Paper Citing NAMD - Abstract
McCullagh, Martin; Saunders, Marissa G.; Voth, Gregory A.
Unraveling the Mystery of ATP Hydrolysis in Actin Filaments
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:13053-13058, SEP 17 2014
Actin performs its myriad cellular functions by the growth and disassembly of its filamentous form. The hydrolysis of ATP in the actin filament has been shown to modulate properties of the filament, thus making it a pivotal regulator of the actin life cycle. Actin has evolved to selectively hydrolyze ATP in the filamentous form, F-actin, with an experimentally observed rate increase over the monomeric form, G-actin, of 4.3 X 10(4). The cause of this dramatic increase in rate is investigated in this paper using extensive QM/MM simulations of both G- and F-actin. To compute the free energy of hydrolysis in both systems, metadynamics is employed along two collective variables chosen to describe the reaction coordinates of hydrolysis. F-actin is modeled as a monomer with restraints applied to coarse-grained variables enforced to keep it in a filament-like conformation. The simulations reveal a barrier height reduction for ATP hydrolysis in F-actin as compared to G-actin of 8 +/- 1 kcal/mol, in good agreement with the experimentally measured barrier height reduction of 7 +/- 1 kcal/mol. The barrier height reduction is influenced by an enhanced rotational diffusion of water in F-actin as compared to G-actin and shorter water wires between Asp 154 and the nucleophilic water in F-actin, leading to more rapid proton transport.
