National Center for Design of
Biomimetic Nanoconductors

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IP3 receptors in the Endoplasmic Reticulum

Snapshot from a simulation of an endoplasmic reticulum (ER) membrane (purple) in the cytoplasm of a mast cell. Stores of Ca ions (yellow particles) inside the ER are being released thru clustered IP3 receptors in the ER membrane (red particles) into the cytoplasm in response to an IP3 signal. The open/close channel states and the resulting eflux of Ca ions are modulated by buffer species (not shown) and a reaction network described in Means et al, Biophys J (to appear). In that paper, the system was modeled via continuum reaction/diffusion equations on a finite element grid. In this work, the proteins and other biomolecules are represnted as individual particles (3 million of them) which diffuse and react with each other; the ER is represented as a triangulated surface. The simulation was performed with ChemCell, a particle-based protein network simulator (www.cs.sandia.gov/~sjplimp/cell.html)

The National Center for Design of Biomimetic Nanoconductors is funded by Grant Number PHS 2 PN2 EY016570B from the National Institutes of Health through the NIH Roadmap for Medical Research and is based at the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. Partner institutions include University of Chicago, Illinois Institute of Technology, Sandia National Laboratories, Wabash College, University of California, Davis, and the University of New Mexico, University of Illinois at Chicago, Weill Cornell Medical College, and the National Institute of Standards and Technology.