Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments

Abstract

Actin filaments continually assemble and disassemble in the cell cytoplasm, during which they age as the nucleotides bound to newly added actin sub-units hydrolyze from ATP to an intermediate ADP-Pi, followed by a slower release of Pi to form ADP. This results into a spatial distribution of all three states of the bound nucleotide along the growing filament. It is not fully understood whether ATP hydrolysis and Pi release in a growing actin filament are spatially cooperative or purely random. Using a bottom-up multi-scale coarse-grained modeling strategy, we design simulations to study cooperativity in these reactions and find that the reactions are indeed cooperative to a certain extent. At first level of coarse-graining, we construct an ultra-coarse-grained (UCG) model based on atomistic simulations of short actin filaments. The UCG model agrees with experiments in terms of mechanical properties such as persistence length, which is governed by the bound nucleotide's state. The model also predicts that states of the bound nucleotides of neighboring sub-units significantly modulate the reaction kinetics, implying cooperativity especially in the slower Pi release reaction. We further coarse-grain the system into a Markov state model that incorporates assembly and disassembly, and the cooperativity predicted by the UCG model. The model reveals that cooperativity in ATP hydrolysis and Pi release has significant effects on the filament growth dynamics, but only near the critical g-actin monomer concentration. Filament dynamics are robust to the mechanism of hydrolysis far from the critical concentration and both cooperative and random mechanisms show similar growth dynamics. On the contrary, the filament composition in terms of the bound nucleotide distribution varies significantly at all monomer concentrations studied. These results provide new insights into the mechanism of ATP hydrolysis and its implications on actin filament properties.