Asymptotic states and topological structure of an activation-deactivation chemical network

Journal of Theoretical Biology

Volumn 245, Issue 3, 2007, Pages 423-432

  Martelli, Carlotta ^a   Giansanti, Andrea ^a   Arisi, Ivan ^b   Rosato, Vittorio ^c,d  

^a UNIVERSITÀ DI ROMA LA SAPIENZA   (Italy)

^b EUROPEAN BRAIN RESEARCH INSTITUTE   (Italy)

^c ENEA   (Italy)

^d ENEA C R CASACCIA   (Italy)

Author keywords

Activation deactivation chemical reactions; Dynamical systems; Protein protein interaction networks; Stability; Stationary states

Indexed keywords

PHOSPHOPROTEIN PHOSPHATASE; PROTEIN KINASE;

ACTIVITY PATTERN; CHEMICAL REACTION; EQUATION; MAPPING; NUMERICAL METHOD; PROTEIN;

ARTICLE; CHEMICAL ANALYSIS; CHEMICAL REACTION; CHEMICAL STRUCTURE; EVOLUTION; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR STABILITY; PHYSICAL PHASE; PRIORITY JOURNAL; PROTEIN DEPHOSPHORYLATION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SIMULATION;

ANIMALS; COMPUTER SIMULATION; MODELS, CHEMICAL; PROTEIN INTERACTION MAPPING; PROTEINS; SIGNAL TRANSDUCTION;

EID: 33847615282     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2006.10.003     Document Type: Article

References (41)

1. Aladana M., and Cluzel P. A natural class of robust networks. Proc. Natl. Acad. Sci. 100 15 (2003) 8710-8714
2. Albert R. Scale-free networks in cell biology. J. Cell. Sci. 118 Pt21 (2005) 4947-4957
3. Albert R., and Barabasi A.-L. Statistical mechanics of complex networks. Rev. Mod. Phys. 74 (2002) 47
4. Albert R., Jeong H., and Barabasi A.-L. Error and attack tolerance of complex networks. Nature 406 (2000) 378
5. Aleksiejuk A., Holyst J.A., and Stauffer D. Ferromagnetic phase transition in Barabasi-Albert networks. Physica A 310 (2002) 260
6. Aluffi-Pentini F., De Fonso V., and Parisi V. A novel algorithm for the numerical integration of systems of ordinary differential equations arising in chemical problems. J. Math. Chem. 33 (2003) 1
7. Arita M. The metabolic world of Escherichia coli is not small. Proc. Natl Acad. Sci. USA 101 6 (2004) 1543-1547
8. Arita M. Scale-freeness and biological networks. J. Biochem. (Tokyo) 138 1 (2005) 1-4
9. Barabasi A.-L., and Albert R. Emergence of scaling in random networks. Science 286 (1999) 509
10. Bhalla U.S., Ram P.T., and Iyengar R. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297 5583 (2002) 1018-1023
11. Binder B., and Heinrich R. Interrelations between dynamical properties and structural characteristics of signal transduction networks. Genome Inform. 15 (2004) 13
12. Christley R.M., Pinchbek G.L., Bowers R.G., Clancy D., French N.P., Bennett R., and Turner J. Infection in social networks: using network analysis to identify high-risk individuals. Am. J. Epidem. 162 10 (2005) 1024-1031
13. Cusick M.E., Klitgord N., Vidal M., and Hill D.E. Interactome: gateway into Systems Biology. Hum. Mol. Genet. 14 Spec.Num.2 (2005) R171
14. Dorogovtsev S.N., Goltsev A.V., and Mendes J.F.F. Ising model on networks with an arbitrary distribution of connections. Phys. Rev. E 66 (2002) 016104
15. Eguiluz V.M., Chialvo D.R., Cecchi D.A., Baliki M., and Apkarian A.V. Scale-free brain functional networks. Phys. Rev. Lett. 94 1 (2005) 018102
16. Haugh J.M., Schneider I.C., and Lewis J.M. On the cross-regulation of protein tyrosine phosphatases and receptor tyrosine kinases in intracellular signaling. J. Theor. Biol. 230 1 (2004) 119-132
17. Hautamiemi S., Kharait S., Iwabu A., Wells A., and Lauffenburger D.A. Modelling of signal-response cascades using decision tree analysis. Bioinformatics 21 9 (2005) 2027-2035
18. Hirano K., Derkach D.N., Hirano M., Nishimura J., and Kanaide H. Protein kinase network in the regulation of phosphorylation and dephosphorylation of smooth muscle myosin light chain. Mol. Cell. Biochem. 248 1-2 (2003) 105-114
19. Homberg J.J., Bruggeman F.J., Binder B., Geest C.R., de Vaate A.J., Lankeima J., Heinrich R., and Westerhoff H.V. Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control. FEBS 272 1 (2005) 244-258
20. Ibarra R.U., Edwards J.S., and Palsson B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420 6912 (2002) 186-189
21. Joy M.P., Brock A., Ingber D.E., and Huang S. High-betweenness proteins in the yeast protein interaction network. J. Biomed. Biotechnol. 2005 2 (2005) 96-103
22. Kashtan N., and Alon U. Spontaneous evolution of modularity and network motifs. Proc. Natl Acad. Sci. USA 102 309 (2005) 13773-13778
23. Kauffman S.A. Requirements for evolvability in complex systems: orderly dynamics and frozen components. Physica D 42 (1990) 135
24. Klemm, K., Bornholdt, S., 2005. Topology of biological networks and reliability of information processing. Proc. Natl Acad. Sci. USA 102 (51) 18414-18419.
25. Lee R.E., and Megeney L.A. The yeast kinome displays scale free topology with functional hub clusters. BMC Bioinform. 6 (2005) 271
26. Li F., Long T., Lu Y., Ouyang Q., and Tang C. The yeast cell-cycle is robustly designed. Proc. Natl Acad. Sci. 101 14 (2004) 4781-4786
27. Martin H., Flandez M., Nombela C., and Molina M. Protein phosphatases in MAPK signalling: we keep learning from yeast. Mol. Microbiol. 58 1 (2005) 6-16
28. Mazurie A., Bottani S., and Vergassola M. An evolutionary and functional assessment of regulatory network motifs. Genome Biol. 6 4 (2005) R35
29. Middendorf M., Ziv E., Adams C., Hom J., Koytcheff R., Levovitz C., Woods G., Chen L., and Wiggins C. Discriminative topological features reveal biological network mechanism. BMC Bioinform. 5 (2004) 181
30. Newman M.E.J. The structure and function of complex networks. SIAM Rev. 45 (2003) 167-256
31. Rodriguez-Caso D., Medina M.A., and Sole R.V. Topology, tinkering and evolution of the human transcription factor network. FEBS 272 24 (2005) 6423-6434
32. Saramaki J., and Kaski K. Modelling development of epidemics with dynamic small-world networks. J. Theor. Biol. 234 3 (2005) 413-421
33. Sauro H.M., and Kholodenko B.N. Quantitative analysis of signaling networks. Prog. Biophys. Mol. Biol. 148 1-2 (2004) 5-43
34. Segre D., Vitkup D., and Church G.M. Analysis of optimality in natural and perturbated metabolic networks. Proc. Natl Acad. Sci. USA 99 23 (2002) 15112
35. Song C., Havlin S., and Makse H.A. Self-similarity of complex networks. Nature 433 7024 (2005) 392-395
36. Soyer O.S., Salathé M., and Bonhoeffer S. Signal transduction networks: topology, response and biochemical processes. J. Theor. Biol. 238 (2006) 416-425
37. Sweetlove L.J., and Fernie A.R. Regulation of metabolic network: understanding metabolic complexity in the systems biology era. New Phytol. 168 1 (2005) 9-24
38. Steffen M., Petti A., Aach J., D'haeseleer P., and Church G. Automated modelling of signal transduction network. BMC Bioinform. 3 (2002) 34
39. Tari, L., Baral, C., Dasgupta, P., 2005. Understanding the global properties of functionally-related gene networks using the gene ontology, Pac. Symp. Biocomput. 209-220.
40. Titz B., Schlesner M., and Uetz P. What do we learn from high-throughput protein interaction data?. Expert Rev. Proteomics 1 1 (2004) 111-121
41. Watts D.J., and Strogartz S.H. Collective dynamics of "small-world" networks. Nature 393 (1998) 393