MOLECULAR-DYNAMICS SIMULATION OF A CLASS-A BETA-LACTAMASE - STRUCTURAL AND MECHANISTIC IMPLICATIONS

A molecular dynamics (MD) simulation of the class A beta-lactamase fro m S. aureus PC1 has been carried out based on the GROMOS force field. The simulation treats the enzyme solvated by 7295 molecules of water i n a hexagonal prism cell using periodic boundary conditions. The overa ll structural integrity of the molecule is well preserved. Calculated temperature factors show no dramatic increase in the flexibility of th e Omega loop, a loosely packed 17-residue segment (residues 163-179) a djacent to the active site. The salt bridge between Arg164 and Asp179, believed to be the main stabilizing interaction for the Omega loop, w as observed to be destabilized in the theoretical model but is compens ated in part by a new interaction between Arg164 and Glu168. Early in the simulation, however, a rigid flap-like motion was observed for the Omega loop which results in a repositioning of the carboxylate group of Glu166 within hydrogen-bonding distance of the primary nucleophile, the Ser70 hydroxyl group, coupled with displacement of the ''hydrolyt ic'' water molecule. The significant repositioning of Glu166 suggests that its position in the crystal structures of class A beta-lactamases cannot be taken as conclusive evidence that an acylation mechanism in volving direct general base catalysis by the Glu166 carboxylate is inc orrect. Analysis of the mobility of active site water molecules sugges ts that most of them, including the ''hydrolytic'' and ''oxyanion hole '' water molecules, exchange with bulk solvent much faster than the ca talytic time scale.