메뉴 건너뛰기




Volumn 207, Issue 1, 2007, Pages 40-57

Approximations and their consequences for dynamic modelling of signal transduction pathways

Author keywords

Approximations; Conservation laws; Dynamical modelling; Feedback loops; Neglect of components; Signal transduction; Signalling cascades; Stationary states

Indexed keywords

APPROXIMATION THEORY; BIOCHEMISTRY; CELLS; COMPUTER SIMULATION; DIFFERENTIAL EQUATIONS; REACTION KINETICS;

EID: 34147183345     PISSN: 00255564     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mbs.2006.08.012     Document Type: Article
Times cited : (37)

References (47)
  • 1
    • 0035859030 scopus 로고    scopus 로고
    • The ins and outs of signalling
    • Downward J. The ins and outs of signalling. Nature 411 6839 (2001) 759
    • (2001) Nature , vol.411 , Issue.6839 , pp. 759
    • Downward, J.1
  • 5
    • 0033136109 scopus 로고    scopus 로고
    • Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era
    • Schilling C.H., Schuster S., Palsson B.O., and Heinrich R. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15 3 (1999) 296
    • (1999) Biotechnol. Prog. , vol.15 , Issue.3 , pp. 296
    • Schilling, C.H.1    Schuster, S.2    Palsson, B.O.3    Heinrich, R.4
  • 7
    • 0035579883 scopus 로고    scopus 로고
    • Mathematical model of the cell division cycle of fission yeast
    • Novak B., Pataki Z., Ciliberto A., and Tyson J.J. Mathematical model of the cell division cycle of fission yeast. Chaos 11 1 (2001) 277
    • (2001) Chaos , vol.11 , Issue.1 , pp. 277
    • Novak, B.1    Pataki, Z.2    Ciliberto, A.3    Tyson, J.J.4
  • 10
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: a literature review
    • De Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comp. Biology 9 1 (2002) 67
    • (2002) J. Comp. Biology , vol.9 , Issue.1 , pp. 67
    • De Jong, H.1
  • 11
    • 3142617691 scopus 로고    scopus 로고
    • Mathematical and computational techniques to deduce complex biochemical reaction mechanisms
    • Crampin E.J., Schnell S., and McSharry P.E. Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Prog. Biophys. Mol. Biol. 86 1 (2004) 77
    • (2004) Prog. Biophys. Mol. Biol. , vol.86 , Issue.1 , pp. 77
    • Crampin, E.J.1    Schnell, S.2    McSharry, P.E.3
  • 12
    • 0004207135 scopus 로고    scopus 로고
    • Fall C.P., Marland E.S., Wagner J.M., and Tyson J.J. (Eds), Springer, New York
    • In: Fall C.P., Marland E.S., Wagner J.M., and Tyson J.J. (Eds). Computational Cell Biology (2002), Springer, New York
    • (2002) Computational Cell Biology
  • 13
    • 0029790351 scopus 로고    scopus 로고
    • Ultrasensitivity in the mitogen-activated protein kinase cascade
    • Huang C.-Y.F., and Ferrell Jr. J.E. Ultrasensitivity in the mitogen-activated protein kinase cascade. PNAS 93 19 (1996) 10078
    • (1996) PNAS , vol.93 , Issue.19 , pp. 10078
    • Huang, C.-Y.F.1    Ferrell Jr., J.E.2
  • 14
    • 0034914737 scopus 로고    scopus 로고
    • A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (MAPK) pathway model
    • Asthagiri A.R., and Lauffenburger D.A. A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (MAPK) pathway model. Biotechnol. Prog. 17 2 (2001) 227
    • (2001) Biotechnol. Prog. , vol.17 , Issue.2 , pp. 227
    • Asthagiri, A.R.1    Lauffenburger, D.A.2
  • 15
    • 0036212767 scopus 로고    scopus 로고
    • Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors
    • Schoeberl B., Eichler-Jonsson C., Gilles E.D., and Müller G. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nature Biotech. 20 4 (2002) 370
    • (2002) Nature Biotech. , vol.20 , Issue.4 , pp. 370
    • Schoeberl, B.1    Eichler-Jonsson, C.2    Gilles, E.D.3    Müller, G.4
  • 16
    • 0030746219 scopus 로고    scopus 로고
    • Mechanistic studies of the dual phosphorylation of mitogen activated protein kinase
    • Ferrell Jr. J.E., and Bhatt R.R. Mechanistic studies of the dual phosphorylation of mitogen activated protein kinase. J. Biol. Chem. 272 30 (1997) 19008
    • (1997) J. Biol. Chem. , vol.272 , Issue.30 , pp. 19008
    • Ferrell Jr., J.E.1    Bhatt, R.R.2
  • 17
    • 0036285634 scopus 로고    scopus 로고
    • Mathematical models of protein kinase
    • Heinrich R., Nell B.G., and Rapoport T.A. Mathematical models of protein kinase. Mol. Cell 9 5 (2002) 957
    • (2002) Mol. Cell , vol.9 , Issue.5 , pp. 957
    • Heinrich, R.1    Nell, B.G.2    Rapoport, T.A.3
  • 18
    • 0037417886 scopus 로고    scopus 로고
    • Identification of nucleocyroplasmic cycling as a remote sensor in cellular signaling by databased modeling
    • Swameye I., Müller T.G., Timmer J., Sandra O., and Klingmüller U. Identification of nucleocyroplasmic cycling as a remote sensor in cellular signaling by databased modeling. PNAS 100 3 (2003) 1028
    • (2003) PNAS , vol.100 , Issue.3 , pp. 1028
    • Swameye, I.1    Müller, T.G.2    Timmer, J.3    Sandra, O.4    Klingmüller, U.5
  • 20
    • 0031900740 scopus 로고    scopus 로고
    • Signal transduction through MAP kinase cascades
    • Lewis T.S., Shapiro P.S., and Ahn N.G. Signal transduction through MAP kinase cascades. Adv. Cancer Res. 74 (1998) 49
    • (1998) Adv. Cancer Res. , vol.74 , pp. 49
    • Lewis, T.S.1    Shapiro, P.S.2    Ahn, N.G.3
  • 21
    • 14844317354 scopus 로고    scopus 로고
    • The dynamic systems approach to control and regulation of intracellular networks
    • Wolkenhauer O., Ullah M., Wellstead P., and Cho K.-H. The dynamic systems approach to control and regulation of intracellular networks. FEBS Lett. 579 8 (2005) 1846
    • (2005) FEBS Lett. , vol.579 , Issue.8 , pp. 1846
    • Wolkenhauer, O.1    Ullah, M.2    Wellstead, P.3    Cho, K.-H.4
  • 22
    • 33644807093 scopus 로고    scopus 로고
    • Feedback dynamics and cell function: why systems biology is called systems biology
    • Wolkenhauer O., and Mesarovic M. Feedback dynamics and cell function: why systems biology is called systems biology. Mol. BioSyst. 1 1 (2005) 14
    • (2005) Mol. BioSyst. , vol.1 , Issue.1 , pp. 14
    • Wolkenhauer, O.1    Mesarovic, M.2
  • 25
    • 0001424903 scopus 로고
    • An amplified sensitivity arising from covalent modification in biological systems
    • Goldbeter A., and Koshland Jr. D.E. An amplified sensitivity arising from covalent modification in biological systems. PNAS 78 11 (1981) 6840
    • (1981) PNAS , vol.78 , Issue.11 , pp. 6840
    • Goldbeter, A.1    Koshland Jr., D.E.2
  • 27
    • 0034019315 scopus 로고    scopus 로고
    • Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades
    • Kholodenko B.N. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267 6 (2000) 1583
    • (2000) Eur. J. Biochem. , vol.267 , Issue.6 , pp. 1583
    • Kholodenko, B.N.1
  • 29
    • 0000870544 scopus 로고
    • Die Kinetik der Invertinwirkung
    • Michaelis L., and Menten M.L. Die Kinetik der Invertinwirkung. Biochem. Z. 49 (1913) 333
    • (1913) Biochem. Z. , vol.49 , pp. 333
    • Michaelis, L.1    Menten, M.L.2
  • 30
    • 0000292524 scopus 로고
    • A note on the kinetics of enzyme action
    • Briggs G.E., and Haldane J.B.S. A note on the kinetics of enzyme action. Biochem. J. 19 (1925) 338
    • (1925) Biochem. J. , vol.19 , pp. 338
    • Briggs, G.E.1    Haldane, J.B.S.2
  • 31
    • 0031582628 scopus 로고    scopus 로고
    • Closed form solution for time-dependent enzyme kinetics
    • Schnell S., and Mendoza C. Closed form solution for time-dependent enzyme kinetics. J. Theor. Biol. 187 2 (1997) 207
    • (1997) J. Theor. Biol. , vol.187 , Issue.2 , pp. 207
    • Schnell, S.1    Mendoza, C.2
  • 32
    • 0344393718 scopus 로고    scopus 로고
    • The total quasi-steady state approximation is valid for reversible enzyme kinetics
    • Tzafriri A.R., and Edelmann E.R. The total quasi-steady state approximation is valid for reversible enzyme kinetics. J. Theor. Biol. 226 3 (2004) 303
    • (2004) J. Theor. Biol. , vol.226 , Issue.3 , pp. 303
    • Tzafriri, A.R.1    Edelmann, E.R.2
  • 35
    • 0030445778 scopus 로고    scopus 로고
    • Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs
    • Ferrell Jr. J.E. Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. TIBS 21 12 (1996) 460
    • (1996) TIBS , vol.21 , Issue.12 , pp. 460
    • Ferrell Jr., J.E.1
  • 38
    • 0034613112 scopus 로고    scopus 로고
    • Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells
    • Brightmann F.A., and Fell D.A. Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells. FEBS Lett. 482 3 (2000) 169
    • (2000) FEBS Lett. , vol.482 , Issue.3 , pp. 169
    • Brightmann, F.A.1    Fell, D.A.2
  • 39
    • 33644524741 scopus 로고    scopus 로고
    • Cell-signalling dynamics in time and space
    • Kholodenko B.N. Cell-signalling dynamics in time and space. Nat. Rev. Mol. Biol. 7 (2006) 165
    • (2006) Nat. Rev. Mol. Biol. , vol.7 , pp. 165
    • Kholodenko, B.N.1
  • 40
    • 0842288229 scopus 로고    scopus 로고
    • Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades
    • Markevich N.I., Hoek J.B., and Kholodenko B.N. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J. Cell Biol. 164 3 (2004) 353
    • (2004) J. Cell Biol. , vol.164 , Issue.3 , pp. 353
    • Markevich, N.I.1    Hoek, J.B.2    Kholodenko, B.N.3
  • 42
    • 21044435948 scopus 로고    scopus 로고
    • A systems- and signal-oriented approach to intracellular dynamics
    • Wolkenhauer O., Ullah M., Wellstead P., and Cho K.-H. A systems- and signal-oriented approach to intracellular dynamics. Biochem. Soc. Trans. 33 3 (2005) 507
    • (2005) Biochem. Soc. Trans. , vol.33 , Issue.3 , pp. 507
    • Wolkenhauer, O.1    Ullah, M.2    Wellstead, P.3    Cho, K.-H.4
  • 43
    • 0037376655 scopus 로고    scopus 로고
    • Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
    • Tyson J.J., Chen K.C., and Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15 2 (2003) 221
    • (2003) Curr. Opin. Cell Biol. , vol.15 , Issue.2 , pp. 221
    • Tyson, J.J.1    Chen, K.C.2    Novak, B.3
  • 44
    • 0033230728 scopus 로고    scopus 로고
    • Multistability: a major means of differentiation and evolution in biological systems
    • Laurent M., and Kellershohn N. Multistability: a major means of differentiation and evolution in biological systems. Trends Biochem. Sci. 24 11 (1999) 418
    • (1999) Trends Biochem. Sci. , vol.24 , Issue.11 , pp. 418
    • Laurent, M.1    Kellershohn, N.2
  • 45
    • 0032496358 scopus 로고    scopus 로고
    • The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes
    • Ferrell Jr. J.E., and Machleder E.M. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280 (1998) 895
    • (1998) Science , vol.280 , pp. 895
    • Ferrell Jr., J.E.1    Machleder, E.M.2
  • 46
    • 4344674786 scopus 로고    scopus 로고
    • Bistability analyses of a caspase activation model for receptor-induced apoptosis
    • Eissing T., Conzelmann H., Gilles E.D., Allgöwer F., and Bullinger E. Bistability analyses of a caspase activation model for receptor-induced apoptosis. J. Biol. Chem. 279 35 (2004) 36892
    • (2004) J. Biol. Chem. , vol.279 , Issue.35 , pp. 36892
    • Eissing, T.1    Conzelmann, H.2    Gilles, E.D.3    Allgöwer, F.4    Bullinger, E.5
  • 47
    • 0342901749 scopus 로고    scopus 로고
    • Generalisation of the theory of transition times in metabolic pathways: a geometrical approach
    • Llórens M., Nuño J.C., Rodríguez Y., Meléndez-Hevia E., and Montero F. Generalisation of the theory of transition times in metabolic pathways: a geometrical approach. Biophys. J. 77 1 (1999) 23
    • (1999) Biophys. J. , vol.77 , Issue.1 , pp. 23
    • Llórens, M.1    Nuño, J.C.2    Rodríguez, Y.3    Meléndez-Hevia, E.4    Montero, F.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.