The impact of retroactivity on the input/output static characteristics of a signaling component

ASME 2010 Dynamic Systems and Control Conference, DSCC2010

Volumn 1, Issue , 2010, Pages 313-320

  Ventura, A C ^a   Jiang, P ^a   Ninfa, A J ^a   Van Wassenhove, L ^a   Merajver, S D ^a   Del Vecchio, D ^b  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR SYSTEM; COVALENT MODIFICATIONS; DOWNSTREAM TARGET; ENGINEERING SYSTEMS; INPUT/OUTPUT; SIGNALING COMPONENTS; STATIC CHARACTERISTIC;

SIGNALING;

EID: 79958183032     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1115/DSCC2010-4061     Document Type: Conference Paper

References (30)

1. Klipp, E., Herwig, R., Kowald, A., Wierling, C., and Lehrach, H., 2005. SYstems Biology in Practice. Wiley.
2. Blume-Jensen, P., and Hunter, T., 2001. "Oncogenic kinase signalling". Nature, 411, pp. 355-365. (Pubitemid 32467045)
3. Behar, M., Dohlman, H. G., and Elston, T. C., 2007. "Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks". Proc. Natl. Acad. Sci. USA, 104(41), pp. 16147-16151.
4. Fell, D., 1997. Understanding the control of metabolism. Portland Press.
5. Seger, R., and Krebs, E. G., 1995. "The MAPK signaling cascade". The FASEB Journal, 9, pp. 726-735.
6. Rubinfeld, H., and Seger, R., 2005. "The ERK cascade: a prototype of MAPK signaling". Mol Biotechnol, 31(2), pp. 151-174. (Pubitemid 41306584)
7. Stadtman, E. R., and Chock, P. B., 1977. "Superiority of interconvertible enzyme cascades in metabolic regulation: Analysis of monocyclic systems". Proc. Natl. Acad. Sci. USA, 74(7), pp. 2761-2765. (Pubitemid 8150816)
8. Chock, P. B., and Stadtman, E. R., 1977. "Superiority of interconvertible enzyme cascades in metabolite regulation: analysis of multicyclic systems". Proc. Natl. Acad. Sci. USA, 74(7), pp. 2766-2770. (Pubitemid 8150817)
9. Goldbeter, A., and Koshland, D. E., 1981. "An amplified sensitivity arising from covalent modification in biological systems". Proc. Natl. Acad. Sci. USA, pp. 6840-6844. (Pubitemid 12216857)
10. A, A. G., and Jr., D. E. K. "Ultrasensitivity in biochemical systems controlled by covalent modification. interplay between zero-order and multistep effects". J. Biol. Chem., 259(23).
11. Cárdenas, M. L., and Cornish-Bowden, A., 1989. "Characteristics necessary for an interconvertible enzyme cascade to generate a highly sensitive response to an effector". Biochem. J., 257(2), pp. 339-345. (Pubitemid 19040902)
12. Del Vecchio, D., Ninfa, A. J., and Sontag, E. D., 2008. "Modular cell biology: Retroactivity and insulation". Nature/EMBO Molecular Systems Biology, 4:161.
13. Del Vecchio, D., and Sontag, E. D., 2009. "Engineering principles in bio-molecular systems: From retroactivity to modularity". European Journal of Control (Special Issue).
14. Del Vecchio, D., Ninfa, A. J., and Sontag, E. D., 2008. "A systems theory with retroactivity: Application to transcriptional modules". Proc. of American Control Conference, pp. 1368-1373.
15. Del Vecchio, D., and Jayanthi, S., 2008. "Retroactivity attenuation in transcriptional networks: Design and analysis of an insulation device". Proc. Conference on Decision and Control.
16. Saez-Rodriguez, J., Kremling, A., Conzelmann, H., Bettenbrock, K., and Gilles, E. D., 2004. "Modular analysis of signal transduction networks". IEEE Control Systems Magazine, pp. 35-52.
17. Saez-Rodriguez, J., Kremling, A., and Gilles, E., 2005. "Dissecting the puzzle of life: modularization of signal transduction networks". Computers and Chemical Engineering, 29, pp. 619-629. (Pubitemid 40417807)
18. Ventura, A. C., Sepulchre, J.-A., and Merajver, S. D., 2008. "A hidden feedback in signaling cascades is revealed". PLoS Comput Biol, 4(3).
19. Jayanthi, S., and Del Vecchio, D., 2009. "On the compromise between retroactivity attenuation and noise amplification in gene regulatory networks". In Proc. Conf. Decision and Control.
20. Franco, E., Del Vecchio, D., and Murray, R. M., 2009. "Design of insulating devices for in vitro synthetic circuits". In Proc. Conf. on Decision and Control.
21. Jr, F. E. F., 1996. "Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switchlike outputs". Trends Biochem Sci., 21(12), pp. 460-466.
22. Huang, C. Y., and Jr., J. E. F., 1996. "Ultrasensitivity in the mitogen-activated protein kinase cascade". Proc. Natl. Acad. Sci. USA, 93(19), pp. 10078-83.
23. Alon, U., 2007. An introduction to systems biology. Design principles of biological circuits. Chapman-Hall.
24. Kholodenko, B. N., 2006. "Cell signaling dynamics in time and space". Nat. Rev. Mol. Cell Biol., 7(3), pp. 165-176.
25. Kholodenko, B. N., Kiyatkin, A., Bruggeman, F. J., Sontag, E., Westerhoff, H. V., and Hoek, J. B., 2002. "Untangling the wires: A strategy to trace functional interactions in signaling and gene networks". Proc. Natl. Acad. Sci. USA, 99(20), pp. 12841-12846.
26. Pioszak, A. A., Jiang, P., and Ninfa, A. J., 2000. "The Escherichia coli PII signal transduction protein regulates the activities of the two-component system transmitter protein NRII by direct interaction with the kinase domain of the transmitter module.". Biochemistry, 39(44), pp. 13450-13461.
27. Jiang, P., Mayo, A. E., and Ninfa, A. J., 2007. "Escherichia coli glutamine synthetase adenylyltransferase (ATase, EC 2.7.7.49): kinetic characterization of regulation by PII, PII-UMP, glutamine, and alpha-ketoglutarate.". Biochemistry, 46(13), pp. 4133-46. (Pubitemid 46536075)
28. Ninfa, A. J., and Jiang, P., 2005. "PII signal transduction proteins: sensors of α-ketoglutarate that regulate nitrogen metabolism". Curr Opinion Microbiol., 8, pp. 168-173. (Pubitemid 40417958)
29. Jiang, P., and Ninfa, A. J., 2007. "Escherichia coli PII signal transduction protein controlling nitrogen assimilation acts as a sensor of adenylylate energy charge in vitro". Biochemistry, 46, pp. 12979-12996. (Pubitemid 350086218)
30. Ventura, A. C., Jiang, P., Wassenhove, L. V., Del Vecchio, D., Merajver, S. D., and Ninfa, A. J., 2010. "Signaling properties of a covalent modification cycle are altered by a downstream target". Proc. Natl. Acad. Sci. USA, In Press.