Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations

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 c...

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Main Authors:	Hituri, Katri, Linne, Marja-Leena
Format:	Online
Language:	English
Published:	Public Library of Science 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3629942/

id	pubmed-3629942
recordtype	oai_dc
spelling	pubmed-36299422013-04-29 Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations Hituri, Katri Linne, Marja-Leena Research Article 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. Public Library of Science 2013-04-10 /pmc/articles/PMC3629942/ /pubmed/23630568 http://dx.doi.org/10.1371/journal.pone.0059618 Text en © 2013 Hituri, Linne http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Hituri, Katri Linne, Marja-Leena
spellingShingle	Hituri, Katri Linne, Marja-Leena Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations
author_facet	Hituri, Katri Linne, Marja-Leena
author_sort	Hituri, Katri
title	Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations
title_short	Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations
title_full	Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations
title_fullStr	Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations
title_full_unstemmed	Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations
title_sort	comparison of models for ip3 receptor kinetics using stochastic simulations
description	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.
publisher	Public Library of Science
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3629942/
_version_	1611971147445829632

Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations

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