Ab Initio QM/MM Dynamics Simulation of the Tetrahedral Intermediate of Serine Proteases:  Insights into the Active Site Hydrogen-Bonding Network

Ab initio QM/MM dynamics simulation is employed to examine the stability of the tetrahedral intermediate during the deacylation step in elastase-catalyzed hydrolysis of a simple peptide. An extended quantum region includes the catalytic triad, the tetrahedral structure, and the oxyanion hole. The calculations indicate that the tetrahedral intermediate of serine proteases is a stable species on the picosecond time scale. On the basis of geometrical and dynamical properties, and in agreement with many experimental and theoretical studies, it is suggested that the crucial hydrogen bonds involved in stabilizing this intermediate are between Asp-102 and His-57 and between the charged oxygen of the intermediate and the backbone N−H group of Gly-193 in the oxyanion hole. The mobility of the imidazolium ring between Ow and Oγ, two of the oxygens of the tetrahedral structure, shows how the intermediate could proceed toward the product state without a “ring-flip mechanism”, proposed earlier on the basis of NMR data. In addition to the proposed Cε1−H···O hydrogen bond between the imidazolium ring and the backbone carbonyl of Ser-214, we observe an alternative Cε1−H···O hydrogen bond with the backbone carbonyl of Thr-213, that can stabilize the intermediate during the imidazolium movement. Proton hopping occurs between Asp-102 and His-57 during the simulation. The proton is, however, largely localized on the nitrogen, and hence it does not participate in a low-barrier hydrogen bond. The study also suggests factors that may be implicated in product release: breaking the hydrogen bond of the charged oxygen with the backbone of Ser-195 in the oxyanion hole and a loop opening between residues 216−225 that enables the breaking of a hydrogen bond in subsite S3.