Multi-contact description of protein-protein interactions

Abstract

Binding and unbinding between proteins generally involve multiple contacts between individual amino acids at the interface that dynamically form and break on time scales shorter than those associated with the meso-scale ‘bond’ between two proteins. To understand how properties of the micro-scale contacts affect the binding kinetics and lifetime of protein-protein interactions, we develop theoretical and computational models of increasing complexity. In the case when contacts form and break independently, the steady-state solution of the corresponding master equation can be analytically obtained, which relates the fraction of contacts formed as a function of the rate constants characterizing the contacts.