Molecular dynamics simulations of the mononuclear zinc-beta-lactamase fromBacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism

Herein, we present results from MD simulations of the Michaelis complex for med between the B. cereus zinc-beta -lactamase enzyme and benzylpenicillin. The structural and dynamical effects induced by substrate-binding, the spe cific role of the conserved residues, and the near attack conformers of the Michaelis complex are discussed. Quantum chemical methods (HF/6-31G* and B 3LYP/6-31G*) are also applied to study the hydrolysis reaction of N-methyla zetidinone catalyzed by a monozinc system consisting of the side chains of the histidine residues (His86, His88, and His149) complexed with Zn-OH and the side chains of Asp90 and His210. From this model system, we built molec ular-mechanics representations of the prereactive complex and transition st ate configurations docked into the active site. Linear-scaling semiempirica l calculations coupled with a continuum solvent model were then performed o n these static models. We propose that the experimental rate data for the B . cereus enzyme is compatible with a one-step mechanism for the hydrolysis of beta -lactam substrates in which His210 acts as a proton donor.