| Abstract
| - Ab initio QM/MM dynamics simulation is employed to examine the stability of the tetrahedralintermediate during the deacylation step in elastase-catalyzed hydrolysis of a simple peptide. An extendedquantum region includes the catalytic triad, the tetrahedral structure, and the oxyanion hole. The calculationsindicate that the tetrahedral intermediate of serine proteases is a stable species on the picosecond timescale. On the basis of geometrical and dynamical properties, and in agreement with many experimentaland theoretical studies, it is suggested that the crucial hydrogen bonds involved in stabilizing this intermediateare between Asp-102 and His-57 and between the charged oxygen of the intermediate and the backboneN−H group of Gly-193 in the oxyanion hole. The mobility of the imidazolium ring between Ow and Oγ, twoof the oxygens of the tetrahedral structure, shows how the intermediate could proceed toward the productstate without a “ring-flip mechanism”, proposed earlier on the basis of NMR data. In addition to the proposedCε1−H···O hydrogen bond between the imidazolium ring and the backbone carbonyl of Ser-214, we observean alternative Cε1−H···O hydrogen bond with the backbone carbonyl of Thr-213, that can stabilize theintermediate during the imidazolium movement. Proton hopping occurs between Asp-102 and His-57 duringthe simulation. The proton is, however, largely localized on the nitrogen, and hence it does not participatein 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 anda loop opening between residues 216−225 that enables the breaking of a hydrogen bond in subsite S3.
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