Structural ontogeny of protein-protein interactions

Natural protein binding sites are often the most “druggable” sites on
proteins, while alternative protein surfaces can be difficult targets. To
explore the structural basis of this phenomenon, we used synthetic
coevolution to engineer new interactions between naïve surfaces,
simulating the de novo formation of protein complexes. We isolated seven
distinct structural families of protein Z-domain complexes and found that
synthetic complexes explore multiple shallow energy wells through
ratchet-like docking modes, while complexes co-evolved from a natural
binding surface converged in a deep energy well with a relatively fixed
docking geometry. Epistasis analysis using machine learning to
estimate fitness landscapes extracted “seed” contacts emerging from silent
surfaces between binding partners that anchored the earliest stages of
encounter complex formation. These data suggest why natural binding sites
attract binders: alternative surfaces have a shallow energy landscape that
disfavors tight binding, likely due to evolutionary counter-selection. Our
findings have implications for understanding druggable versus undruggable
surfaces.