Signaling in small subcellular volumes. I. Stochastic and diffusion effects on individual pathways

Biophysical Journal

Volumn 87, Issue 2, 2004, Pages 733-744

  Bhalla, Upinder S ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN KINASE;

ARTICLE; CELL VOLUME; CHEMICAL REACTION; DIFFUSION; DYNAMICS; MONTE CARLO METHOD; PROTEIN FUNCTION; REACTION ANALYSIS; SIGNAL TRANSDUCTION; STOCHASTIC MODEL;

EID: 4143118798     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.040469     Document Type: Article

References (45)

1. Arkin, A., J. Ross, and H. H. McAdams. 1998. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics. 149:1633-1648.
2. Bayer, K. U., and H. Schulman. 2001. Regulation of signal transduction by protein targeting: the case for CaMKII. Biochem. Biophys. Res. Commun. 289:917-923.
3. 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.
4. Bhalla, U. S. 1998. The network within: signaling pathways. In The Book of GENESIS: Exploring Realistic Neural Models with the GEneral NEural SImulation System. J. M. Bower and D. Beeman, editors. Springer-Verlag, New York. 169-190.
5. Bhalla, U. S. 2002a. Mechanisms for temporal tuning and filtering by postsynaptic signaling pathways. Biophys. J. 83:740-752.
6. Bhalla, U. S. 2002b. Use of Kinetikit and GENESIS for modeling signaling pathways. In Methods in Enzymology. J. D. Hildebrandt and R. Iyengar, editors: Academic Press, New York. 3-23.
7. Bower, J. M., and D. Beeman. 1998. The Book of GENESIS. Springer-Verlag, New York.
8. Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain. 2002. Stochastic gene expression in a single cell. Science. 297:1183-1186.
9. Falcke, M. 2003. On the role of stochastic channel behavior in intracellular Ca2+ dynamics. Biophys. J. 84:42-56.
10. Fink, C.C., B. Slepchenko, I. I. Moraru, J. Watras, J. C. Schaff, and L. M. Loew. 2000. An image-based model of calcium waves in differentiated neuroblastoma cells. Biophys. J. 79:163-183.
11. Franks, K. M., T. M. J. Bartol, and T. J. Sejnowski. 2002. A Monte Carlo model reveals independent signaling at central glutamatergic synapses. Biophys. J. 83:2333-2348.
12. Gibson, M. A., and J. Bruck. 2000. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A. 104:1876-1889.
13. Gillespie, D. T. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81:2340-2361.
14. Goldberg, J. H., G. Tamas, D. Aronov, and R. Yuste. 2003. Calcium microdomains in aspiny dendrites. Neuron. 40:807-821.
15. 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.
16. Gonze, D., J. Halloy, and A. Goldbeter. 2002. Robustness of circadian rhythms with respect to molecular noise. Proc. Natl. Acad. Sci. USA. 99:673-678.
17. Harrison, L. G. 1993. Kinetic Theory of Living Pattern. Cambridge University Press, Cambridge.
18. Kepler, T. B., and T. C. Elston. 2001. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys. J. 81:3116-3136.
19. Kholodenko, B. N. 2003. Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors. J. Exp. Biol. 206:2073-2082.
20. Kholodenko, B. N., G. C. Brown, and J. B. Hoek. 2000. Diffusion control of protein phosphorylation in signal transduction pathways. Biochem. J. 350:901-907.
21. Kierzek, A. M., J. Zaim, and P. Zielenkiewicz. 2001. The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. J. Biol. Chem. 276:8165-8172.
22. Levchenko, A., J. Bruck, and P. W. Sternberg. 2000. Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc. Natl. Acad. Sci. USA. 97:5818-5823.
23. Levin, M. D., T. S. Shimizu, and D. Bray. 2002. Binding and diffusion of CheR molecules within a cluster of membrane receptors. Biophys. J. 82:1809-1817.
24. MacGregor, R. J. 1987. Neural and Brain Modeling. Academic Press, San Diego.
25. Meyer, T., and K. Shen. 2000. In and out of the postsynaptic region: signaling proteins on the move. Trends Cell Biol. 10:238-244.
26. Morrison, D. K., and R. J. Davis. 2003. Regulation of MAP kinase signaling modules by scaffold proteins in mammals. Annu. Rev. Cell Dev. Biol. 19:91-118.
27. Morton-Firth, C. J., T. S. Shimizu, and D. Bray. 1999. A free-energy-based stochastic simulation of the Tar receptor complex. J. Mol. Biol. 286:1059-1074.
28. Ortiz, J., H. W. Harris, X. Guitart, R. Z. Terwillinger, J. W. Haycock, and E. J. Nestler. 1995. Extracellular signal-regulated protein kinases (ERKs) and ERK Kinase (MEK): Regional distribution and regulation by chronic morphine. J. Neurosci. 15:1285-1297.
29. Ozbudak, E. M., M. Thattai, I. Kurster, A. D. Grossman, and A. van Oudenaarden. 2002. Regulation of noise in the expression of a single gene. Nat. Genet. 31:69-73.
30. Paulsson, J., O. G. Berg, and M. Ehrenberg. 2000. Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. Proc. Natl. Acad. Sci. USA. 97:7148-7153.
31. Rao, C. V., D. M. Wolf, and A. P. Arkin. 2002. Control, exploitation and tolerance of intracellular noise. Nature. 420:231-237.
32. Resat, H., J. A. Ewald, D. A. Dixon, and H. S. Wiley. 2003. An integrated model of epidermal growth factor receptor trafficking and signal transduction. Biophys. J. 85:730-743.
33. Rich, T. C., K. A. Fagan, H. Nakata, J. Schaack, D. M. Cooper, and J. W. Karpen. 2000. Cyclic nucleotide-gated channels colocalize with adenylyl cyclase in regions of restricted cAMP diffusion. J. Gen. Physiol. 116:147-161.
34. Sabatini, B. L., and K. Svoboda. 2000. Analysis of calcium channels in single spines using optical fluctuation analysis. Nature. 408:589-593.
35. Shen, K., M. N. Teruel, J. H. Connor, S. Shenolikar, and T. Meyer. 2000. Molecular memory by reversible translocation of calcium/calmodul-independent protein kinase II. Nat. Neurosci. 3:881-886.
36. Shimizu, T. S., S. V. Aksenov, and D. Bray. 2003. A spatially extended stochastic model of the bacterial chemotaxis signaling pathway. J. Mol. Biol. 329:291-309.
37. Sivakumaran, S., S. Hariharaputran, J. Mishra, and U.S. Bhalla. 2003. The database of quantitative cellular signaling: management and analysis of chemical kinetic models of signaling networks. Bioinformatics. 19:408-415.
38. Smith, F. D., and J. D. Scott. 2002. Signaling complexes: junctions on the intracellular information super highway. Curr. Biol. 12:32-40.
39. Stiles, J. R., and T. M. Bartol. 2000. Monte Carlo methods for simulating realistic synaptic microphysiology using mcell. In Computational Neuroscience: Realistic Modeling for experimentalists. E. De Schutter, editor. CRC Press, Boca Raton, FL. 87-128.
40. Strack, S., M. A. Barban, B. E. Wadzinski, and R. J. Colbran. 1997. Differential inactivation of postsynaptic density-associated and soluble Ca2+/Calmodulin-dependent protein kinase II by protein phosphatases I and 2A. J. Neurochem. 68:2119-2128.
41. Strack, S., and R. J. Colbran. 1998. Autophosphorylation-dependent targeting of calcium/calmodulin-dependent protein kinase II by the NR2B subunit of the N-methyl- D-aspartate receptor. J. Biol. Chem. 273:20689-20692.
42. Strier, D. E., A. C. Ventura, and S. P. Dawson. 2003. Saltatory and continuous calcium waves and the rapid buffering approximation. Biophys. J. 85:3575-3586.
43. Thattai, M., and A. van Oudenaarden. 2001. Intrinsic noise in gene regulatory networks. Proc. Natl. Acad. Sci. USA. 98:8614-8619.
44. Vasudeva, K., and U. S. Bhalla. 2004. Adaptive stochastic-deterministic chemical kinetic simulations. Bioinformatics. 20:78-84.
45. Vilar, J. M., H. Y. Kueh, N. Barkai, and S. Leibler. 2002. Mechanisms of noise-resistance in genetic oscillators. Proc. Natl. Acad. Sci. USA. 99:5988-5992.