Mobility of the active site bound paraoxon and sarin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation

The kinetic data published on phosphotriesterase (PTE), with various comple xed metals, clearly indicates that the P=O and P=S bonds of phosphotriester and thiophosphotriester substrates, respectively, are strongly polarized b y one or both of the active site complexed metal ions. However, this observ ation is not consistent with the three-dimensional X-ray crystal structure of zinc-substituted PTE with active site bound substrate analogue diethyl 4 -methylbenzylphosphonate. In this structure, the distance between the phosp horyl oxygen and the nearest zinc is 3.4 Angstrom, a distance too large to afford strong polarization. In the present paper, the geometry and mobility of various PTE active site-substrate complexes are examined by performing both molecular dynamics (MD) simulations and quantum mechanical calculation s, Two known substrates are considered, paraoxon and sarin, although their turnover rates vary about 100-fold, The results indicate that PTE forms a c omplex with either substrate in which the phosphoryl oxygen becomes strongl y coordinated with the less buried zinc atom. It is shown that the geometry of the active site is changed when the protein is immersed in a water bath and relaxed by MD. The most substantial conformational change is the openi ng of the gateway in a pocket where the location of the leaving group is ex pected. The opening is observed for the pure enzyme as well as for the enzy me/substrate complexes and it ranges from 11 to 18 Angstrom. It is also sho wn that the pockets, in which the substrate substituents are localized, exh ibit different flexibility and interact with the substrate with coordinated conformational adjustments.