The effects of reversibility and noise on stochastic phosphorylation cycles and cascades

Biophysical Journal

Volumn 95, Issue 5, 2008, Pages 2183-2192

  Miller, Clark A ^a   Beard, Daniel A ^b  

^a University of Wisconsin Madison   (United States)

^b MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; PHOSPHOTRANSFERASE;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; ENZYME STABILITY; HYDROLYSIS; KINETICS; METABOLISM; PHOSPHORYLATION; SIGNAL TRANSDUCTION; STATISTICS; THERMODYNAMICS;

ADENOSINE TRIPHOSPHATE; ALGORITHMS; ENZYME STABILITY; HYDROLYSIS; KINETICS; MODELS, BIOLOGICAL; PHOSPHORYLATION; PHOSPHOTRANSFERASES; SIGNAL TRANSDUCTION; STOCHASTIC PROCESSES; THERMODYNAMICS;

EID: 51649085888     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.126185     Document Type: Article

References (28)

1. Swain, P. S., M. B. Elowitz, and E. D. Siggia. 2002. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl. Acad. Sci. USA. 99:12795-12800.
2. Süel, G. M., R. P. Kulkarni, J. Dworkin, J. Garcia-Ojalvo, and M. B. Elowitz. 2007. Tunability and noise dependence in differentiation dynamics. Science. 315:1716-1719.
3. Lestas, I., J. Paulsson, N. E. Ross, and G. Vinnicombe. 2008. Noise in gene regulatory networks. IEEE Trans. Automat. Contr. 53:189-200.
4. Paulsson, J. 2004. Summing up the noise in gene networks. Nature. 427:415-418.
5. Chickarmane, V., B. N. Kholodenko, and H. M. Sauro. 2007. Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation. J. Theor. Biol. 244:68-76.
6. Wang, X., N. Hao, H. G. Dohlman, and T. C. Elstonz. 2006. Bistability, stochasticity, and oscillations in the mitogen-activated protein kinase cascade. Biophys. J. 90:1961-1978.
7. Morishita, Y., T. J. Kobayashi, and K. Aihara. 2006. An optimal number of molecules for signal amplification and discrimination in a chemical cascade. Biophys. J. 91:2072-2081.
8. Shibata, T., and K. Fujimoto. 2005. Noisy signal amplification in ultrasensitive signal transduction. Proc. Natl. Acad. Sci. USA. 102:331-336.
9. Thattai, M., and A. van Oudenaarden. 2002. Attenuation of noise in ultrasensitive signaling cascades. Biophys. J. 82:2943-2950.
10. Levine, J., H. Y. Kueh, and L. Mirny. 2007. Intrinsic fluctuations, robustness, and tunability in signaling cycles. Biophys. J. 92:4473-4481.
11. Berg, O. G., J. Paulsson, and M. Ehrenberg. 2000. Fluctuations and quality of control in biological cells: zero-order ultrasensitivity reinvestigated. Biophys. J. 79:1228-1236.
12. Samoilov, M., S. Plyasunov, and A. P. Arkin. 2005. Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc. Natl. Acad. Sci. USA. 102:2310-2315.
13. Samoilov, M. S., and A. P. Arkin. 2006. Deviant effects in molecular reaction pathways. Nat. Biotechnol. 24:1235-1240.
14. Goldbeter, A., and D. E. Koshland, Jr. 1981. An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl. Acad. Sci. USA. 78:6840-6844.
15. Craciun, G., Y. Tang, and M. Feinberg. 2006. Understanding bistability in complex enzyme-driven reaction networks. Proc. Natl. Acad. Sci. USA. 103:8697-8702.
16. Artyomov, M. N., J. Das, M. Kardar, and A. K. Chakraborty. 2007. Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities. Proc. Natl. Acad. Sci. USA. 104:18958-18963.
17. Qian, H. 2003. Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction. Biophys. Chem. 105:585-593.
18. Feinberg, M., and P. Ellison. 1998. The Chemical Reaction Network Toolbox Ver. 1.1. Ohio State University, Columbus, OH. http://www.chbmeng.ohio-state. edu/feinberg/crnt.
19. Feinberg, M. 1987. Chemical reaction network structure and the stability of complex isothermal reactors. I. The deficiency zero and deficiency one theorems. Chem. Eng. Sci. 42:2229-2268.
20. Feinberg, M. 1988. Chemical reaction network structure and the stability of complex isothermal reactors. II: Multiple steady states for networks of deficiency one. Chem. Eng. Sci. 43:1-25.
21. Ellison, P., and M. Feinberg. 2000. How catalytic mechanisms reveal themselves in multiple steady-state data: I. Basic principles. J. Mol. Catal. Chem. 154:155-167.
22. Beard, D. A., and H. Qian. 2008. Biochemical signaling modules. In Chemical Biophysics: Quantitative Analysis of Cellular Systems. Cambridge University Press, Cambridge, UK.
23. Gillespie, D. T. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81:2340-2361.
24. Kierzek, A. M. 2002. STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm. Bioinformatics. 18:470-481.
25. Angeli, D., and E. D. Sontag. 2008. Translation-invariant monotone systems, and a global convergence result for enzymatic futile cycles. Nonlinear Anal. Real World Appl. 9:128-140.
26. Qian, H. 2007. Phosphorylation energy hypothesis: open chemical systems and their biological functions. Annu. Rev. Phys. Chem. 58:113-142.
27. Gómez-Uribe, C. A., and G. C. Verghese. 2007. Mass fluctuation kinetics: capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations. J. Chem. Phys. 126:024109.
28. Goutsias, J. 2007. Classical versus stochastic kinetics modeling of biochemical reaction systems. Biophys. J. 92:2350-2365.