Time evolution of the substrate-induced millisecond allosteric activation of imidazole glycerol phosphate synthase.

Abstract

Deciphering the molecular mechanisms of enzymatic allosteric regulation requires the structural characterization of functional states and also their time evolution toward the formation of the allosterically activated ternary complex. The transient nature and usually slow millisecond time scale interconversion between these functional states hamper their experimental and computational characterization. Here, we design a computational strategy that combines molecular dynamics simulations, enhanced sampling techniques, and dynamical networks to describe the millisecond allosteric activation of imidazole glycerol phosphate synthase (IGPS) from the inactive substrate-free form to the formation of the enzyme active complex. IGPS is a heterodimeric enzyme complex whose HisH subunit is responsible for hydrolysing glutamine and delivering ammonia for the cyclase activity in HisF. Essential molecular details of the long-range millisecond allosteric activation of IGPS remain hidden. Without using a priori information of the active state, our simulations uncover how IGPS, with the allosteric effector bound, spontaneously captures glutamine in a catalytically inactive HisH conformation, subsequently attains a closed HisF:HisH interface, and finally forms the oxyanion hole in HisH for efficient glutamine hydrolysis. We show that the combined effector and substrate binding dramatically decreases the conformational barrier associated with the oxyanion hole formation, in line with experimentally observed 4500-fold activity increase in glutamine hydrolysis. This computational strategy tailored to describe millisecond timescale events can be generalized to study other allosterically regulated enzymes.