Catalysis of Phosphoanhydride Hydrolysis in Water: How Protonation and the Magnesium Ion Shape Transition-State Diversity
Abstract
Phosphoanhydride hydrolysis is a central reaction in biochemistry, powering processes from biosynthesis to molecular motors. Yet, its solution mechanism and the molecular origins of catalysis by protonation and magnesium ions remain elusive. Here we use machine learning potentials trained at density functional theory accuracy combined with extensive reaction path sampling and free-energy methods to dissect pyrophosphate hydrolysis in solution, a model for ATP and GTP reactivity. Our simulations reveal multiple mechanistic pathways and identify a dominant mechanism involving synchronous P-O bond formation and cleavage, followed by solvent-assisted proton transfer. Protonation and Mg²⁺ coordination both stabilize tighter transition-state ensembles and lower activation barriers, although our simulations show that the intrinsic catalytic effect of the ion has been overestimated. These results establish the key drivers of phosphate hydrolysis and demonstrate the power of machine learning-driven simulations to resolve elusive mechanisms in biochemistry.
Adrián García-Martínez
PhD Student
Kirill Zinovjev
Group member
