A Stochastic Model of Calcium Puffs Based on Single-Channel Data

Berridge, 1997, Elementary and global aspects of calcium signalling, J. Physiol., 499, 291, 10.1113/jphysiol.1997.sp021927 Berridge, 2000, The versatility and universality of calcium signalling, Nat. Rev. Mol. Cell Biol., 1, 11, 10.1038/35036035 Keener, 2009 Bergner, 2002, Acetylcholine-induced calcium signaling and contraction of airway smooth muscle cells in lung slices, J. Gen. Physiol., 119, 187, 10.1085/jgp.119.2.187 Thurley, 2012, Fundamental properties of Ca2+ signals, Biochim. Biophys. Acta, 1820, 1185, 10.1016/j.bbagen.2011.10.007 De Young, 1992, A single-pool inositol 1,4,5-trisphosphate-receptor-based model for agonist-stimulated oscillations in Ca2+ concentration, Proc. Natl. Acad. Sci. USA, 89, 9895, 10.1073/pnas.89.20.9895 Atri, 1993, A single-pool model for intracellular calcium oscillations and waves in the Xenopus laevis oocyte, Biophys. J., 65, 1727, 10.1016/S0006-3495(93)81191-3 Bezprozvanny, 1991, Bell-shaped calcium-response curves of ins(1,4,5)P3- and calcium-gated channels from endoplasmic reticulum of cerebellum, Nature, 351, 751, 10.1038/351751a0 Sneyd, 2004, A comparison of three models of the inositol trisphosphate receptor, Prog. Biophys. Mol. Biol., 85, 121, 10.1016/j.pbiomolbio.2004.01.013 Sneyd, 2005, Models of the inositol trisphosphate receptor, Prog. Biophys. Mol. Biol., 89, 207, 10.1016/j.pbiomolbio.2004.11.001 Foskett, 2007, Inositol trisphosphate receptor Ca2+ release channels, Physiol. Rev., 87, 593, 10.1152/physrev.00035.2006 Wagner, L. E., and D. I. Yule. 2011. Differential regulation of the inositol 1,4,5-trisphosphate receptor type-1 and -2 single channel properties by InsP3, Ca2+ and ATP. J. Physiol. http://jp.physoc.org/content/early/2012/04/30/jphysiol.2012.228320. Abstract. Mak, 2007, Rapid ligand-regulated gating kinetics of single inositol 1,4,5-trisphosphate receptor Ca2+ release channels, EMBO Rep., 8, 1044, 10.1038/sj.embor.7401087 Gin, 2009, A kinetic model of the inositol trisphosphate receptor based on single-channel data, Biophys. J., 96, 4053, 10.1016/j.bpj.2008.12.3964 Ullah, 2012, A data-driven model of a modal gated ion channel: the inositol 1,4,5-trisphosphate receptor in insect Sf9 cells, J. Gen. Physiol., 140, 159, 10.1085/jgp.201110753 Siekmann, 2012, A kinetic model for type I and II IP3R accounting for mode changes, Biophys. J., 103, 658, 10.1016/j.bpj.2012.07.016 Shuai, 2006, The number and spatial distribution of IP3 receptors underlying calcium puffs in Xenopus oocytes, Biophys. J., 91, 4033, 10.1529/biophysj.106.088880 Dickinson, 2012, The probability of triggering calcium puffs is linearly related to the number of inositol trisphosphate receptors in a cluster, Biophys. J., 102, 1826, 10.1016/j.bpj.2012.03.029 Thul, 2004, Release currents of IP(3) receptor channel clusters and concentration profiles, Biophys. J., 86, 2660, 10.1016/S0006-3495(04)74322-2 Swaminathan, 2009, A simple sequential-binding model for calcium puffs, Chaos, 19, 037109, 10.1063/1.3152227 Shuai, 2007, A kinetic model of single and clustered IP3 receptors in the absence of Ca2+ feedback, Biophys. J., 93, 1151, 10.1529/biophysj.107.108795 Solovey, 2008, Simplified model of cytosolic Ca2+ dynamics in the presence of one or several clusters of Ca2+-release channels, Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 78, 041915, 10.1103/PhysRevE.78.041915 Higgins, 2009, Waiting time distributions for clusters of IP3 receptors, J. Theor. Biol., 259, 338, 10.1016/j.jtbi.2009.03.018 Rüdiger, 2010, Law of mass action, detailed balance, and the modeling of calcium puffs, Phys. Rev. Lett., 105, 048103, 10.1103/PhysRevLett.105.048103 Rüdiger, 2012, Termination of Ca²+ release for clustered IP3R channels, PLoS Comput. Biol., 8, e1002485, 10.1371/journal.pcbi.1002485 Nguyen, 2005, A stochastic automata network descriptor for Markov chain models of instantaneously coupled intracellular Ca2+ channels, Bull. Math. Biol., 67, 393, 10.1016/j.bulm.2004.08.010 Ullah, 2012, Multi-scale data-driven modeling and observation of calcium puffs, Cell Calcium, 52, 152, 10.1016/j.ceca.2012.04.018 Thurley, 2011, Timescales of IP(3)-evoked Ca(2+) spikes emerge from Ca(2+) puffs only at the cellular level, Biophys. J., 101, 2638, 10.1016/j.bpj.2011.10.030 Siekmann, 2011, MCMC estimation of Markov models for ion channels, Biophys. J., 100, 1919, 10.1016/j.bpj.2011.02.059 Smith, 2009, Imaging the quantal substructure of single IP3R channel activity during Ca2+ puffs in intact mammalian cells, Proc. Natl. Acad. Sci. USA, 106, 6404, 10.1073/pnas.0810799106 Rüdiger, 2007, Hybrid stochastic and deterministic simulations of calcium blips, Biophys. J., 93, 1847, 10.1529/biophysj.106.099879 Rose, 2006, “Trigger” events precede calcium puffs in Xenopus oocytes, Biophys. J., 91, 4024, 10.1529/biophysj.106.088872 Fraiman, 2006, Analysis of puff dynamics in oocytes: interdependence of puff amplitude and interpuff interval, Biophys. J., 90, 3897, 10.1529/biophysj.105.075911 Bruno, 2010, Quantifying calcium fluxes underlying calcium puffs in Xenopus laevis oocytes, Cell Calcium, 47, 273, 10.1016/j.ceca.2009.12.012 Solovey, 2011, Mean field strategies induce unrealistic non-linearities in calcium puffs, Front. Physiol., 2, 46, 10.3389/fphys.2011.00046