MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics
Fig 2
Enzyme modules are explicit representations of enzymatic regulatory mechanisms.
(A) The reaction catalyzed by pyruvate kinase is replaced with the stoichiometric description of the enzymatic mechanism. The steady state values obtained after simulating a 50% increase of ATP utilization are mapped onto a metabolic pathway map drawn using Escher [44]. The colors represent flux values and range from red to purple to gray, with red indicating higher flux values and gray indicating lower flux values. (B) Enzyme modules provide a network-level perspective of regulation mechanisms by plotting systemic quantities against fractional states of enzymes as described in Yurkovich et al. [24]. (C) The different signals of the enzyme module can be observed to provide enzyme-level resolution of the regulatory response.