Sensitivity or specificity in protein interactions are independently regulated upon recognition: An SH2 case study.

Abstract

Molecular recognition in protein-protein interactions is prompted by anchor residues that are pre-formed in a mostly bound-like ensemble before docking into their evolutionarily designed pockets. For non-competitive interactions, receptors must be sensitive to the ligand and readily bind upon recognition. On the other hand, for competitive interactions receptors must specifically distinguish among cognate ligands, limiting the free energy of the encounter complex to avoid arbitrarily locking their first approach partner. SH2 domains bind phosphorylated tyrosine (pY) sequences and use a dual pocket architecture to both specifically distinguish among ligands and auto-interact with a covalently linked ligand. Using molecular dynamics, we find that non-competitive sensors recognize sequences where pY is the anchor and can readily bind. In contrast, non-covalently linked ligands present a non-polar anchor side chain that is +2 or +3 C-terminal of pY. These distinct phenotypes define recognition by docking to separate pockets in the overall binding interface. Additionally, we show cognate interactions driven by pY anchor residues are limited to autoinhibitory sensors of multi-domain kinases, strongly suggesting the driving force for diversifying SH2 domains to bind pY residues was the arising need for an autoinhibitory sensor. Collectively, our results provide novel mechanistic insights to how the anchor ensemble can be used to dissect regulatory networks and design functional modulators targeting either sensitive or specific interactions.