title: Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations.
abstract: Kinesin is a molecular motor that hydrolyzes adenosine triphosphate (ATP) and moves along microtubules against load. While motility and atomic structures have been well-characterized for various members of the kinesin family, not much is known about ATP hydrolysis inside the active site. Here, we study ATP hydrolysis mechanisms in the kinesin-5 protein Eg5 by using combined quantum mechanics/molecular mechanics metadynamics simulations. Approximately 200 atoms at the catalytic site are treated by a dispersion-corrected density functional and, in total, 13 metadynamics simulations are performed with their cumulative time reaching ~0.7 ns. Using the converged runs, we compute free energy surfaces and obtain a few hydrolysis pathways. The pathway with the lowest free energy barrier involves a two-water chain and is initiated by the Pγ-Oβ dissociation concerted with approach of the lytic water to PγO3-. This immediately induces a proton transfer from the lytic water to another water, which then gives a proton to the conserved Glu270. Later, the proton is transferred back from Glu270 to HPO(4)2- via another hydrogen-bonded chain. We find that the reaction is favorable when the salt bridge between Glu270 in switch II and Arg234 in switch I is transiently broken, which facilitates the ability of Glu270 to accept a proton. When ATP is placed in the ADP-bound conformation of Eg5, the ATP-Mg moiety is surrounded by many water molecules and Thr107 blocks the water chain, which together make the hydrolysis reaction less favorable. The observed two-water chain mechanisms are rather similar to those suggested in two other motors, myosin and F1-ATPase, raising the possibility of a common mechanism.
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan. mcgrath@theory.biophys.kyoto-u.ac.jp
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: McGrath
authors.forename: I-F Will
authors.initials: IF
authors.lastname: Kuo
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Hayashi
authors.forename: Shoji
authors.initials: S
authors.lastname: Takada
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism*; D020134:Catalytic Domain; D006801:Humans; D006868:Hydrolysis; D016547:Kinesins / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular
chemical_list: C470243:KIF11 protein, human; D000255:Adenosine Triphosphate; D016547:Kinesins