol.47 , Issue.6 , pp. 974-986
    • Levskii, M.1
  • 34
    • 4444257007 scopus 로고    scopus 로고
    • A theory of optimal differential gene expression
    • Liebermeister W., Klipp E., Schuster S., Heinrich R. A theory of optimal differential gene expression. Biosystems 2004, 76(1-3):261-278.
    • (2004) Biosystems , vol.76 , Issue.1-3 , pp. 261-278
    • Liebermeister, W.1    Klipp, E.2    Schuster, S.3    Heinrich, R.4
  • 35
    • 0342901749 scopus 로고    scopus 로고
    • Generalization of the theory of transition times in metabolic pathways: a geometrical approach
    • Llorens M., Nuno J.C., Rodriguez Y., Melendez-Hevia E., Montero F. Generalization of the theory of transition times in metabolic pathways: a geometrical approach. Biophys. J. 1999, 77(1):23-36.
    • (1999) Biophys. J. , vol.77 , Issue.1 , pp. 23-36
    • Llorens, M.1    Nuno, J.C.2    Rodriguez, Y.3    Melendez-Hevia, E.4    Montero, F.5
  • 36
    • 0037351676 scopus 로고    scopus 로고
    • A golden section approach to optimization of automotive friction materials
    • Lu Y. A golden section approach to optimization of automotive friction materials. J. Mater. Sci. 2003, 38(5):1081-1085.
    • (2003) J. Mater. Sci. , vol.38 , Issue.5 , pp. 1081-1085
    • Lu, Y.1
  • 37
    • 0036708443 scopus 로고    scopus 로고
    • Dynamic flux balance analysis of diauxic growth in Escherichia coli
    • Mahadevan R., Edwards J.S., Doyle F.J. Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 2002, 83(3):1331-1340.
    • (2002) Biophys. J. , vol.83 , Issue.3 , pp. 1331-1340
    • Mahadevan, R.1    Edwards, J.S.2    Doyle, F.J.3
  • 38
    • 33845460324 scopus 로고    scopus 로고
    • Role of cascades in converting oscillatory signals into stationary step-like responses
    • Marhl M., Grubelnik V. Role of cascades in converting oscillatory signals into stationary step-like responses. BioSystems 2007, 87(1):58-67.
    • (2007) BioSystems , vol.87 , Issue.1 , pp. 58-67
    • Marhl, M.1    Grubelnik, V.2
  • 39
    • 58049147181 scopus 로고    scopus 로고
    • Maximum principle of optimal control of the primitive equations of the ocean with state constraint
    • Medjo T.T. Maximum principle of optimal control of the primitive equations of the ocean with state constraint. Numer. Funct. Anal. Optim. 2008, 29(11-12).
    • (2008) Numer. Funct. Anal. Optim. , vol.29 , Issue.11-12
    • Medjo, T.T.1
  • 40
    • 24944479613 scopus 로고    scopus 로고
    • A variation of Schwarzschild telescope: golden section solution with two concentric spheres and its extension to finite distance solutions
    • Nariai K., Iwamoto H. A variation of Schwarzschild telescope: golden section solution with two concentric spheres and its extension to finite distance solutions. Opt. Rev. 2005, 12(3):190-195.
    • (2005) Opt. Rev. , vol.12 , Issue.3 , pp. 190-195
    • Nariai, K.1    Iwamoto, H.2
  • 41
    • 70350391935 scopus 로고    scopus 로고
    • Optimal metabolic regulation by temporal variation of enzyme activities: a control theoretic approach
    • Oyarzún D., Ingalls B., Kalamatianos D. Optimal metabolic regulation by temporal variation of enzyme activities: a control theoretic approach. Proceedings of the 2nd Conference on FSOBE 2007, 491-496.
    • (2007) Proceedings of the 2nd Conference on FSOBE , pp. 491-496
    • Oyarzún, D.1    Ingalls, B.2    Kalamatianos, D.3
  • 42
    • 70350400430 scopus 로고    scopus 로고
    • Sequential activation of metabolic pathways: a dynamic optimization approach
    • Oyarzún D., Ingalls B., Middleton R., Kalamatianos D. Sequential activation of metabolic pathways: a dynamic optimization approach. Bull. Math. Biol. 2009, 71(8):1851-1872.
    • (2009) Bull. Math. Biol. , vol.71 , Issue.8 , pp. 1851-1872
    • Oyarzún, D.1    Ingalls, B.2    Middleton, R.3    Kalamatianos, D.4
  • 43
    • 11844280852 scopus 로고    scopus 로고
    • Game-theoretical approaches to studying the evolution of biochemical systems
    • Pfeiffer T., Schuster S. Game-theoretical approaches to studying the evolution of biochemical systems. Trends Biochem. Sci. 2005, 30(1):20-25.
    • (2005) Trends Biochem. Sci. , vol.30 , Issue.1 , pp. 20-25
    • Pfeiffer, T.1    Schuster, S.2
  • 45
    • 0036678794 scopus 로고    scopus 로고
    • Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
    • Ronen M., Rosenberg R., Shraiman B.I., Alon U. Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. 2002, 99(16):10555-10560.
    • (2002) Proc. Natl. Acad. Sci. , vol.99 , Issue.16 , pp. 10555-10560
    • Ronen, M.1    Rosenberg, R.2    Shraiman, B.I.3    Alon, U.4
  • 46
    • 36949025593 scopus 로고    scopus 로고
    • The predictive power of molecular network modelling-case studies of predictions with subsequent experimental verification
    • Landes Bioscience, Georgetown, E. Frank (Ed.)
    • Schuster S., Klipp E., Marhl M. The predictive power of molecular network modelling-case studies of predictions with subsequent experimental verification. Discovering Biomolecular Mechanisms with Computational Biology 2006, 95-103. Landes Bioscience, Georgetown. E. Frank (Ed.).
    • (2006) Discovering Biomolecular Mechanisms with Computational Biology , pp. 95-103
    • Schuster, S.1    Klipp, E.2    Marhl, M.3
  • 47
    • 43449132092 scopus 로고    scopus 로고
    • Is maximization of molar yield in metabolic networks favoured by evolution?
    • Schuster S., Pfeiffer T., Fell D.A. Is maximization of molar yield in metabolic networks favoured by evolution?. J. Theor. Biol. 2008, 252(3):497-504.
    • (2008) J. Theor. Biol. , vol.252 , Issue.3 , pp. 497-504
    • Schuster, S.1    Pfeiffer, T.2    Fell, D.A.3
  • 48
    • 67049144867 scopus 로고    scopus 로고
    • Effects of recombinant protein expression on green fluorescent protein diffusion in Escherichia coli
    • Slade K.M., Baker R., Chua M., Thompson N.L., Pielak G.J. Effects of recombinant protein expression on green fluorescent protein diffusion in Escherichia coli. Biochemistry 2009, 48(23):5083-5089.
    • (2009) Biochemistry , vol.48 , Issue.23 , pp. 5083-5089
    • Slade, K.M.1    Baker, R.2    Chua, M.3    Thompson, N.L.4    Pielak, G.J.5
  • 50
    • 0033005128 scopus 로고    scopus 로고
    • Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries
    • Varner J., Ramkrishna D. Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries. Biotechnol. Prog. 1999, 15(3):407-425.
    • (1999) Biotechnol. Prog. , vol.15 , Issue.3 , pp. 407-425
    • Varner, J.1    Ramkrishna, D.2
  • 51
    • 73449095722 scopus 로고    scopus 로고
    • Selection advantage of metabolic over non-metabolic replicators: a kinetic analysis
    • Wagner N., Pross A., Tannenbaum E. Selection advantage of metabolic over non-metabolic replicators: a kinetic analysis. BioSystems 2010, 99(2):126-129.
    • (2010) BioSystems , vol.99 , Issue.2 , pp. 126-129
    • Wagner, N.1    Pross, A.2    Tannenbaum, E.3


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