Alternative ways to represent a catalytic (enzymatic) reaction. a) An enzymatic reaction converting substrate S into product P is represented in the form of a place/transition Petri net by modeling the formation and decay of the enzyme-substrate complex ES. Upon firing of T1, enzyme E is consumed and released upon firing of T2. b) In the framework of an Extended Petri net, an enzymatic reaction can be modeled with a test arc (bidirected arc) connecting the Enzyme place E with the transition that converts substrate S into product P. The transition can only fire if there is at least one token in E. Upon firing of the transition, the token is consumed from and immediately redelivered into place E, i.e. unlike in a), the marking of E does not change while the token of place S moves to place P.
Durzinsky et al. BMC Systems Biology 2011 5:113 doi:10.1186/1752-0509-5-113