Mechanistic systems models of cell signaling networks: A case study of myocyte adrenergic regulation

Progress in Biophysics and Molecular Biology

Volumn 85, Issue 2-3, 2004, Pages 261-278

  Saucerman, Jeffrey J ^a   McCulloch, Andrew D ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Adrenergic regulation; Mathematical model; Myocyte

Indexed keywords

BETA ADRENERGIC RECEPTOR; CALCIUM BINDING PROTEIN; CALCIUM CHANNEL L TYPE; PHOSPHOLAMBAN; RYANODINE RECEPTOR;

ANIMAL; BIOLOGICAL MODEL; CALCIUM SIGNALING; CELL CULTURE; COMPARATIVE STUDY; COMPUTER SIMULATION; CONFERENCE PAPER; EVALUATION; FEEDBACK SYSTEM; HEART CONTRACTION; HEART MUSCLE CELL; METABOLISM; PHOSPHORYLATION; PHYSIOLOGY; RAT; SIGNAL TRANSDUCTION; VALIDATION STUDY;

ANIMALS; CALCIUM CHANNELS, L-TYPE; CALCIUM SIGNALING; CALCIUM-BINDING PROTEINS; CELLS, CULTURED; COMPUTER SIMULATION; FEEDBACK; MODELS, CARDIOVASCULAR; MYOCARDIAL CONTRACTION; MYOCYTES, CARDIAC; PHOSPHORYLATION; RATS; RECEPTORS, ADRENERGIC, BETA; RYANODINE RECEPTOR CALCIUM RELEASE CHANNEL; SIGNAL TRANSDUCTION;

EID: 2442587536     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbiomolbio.2004.01.005     Document Type: Conference Paper

References (51)

1. Angeli D., Sontag E. Monotone control systems. IEEE Trans. Automat. Control. 48:2003;1684-1698
2. Asthagiri A.R., Lauffenburger D.A. Bioengineering models of cell signaling. Annu. Rev. Biomed. Eng. 02:2000;31-53
3. Bers, D.M., 2001. Excitation-Contraction Coupling and Cardiac Contractile Force. Kluwer Academic Publishers, Boston, pp. 427.
4. Bers D.M., Stiffel V.M. Ratio of ryanodine to dihydropyridine receptors in cardiac and skeletal muscle and implications for E-C coupling. Am. J. Physiol. 264:1993;C1587-C1593
5. 2+ transport Circ. Res. 93:2003;487-490
6. Bhalla U.S., Iyengar R. Emergent properties of networks of biological signaling pathways. Science. 283:1999;381-387
7. Cohen P., Nimmo G.A., Burchell A., Antoniw J.F. The substrate specificity and regulation of the protein phosphatases involved in the control of glycogen metabolism in mammalian skeletal muscle. Adv. Enzyme Regul. 16:1977;97-119
8. Csete M.E., Doyle J.C. Reverse engineering of biological complexity. Science. 295:2002;1664-1669
9. Eisner D.A., Choi H.S., Diaz M.E., O'Neill S.C., Trafford A.W. Integrative analysis of calcium cycling in cardiac muscle. Circ. Res. 87:2000;1087-1094
10. Fentzke R.C., Buck S.H., Patel J.R., Lin H., Wolska B.M., Stojanovic M.O., Martin A.F., Solaro R.J., Moss R.L., Leiden J.M. Impaired cardiomyocyte relaxation and diastolic function in transgenic mice expressing slow skeletal troponin I in the heart. J. Physiol. 517(Pt 1):1999;143-157
11. Fink M.A., Zakhary D.R., Mackey J.A., Desnoyer R.W., Apperson-Hansen C., Damron D.S., Bond M. AKAP-mediated targeting of protein kinase a regulates contractility in cardiac myocytes. Circ. Res. 88:2001;291-297
12. Gibson R.M., Ji-Buechler Y., Taylor S.S. Interaction of the regulatory and catalytic subunits of cAMP-dependent protein kinase. Electrostatic sites on the type Ialpha regulatory subunit. J. Biol. Chem. 272:1997;16343-16350
13. Gilman A.G., Simon M.I., Bourne H.R., Harris B.A., Long R., Ross E.M., et al. Overview of the alliance for cellular signaling. Nature. 420:2002;703-706
14. Hairer, E., Wanner, G., 1996. Solving Ordinary Differential Equations II. Stiff and Differential-Algebraic Problems. Springer Series in Computational Mathematics, Vol. 14, 2nd Edition, Springer-Verlag, Berlin.
15. 2+ channels revealed by discrete-time Markov analysis of slow gating. Biophys. J. 65:1993;1599-1612
16. Hoffmann A., Levchenko A., Scott M.L., Baltimore D. The IkappaB-NF-kappaB signaling module. temporal control and selective gene activation Science. 298:2002;1241-1245
17. Ideker T., Lauffenburger D. Building with a scaffold. emerging strategies for high- to low-level cellular modeling Trends Biotechnol. 21:2003;255-262
18. Ideker T., Ozier O., Schwikowski B., Siegel A.F. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 18(Suppl 1):2002;S233-S240
19. Karczewski P., Bartel S., Krause E.G. Differential sensitivity to isoprenaline of troponin I and phospholamban phosphorylation in isolated rat hearts. Biochem. J. 266:1990;115-122
20. Katz A.M. Physiology of the Heart. 2001;Lippincott Williams & Wilkins, New York
21. Khalil, H.K., 1996. Nonlinear Systems, Prentice-Hall, Upper Saddle River, NJ, pp. 734.
22. Kohn K.W. Molecular interaction maps as information organizers and simulation guides. Chaos. 11:2001;84-97
23. Konhilas J.P., Irving T.C., Wolska B.M., Jweied E.E., Martin A.F., Solaro R.J., de Tombe P.P. Troponin I in the murine myocardium. influence on length-dependent activation and interfilament spacing J. Physiol. 547:2003;951-961
24. Li S., Petzold L.R. Software and algorithm for sensitivity analysis of large-scale differential algebraic systems. J. Comput. Appl. Math. 125:2000;131-145
25. Li L., Desantiago J., Chu G., Kranias E.G., Bers D.M. Phosphorylation of phospholamban and troponin I in beta-adrenergic-induced acceleration of cardiac relaxation. Am. J. Physiol. Heart Circ. Physiol. 278:2000;H769-H779
26. Li Y., Kranias E.G., Mignery G.A., Bers D.M. Protein kinase a phosphorylation of the ryanodine receptor does not affect calcium sparks in mouse ventricular myocytes. Circ. Res. 90:2002;309-316
27. Luo C.H., Rudy Y. A dynamic model of the cardiac ventricular action potential. I. Simulations of ionic currents and concentration changes. Circ. Res. 74:1994;1071-1096
28. Marks A.R. A guide for the perplexed. towards an understanding of the molecular basis of heart failure Circulation. 107:2003;1456-1459
29. Marx S.O., Reiken S., Hisamatsu Y., Jayaraman T., Burkhoff D., Rosemblit N., Marks A.R. PKA phosphorylation dissociates FKBP12.6 from the calcium release channel (ryanodine receptor). defective regulation in failing hearts Cell. 101:2000;365-376
30. Michel J.J., Scott J.D. AKAP mediated signal transduction. Annu. Rev. Pharmacol. Toxicol. 42:2002;235-257
31. Noble D. Modelling the heart. insights, failures and progress Bioessays. 24:2002;1155-1163
32. Puglisi J.L., Bers D.M. LabHEART. an interactive computer model of rabbit ventricular myocyte ion channels and Ca transport Am. J. Physiol. Cell. Physiol. 281:2001;C2049-C2060
33. Reiken, S., Gaburjakova, M., Guatimosim, S., Gomez, A.M., D'Armiento, J., Burkhoff, D., et al., 2003. Protein kinase a phosphorylation of the cardiac calcium release channel (ryanodine receptor) in normal and failing hearts. Role of phosphatases and response to isoproterenol. J. Biol. Chem. 278, 444-453.
34. Rice J.J., Winslow R.L., Hunter W.C. Comparison of putative cooperative mechanisms in cardiac muscle. length dependence and dynamic responses Am. J. Physiol. 276:1999;H1734-H1754
35. 2+-regulatory site of bovine cardiac troponin. J. Biol. Chem. 257:1982;260-263
36. Sachs, K., Gifford, D., Jaakkola, T., Sorger, P., Lauffenburger, D.A., 2002. Bayesian network approach to cell signaling pathway modeling. Sci STKE 2002, PE38.
37. Sambrano, G.R., 2003. Developing a navigation and visualization system for signaling pathways. AfCS Research Reports 1, Access: http://www.signaling- gateway.org/reports/v1/da0003.
38. Sastry, S., 1999. Nonlinear Systems: Analysis, Stability, and Control. Springer, New York, pp. 704.
39. Saucerman J.J., Brunton L.L., Michailova A.P., McCulloch A.D. Modeling beta-adrenergic control of cardiac myocyte contractility in silico. J. Biol. Chem. 278:2003;47997-48003
40. Savageau M.A. Michaelis-Menten mechanism reconsidered. implications of fractal kinetics J. Theoret. Biol. 176:1995;115-124
41. Schnell S., Maini P.K. Enzyme kinetics at high enzyme concentration. Bull. Math. Biol. 62:2000;483-499
42. Segel, I.H., 1975. Enzyme kinetics: behavior and analysis of rapid equilibrium and steady state enzyme systems. Wiley, New York, pp. xxii, 957.
43. Solaro R.J., Moir A.J., Perry S.V. Phosphorylation of troponin I and the inotropic effect of adrenaline in the perfused rabbit heart. Nature. 262:1976;615-617
44. Song L.S., Wang S.Q., Xiao R.P., Spurgeon H., Lakatta E.G., Cheng H. Beta-adrenergic stimulation synchronizes intracellular Ca(2+) release during excitation-contraction coupling in cardiac myocytes. Circ. Res. 88:2001;794-801
45. Steenaart N.A., Ganim J.R., Di Salvo J., Kranias E.G. The phospholamban phosphatase associated with cardiac sarcoplasmic reticulum is a type 1 enzyme. Arch. Biochem. Biophys. 293:1992;17-24
46. Stemmer P.M., Ledyard T.H., Watanabe A.M. Protein dephosphorylation rates in myocytes after isoproterenol withdrawal. Biochem. Pharmacol. 59:2000;1513-1519
47. Takai A., Tsuboi K., Koyasu M., Isobe M. Effects of modification of the hydrophobic C-1-C-16 segment of tautomycin on its affinity to type-1 and type-2A protein phosphatases. Biochem. J. 350(Pt 1):2000;81-88
48. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., et al. The sequence of the human genome. Science. 291:2001;1304-1351
49. Viatchenko-Karpinski S., Gyorke S. Modulation of the Ca(2+)-induced Ca(2+) release cascade by beta-adrenergic stimulation in rat ventricular myocytes. J. Physiol. 533:2001;837-848
50. Wuchty S., Oltvai Z.N., Barabasi A.L. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat. Genet. 35:2003;176-179
51. Zhang J., Ma Y., Taylor S.S., Tsien R.Y. Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering. Proc. Natl. Acad. Sci. USA. 98:2001;14997-15002