Figure 3

A model of a non-covalent interaction between a PI3K-p110 and a Ras. The figure was graphed from the developed SN to illustrate the relationships among different agents. The figure visualizes the agents as icons and their relationship as arrows. The left panel illustrates that a PI3K-p110 contains a "Not Bound" Ras-binding site and a "Non-Functional" catalytic domain. The right panel shows that when the PI3K-p110 has bound to a Ras, its Ras-binding site has switched to "Bound", and the catalytic domain has become "Functional" due to a positive allosteric regulation event. State changes as a result of the interaction are shown in bold. Note that the model stores the information, which specifies the non-covalent event between the prototypic Ras and the prototypic PI3K-p110, and the condition for the event to occur. This figure illustrates an instance of the Ras-binding event occurred during a simulation. The PI3K-p110 is an instance of the PI3K-p110 prototype, and it is the same agent before and after it binds to the Ras. Figure 8 shows the description of each icon.