Packing defects functionalize soluble proteins

•We validate the conjecture that protein packing defects participate in biochemical events.•Packing defects promote deprotonation of nearby nucleophilic groups.•Packing defects induce basicity in nearby interfacial water.•Packing defects prepare the aqueous interface for enzyme catalysis.•Mutations that create packing defects stimulate enzyme catalysis.

This work explores the participation of protein packing defects, the so-called dehydrons, in biochemical events. We delineate the enabling role of dehydrons as activators of nucleophilic groups. This activation results from the induction of chemical basicity in interfacial water molecules, promoting deprotonation of adjacent nucleophiles. Through multiple steering molecular dynamics with pulling along the proton-displacement coordinate, we show that nucleophilic groups are functionally enabled by nearby dehydrons that promote proton transference. The computations are validated against experimentally determined pKa decreases at functional sites and biochemical probes of deregulated catalytic activity arising from dehydron-generating mutations.