Abstract
The motion of catalytic residues and water molecules in the active site of acyl-chymotrypsin was studied with stochastic boundary molecular dynamics. A water molecule expected to provide the nucleophilic OH- for the deacylation reaction was found trapped between His57 and the ester linkage of the acyl group. The trapped water oxygen and hydrogen occasionally approach the carbonyl carbon and the ester oxygen, respectively, while keeping the hydrogen bond to His57 Nε2. Such configurations lead us a stepwise mechanism with very small imidazole movement or one step mechanism in which the tetrahedral intermediate is at the saddle point of the reaction.
