Structured Random Binding: a minimal model of protein-protein interactions

Abstract

We describe Structured Random Binding (SRB), a minimal model of protein-protein interactions rooted in the statistical physics of disordered systems. In this model, nonspecific binding is a generic consequence of the interaction between random proteins, exhibiting a phase transition from a high temperature state where nonspecific complexes are transient and lack well-defined interaction interfaces, to a low temperature state where the complex structure is frozen and a definite interaction interface is present. Numerically, weakly-bound nonspecific complexes can evolve into tightly-bound, highly specific complexes, but only if the structural correlation length along the peptide backbone is short; moreover, evolved tightly-bound homodimers favor the same interface structure that is predominant in real protein homodimers.