A rule-based model of base excision repair

Abstract

There are ongoing debates in the DNA repair community on whether the coordination of DNA repair is achieved by means of direct protein-protein interactions or whether substrate specificity is sufficient to explain how DNA intermediates are channeled from one repair enzyme to the other. In order to address these questions we designed a model of the Base Excision Repair pathway in Kappa, a rule based formalism for modeling protein-protein and protein-DNA interactions. We use this model to shed light on the key role of the scaffolding protein XRCC1 in coordinating the repair process.