Figure 1

Types of interactions between processes. Reactions are indicated by arrows. The reaction rate for each reaction is denoted as d _i and parameterized by k _i and k_-i. A) Visualization of a graded interaction between the processes of L binding and D phosphorylation. The same scheme can be taken to demonstrate non-interacting processes. For non-interacting processes the parameter restrictions k₁ = k₃, k_-1 = k_-3, k₂ = k₄ and k_-2 = k_-4 hold. B) Visualization of an all-or-none interaction between the processes of binding site phosphorylation and E binding. E can only bind to phosphorylated sites, while the dephosphorylation of D is only possible in the absence of a bound effector. C) The cyclic reaction scheme degenerates to a reaction chain, as the species D[0, 0, E] does not exist. In this case, the notation can be simplified by describing binding site phosphorylation and E binding as modifications of the same site.