Fig. 1.
Modular organization of the yeast PCD protein interaction network. (A) Visualization of the modularized PCD protein interaction network. Five modules with distinct functions constitute this network: Signaling (red), Transport (brown), Endocytosis (blue), Exocytosis (green), and Mitosis Exit regulation (gray). The different node shapes represent different universal roles as indicated. Cdc42 protein is used as an example to explain the method for reduction of the local connectivity of each node to the global connectivity to the modules with assigned kinetic parameters. (B) Description of the interactions (colored lines) of Cdc42 with proteins in different modules (large circles). (C) Mathematical representation of PCD protein interaction network and dynamics. The global connectivity of Cdc42 is represented by a 5D integer vector composed of the number of Cdc42’s linkages with each of the five modules. Each module is also assigned a characteristic time constant, τi (τ1–5 for Signaling, Endocytosis, Transport, Mitotic Exit, and Exocytosis, respectively).