A kinetic Monte Carlo simulation study of inositol 1,4,5-trisphosphate receptor (IP3R) calcium release channel

Most of the previously theoretical studies about the stochastic nature of the IP3R calcium release channel gating use the chemical master equation (CME) approach. Because of the limitations of this approach we have used a stochastic simulation algorithm (SSA) presented by Gillespie. A single subunit...

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Vydáno v:Computational biology and chemistry Ročník 31; číslo 2; s. 99 - 109
Hlavní autoři: Haeri, H.H., Hashemianzadeh, S.M., Monajjemi, M.
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Elsevier Ltd 01.04.2007
Témata:
Algorithms
Calcium - metabolism
Calcium Signaling
Complex reactions
Computational Biology - statistics & numerical data
De Young–Keizer model
Gillespie algorithm
Inositol 1,4,5-Trisphosphate Receptors - metabolism
Ion channel
Ion Channel Gating
Models, Biological
Monte Carlo
Monte Carlo Method
Stochastic Processes
Stochastisity
Stochastisity
Complex reactions
Monte Carlo
Ion channel
Gillespie algorithm
De Young–Keizer model
ISSN:1476-9271, 1476-928X
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Shrnutí:Most of the previously theoretical studies about the stochastic nature of the IP3R calcium release channel gating use the chemical master equation (CME) approach. Because of the limitations of this approach we have used a stochastic simulation algorithm (SSA) presented by Gillespie. A single subunit of De Young–Keizer (DYK) model was simulated using Gillespie algorithm. The model has been considered in its complete form with eight states. We investigate the conditions which affect the open state of the model. Calcium concentrations were the subject of fluctuation in the previous works while in this study the population of the states is the subject of stochastic fluctuations. We found out that decreasing open probability is a function of Ca 2+ concentration in fast time domain, while in slow time domain it is a function of IP3 concentration. Studying the population of each state shows a time dependent reaction pattern in fast and medium time domains (10 −4 and 10 −3 s). In this pattern the state of X 0 1 0 has a determinative role in selecting the open state path. Also, intensity and frequency of fluctuations and Ca 2+ inhibitions have been studied. The results indicate that Gillespie algorithm can be a better choice for studying such systems, without using any approximation or elimination while having acceptable accuracy. In comparison with the chemical master equation, Gillespie algorithm is also provides a wide area for studying biological systems from other points of view.
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ISSN:1476-9271
1476-928X
DOI:10.1016/j.compbiolchem.2007.02.009