Reference : Mesoscopic behavior from microscopic Markov dynamics and its application to calcium r...
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
Physical, chemical, mathematical & earth Sciences : Physics
http://hdl.handle.net/10993/15782
Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels.
English
Christian, Nils mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Skupin, Alexander mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Morante, Silvia [> >]
Karl, Jansen [> >]
Rossi, Giancarlo [> >]
Ebenhöh, Oliver [> >]
2014
Journal of Theoretical Biology
Elsevier
343
102--112
Yes (verified by ORBilu)
0022-5193
1095-8541
Amsterdam
The Netherlands
[en] Gillespie algorithm ; ip3 receptor ; calcium signaling
[en] A major challenge in biology is to understand how molecular processes determine phenotypic features. We address this fundamental problem in a class of model systems by developing a general mathematical framework that allows the calculation of mesoscopic properties from the knowledge of microscopic Markovian transition probabilities. We show how exact analytic formulae for the first and second moments of resident time distributions in mesostates can be derived from microscopic resident times and transition probabilities even for systems with a large number of microstates. We apply our formalism to models of the inositol trisphosphate receptor, which plays a key role in generating calcium signals triggering a wide variety of cellular responses. We demonstrate how experimentally accessible quantities such as opening and closing times and the coefficient of variation of inter-spike intervals, and other, more elaborated, quantities can be analytically calculated from the underlying microscopic Markovian dynamics. A virtue of our approach is that we do not need to follow the detailed time evolution of the whole system, as we derive the relevant properties of its steady state without having to take into account the often extremely complicated transient features. We emphasize that our formulae fully agree with results obtained by stochastic simulations and approaches based on a full determination of the microscopic system's time evolution. We also illustrate how experiments can be devised to discriminate between alternative molecular models of the inositol trisphosphate receptor. The developed approach is applicable to any system described by a Markov process and, owing to the analytic nature of the resulting formulae, provides an easy way to characterize also rare events that are of particular importance to understand the intermittency properties of complex dynamic systems.
Luxembourg Centre for Systems Biomedicine (LCSB): Integrative Cell Signalling (Skupin Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
University of Aberdeen, Department of Physics, Meston Walk, Aberdeen AB24 3UE, UK; Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, 14473 Potsdam, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, D-40225 Düsseldorf, Germany. Electronic address: ebenhoeh@abdn.ac.uk.
http://hdl.handle.net/10993/15782
10.1016/j.jtbi.2013.11.010
http://dx.doi.org/10.1016/j.jtbi.2013.11.010

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