12.12. FceRI MCell rule Model

12.12.1. Description

This example illustrates the implementation of a BioNetGen model in MCell (details of the model can be found here.). As in BioNetGen molecules can have components and states, here volume molecules Lig have two components l and l, surface molecules Lyn have two components U and SH2, volume molecules Syk have three components, tSH2, l and a, and components l and a can be in two states Y and pY, and finally surface molecules Rec have three components a, b and g, and components b and g can be in two states Y and pY. In BioNetGen notation this is written as Lig(l,l), Lyn(U, SH2), Syk(tSH2,l~Y~pY,a~Y~pY) and Rec(a,b~y~pY,g~Y~Py). Complexes can be formed by linking two components, for instance, molecules Rec(a) and Lig(l,l) form a complex through the reaction Rec(a) + Lig(l,l) -> Rec(a!1).Lig(l!1,l). Several reactions drive the dynamic of this system, see the tab reactions in the CellBlender version of this model to find all of them. Complexes can also react, for instance Lig(l!1,l!2).Lyn(U!3,SH2).Rec(a!2,b~Y!3).Rec(a!1,g~pY!4).Syk(tSH2!4,l~Y) can form Lig(l!1,l!2).Lyn(U!3,SH2).Rec(a!2,b~Y!3).Rec(a!1,g~pY!4).Syk(tSH2!4,l~pY) where the component Syk(tSH2!4,l~Y) change to state Syk(tSH2!4,l~pY).

12.12.2. Demonstrated features

  • Definition of molecules with components and states as in BioNetGen.

  • Reactions with absolute orientation.

  • Usage of BioNetGen compartments.

  • Complexes are formed.

  • Count complexes.