Signal amplification in biological and electrical engineering systems. Universal role of cascades

Biophysical Chemistry

Volumn 143, Issue 3, 2009, Pages 132-138

  Grubelnik, Vladimir ^a   Dugonik, Bogdan ^a   Osebik, Davorin ^a   Marhl, Marko ^a  

^a UNIVERSITY OF MARIBOR   (Slovenia)

Author keywords

Cellular signaling; Laplacean transformation; Multi stage amplifier; Protein cascade

Indexed keywords

ARTICLE; BIOENGINEERING; BIOTECHNOLOGY; CELL FUNCTION; CONTROLLED STUDY; ELECTRIC CAPACITANCE; IMPEDANCE; MATHEMATICAL MODEL; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR MECHANICS; PRIORITY JOURNAL; RELIABILITY; SIGNAL DETECTION;

ALGORITHMS; COMPUTER SIMULATION; ELECTRONICS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION;

LAPLACEA;

EID: 67349176597     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2009.04.009     Document Type: Article

References (53)

1. Alves R., and Savageau M.A. Comparative analysis of prototype two-component systems with either bifunctional or monofunctional sensors: differences in molecular structure and physiological function. Mol. Microbiol. 48 (2003) 25-51
2. Ulrich L.E., Koonin E.V., and Zhulin I.B. One-component systems dominate signal transduction in prokaryotes. Trends Microbiol. 13 (2005) 52-56
3. Sauro H.M., and Kholodenko B.N. Quantitative analysis of signaling networks. Prog. Biophys. Mol. Biol. 86 (2004) 5-43
4. Neves R.S., and Iyengar R. Modeling of signaling networks. BioEssays 24 (2002) 1110-1117
5. Bray D. Protein molecules as computational elements in living cells. Nature 376 (1995) 307-312
6. Wray G.A. Promoter logic. Science 279 (1998) 1871-1872
7. M. Ptashne, Genetic Switch: Phage Lambda and Higher Organisms (Cell Press, Blackwell Scientific Publications, 2nd edn. 1992).
8. Reed R.R. How does the nose know?. Cellular 60 (1990) 1-2
9. Stryer L. Visual excitation and recovery. J. Biol. Chem. 266 (1991) 10711-10714
10. Koshland D.E. Biochemistry of sensing and adaptation. Trends Biochem. Sci. 5 (1980) 297
11. Detwiler P.B., Ramanathan S., Sengupta A., and Shraiman B.I. Engineering aspects of enzymatic signal transduction: photoreceptors in the retina. Biophys J. 79 (2000) 2801-2817
12. Wald G. Visual excitation and blood clotting. Science 150 (1965) 1028-1030
13. Levine S.M. Enzyme amplifier kinetics. Science 152 (1966) 651-653
14. Ferrell J.E. Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem. Sci. 21 (1996) 460-466
15. Brown G.C., Hoek J.B., and Kholodenko B.N. Why do proteins have more than one level?. Trends Biochem. Sci. 22 (1997) 288
16. Pearson G., Robinson F., Gibson T., Xu B.E., Karandikar M., Berman K., and Cobb M. Mitogen-activated protein (MAP) kinase pathways: regulation and physiological functions. Endocr. Rev. 22 (2001) 153-183
17. Stadtman E.R., and Chock P.B. Superiority of interconvertible enzyme cascades in metabolic regulation: analysis of multicyclic systems. Proc. Natl. Acad. Sci. USA. 74 (1977) 2766-2770
18. Koshland D.E., Goldbeter A., and Stock J.B. Amplification and adaptation in regulatory and sensory systems. Science 217 (1982) 220-225
19. Widmann C., Gibson S., Jarpe M.B., and Johnson G.L. Mitogen-activated protein kinase: conservation of a three-kinase module from yeast to human. Physiol. Rev. 79 (1999) 143-180
20. Chock P.B., Rhee S.G., and Stadtman E.R. Interconvertible enzyme cascades in cellular regulation. Annu. Rev. Biochem. 49 (1980) 813-843
21. Goldbeter A., and Koshland D.E. An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl. Acad. Sci. USA 78 (1981) 6840-6844
22. Goldbeter A., and Koshland D.E. Sensitivity amplification in biochemical systems. Q. Rev. Biophys. 15 (1982) 555-591
23. Goldbeter A., and Koshland D.E. Ultrasensitivity in biochemical systems controlled by covalent modification. Interplay between zero-order and multisteps effects. J. Biol. Chem. 259 (1984) 14441-14447
24. Mutalik V.K., Singh A.P., Edwards J.S., and Venkatesh K.V. Robust global sensitivity in multiple enzyme cascade system explains how the downstream cascade structure may remain unaffected by cross-talk. FEBS Lett. 558 (2004) 79-84
25. Kholodenko B.N., Hoek J.B., Westerhoff H.V., and Brown G.C. Quantification of information transfer via cellular signal transduction pathways. FEBS Lett. 414 (1997) 430-434
26. Heinrich R., Neel B.G., and Rapoport T.A. Mathematical models of protein kinase signal transduction. Mol. Cell. 9 (2002) 957-970
27. Mayawala K., Gelmi C.A., and Edwards J.S. MAPK cascade possesses decoupled controllability of signal amplification and duration. Biophys. J. 87 (2004) L01-L03
28. Chaves M., Sontag E.D., and Dinerstein R.J. Optimal length an signal amplification in weakly activated signal transduction cascades. J. Phys. Chem. B 108 (2004) 15311-15320
29. Nakabayashi J., and Sasaki A. Optimal phosphorylation step number of intracellular signal-transduction pathway. J. Theor. Biol. 233 (2005) 413-421
30. Marhl M., and Grubelnik V. Role of cascades in converting oscillatory signals into stationary step-like responses. Biosystems 87 (2007) 58-67
31. Koshland D.E., Goldbeter A., and Stock J.B. Amplification and adaptation in regulatory and sensory systems. Science 217 (1982) 220-225
32. Fell D. Understanding the Control of Metabolism (1997), Portland Press
33. Balaji S., and Lakshminarayanan S. Conceptual comparison of metabolic pathways with electronic circuits. J. Bionics Eng. 1 (2004) 175-182
34. Chiam K.H., Bhargava V., and Rajagopal G. Oscillatory dynamics in the mitogen-activated protein kinase cascade. Computational Systems Bioinformatics Conference (2005), Stanford, California 164-165
35. Hersen P., Mclean M.N., Mahadevan L., and Ramanathan S. Signal processing by HOG MAP kinase pathway. PNAS 105 (2008) 7165-7170
36. Arkin A.P. Signal processing by biochemical reaction networks. In: Walleczek J. (Ed). Self-Organized Biodynamics and Nonlinear Control (2000), Cambridge University Press 112-144
37. Marhl M., Perc M., and Schuster S. Selective regulation of cellular processes via protein cascades acting as band-pass filters for time-limited oscillations. FEBS Lett. 579 (2005) 5461-5465
38. Ferrell J.E. Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem. Sci. 21 (1996) 460-466
39. Ragazzini J.R., Randall R.H., and Russell F.A. Analysis of problems in dynamics by electronic circuits. Proc. IRE 35 (1947) 444-452
40. Theodore F.B., Jeffrey S.B., and Guillermo R. Electronic Devices and Circuits. 6th edn. (2004), Prentice Hall
41. Juang C., Shiue S.F., Tsai S.Y., and Yang J.N. Transimpedance amplifiers using three cascade variable inverter gain stages. Analog Integr. Circuits Signal Process. 49 (2006) 299-302
42. Maxim A. A 10.7 GHz SiGe BICMOS limiting amplifier using multiple offset cancellation loops, Custom Integrated Circuits Conference. Proceedings of the IEEE (2005) 127-130
43. Trotta S., Knapp H., Aufinger K., Meister T.F., Bock J., Dehlink B., Simburger W., and Scholtz A.L. An 84 GHz bandwidth and 20 dB gain broadband amplifier in SiGe bipolar technology. IEEE Solid-State Circuits Society 42 (2007) 2099-2106
44. Woods N.M., Cuthbertson K.S.R., and Cobbold P.H. Repetitive transient rises in cytoplasmic free calcium in hormone-stimulated hepatocytes. Nature 319 (1986) 600-602
45. 2+ signaling. Adv. Phys. 53 (2004) 255-440
46. Matsuda S., Kosako H., Takenaka K., Moriyama K., Sakai H., Akiyama T., Gotoh Y., and Nishida E. Xenopus MAP kinase activator: identification and function as a key intermediate in the phosphorylation cascade. EMBO J. 3 (1992) 973-982
47. Yew N., Mellini M.L., and Vande Woude G.F. Meiotic initiation by the mos protein in Xenopus. Nature 355 (1992) 649-652
48. Haccard O., Sarcevic B., Lewellyn A., Hartley R.S., Roy L.M., Izumi T., Erikson E., and Maller J.L. Induction of metaphase arrest in cleaving Xenopus embryos by MAP kinase. Science 262 (1993) 1262-1265
49. Adams J. Mastering Electronics Workbench. 1st edn. (2001), McGraw-Hill
50. National Semiconductor Corporation, http://cache.national.com/ds/TL/TL082.pdf, accessed April 2007.
51. C.E. Shannon, A mathematical theory of communication, Bell. Syst.Tech. J. 27 (1948) 379-423 and 623-656.
52. Dolmetsch R.E., Xu K., and Lewis R.S. Calcium oscillations increase the efficiency and specificity of gene expression. Nature 392 (1998) 933-936
53. 2+ spike frequency can optimize gene expression. Nature 392 (1998) 936-1941