Figure 4

Example of multistate species and reactions. Protein Cdh1 has eleven forms (or states): a non-phosphorylated form (Cdh1) and ten phosphorylated forms. These are shown as a Cdh1 molecule surrounded by 1, 2,..., 10 phosphate groups (P). Each form of the protein takes part in specific phosphorylation/dephosphorylation reactions. Intuitively, the form with i phosphate groups has a successor form i+1 and a predecessor form i−1, with the exceptions that i = 0 does not have a predecessor and i = 10 does not have a successor. The classical way of modeling this system of phosphorylation and dephosphorylation reactions is to explicitly write the 20 single-state reactions. With our syntax the user writes just two collective reactions using successor/predecessor operators with ranges covering only the needed subset of states. In the figure, the single reaction for “successor” is shown together with the expanded form of the group of reactions modeling the phosphorylation action of Cdh1 by ClbM.