twoLayerCascadeJ -- an example chemical reaction motif

A combination of two one-site modification cycles in a cascade motif with a specific phosphotase acting in each layer [Feliu, Wiuf].

i1 : twoLayerCascadeJ()

o1 = S_0+E-->X_1
     X_1-->S_0+E
     X_1-->E+S_1
     S_1+F_1-->Y_1
     Y_1-->S_1+F_1
     Y_1-->S_0+F_1
     S_1+P_0-->X_2
     X_2-->S_1+P_0
     X_2-->S_1+P_1
     P_1+F_2-->Y_2
     Y_2-->P_1+F_2
     Y_2-->P_0+F_2

o1 : ReactionNetwork

In the motif Modification of Two-layer Cascade J, the symbols used in the chemical reactions have the following meaning:

S_i and P_i are substrates with i = 0, 1, 2 phosphorylated sites, E is a kinase and F is a phosphotase, X and Y are the intermediate complexes formed by the enzymes E and F, respectively.

To rename species, use substitute(ReactionNetwork,List).