Theoretical studies of the ATP hydrolysis mechanism of myosin.
The ATP hydrolysis mechanism of myosin was studied using quantum chemical (QM) and molecular dynamics calculations. The initial model compound for QM calculations was constructed on the basis of the energy-minimized structure of the myosin(S1dc)-ATP complex, which was determined by molecular mechanics calculations. The result of QM calculations suggested that the ATP hydrolysis mechanism of myosin consists of a single elementary reaction in which a water molecule nucleophilically attacked gamma-phosphorus of ATP. In addition, we performed molecular dynamics simulations of the initial and final states of the ATP hydrolysis reaction, that is, the myosin-ATP and myosin-ADP.Pi complexes. These calculations revealed roles of several amino acid residues (Lys185, Thr186, Ser237, Arg238, and Glu459) in the ATPase pocket. Lys185 maintains the conformation of beta- and gamma-phosphate groups of ATP by forming the hydrogen bonds. Thr186 and Ser237 are coordinated to a Mg(2+) ion, which interacts with the phosphates of ATP and therefore contributes to the stabilization of the ATP structure. Arg238 and Glu459, which consisted of the gate of the ATPase pocket, retain the water molecule acting on the hydrolysis at the appropriate position for initiating the hydrolysis.
Okimoto
N
N
Computational Science Laboratory, Institute of Physical and Chemical Research (RIKEN), Wako-shi, Saitama, 351-0198, Japan. okimoto@atlas.riken.go.jp
Yamanaka
K
K
Ueno
J
J
Hata
M
M
Hoshino
T
T
Tsuda
M
M
D000244:Adenosine Diphosphate / Q000737:chemistry / Q000378:metabolism; D000251:Adenosine Triphosphatases / Q000378:metabolism*; D000255:Adenosine Triphosphate / Q000378:metabolism*; D020816:Amino Acid Motifs / Q000502:physiology; D001665:Binding Sites / Q000502:physiology; D003198:Computer Simulation; D006860:Hydrogen Bonding; D006868:Hydrolysis; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism; D008954:Models, Biological; D016297:Mutagenesis, Site-Directed; D009218:Myosins / Q000378:metabolism*; D010710:Phosphates / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D013816:Thermodynamics; D014867:Water / Q000737:chemistry* / Q000378:metabolism
D010710:Phosphates; D014867:Water; D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases; D009218:Myosins; D008274:Magnesium