Physical Confinement Modulates the Rate-Limiting Transition in the Release of Phosphate from Actin Filaments

Abstract

The nucleotide state and rates of transitions between states regulate the dynamics of ATPases. Slow inorganic phosphate (Pi) release following ATP hydrolysis is often rate-limiting and associated with key conformational changes. Actin filaments offer a unique opportunity to understand the fundamentals of Pi release, because identical subunits at filament ends and the interior release Pi at markedly different rates. The molecular origin of this difference is debated, so we employed extensive all-atom molecular dynamics simulations to characterize Pi release from different subunits within an actin filament. The calculated dissociation rates of Pi from ADP-Mg2+ in the active site correlate with experimentally measured Pi release rates and scale inversely with the numbers of water molecules in the cavity surrounding the {gamma}-phosphate. Simulations show that egress of Pi through the protein channels, including through the N111-R177 backdoor, is not rate-limiting and, importantly, that subunits at the filament ends use alternative egress pathways. TeaserMolecular dynamics simulations show that dissociation of phosphate from Mg2+ limits release from all parts of actin filaments