Markov chain Monte Carlo fitting of single-channel data from inositol trisphosphate receptors

Journal of Theoretical Biology

Volumn 257, Issue 3, 2009, Pages 460-474

  Gin, Elan ^a   Falcke, Martin ^b   Wagner, Larry E ^c   Yule, David I ^c   Sneyd, James ^a  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^c UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

Author keywords

Bayesian inference; Markov model

Indexed keywords

CALCIUM CHANNEL; INOSITOL 1,4,5 TRISPHOSPHATE RECEPTOR;

BAYESIAN ANALYSIS; CALCIUM; MARKOV CHAIN; MONTE CARLO ANALYSIS; NUMERICAL MODEL;

ARTICLE; CALCIUM CELL LEVEL; INTRACELLULAR TRANSPORT; MATHEMATICAL COMPUTING; MONTE CARLO METHOD; NONHUMAN; PATCH CLAMP; PRIORITY JOURNAL; PROBABILITY; SIMULATION; STEADY STATE;

ANIMALS; CALCIUM; INOSITOL 1,4,5-TRISPHOSPHATE RECEPTORS; ION CHANNEL GATING; MARKOV CHAINS; MODELS, BIOLOGICAL; MONTE CARLO METHOD;

EID: 61449197652     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.12.020     Document Type: Article

References (51)

1. 2 +. Curr. Biol. 9 (1999) 1115-1118
2. Adkins C.E., Wissing F., Potter B.V.L., and Taylor C.W. Rapid activation and partial inactivation of inositol trisphosphate receptors by adenophostin A. Biochem. J. 352 (2000) 929-933
3. Ball F., Cai Y., Kadane J., and O'Hagan A. Bayesian inference for ion-channel gating mechanisms directly from single-channel recordings using Markov chain. Monte Carlo. Proc. R. Soc. London A 455 (1999) 2879-2932
4. Ball F.G., and Sansom M. Ion-channel gating mechanisms: model identification and parameter estimation from single channel recordings. Proc. R. Soc. London B 236 (1989) 385-416
5. Beard D., Liang S., and Qian H. Energy balance analysis of complex metabolic networks. Biophys. J. 83 (2002) 79-86
6. 3) receptor functional properties. Cell Calcium 16 (1994) 151-166
7. 3- and calcium-gated channels from endoplasmic reticulum cerebellum. Nature 351 (1991) 751-754
8. Blatz A.L., and Magleby K.L. Correcting single channel data for missed events. Biophys. J. 49 (1986) 967-980
9. Bruno W.J., Yang J., and Pearson J.E. Using independent open-to-closed transitions to simplify aggregated Markov models of ion channel gating kinetics. Proc. Natl. Acad. Sci. USA 102 (2005) 6326-6331
10. Colquhoun D., and Hawkes A.G. Relaxation and fluctuations of membrane currents that flow through drug-operated ion channels. Proc. R. Soc. London B 199 (1977) 231-262
11. Colquhoun D., and Hawkes A. On the stochastic properties of single ion channels. Proc. R. Soc. London B 211 (1981) 205-235
12. Colquhoun D., Hawkes A., and Srodzinski K. Joint distributions of apparent open and shut times of single-ion channels and maximum likelihood fitting of mechanisms. Philos. Trans. R. Soc. London A 354 (1996) 2555-2590
13. Crouzy S.C., and Sigworth F.J. Yet another approach to the dwell-time omission problem of single-channel analysis. Biophys. J. 58 (1990) 731-743
14. + outward-rectifier in barley leaf. J. Math. Biol. 50 (2005) 233-256
15. 3 receptors. Science 313 (2006) 229-233
16. 2 + concentration. Proc. Natl. Acad. Sci. USA 89 (1992) 9895-9899
17. Ehrlich B., and Watras J. Inositol 1,4,5-trisphosphate activates a channel from smooth muscle sarcoplasmic reticulum. Nature 336 (1988) 583-586
18. Fall, C., Marland, E., Wagner, J., Tyson, J. (Eds.), 2002. Computational Cell Biology. Springer, Berlin.
19. Feinberg M. Necessary and sufficient conditions for detailed balancing in mass action systems of arbitrary complexity. Chem. Eng. Sci. 44 (1989) 1819-1827
20. 2 + release channels. Physiol. Rev. 87 (2007) 593-658
21. Fredkin D.R., and Rice J.A. On aggregated Markov processes. J. Appl. Prob. 23 (1986) 208-214
22. Fredkin D.R., and Rice J.A. Bayesian restoration of single-channel patch clamp recordings. Biometrics 48 (1992) 427-448
23. Gilks, W., Richardson, S., Spiegelhalter, D. (Eds.), 1996. Markov Chain Monte Carlo in Practice. Chapman & Hall, London.
24. Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (1977) 2340-2361
25. Green P.J. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 88 (1995) 1035-1053
26. Hastings W. Monte carlo sampling methods using Markov chains and their applications. Biometrika 57 (1970) 97-109
27. Hawkes A., Jalali A., and Colquhoun D. The distributions of the apparent open times and shut times in a single channel record when brief events cannot be detected. Phil. Trans. R. Soc. London A 332 (1990) 511-538
28. Hodgson M. A Bayesian restoration of an ion channel signal. J. R. Stat. Soc. B 61 (1999) 95-114
29. Hodgson M.E., and Green P.J. Bayesian choice among Markov models of ion channels using Markov chain Monte Carlo. Proc. R. Soc. London A 455 (1999) 2448-3425
30. Horn R., and Lange K. Estimating kinetic constants from single channel data. Biophys. J. 43 (1983) 207-223
31. Keener J., and Sneyd J. Mathematical Physiology vol. 1 (2008), Springer, New York
32. Magleby K.L., and Weiss D.S. Estimating kinetic parameters for single channels with simulation a general method that resolves the missed event problem and accounts for noise. Biophys. J. 58 (1990) 1411-1426
33. 3) receptors in Xenopus oocyte nucleus. J. Gen. Physiol. 109 (1997) 571-587
34. 2 + inhibition. Proc. Natl. Acad. Sci. USA 95 (1998) 15821-15825
35. Mak D.-O.D., McBride S., Raghuram V., Yue Y., Joseph S., and Foskett J.K. Single-channel properties in endoplasmic reticulum membrane of recombinant type 3 inositol trisphosphate receptor. J. Gen. Physiol. 115 (2000) 241-256
36. 3 receptors. J. Gen. Physiol. 117 (2001) 435-446
37. 2 + release channels. EMBO 8 (2007) 1044-1051
38. 2 + safeguards against spontaneous activity. Curr. Biol. 7 (1997) 510-518
39. Marchant J.S., and Taylor C.W. Rapid activation and partial inactivation of inositol trisphosphate receptors by inositol trisphosphate. Biochemistry 37 (1998) 11524-11533
40. McManus O., Blatz A., and Magleby K. Sampling, log binning, fitting, and plotting durations of open and shut intervals form single channels and the effects of noise. Pflugers Arch. 410 (1987) 530-553
41. Metropolis N., Rosenbluth A., Rosenbluth M., Teller A., and Teller E. Equations of state calculations by fast computing machines. J. Chem. Phys. 21 (1953) 1087-1092
42. Neher E., and Sakmann B. Single-channel currents recorded from membrane of denervated frog muscle fibres. Nature 260 (1976) 799-802
43. Rosales R., Stark J.A., Fitzgerald W.J., and Hladky S.B. Bayesian restoration of ion channel records using hidden Markov models. Biophys. J. 80 (2001) 1088-1103
44. Rosales R.A., Fill M., and Escobar A.L. Calcium regulation of single ryanodine receptor channel gating analyzed using HMM/MCMC statistical methods. J. Gen. Physiol. 121 (2004) 533-553
45. Sigworth F.J., and Sine S. Data transformations for improved display and fitting of single-channel dwell time histograms. Biophys. J. 52 (1987) 1047-1054
46. Sneyd J., and Dufour J. A dynamic model of the type-2 inositol trisphosphate receptor. Proc. Natl. Acad. Sci. USA 99 (2002) 2398-2403
47. Sneyd J., and Falcke M. Models of inositol trisphosphate receptor. Prog Biophys Mol Bio. 89 (2005) 207-245
48. Thul R., and Falcke M. Waiting time distributions for clusters of complex molecules. EPL 79 (2007) 38003
49. Wagner II L.E., Li W.-H., and Yule D.I. Phosphorylation of type-1 inositol 1,4,5-trisphosphate receptors by cyclic nucleotide-dependent protein kinases. J. Biol. Chem. 278 (2003) 45811-45817
50. Wagner II L.E., Li W.-H., Joseph S.K., and Yule D.I. Functional consequences of phosphomimetic mutations at key cAMP-dependent protein kinase phosphorylation sites in the type 1 inositol 1,4,5-trisphosphate receptor. J. Biol. Chem. 279 (2004) 46242-46252
51. Wagner II L., Joseph S., and Yule D. Regulation of single inositol 1,4,5-trisphosphate receptor channel activity by protein kinase A phosphorylation. J. Physiol. 586 (2008) 3577-3596