Quantitative analysis of signaling networks

Progress in Biophysics and Molecular Biology

Volumn 86, Issue 1, 2004, Pages 5-43

  Sauro, Herbert M ^a,b   Kholodenko, Boris N ^c  

^a KECK GRADUATE INSTITUTE   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

Biological signal transduction; Control systems; Engineering; Quantitative; Simulation; Systems biology

Indexed keywords

EUKARYOTA; PROKARYOTA;

EID: 3242729569     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbiomolbio.2004.03.002     Document Type: Article

References (142)

1. Alm E., Arkin A. Biological networks. Current Opin. Struct. Biol. 13:2003;193-202
2. AMD, 2003. AMD corporation. URL: http://www.amd.com.
3. Arkin A., Ross J. Computational functions in biochemical reaction networks. Biophys. J. 67:1994;560-578
4. Arkin A., Ross J., McAdams H.H. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics. 149:1998;1633-1648
5. Asthagiri A.R., Lauffenburger D.A. Bioengineering models of cell signaling. Annu. Rev. Biomed. Eng. 2:2000;31-53
6. Asthagiri A.R., Lauffenburger D.A. A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (mapk) pathway model. Biotechnol. Prog. 17:2001;227-239
7. Bagowski C.P., Besser J., Frey C.R., Ferrell J.E. The jnk cascade as a biochemical switch in mammalian cells. Ultrasensitive and all-or-none responses. Curr. Biol. 13:2003;315-320
8. Becskei A., Serrano L. Engineering stability in gene networks by autoregulation. Nature. 405:2000;590-593
9. Berg H.C., Purcell E.M. Physics of chemoreception. Biophys. J. 20:1977;193-219
10. Bhalla U.S. Understanding complex signaling networks through models and metaphors. Prog. Biophys. Mol. Biol. 81:2003;45-65
11. Bhalla U.S. Understanding complex signaling networks through models and metaphors. Prog. Biophys. Mol. Biol. 81:2003;45-65
12. Bhalla U., Ram P., Iyengar R. Map kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science. 297:2002;1018-1023
13. Black H.S. Inventing the negative feedback amplifier. IEEE Spectrum. 14:1977;55-60
14. Bluethgen N., Herzel H. Map-kinase-cascade: switch, amplifier or feedback controller. Gauges R., van Gend C. Second Workshop on Computation of Biochemical Pathways and Genetic Networks. 2001;55-62 Logos Verlag, Berlin, U.K.
15. Bolouri H., Davidson E.H. Modeling transcriptional regulatory networks. BioEssays. 24:2002;1118-1129
16. Bourret R.B., Stock A.M. Molecular information processing. lessons from bacterial chemotaxis J. Biol. Chem. 277:2002;9625-9628
17. Bray D. Intracellular signaling as a parallel distributed process. J. Theor. Biol. 143:1990;215-231
18. Bray D. Protein molecules as computational elements in living cells. Nature. 376:1995;307-312
19. Brazhnik P., de la Fuente A., Mendes P. Gene networks. how to put the function in genomics Trends Biotechnol. 20:2002;467-472
20. Brightman F.A., Fell D.A. Differential feedback regulation of the mapk cascade underlies the quantitative differences in egf and ngf signaling in pc12 cells. FEBS Lett. 482:2000;169-174
21. Brown G., Hoek J.B., Kholodenko B.N. Why do protein kinase cascades have more than one level? Trends Biochem. Sci. 22:1997;288-288
22. Brown G.C., Hoek J.B., Kholodenko B.N. Why do protein kinase cascades have more than one level? Trends Biochem. Sci. 22:1997;288
23. Bruggeman F.J., Westerhoff H.V., Hoek J.B., Kholodenko B.N. Modular response analysis of cellular regulatory networks. J. Theor. Biol. 218:2002;507-520
24. Burns, J.A., 1971. Studies on complex enzyme systems. Ph.D. Thesis, University of Edinburgh. URL: http://www.cds.caltech.edu/hsauro/Burns/jimBurns. pdf.
25. Cárdenas M.L., Cornish-Bowden A. Characteristics necessary for an interconvertible enzyme cascade to generate a highly sensitive response to an effector. Biochem. J. 257:1989;339-345
26. Chang L., Karin M. Mammalian map kinase signaling cascades. Nature. 410:2001;37-40
27. Chock P.B., Stadtman E.R. Superiority of interconvertible enzyme cascades in metabolic regulation. analysis of monocyclic systems Proc. Natl. Acad. Sci. USA. 74:1977;2761-2765
28. Chock P.B., Stadtman E.R. Superiority of interconvertible enzyme cascades in metabolite regulation. analysis of multicyclic systems Proc. Natl. Acad. Sci. USA. 74:1977;2766-2770
29. Cinquin O., Demongeot J. Roles of positive and negative feedback in biological systems. C.R. Biol. 325:2002;1085-1095
30. Decroly O., Goldbeter A. Birhythmicity, chaos, and other patterns of temporal self-organization in a multiply regulated biochemical system. Proc. Natl. Acad. Sci. USA. 79:1982;6917-6921
31. Dibrov B.F., Zhabotinsky A.M., Kholodenko B.N. Dynamic stability of steady states and static stabilization in unbranched metabolic pathways. J. Math. Biol. 15:1982;51-63
32. Edelstein B. A biochemical model with multiple steady states. J. Theor. Biol. 29:1970;57-62
33. Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 403:2000;335-338
34. Eschrich K., Schellenberger W., Hofmann E. A hysteretic cycle in glucose-6-phosphate metabolism observed in a cell-free yeast extract. Eur. J. Biochem. 188:1990;697-703
35. Falke J.J., Bass R.B., Butler S.L., Chervitz S.A., Danielson M.A. The two-component singaling pathway of batercial chemotaxis. Annu. Rev. Cell Dev. Biol. 13:1997;457-512
36. Fell D. Understanding the Control of Metabolism. 1997;Portland Press, London
37. Fell D., Small J. Theoretical aspects of covalent modification in metabolic control. Biochem. Soc. Trans. 14:1986;623-624
38. Fell D.A., Sauro H.M. Metabolic control analysis. additional relationships between elasticities and control coefficients Eur. J. Biochem. 148:1985;555-561
39. Ferrell J.E. Tripping the switch fantastic. how a protein kinase cascade can convert graded inputs into switch-like outputs Trends Biochem. Sci. 21:1996;460-466
40. Ferrell J.E. How responses get more switch-like as you move down a protein kinase cascade. Trends Biochem. Sci. 22:1997;288-289
41. Ferrell J.E. Self-perpetuating states in signal transduction. positive feedback, double-negative feedback and bistability Curr. Opin. Cell Biol. 14:2002;140-148
42. Ferrell J.E.J. Building a cellular switch. more lessons from a good egg BioEssays. 21:1999;866-870
43. Ferrell J.E., Machleder E.M. The biochemical basis of an all-or-none cell fate switch in xenopus oocytes. Science. 280:1998;895-898
44. Ford B.J. Single Lens, The Story of the Simple Microscope. 1985;Harper & Row Publishers, New York
45. Gardner T.S., Collins J.J. Neutralizing noise in gene networks. Nature. 405:2000;520-521
46. Gardner T.S., Cantor C.R., Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature. 403:2000;339-342
47. Goldbeter A., Decroly O. Temporal self-organization in biochemical systems. periodic behaviour vs. chaos Am. J. Physiol. 245:1983;R478-R483
48. Goldbeter A., Koshland D.E. An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl. Acad. Sci. 78:1981;6840-6844
49. Goldbeter A., Koshland D.E. Ultrasensitivity in biochemical systems controlled by covalent modification. interplay between zero-order and multistep effects. J. Biol. Chem. 259:1984;14441-14447
50. Gomperts B.D., Mramer I.M., Tatham P.E.R. Signal Transduction. 2002;Academic Press, New York
51. Gonze D., Goldbeter A. A model for a network of phosphorylation- dephosphorylation cycles displaying the dynamics of dominoes and clocks. J. Theor. Biol. 210:2001;167-186
52. Grossman A.D. Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilus. Ann. Rev. Genet. 29:1995;477-508
53. Hasty J., McMillen D., Isaacs F., Collins J.J. Computational studies of gene regulatory networks. in numero molecular biology Nat. Rev. Genet. 2:2001;268-279
54. Hasty J., McMillen D., Collins J.J. Engineered Gene Circuits. Nature. 420:2002;224-230
55. Hayes B. Computing omes to life. Am. Sci. 89:2001;204-208
56. Hazzalin C., Mahadevan L.C. Mapk-regulated transcription. a continuously variable gene switch? Nat. Rev. Mol. Cell Biol. 3:2002;30-40
57. Hecker M., Volker U. General stress response of Bacillus subtilis and other bacteria. Adv. Microb. Physiol. 44:2001;35-91
58. Heinrich R., Schuster S. The Regulation of Cellular Systems. 1996;Chapman & Hall, London
59. Hervagault J.-F., Canu S. Bistability and irreversible transitions in a simple substrate cycle. J. Theor. Biol. 127:1987;439-449
60. Hervagault J.-F., Cimino A. Dynamic behaviours of an open substrate cycle. a graphical approach J. Theor. Biol. 140:1989;399-416
61. Hjelmfelt A., Weinberger E.D., Ross J. Chemical implementation of neural networks and turing machines. Proc. Natl. Acad. Sci. 88:1991;10983-10987
62. Hjelmfelt A., Weinberger E.D., Ross J. Chemical implementation of finite-state machines. Proc. Natl. Acad. Sci. 89:1992;383-387
63. Hofmeyr J.-H., Westerhoff H.V. Building the cellular puzzle. control in multi-level reaction networks J. Theor. Biol. 208:2001;261-285
64. Hofmeyr J.-H.S., Kacser H., van der Merwe K.J. Metabolic control analysis of moiety-conserved cycles. Eur. J. Biochem. 155:1986;631-641
65. Horowitz P., Winfield H. The Art of Electronics. 1990;Cambridge University Press, Cambridge
66. Huang C.F., Ferrell J.E. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc. Natl. Acad. Sci. 93:1996;10078-10083
67. Hunting A. Limit-cycles in enzyme-systems with nonlinear negative feedback. Biophys. Struct. Mech. 1:1974;47-54
68. Intel, 2003. Intel corporation. URL: http://www.intel.com.
69. Jung W.G. IC Op-Amp Cookbook. 3rd Edition:1986;Prentice-Hall PTR, Englewood Cliffs, NJ
70. Kacser H., Burns J.A. The control of flux. Davies D.D. Rate Control of Biological Processes. Symposium of the Society Exponential Biology. Vol. 27:1973;65-104 Cambridge University Press, Cambridge, MA
71. Kahn D., Westerhoff H.V. Control theory of regulatory cascades. J. Theor. Biol. 153:1991;255-285
72. Kholodenko B.N. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267:2000;1583-1588
73. Kholodenko B.N., Hoek J.B., Westerhoff H.V., Brown G.C. Quantification of information transfer via cellular signal transduction pathways. FEBS Lett. 414:1997;430-434
74. Kholodenko, B.N., Hoek, J., Westerhoff, H.W., Brown, G.C., 1998. Control analysis of cellular signal transduction pathways. In: Larsson, C., Pahlman, I.-L., Gustafsson, L. (Eds.), Proceedings of the Eigth International Meeting on BioThermoKinetics, BioThermoKinetics in the Post Genomic Era. Chalmers Reproservice, Göteborg, pp. 102-107.
75. Kholodenko B.N., Demin O.V., Moehren G., Hoek J.B. Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem. 274:1999;30169-30181
76. Kholodenko B.N., Kiyatkin A., Bruggeman F.J., Sontag E., Westerhoff H.V., Hoek J.B. Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc. Natl. Acad. Sci. USA. 99:2002;12841-12846
77. Koza, III, J.R., F.H.B., Bennett, H.F., Andre, D., 1999. Genetic Programming III: Automatic Programming and Automatic Circuit Synthesis. Morgan Kaufmann, Los Altos, LA.
78. Koza J.R., Keane M.A., Streeter M.J. Evolving inventions. Sci. Am. 288:2003;52-59
79. Kyriakis J.M., Avruch J. Mammalian mitogen-activated protein kinase signal transduction pathways activated by stress and inflamation. Physiol. Rev. 81:2002;807-869
80. Lancaster, D., Lancaster, D., 1980. TTL Cookbook. Sams.
81. Laurent M., Kellershohn N. Multistability. a major means of differentiation and evolution in biological systems Trends Biochem. Sci. 24:1999;418-422
82. Levine S.M. Enzyme amplifier kinetics. Science. 152:1966;651-653
83. Lisman J.E. A mechanism for memory storage insensitive to molecular turnover. a bistable autophosphorylating kinase Proc. Natl. Acad. Sci. 82:1985;3055-3057
84. Loew L.M., Schaff J.C. The virtual cell: a software environment for computational cell biology. Trends Biotechnol. 19:2001;401-406
85. Manning G., Whyte D.B., Martinez R., Hunter T., Sudarsanam S. The protein kinase complement of the human genome. Science. 298:2000;1912-1934
86. Manning G., Plowman G.D., Hunter T., Sudarsanam S. Evolution of protein kinase signaling from yeast to man. Trends Biochem. Sci. 27:2002;514-520
87. Markevich N.I., Hoek J.B., Kholodenko B.N. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J. Cell Biol. 164:2004;353-359
88. Marshall C.J. Map kinase kinase kinase, map kinase kinase and map kinase. Curr. Opin. Genet. Dev. 4:1994;82-89
89. McAdams H.H., Arkin A. Simulation of prokaryotic genetic circuits. Annu. Rev. Biophys. Biomol. Struct. 27:1998;199-224
90. Mendes P. Gepasi. a software package for modelling the dynamics, steady states and control of biochemical and other systems Comput. Appl. Biosci. 9:1993;563-571
91. Mindell D. Opening black's box. Technol. Culture. 14:2000;405-434
92. Moehren G., Markevich N., Demin O., Kiyatkin A., Goryanin I., Hoek J.B., Kholodenko B.N. Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model. Biochemistry. 41:2002;306-320
93. Morales M., McKay D. Biochemical oscillations in controlled systems. Biophys. J. 7:1967;621-625
94. Okamoto M., Katsurayama A., Tsukiji M., Aso Y., Hayashi K. Dynamic behavior of enzymatic system realizing two-factor model. J. Theor. Biol. 83:1980;1-16
95. Okamoto M., Sakai T., Hayashi K. Switching mechanisms of a cyclic enzyme system. role as a "chemical diode" Biosystems. 21:1987;1-11
96. Okamoto M., Sakai T., Hayashi K. Biochemical switching device - monocyclic enzyme-system. Biotechnol. Bioeng. 32:1988;527-537
97. Okamoto M., Sakai T., Hayashi K. Biochemical switching device - how to turn on (off) the switch. Biosystems. 22:1989;155-162
98. Othmer H.H. The quantitative dynamics of a class of biochemical control circuits. J. Math. Biol. 37:1976;53-78
99. Pomerening J.R., Sontag E.D., Ferrell J.E. Building a cell cycle oscillator. hysteresis and bistability in the activation of cdc2 Nat. Cell. Biol. 5:2003;346-351
100. Poritz M.A., Malmstrom S., Kim M.-H., Rossmeissl P.J., Kamb A. Graded mode of transcriptional induction in yeast pheromone signaling revealed by single-cell analysis. Yeast. 18:2001;1331-1338
101. Rao C.V., Arkin A. Control motifs for intracellular regulatory networks. Annu. Rev. Biomed. Eng. 3:2001;391-419
102. Ravasz E., Somera A.L., Mongru D.A., Oltvai Z.N., Barabasi A.-L. Hierarchical organization of modularity in metabolic networks. Science. 297:2002;1551-1555
103. Rohwer J.M., Schuster S., Westerhoff H.V. How to recognize monofunctional units in a metabolic system. J. Theor. Biol. 179:1996;213-228
104. Ryan K.R., Shapiro L. Temporal and spatial regulation in prokaryotic cell cycle progression and development. Annu. Rev. Biochem. 72:2003;367-394
105. Sauro H.M. A biochemical nand gate and assorted circuits. Schuster S., Rigoulet M., Ouhabi R., Mazat J.-P. Modern Trends in Biothermokinetics. 1993;133-140 Plenum Press, New York, London
106. Sauro, H.M., 2000. Jarnac: a system for interactive metabolic analysis. In: Hofmeyr, J.-H.S., Rohwer, J.M., Snoep, J.L. (Eds.), Animating the Cellular Map: Proceedings of the Ninth International Meeting on BioThermoKinetics, Stellenbosch University Press.
107. Sauro, H.M., 2001. A rationale for the 'design' of the MAP kinase pathway. In: Yi, T.-M., Hucka, M.(Eds.), Second International Conference on Systems Biology. Caltech, Pasadena, pp. 13; http://www.sys - bio.org.
108. Sauro H.M., Fell D.A. Scamp. a metabolic simulator and control analysis program Math. Comput. Model. 15:1991;15-28
109. Sauro H.M., Hucka M., Finney A., Wellock C., Bolouri H., Doyle J., Kitano H. Next generation simulation tools. the systems biology workbench and biospice integration OMICS. 7(4):2003;355-372
110. Savageau M.A. The behaviour of intact biochemical control systems. Curr. Topics Cell. Reg. 6:1972;63-130
111. Savageau M.A. Optimal design of feedback control by inhibition. steady-state considerations J. Mol. Evol. 4:1974;139-156
112. Savageau M.A. Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology. 1976;Addison-Wesley, Reading, MA
113. Schoeberl B., Eichler-Jonsson C., Gilles E.D., Muller G. Computational modeling of the dynamics of the map kinase cascade activated by surface and internalized egf receptors. Nat. Biotechnol. 20:2002;370-375
114. Segall J.E., Block S.M., Berg H.C. Temporal comparisons in bacterial chemotaxis. Proc. Natl. Acad. Sci. USA. 83:1986;8987-8991
115. Seno M., Iwamoto K., Sawada K. Instability and oscillatory behavior of membrane-chemical reaction systems. J. Theor. Biol. 72:1978;577-588
116. Sha W., Moore J., Chen K., Lassaletta A.D., Yi C.-S., Tyson J.J., Sible J.C. From the cover. hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts Proc. Natl. Acad. Sci. USA. 100:2003;975-980
117. Shapiro B.E., Levchenko A., Meyerowitz E.M., Wold B.J., Mjolsness E.D. Cellerator. extending a computer algebra system to include biochemical arrows for signal transduction simulations Bioinformatics. 19:2003;677-678
118. Shen-Orr S.S., Milo R., Mangan S., Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31:2002;64-68
119. Shvartsman S.Y., Muratov C.B., Lauffenburger D.A. Modeling and computational analysis of egf receptor-mediated cell communication in drosophila oogenesis. Development. 129:2002;2577-2589
120. Small, J.R., 1988. Theoretical aspects of metabolic control. Ph.D. Thesis, Oxford Polytechnic.
121. Small J.R., Fell D.A. Covalent modification and metabolic control analysis. modification to the theorems and their application to metabolic systems containing covalently-modified enzymes Eur. J. Biochem. 191:1990;405-411
122. Smolen P., Baxter D.A., Byrne J.H. Modeling transcriptional control in gene networks-methods, recent results, and future directions. Bull. Math. Biol. 62:2000;247-292
123. Solée R.V., Cancho R.F., Valverde S., Montoya J.M. Selection, tinkering, and emergence in complex networks. Complexity. 8:2002;20-33
124. Soroka W.W. Analog Methods in Computation and Simulation. 1954;McGraw-Hill Book Company Inc., New York
125. Thar R., Kuhl M. Bacteria are not too small for spatial sensing of chemical gradients. an experimental evidence Proc. Acad. Natl. Sci. 100:2003;5748-5753
126. The-Arabidopsis-Initiative, 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
127. Thron C.D. A model for a bistable biochemical trigger of mitosis. Biophys. Chem. 57:1996;239-251
128. Tomita M., Hashimoto K., Takahashi K., Shimizu T.S., Matsuzaki Y., Miyoshi F S.K., Tanida S., Yugi K., Venter J.C., Hutchison C.A. E-cell. software environment for whole-cell simulation Bioinformatics. 15:1999;72-84
129. Tyson, J., Othmer, H.G., 1978. The dynamics of feedback control circuits in biochemical pathways. In: Rosen, R., Snell, F.M. (Eds.), Progress in Theoretical Biology, Vol. 5, pp. 1-62.
130. Tyson J.J., Chen K., Novak B. Network dynamics and cell physiology. Nat. Rev. Mol. Cell Biol. 2:2001;908-916
131. Tyson J.J., Csikasz-Nagy A., Novak B. The dynamics of cell cycle regulation. BioEssays. 24:2002;1095-1109
132. Tyson J.J., Chen K.C., Novak B. Sniffers, buzzers, toggles and blinkers. dynamics of regulatory and signaling pathways in the cell Curr. Opin. Cell Biol. 15:2003;221-231
133. Umbarger H.E. Evidence for a negative-feedback mechanism in the biosynthesis of leucine. Science. 123:1956;848
134. Wald G. Visual excitation and blodd clotting. Science. 150:1965;1028-1030
135. West A.H., Stock A.M. Histidine kinases and response regulator proteins in two-compartment signaling systems. Trends Biochem. Sci. 26:2001;369-376
136. Wiley H.S., Shvartsman S.Y., Lauffenburger D.A. Computational modeling of the egf-receptor system. a paradigm for systems biology Trends Cell. Biol. 13:2003;43-50
137. Wolf D.M., Arkin A.P. Fifteen minutes of fim: control of type 1 pili expression in E. coli. OMICS. 6:2002;91-114
138. Wolf D.M., Arkin A.P. Motifs, modules and games in bacteria. Curr. Opin. Microbiol. 6:2003;125-134
139. Wong Y.J., Ott W.E. Function Circuits: Design and Applications. 1976;McGraw-Hill Book Company, New York
140. Yates R.A., Pardee A.B. Control of pyrimidine biosynthesis in Escherichia coli by a feed-back mechanism. J. Biol. Chem. 221:1956;757-770
141. Yi T., Huang Y., Simon M.I., Doyle J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc. Natl. Acad. Sci. USA. 97:2000;4649-4653
142. Yildirim N., Mackey M.C. Feedback regulation in the lactose operon. a mathematical modeling study and comparison with experimental data Biophys. J. 84:2003;2841-2851