A Characterization of Scale Invariant Responses in Enzymatic Networks

PLoS Computational Biology

Volumn 8, Issue 11, 2012, Pages

  Skataric, Maja ^a   Sontag, Eduardo D ^b  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL RESPONSE; LINEARISATION; PHYSIOLOGICAL RESPONSE; PROPERTY; SCALE INVARIANCE; SCALE-INVARIANT; SENSITIVITY RANGE; SENSORY SYSTEM; SINGLE-CELL LEVEL; STIMULUS LEVELS;

PHYSIOLOGICAL MODELS;

ARTICLE; CALCULATION; CONCENTRATION (PARAMETERS); ENZYME ACTIVATION; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME MECHANISM; LINEAR SYSTEM; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; RATING SCALE; SIGNAL TRANSDUCTION;

EID: 84870706819     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002748     Document Type: Article

References (52)

1. Alon U (2006) An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall.
2. Keener J, Sneyd J (1998) Mathematical Physiology. New York: Springer.
3. Block SM, Segall JE, Berg HC, (1983) Adaptation kinetics in bacterial chemotaxis. J Bacteriol 154: 312-323.
4. Shimizu TS, Tu Y, Berg HC, (2010) A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli. Mol Syst Biol 6: 382.
5. Mello BA, Tu Y, (2003) Perfect and near-perfect adaptation in a model of bacterial chemotaxis. Biophys J 84: 2943-2956.
6. Laming D (1986) Sensory Analysis. London: Academic Press.
7. Thompson R (1967) Foundations of physiological psychology. New York: Harper and Row.
8. Kalinin YV, Jiang LL, Tu YH, Wu M, (2009) Logarithmic sensing in Escherichia coli bacterial chemotaxis. Biophysical Journal 96: 2439-2448.
9. R Mesibov GWO, Adler J, (1973) The range of attractant concentrations for bacterial chemotaxis and the threshold and size of response over this range. J Gen Physiol 62: 203-223.
10. Paliwal S, Iglesias PA, Campbell K, Hilioti Z, Groisman A, et al. (2007) MAPK-mediated bimodal gene expression and adaptive gradient sensing in yeast. Nature 446: 46-51.
11. Goentoro L, Kirschner MW, (2009) Evidence that fold-change, and not absolute level, of β-catenin dictates Wnt signaling. Molecular Cell 36: 872-884.
12. Cohen-Saidon C, Cohen AA, Sigal A, Liron Y, Alon U, (2009) Dynamics and variability of ERK2 response to EGF in individual living cells. Molecular Cell 36: 885-893.
13. Shoval O, Goentoro L, Hart Y, Mayo A, Sontag E, et al. (2010) Fold change detection and scalar symmetry of sensory input _elds. Proc Natl Acad Sci U S A 107: 15995-16000.
14. Shoval O, Alon U, Sontag E, (2011) Symmetry invariance for adapting biological systems. SIAM Journal on Applied Dynamical Systems 10: 857-886.
15. Lazova MD, Ahmed T, Bellomo D, Stocker R, Shimizu TS, (2011) Response-rescaling in bacterial chemotaxis. Proc Natl Acad Sci U S A 108: 13870-13875.
16. Sontag E (1998) Mathematical Control Theory. Deterministic Finite-Dimensional Systems, volume 6 of Texts in Applied Mathematics, second edition. New York: Springer-Verlag. xvi+531 pp.
17. Yi TM, Huang Y, Simon M, Doyle J, (2000) Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci U S A 97: 4649-4653.
18. Sontag E, (2003) Adaptation and regulation with signal detection implies internal model. Systems Control Lett 50: 119-126.
19. Iglesias P, (2003) Feedback control in intracellular signaling pathways: Regulating chemotaxis in dictyostelium discoideum. European J Control 9: 216-225.
20. Ma W, Trusina A, El-Samad H, Lim WA, Tang C, (2009) Defining network topologies that can achieve biochemical adaptation. Cell 138: 760-773.
21. Bijlsma J, Groisman E, (2003) Making informed decisions: regulatory interactions between two-component systems. Trends Microbiol 11: 359-366.
22. Grossman A, (1995) Genetic networks controlling the initiation of sporulation and the development of genetic competence in bacillus subtilis. Annu Rev Genet 29: 477-508.
23. Chen H, Bernstein B, Bamburg J, (2000) Regulating actin filament dynamics in vivo. Trends Biochem Sci 25: 19-23.
24. Donovan S, Shannon K, Bollag G, (2002) GTPase activating proteins: critical regulators of intracellular signaling. Biochim Biophys Acta 1602: 23-45.
25. Karp G (2002) Cell and Molecular Biology. Wiley.
26. Stryer L (1995) Biochemistry. Freeman.
27. Sulis M, Parsons R, (2003) PTEN: from pathology to biology. Trends Cell Biol 13: 478-483.
28. Lew D, Burke D, (2003) The spindle assembly and spindle position checkpoints. Annu Rev Genet 37: 251-282.
29. Asthagiri A, Lauffenburger D, (2001) A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (mapk) pathway model. Biotechnol Prog 17: 227-239.
30. Chang L, Karin M, (2001) Mammalian MAP kinase signaling cascades. Nature 410: 37-40.
31. Huang CY, Jr JF, (1996) Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci U S A 93: 10078-10083.
32. Widmann C, Spencer G, Jarpe M, Johnson G, (1999) Mitogen-activated protein kinase: Conservation of a three-kinase module from yeast to human. Physiol Rev 79: 143-180.
33. Angeli D, Ferrell JE, Sontag E, (2004) Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc Natl Acad Sci U S A 101: 1822-1827.
34. Takeda K, Shao D, Adler M, Charest P, Loomis W, et al. (2012) Incoherent feedforward control governs adaptation of activated Ras in a eukaryotic chemotaxis pathway. Sci Signal 5 (205):: ra2.
35. Shah NA, Sarkar CA, (2011) Robust network topologies for generating switch-like cellular responses. PLoS Comput Biol 7: e1002085.
36. Yao G, Tan C, West M, Nevins JR, You L, (2011) Origin of bistability underlying mammalian cell cycle entry. Mol Syst Biol 7: 485.
37. Francois P, Siggia ED, (2008) A case study of evolutionary computation of biochemical adaptation. Phys Biol 5: 026009.
38. Andrews B, Sontag E, Iglesias P (2008) An approximate internal model principle: Applications to nonlinear models of biological systems. In: Proceedings of the 17th IFAC World Congress; 6-11 July 2008; Seoul, Korea. pp. Paper FrB25.3, 6 pages.
39. Sontag E, (2010) Remarks on feedforward circuits, adaptation, and pulse memory. IET Systems Biology 4: 39-51.
40. Mangan S, Itzkovitz S, Zaslaver A, Alon U, (2006) The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J Mol Biol 356: 1073-1081.
41. Kremling A, Bettenbrock K, Gilles ED, (2008) A feed-forward loop guarantees robust behavior in escherichia coli carbohydrate uptake. Bioinformatics 24: 704-710.
42. Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, et al. (2005) Formation of regulatory patterns during signal propagation in a Mammalian cellular network. Science 309: 1078-1083.
43. Mahaut-Smith MP, Ennion SJ, Rolf MG, Evans RJ, (2000) ADP is not an agonist at P2X(1) receptors: evidence for separate receptors stimulated by ATP and ADP on human platelets. Br J Pharmacol 131: 108-114.
44. Marsigliante S, Elia MG, Di Jeso B, Greco S, Muscella A, et al. (2002) Increase of [Ca(2+)](i) via activation of ATP receptors in PC-Cl3 rat thyroid cell line. Cell Signal 14: 61-67.
45. Sasagawa S, Ozaki Y, Fujita K, Kuroda S, (2005) Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nat Cell Biol 7: 365-373.
46. Nagashima T, Shimodaira H, Ide K, Nakakuki T, Tani Y, et al. (2007) Quantitative transcriptional control of ErbB receptor signaling undergoes graded to biphasic response for cell differentiation. J Biol Chem 282: 4045-4056.
47. Menè P, Pugliese G, Pricci F, Di Mario U, Cinotti GA, et al. (1997) High glucose level inhibits capacitative Ca2+ inux in cultured rat mesangial cells by a protein kinase C-dependent mechanism. Diabetologia 40: 521-527.
48. Nesher R, Cerasi E, (2002) Modeling phasic insulin release: immediate and time-dependent effects of glucose. Diabetes 51 (Suppl 1): S53-59.
49. Ridnour LA, Windhausen AN, Isenberg JS, Yeung N, Thomas DD, et al. (2007) Nitric oxide regulates matrix metalloproteinase-9 activity by guanylyl-cyclase-dependent and-independent pathways. Proc Natl Acad Sci U S A 104: 16898-16903.
50. Tsang J, Zhu J, van Oudenaarden A, (2007) MicroRNA-mediated feedback and feedfor-ward loops are recurrent network motifs in mammals. Mol Cell 26: 753-767.
51. Bleris L, Xie Z, Glass D, Adadey A, Sontag E, et al. (2011) Synthetic incoherent feed-forward circuits show adaptation to the amount of their genetic template. Nature Molecular Systems Biology 7: 519.
52. Iman RL, (2001) Appendix A: Latin Hypercube Sampling 1. Encyclopedia of Statistical Sciences, Update 3: 408-411.