We describe the application of Maude, a symbolic language founded on rewriting logic, to the modeling of functional domains within signaling proteins, within the framework of the Pathway Logic project. Protein functional domains (PFDs) are a critical focus of modern signal transduction research. Recently, it has become apparent that signaling proteins must behave combinatorially to generate the high levels of complexity and versatility observed in signaling networks, and that PFDs are responsible for at least part of this capability. In our approach, the state of a system consisting of proteins and PFDs is represented as a term in an equational theory and rewrite rules.