Signaling in small subcellular volumes. II. Stochastic and diffusion effects on synaptic network properties

Biophysical Journal

Volumn 87, Issue 2, 2004, Pages 745-753

  Bhalla, Upinder S ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALCULATION; COMPLEX FORMATION; DIFFUSION; PHASE TRANSITION; SCALE UP; SIGNAL TRANSDUCTION; SIMULATION; STOCHASTIC MODEL; SYNAPSE;

EID: 4143144113     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.040501     Document Type: Article

References (35)

1. Abeliovich, A., C. Chen, Y. Goda, A. Silva, C. F. Stevens, and S. Tonegawa. 1993. Modified hippocampal long-term potentiation in PKC gamma-mutant mice. Cell. 75:1253-1262.
2. 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.
3. Bhalla, U. S. 2002a. Mechanisms for temporal tuning and filtering by postsynaptic signaling pathways. Biophys. J. 83:740-752.
4. Bhalla, U. S. 2002b. Temporal pattern decoding by synaptic signaling pathways. J. Comput. Neurosci. 13:49-62.
5. Bhalla, U. S. 2002c. Use of Kinetikit and GENESIS for modeling signaling pathways. In Methods in Enzymology. J. D. Hildebrandt and R. Iyengar, editors. Academic Press. 3-23.
6. Bhalla, U. S., and R. Iyengar. 1999. Emergent properties of networks of biological signaling pathways. Science. 283:381-387.
7. Bhalla, U. S., and R. Iyengar. 2001. Robustness of the bistable behavior of a biological signaling feedback loop. Chaos. 11:221-226.
8. Bhalla, U. S., P. T. Ram, and R. Iyengar. 2002. MAP Kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science. 297:1018-1023.
9. Bialek, W. 2001. Stability and noise in biochemical switches. NIPS. 13:103-109.
10. Blitzer, R. D., J. H. Connor, G. P. Brown, T. Wong, S. Shenolikar, R. Iyengar, and E. M. Landau. 1998. Gating of CaMKII by cAMP-regulated protein phosphatase activity during LTP. Science. 280:1940-1942.
11. Bolshakov, V. Y., L. Carboni, M. H. Cobb, S. A. Siegelbaum, and F. Belardetti. 2000. Dual MAP kinase pathways mediate opposing forms of long-term plasticity at CA3-CA1 synapses. Nat. Neurosci. 3:1107-1112.
12. Bray, D. 2001. Cell Movements: from Molecules to Motility. Garland Publishing, New York.
13. Collins, J. J., C. C. Chow, and T. T. Imhoff. 1995. Stochastic resonance without tuning. Nature. 376:236-238.
14. Haustein, E., and P. Schwille. 2003. Ultrasensitive investigations of biological systems by fluorescence correlation spectroscopy. Methods. 29:153-166.
15. Horton, A. C., and M. D. Ehlers. 2003. Neuronal polarity and trafficking. Neuron. 40:277-295.
16. Hur, E. M., and K. T. Kim. 2002. G protein-coupled receptor signalling and cross-talk: achieving rapidity and specificity. Cell. Signal. 14:397-405.
17. 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.
18. Lisman, J. E., and M. A. Goldring. 1988. Feasibility of long-term storage of graded information by the Ca2+/calmodulin-dependent protein kinase molecules of the postsynaptic density. Proc. Natl. Acad. Sci. USA. 85:5320-5324.
19. Lisman, J. E., and C. C. McIntyre. 2001. Synaptic plasticity: a molecular memory switch. Curr. Biol. 11:R788-R791.
20. Moore, P. B., and T. A. Steitz. 2003. The structural basis of large ribosomal subunit function. Annu. Rev. Biochem. 72:813-850.
21. 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.
22. Paddock, M. L., G. Feher, and M. Y. Okamura. 2003. Proton transfer pathways and mechanism in bacterial reaction centers. FEBS Lett. 555:45-50.
23. 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.
24. Selcher, J. C., E. J. Weeber, J. Christian, T. Nekrasova, G. E. Landreth, and J. D. Sweatt. 2003. A role for ERK MAP Kinase in physiologic temporal integration in hippocampal area CA1. Learn. Mem. 10:26-39.
25. Sheng, M., and M. J. Kim. 2002. Postsynaptic signaling and plasticity mechanisms. Science. 298:776-780.
26. Sivakumaran, S., S. Hariharaputran, J. Mishra, and U. S. Bhalla. 2003. The database of quantitative cellular signaling: repository and analysis tools for chemical kinetic models of signaling networks. Bioinformatics. 19:408-415.
27. Soderling, T. R., and V. A. Derkach. 2000. Postsynaptic protein phosphorylation and LTP. Trends Neurosci. 23:75-80.
28. Svoboda, K., D. W. Tank, and W. Denk. 1996. Direct measurement of coupling between dendritic spines and shafts. Science. 272:716-719.
29. Tsodyks, M. 2002. Spike-timing-dependent synaptic plasticity-the long road towards understanding neuronal mechanisms of learning and memory. Trends Neurosci. 25:599-600.
30. Vasudeva, K., and U. S. Bhalla. 2004. Adaptive stochastic-deterministic chemical kinetic simulations. Bioinformatics. 20:78-84.
31. Vilar, J. M. G., and S. Leibler. 2003. DNA looping and physical constraints on transcription regulation. J. Mol. Biol. 331:981-989.
32. Weiss, M., H. Hashimoto, and T. Nilsson. 2003. Anomalous protein diffusion in living cells as seen by fluorescence correlation spectroscopy. Biophys. J. 84:4043-4052.
33. Wu, G.-Y., K. Deisseroth, and R. W. Tsien. 2001. Spaced stimuli stabilize MAPK pathway activation and its effects on dendritic morphology. Nat. Neurosci. 4:151-158.
34. Yamauchi, T. 2002. Molecular constituents and phosphorylation-dependent regulation of the post-synaptic density. Mass Spectrom. Rev. 21:266-286.
35. Zeng, H., S. Chattarji, M. Barbarosie, L. Rondi-Reig, B. D. Philpot, T. Miyakawa, M. F. Bear, and S. Tonegawa. 2001. Forebrain-specific calcineurin knockout selectively impairs bidirectional synaptic plasticity and working/episodic-like memory. Cell. 107:617-629.