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Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations

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Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations. / Hituri, Katri; Linne, Marja-Leena.

julkaisussa: PLoS ONE, Vuosikerta 8, Nro 4, e59618, 2013, s. 1-13.

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Hituri, Katri ; Linne, Marja-Leena. / Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations. Julkaisussa: PLoS ONE. 2013 ; Vuosikerta 8, Nro 4. Sivut 1-13.

Bibtex - Lataa

@article{7f8eb6388ac3413fafa087bd570b5327,
title = "Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations",
abstract = "Inositol 1,4,5-trisphosphate receptor (IP3R) is a ubiquitous intracellular calcium (Ca2+) channel which has a major role in controlling (Ca2+) levels in neurons. A variety of computational models have been developed to describe the kinetic function of IP3R under different conditions. In the field of computational neuroscience, it is of great interest to apply the existing models of IP3R when modeling local Ca2+ transients in dendrites or overall Ca2+ dynamics in large neuronal models. The goal of this study was to evaluate existing IP3R models, based on electrophysiological data. This was done in order to be able to suggest suitable models for neuronal modeling. Altogether four models (Othmer and Tang, 1993; Dawson et al.,2003; Fraiman and Dawson, 2004; Doi et al., 2005) were selected for a more detailed comparison. The selection was based on the computational efficiency of the models and the type of experimental data that was used in developing the model. The kinetics of all four models were simulated by stochastic means, using the simulation software STEPS, which implements the Gillespie stochastic simulation algorithm. The results show major differences in the statistical properties of model functionality. Of the four compared models, the one by Fraiman and Dawson (2004) proved most satisfactory in producing the specific features of experimental findings reported in literature. To our knowledge, the present study is the first detailed evaluation of IP3R models using stochastic simulation methods, thus providing an important setting for constructing a new, realistic model of IP3R channel kinetics for compartmental modeling of neuronal functions. We conclude that the kinetics of IP3R with different concentrations of Ca2+ and IP3 should be more carefully addressed when new models for IP3R are developed.",
author = "Katri Hituri and Marja-Leena Linne",
note = "Contribution: organisation=sgn,FACT1=1<br/>Portfolio EDEND: 2013-12-29<br/>Publisher name: Public Library of Science",
year = "2013",
doi = "10.1371/journal.pone.0059618",
language = "English",
volume = "8",
pages = "1--13",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "4",

}

RIS (suitable for import to EndNote) - Lataa

TY - JOUR

T1 - Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations

AU - Hituri, Katri

AU - Linne, Marja-Leena

N1 - Contribution: organisation=sgn,FACT1=1<br/>Portfolio EDEND: 2013-12-29<br/>Publisher name: Public Library of Science

PY - 2013

Y1 - 2013

N2 - Inositol 1,4,5-trisphosphate receptor (IP3R) is a ubiquitous intracellular calcium (Ca2+) channel which has a major role in controlling (Ca2+) levels in neurons. A variety of computational models have been developed to describe the kinetic function of IP3R under different conditions. In the field of computational neuroscience, it is of great interest to apply the existing models of IP3R when modeling local Ca2+ transients in dendrites or overall Ca2+ dynamics in large neuronal models. The goal of this study was to evaluate existing IP3R models, based on electrophysiological data. This was done in order to be able to suggest suitable models for neuronal modeling. Altogether four models (Othmer and Tang, 1993; Dawson et al.,2003; Fraiman and Dawson, 2004; Doi et al., 2005) were selected for a more detailed comparison. The selection was based on the computational efficiency of the models and the type of experimental data that was used in developing the model. The kinetics of all four models were simulated by stochastic means, using the simulation software STEPS, which implements the Gillespie stochastic simulation algorithm. The results show major differences in the statistical properties of model functionality. Of the four compared models, the one by Fraiman and Dawson (2004) proved most satisfactory in producing the specific features of experimental findings reported in literature. To our knowledge, the present study is the first detailed evaluation of IP3R models using stochastic simulation methods, thus providing an important setting for constructing a new, realistic model of IP3R channel kinetics for compartmental modeling of neuronal functions. We conclude that the kinetics of IP3R with different concentrations of Ca2+ and IP3 should be more carefully addressed when new models for IP3R are developed.

AB - Inositol 1,4,5-trisphosphate receptor (IP3R) is a ubiquitous intracellular calcium (Ca2+) channel which has a major role in controlling (Ca2+) levels in neurons. A variety of computational models have been developed to describe the kinetic function of IP3R under different conditions. In the field of computational neuroscience, it is of great interest to apply the existing models of IP3R when modeling local Ca2+ transients in dendrites or overall Ca2+ dynamics in large neuronal models. The goal of this study was to evaluate existing IP3R models, based on electrophysiological data. This was done in order to be able to suggest suitable models for neuronal modeling. Altogether four models (Othmer and Tang, 1993; Dawson et al.,2003; Fraiman and Dawson, 2004; Doi et al., 2005) were selected for a more detailed comparison. The selection was based on the computational efficiency of the models and the type of experimental data that was used in developing the model. The kinetics of all four models were simulated by stochastic means, using the simulation software STEPS, which implements the Gillespie stochastic simulation algorithm. The results show major differences in the statistical properties of model functionality. Of the four compared models, the one by Fraiman and Dawson (2004) proved most satisfactory in producing the specific features of experimental findings reported in literature. To our knowledge, the present study is the first detailed evaluation of IP3R models using stochastic simulation methods, thus providing an important setting for constructing a new, realistic model of IP3R channel kinetics for compartmental modeling of neuronal functions. We conclude that the kinetics of IP3R with different concentrations of Ca2+ and IP3 should be more carefully addressed when new models for IP3R are developed.

U2 - 10.1371/journal.pone.0059618

DO - 10.1371/journal.pone.0059618

M3 - Article

VL - 8

SP - 1

EP - 13

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 4

M1 - e59618

ER -