How molecular should your molecular model be? on the level of molecular detail required to simulate biological networks in systems and synthetic biology

Methods in Enzymology

Volumn 487, Issue C, 2011, Pages 171-215

  Gonze, Didier ^a   Abou Jaoudé, Wassim ^b   Ouattara, Djomangan Adama ^c,d   Halloy, José ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b INRIA   (France)

^c INSTITUT NATIONAL DE L ENVIRONNEMENT INDUSTRIEL ET DES RISQUES INERIS   (France)

^d UNIVERSITÉ DE TECHNOLOGIE DE COMPIÈGNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

ACCURACY; ARTICLE; BINDING SITE; DYNAMICS; ENZYME KINETICS; GENETIC TRANSCRIPTION; MASS ACTION; MATHEMATICAL MODEL; MICHAELIS MENTEN KINETICS; MOLECULAR MODEL; NONLINEAR SYSTEM; OSCILLATION; OSCILLATOR; PERFORMANCE; PRIORITY JOURNAL; REACTION ANALYSIS; SIMULATION; STOCHASTIC MODEL; SYNTHETIC BIOLOGY; VALIDITY;

GENES, REGULATOR; MODELS, BIOLOGICAL; MODELS, MOLECULAR; SYSTEMS BIOLOGY;

EID: 78650885887     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381270-4.00007-X     Document Type: Article

References (85)

1. Abou-Jaoudé, W., Ouattara, D. A., and Kaufman, M. (2009). From structure to dynamics: Frequency tuning in the p53-Mdm2 network I. Logical approach. J. Theor. Biol. 258, 561-577.
2. Agutter, P. S., and Wheatley, D. N. (2000). Random walks and cell size. BioEssays 22, 1018-1023.
3. Agutter, P. S., Malone, P. C., and Wheatley, D. N. (1995). Intracellular transport mechanisms: A critique of diffusion theory. J. Theor. Biol. 176, 261-272.
4. Agutter, P. S., Malone, P. C., and Wheatley, D. N. (2000). Diffusion theory in biology: A relic of mechanistic materialism. J. Hist. Biol. 33, 71-111.
5. Alon, U. (2007). An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/CRC, Boca Raton.
6. Arkin, A., Ross, J., and McAdams, H. H. (1998). Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149, 1633-1648.
7. Barik, D., Paul, M. R., Baumann, W. T., Cao, Y., and Tyson, J. J. (2008). Stochastic simulation of enzyme-catalyzed reactions with disparate timescales. Biophys. J. 95, 3563-3574.
8. Barkai, N., and Leibler, S. (2000). Circadian clocks limited by noise. Nature 403, 267-268.
9. Becker-Weimann, S., Wolf, J., Herzel, H., and Kramer, A. (2004). Modeling feedback loops of the mammalian circadian oscillator. Biophys. J. 87, 3023-3034.
10. Berry, R. S., Rice, S. A., and Ross, J. (2001). Physical Chemistry (Topics in Physical Chemistry). Oxford University Press, Oxford.
11. Borghans, J. A. M., De Boer, R. J., and Segel, L. A. (1996). Extending the quasi-steady state approximation by changing variables. Bull. Math. Biol. 58, 43-63.
12. Bowen, J. R., Acrivos, A., and Oppenheim, A. K. (1962). Singular perturbation refinement to quasi-steady state approximation in chemical kinetics. Chem. Eng. Sci. 18, 177-188.
13. Briggs, G. E., and Haldane, J. B. (1925). A note on the kinetics of enzyme action. Biochem. J. 19, 338-339.
14. Brooks, C. L., and Gu, W. (2003). Ubiquitination, phosphorylation and acetylation: The molecular basis for p53 regulation. Curr. Opin. Cell Biol. 15, 164-171.
15. Brooks, S. P., and Storey, K. B. (1992). A kinetic description of sequential, reversible, Michaelis-Menten reactions: Practical application of theory to metabolic pathways. Mol. Cell. Biochem. 115, 43-48.
16. Cagatay, T., Turcotte, M., Elowitz, M. B., Garcia-Ojalvo, J., and Suel, G. M. (2009). Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139, 512-522.
17. Cai, X., and Yuan, Z. M. (2009). Stochastic modeling and simulation of the p53-MDM2/ MDMX loop. J. Comput. Biol. 16, 917-933.
18. Cha, S. (1970). Kinetic behavior at high enzyme concentrations. J. Biol. Chem. 245, 4814-4818.
19. Chen, L., Wang, R., Kobayashi, T. J., and Aihara, K. (2004). Dynamics of gene regulatory networks with cell division cycle. Phys. Rev. E 70, 011909.
20. Ciliberto, A., Capuani, F., and Tyson, J. J. (2007). Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation. PLoS Comput. Biol. 3, e45.
21. Cornish-Bowden, A. (1995). Fundamentals of Enzyme Kinetics. Portland Press, London.
22. Elowitz, M. B., and Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338.
23. Elowitz, M. B., Levine, A. J., Siggia, E. D., and Swain, P. S. (2002). Stochastic gene expression in a single cell. Science 297, 1183-1186.
24. Ferrell, J. E., and Machleder, E. M. (1998). The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280, 895-898.
25. Flach, E. H., and Schnell, S. (2006). Use and abuse of the quasi-steady-state approximation. Syst. Biol. (Stevenage) 153, 187-191.
26. Florescu, A. M., and Joyeux, M. (2010). Comparison of kinetic and dynamical models of DNA-protein interaction and facilitated diffusion (dagger). J. Phys. Chem. A 114, 9662-9672.
27. Forger, D. B., and Peskin, C. S. (2005). Stochastic simulation of the mammalian circadian clock. Proc. Natl. Acad. Sci. USA 102, 321-324.
28. Gardiner, C. W. (2004). Handbook of Stochastic Methods. Springer, Berlin.
29. Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000). Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342.
30. Gérard, C., and Goldbeter, A. (2009). Temporal self-organization of the cyclin/Cdk network driving the mammalian cell cycle. Proc. Natl. Acad. Sci. USA 106, 21643-21648.
31. Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361.
32. Goldbeter, A. (1995). A model for circadian oscillations in the Drosophila period protein (PER). Proc. Biol. Sci. 261, 319-324.
33. Goldbeter, A. (1996). Biochemical Oscillations and Cellular Rhythms. Cambridge University Press, Cambridge, UK.
34. Gonze, D., Halloy, J., and Goldbeter, A. (2002a). Robustness of circadian rhythms with respect to molecular noise. Proc. Natl. Acad. Sci. USA 99, 673-678.
35. Gonze, D., Halloy, J., and Goldbeter, A. (2002b). Deterministic versus stochastic models for circadian rhythms. J. Biol. Phys. 28, 637-653.
36. Gonze, D., Halloy, J., Leloup, J.-C., and Goldbeter, A. (2003). Stochastic models for circadian rhythms: Effect of molecular noise on periodic and chaotic behavior. C. R. Biol. 326, 189-203.
37. Gonze, D., Halloy, J., and Goldbeter, A. (2004). Emergence of coherent oscillations in stochastic models for circadian rhythms. Physica A 342, 221-233.
38. Goutsias, J. (2005). Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems. J. Chem. Phys. 122, 184102.
39. Grima, R. (2009). Noise-induced breakdown of the Michaelis-Menten equation in steadystate conditions. Phys. Rev. Lett. 102, 218103.
40. Kaern, M., Blake, W. J., and Collins, J. J. (2003). The engineering of gene regulatory networks. Annu. Rev. Biomed. Eng. 5, 179-206.
41. Kar, S., Baumann, W. T., Paul, M. R., and Tyson, J. J. (2009). Exploring the roles of noise in the eukaryotic cell cycle. Proc. Natl. Acad. Sci. USA 106, 6471-6476.
42. Keller, A. D. (1995). Model genetic circuits encoding autoregulatory transcription factors. J. Theor. Biol. 172, 169-185.
43. Klenin, K. V., Merlitz, H., Langowski, J., and Wu, C. X. (2006). Facilitated diffusion of DNA-binding proteins. Phys. Rev. Lett. 96, 018104.
44. Kopelman, R. (1988). Fractal reaction kinetics. Science 241, 1620-1626.
45. Kraus, M., Lais, P., and Wolf, B. (1992). Structured biological modelling: A method for the analysis and simulation of biological systems applied to oscillatory intracellular calcium waves. BioSystems 27, 145-169.
46. Leloup, J. C. (2009). Circadian clocks and phosphorylation: Insights from computational modeling. Cent. Eur. J. Biol. 4, 290-303.
47. Leloup, J. C., and Goldbeter, A. (2003). Toward a detailed computational model for the mammalian circadian clock. Proc. Natl. Acad. Sci. USA 100, 7051-7056.
48. Lewin, B. (2010). Gene IX. 9th edn. Jones and Bartlett, Sudbury.
49. Loinger, A., and Biham, O. (2007). Stochastic simulations of the repressilator circuit. Phys. Rev. E 76, 051917.
50. Lomholt, M. A., van den Broek, B., Kalisch, S. M., Wuite, G. J., and Metzler, R. (2009). Facilitated diffusion with DNA coiling. Proc. Natl. Acad. Sci. USA 106, 8204-8208.
51. Longo, D. M., Hoffmann, A., Tsimring, L. S., and Hasty, J. (2009). Coherent activation of a synthetic mammalian gene network. Syst. Synth. Biol. 4, 15-23.
52. Macnamara, S., Bersani, A. M., Burrage, K., and Sidje, R. B. (2008). Stochastic chemical kinetics and the total quasi-steady-state assumption: Application to the stochastic simulation algorithm and chemical master equation. J. Chem. Phys. 129, 095105.
53. May, R. (2004). Uses and abuses of mathematics in biology. Science 303, 790-793.
54. McAdams, H. H., and Arkin, A. (1997). Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA 94, 814-819.
55. McAdams, H. H., and Arkin, A. (1999). It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 15, 65-69.
56. McQuarrie, D. A., and Simon, J. D. (1999). Physical Chemistry: A Molecular Approach. University Science Books, Sausalito.
57. Michaelis, L., and Menten, M. L. (1913). Kinetik der Invertinwirkung. Biochem. Z. 49, 333-369.
58. Minton, A. P. (2006). Macromolecular crowding. Curr. Biol. 16, R269-R271.
59. Murray, Check for Author Initials (2003). Mathematical Biology, Springer, Berlin.
60. Narang, A. (2007). Effect of DNA looping on the induction kinetics of the lac operon. J. Theor. Biol. 247, 695-712.
61. Ouattara, D. A., Abou-Jaoudé, W., and Kaufman, M. (2010). From structure to dynamics: Frequency tuning in the p53-Mdm2 network. II: Differential and stochastic approaches. J. Theor. Biol. 264, 1177-1189.
62. Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D., and van Oudenaarden, A. (2002). Regulation of noise in the expression of a single gene. Nat. Genet. 31, 69-73.
63. Ozbudak, E. M., Thattai, M., Lim, H. N., Shraiman, B. I., and Van Oudenaarden, A. (2004). Multistability in the lactose utilization network of Escherichia coli. Nature 427, 737-740.
64. Pahle, J. (2009). Biochemical simulations: Stochastic, approximate stochastic and hybrid approaches. Brief. Bioinform. 10, 53-64.
65. Pettersson, G. (1993). Optimal kinetic design of enzymes in a linear metabolic pathway. Biochim. Biophys. Acta 1164, 1-7.
66. Ptashne, M. (2004). A Genetic Switch: Phage Lambda Revisited. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
67. Raj, A., and van Oudenaarden, A. (2008). Nature, nurture, or chance: Stochastic gene expression and its consequences. Cell 135, 216-226.
68. Rao, C. V., and Arkin, A. P. (2003). Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm. J. Chem. Phys. 118, 4999-5010.
69. Raser, J. M., and O'Shea, E. K. (2005). Noise in gene expression: Origins, consequences, and control. Science 309, 2010-2013.
70. Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S., and Elowitz, M. B. (2005). Gene regulation at the single-cell level. Science 307, 1962-1965.
71. Rossi, F. M., Kringstein, A. M., Spicher, A., Guicherit, O. M., and Blau, H. M. (2000). Transcriptional control: Rheostat converted to on/off switch. Mol. Cell 6, 723-728.
72. Sabouri-Ghomi, M., Ciliberto, A., Kar, S., Novak, B., and Tyson, J. J. (2008). Antagonism and bistability in protein interaction networks. J. Theor. Biol. 250, 209-218.
73. Savageau, M. A. (1995). Michaelis-Menten mechanism reconsidered: Implications of fractal kinetics. J. Theor. Biol. 176, 115-124.
74. Schnell, S., and Maini, P. K. (2000). Enzyme kinetics at high enzyme concentration. Bull. Math. Biol. 62, 483-499.
75. Segel, I. H. (1976). Biochemical Calculations: How to Solve Mathematical Problems in General Biochemistry. Wiley, New York.
76. Segel, L. (1988). On the validity of the steady state assumption of enzyme kinetics. Bull. Math. Biol. 50, 579-593.
77. Segel, L., and Slemrod, M. (1989). The quasi-steady state assumption: A case study in perturbation. SIAM Rev. 31, 446-477.
78. Song, H., Smolen, P., Av-Ron, E., Baxter, D. A., and Byrne, J. H. (2007). Dynamics of a minimal model of interlocked positive and negative feedback loops of transcriptional regulation by cAMP-response element binding proteins. Biophys. J. 92, 3407-3424.
79. Stoleriu, I., Davidson, F. A., and Liu, J. L. (2004). Quasi-steady state assumptions for nonisolated enzyme-catalysed reactions. J. Math. Biol. 48, 82-104.
80. Stoleriu, I., Davidson, F. A., and Liu, J. L. (2005). Effects of periodic input on the quasisteady state assumptions for enzyme-catalysed reactions. J. Math. Biol. 50, 115-132.
81. Tamanini, F., Yagita, K., Okamura, H., and van der Horst, G. T. (2005). Nucleocytoplasmic shuttling of clock proteins. Methods Enzymol. 393, 418-435.
82. Thomas, R., and D'Ari, R. (1990). Biological Feedback. CRC Press, Boca Raton.
83. van Kampen, N. G. (2007). Stochastic Processes in Physics and Chemistry. Elsevier, Amsterdam.
84. von Hippel, P. H., and Berg, O. G. (1989). Facilitated target location in biological systems. J. Biol. Chem. 264, 675-678.
85. Yang, H. T., Hsu, C. P., and Hwang, M. J. (2007). An analytical rate expression for the kinetics of gene transcription mediated by dimeric transcription factors. J. Biochem. 142, 135-144.