Adaptive dynamics with a single two-state protein

Journal of the Royal Society Interface

Volumn 5, Issue SUPPL. 1, 2008, Pages

  Csikász Nagy, Attila ^a   Soyer, Orkun S ^a  

^a MICROSOFT RESEARCH   (United States)

Author keywords

Adaptive dynamics; Cell cycle; Chemotaxis; Computational modelling; Feed forward loop; Modularity

Indexed keywords

BIOCHEMISTRY; BIOLOGICAL SYSTEMS; PROTEINS;

ADAPTIVE DYNAMICS; CELL CYCLE; CHEMOTAXIS; COMPUTATIONAL MODELLING; FEEDFORWARD LOOPS; MODULARITY;

DYNAMICS;

LIGAND;

ADAPTATION; ARTICLE; CATALYSIS; CHEMOTAXIS; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; PROTEIN DEGRADATION; PROTEIN SYNTHESIS; SIGNAL TRANSDUCTION; SIMULATION;

BACTERIA (MICROORGANISMS);

EID: 46249088921     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2008.0099.focus     Document Type: Article

References (35)

1. Alon, U. 2006 An introduction to systems biology: design principles of biological circuits. New York, NY: Chapman and Hall.
2. Barkai, N. & Leibler, S. 1997 Robustness in simple biochemical networks. Nature 387, 913-917. (doi:10.1038/43199)
3. Behar, M., Hao, N., Dohlman, H. G. & Elston, T. C. 2007 Mathematical and computational analysis of adaptation via feedback inhibition in signal transduction pathways. Biophys. J. 93, 806-821. (doi:10.1529/biophysj.107.107516)
4. Berg, H. C. & Tedesco, P. M. 1975 Transient response to chemotactic stimuli in Escherichia coli. Proc. Natl Acad. Sci. USA 72, 3235-3239. (doi:10.1073/pnas.72.8.3235)
5. Blair, D. F. 1995 How bacteria sense and swim. Annu. Rev. Microbiol. 49, 489-522. (doi:10.1146/annurev.mi.49.100195.002421)
6. Bray, D. 2002 Bacterial chemotaxis and the question of gain. Proc. Natl Acad. Sci. USA 99, 7-9. (doi:10.1073/pnas.022641699)
7. Bray, D., Bourret, R. B. & Simon, M. I. 1993 Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis. Mol. Biol. Cell 4, 469-482.
8. Bray, D., Levin, M. D. & Morton-Firth, C. J. 1998 Receptor clustering as a cellular mechanism to control sensitivity. Nature 393, 85-88. (doi:10.1038/30018)
9. Bray, D., Levin, M. D. & Lipkow, K. 2007 The chemotactic behavior of computer-based surrogate bacteria. Curr. Biol. 17, 12-19. (doi:10.1016/j.cub.2006.11.027)
10. Csikász-Nagy, A., Kapuy, O., Gyorffy, B., Tyson, J. J. & Novak, B. 2007 Modeling the septation initiation network (SIN) in fission yeast cells. Curr. Genet. 51, 245-255. (doi:10.1007/s00294-007-0123-4)
11. Endres, R. G. & Wingreen, N. S. 2006 Precise adaptation in bacterial chemotaxis through "assistance neighborhoods". Proc. Natl Acad. Sci. USA 103, 13 040-13 044. (doi:10. 1073/pnas.0603101103)
12. Goldbeter, A. 1996 Biochemical oscillations and cellular rhythms. Cambridge, UK: Cambridge University Press.
13. Gunawardena, J. 2005 Multisite protein phosphorylation makes a good threshold but can be a poor switch. Proc. Natl Acad. Sci. USA 102, 14 617-14 622. (doi:10.1073/pnas.0507322102)
14. Hansen, C. H., Endres, R. G. & Wingreen, N. S. 2008 Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation. PLoS Comput. Biol. 4, e1. (doi:10.1371/journal.pcbi.0040001)
15. Hartwell, L. H., Hopfield, J. J., Leibler, S. & Murray, A. W. 1999 From molecular to modular cell biology. Nature 402, C47-C52. (doi:10.1038/35011540)
16. Levin, M. D., Shimizu, T. S. & Bray, D. 2002 Binding and diffusion of CheR molecules within a cluster of membrane receptors. Biophys. J. 82, 1809-1817.
17. Lipkow, K. 2006 Changing cellular location of CheZ predicted by molecular simulations. PLoS Comput. Biol. 2, e39. (doi:10.1371/journal. pcbi.0020039)
18. Mangan, S. & Alon, U. 2003 Structure and function of the feed-forward loop network motif. Proc. Natl Acad. Sci. USA 100, 11 980-11 985. (doi:10.1073/pnas.2133841100)
19. Mashukova, A., Spehr, M., Hatt, H. & Neuhaus, E. M. 2006 Beta-arrestin2-mediated internalization of mammalian odorant receptors. J. Neurosci. 26, 9902-9912. (doi:10.1523/JNEUROSCI.2897-06.2006)
20. Morgan, D. O. 1995 Principles of CDK regulation. Nature 374, 131-134. (doi:10.1038/374131a0)
21. Nash, P., Tang, X., Orlicky, S., Chen, Q., Gertier, F. B., Mendenhall, M. D., Sicheri, F., Pawson, T. & Tyers, M. 2001 Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature 414, 514-521. (doi:10.1038/35107009)
22. Piatti, S., Bohm, T., Cocker, J. H., Diffley, J. F. & Nasmyth, K. 1996 Activation of S-phase-promoting CDKs in late G1 defines a "point of no return" after which Cdc6 synthesis cannot promote DNA replication in yeast. Genes Dev. 10, 1516-1531. (doi:10.1101/gad.10.12.1516)
23. Rao, C. V., Kirby, J. R. & Arkin, A. P. 2004 Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. PLoS Biol. 2, E49. (doi:10.1371/journal.pbio. 0020049)
24. Ruoff, P., Zakhartsev, M. & Westerhoff, H. V. 2007 Temperature compensation through systems biology. FEBS J. 274, 940-950. (doi:10.1111/j.1742-4658.2007.05641.x)
25. Segall, J. E., Block, S. M. & Berg, H. C. 1986 Temporal comparisons in bacterial chemotaxis. Proc. Natl Acad. Sci. USA 83, 8987-8991. (doi:10.1073/pnas.83.23.8987)
26. Shankaran, H., Wiley, H. S. & Resat, H. 2007 Receptor downregulation and desensitization enhance the information processing ability of signalling receptors. BMC Syst. Biol. 1, 48. (doi:10.1186/1752-0509-1-48)
27. Shinar, G., Milo, R., Martinez, M. R. & Alon, U. 2007 Input output robustness in simple bacterial signaling systems. Proc. Natl Acad. Sci. USA 104, 19 931-19 935. (doi:10.1073/pnas.0706792104)
28. Sorkin, A. & Von Zastrow, M. 2002 Signal transduction and endocytosis: close encounters of many kinds. Nat. Rev. Mol. Cell Biol. 3, 600-614. (doi:10.1038/nrm883)
29. Sourjik, V. & Berg, H. C. 2002a Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer. Proc. Natl Acad. Sci. USA 99, 12 669-12 674. (doi:10.1073/pnas.192463199)
30. Sourjik, V. & Berg, H. C. 2002b Receptor sensitivity in bacterial chemotaxis. Proc. Natl Acad. Sci. USA 99, 123-127. (doi:10.1073/pnas.011589998)
31. Sourjik, V. & Berg, H. C. 2004 Functional interactions between receptors in bacterial chemotaxis. Nature 428, 437-441. (doi:10.1038/nature02406)
32. Soyer, O. S., Salathé, M. & Bonhoeffer, S. 2006 Signal transduction networks: topology, response and biochemical processes. J. Theor. Biol. 238, 416-425. (doi:10.1016/j.jtbi.2005.05.030)
33. Stock, A. M., Robinson, V. L. & Goudreau, P. N. 2000 Two-component signal transduction. Annu. Rev. Biochem. 69, 183-215. (doi:10.1146/annurev.biochem.69.1.183)
34. Tyson, J. J., Chen, K. C. & Novak, B. 2003 Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15, 221-231. (doi:10.1016/S0955-0674(03) 00017-6)
35. Yi, T. M., Huang, Y., Simon, M. I. & Doyle, J. 2000 Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc. Natl Acad. Sci. USA 97, 4649-4653. (doi:10.1073/pnas.97.9.4649)