Skip to main content

Research Repository

Advanced Search

Time to blip – stochastic simulation of single channel opening

Thul, Ruediger

Authors



Abstract

The stochastic dynamics of the inositol-1,4,5-trisphosphate (IP3) receptor (IP3R) is key to understanding a wide range of observed calcium (Ca2+) signals (Falcke 2004). The stochastic nature results from the constant binding and unbinding of Ca2+ and IP3 to and from their respective binding sites and is especially important in the initiation of a Ca2+ puff, i.e. the release of Ca2+ through a cluster of IP3Rs. Once the first IP3R opens, the Ca2+ concentration rises significantly around the ion channel and hence increases the open probability for neighboring IP3Rs. In turn this may trigger the activation of further receptors giving rise to a Ca2+ puff (Thul et al. 2009; Thurley et al. 2012). In this protocol, we determine the time that it takes for a single IP3R to open from rest. We explicitly take into account the tetrameric structure of the IP3R and the fact that multiple subunits need to be active before the channel opens (Bezprozvanny et al. 1991; Watras et al. 1991). We develop code for a stochastic simulation of the IP3R and simulate it using the software package Matlab (Attaway 2011). This protocol demonstrates the basic form of a stochastic simulation algorithm and may serve as a starting point to investigate more complex gating dynamics.

Journal Article Type Article
Publication Date May 15, 2014
Journal Cold Spring Harbor Protocols
Electronic ISSN 1559-6095
Peer Reviewed Peer Reviewed
APA6 Citation Thul, R. (2014). Time to blip – stochastic simulation of single channel opening. Cold Spring Harbor protocols, https://doi.org/10.1101/pdb.prot073239
DOI https://doi.org/10.1101/pdb.prot073239
Publisher URL http://cshprotocols.cshlp.org/content/2014/5/pdb.prot073239
Copyright Statement Copyright information regarding this work can be found at the following address: http://eprints.nottingh.../end_user_agreement.pdf

Files

Time to blip – stochastic simulation of single channel opening-Thul.pdf (453 Kb)
PDF

Copyright Statement
Copyright information regarding this work can be found at the following address: http://eprints.nottingham.ac.uk/end_user_agreement.pdf





You might also like



Downloadable Citations

;