A Rule-Based Model of Base Excision Repair

Agnes Köhler1, Jean Krivine2 and Jakob Vidmar2

1 - INRIA-Rocquencourt, Domaine de Voluceau - Rocquencourt B.P. 105 - 78153 Le Chesnay, France
2 - Univ. Paris Diderot, Sorbonne Paris Cité, Laboratoire PPS, UMR 7126, F-75205 Paris, France

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.

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