pKa, MM, and QM studies of mechanisms of β‐lactamases and penicillin‐binding proteins: Acylation step

Abstract

AbstractThe acylation step of the catalytic mechanism of β‐lactamases and penicillin‐binding proteins (PBPs) has been studied with various approaches. The methods applied range from molecular dynamics (MD) simulations to multiple titration calculations using the Poisson–Boltzmann approach to quantum mechanical (QM) methods. The mechanism of class A β‐lactamases was investigated in the greatest detail. Most approaches support the critical role of Glu‐166 and hydrolytic water in the acylation step of the enzymatic catalysis in class A β‐lactamases. The details of the catalytic mechanism have been revealed by the QM approach, which clearly pointed out the critical role of Glu‐166 acting as a general base in the acylation step with preferred substrates. Lys‐73 shuffles a proton abstracted by Glu‐166 Oε to the β‐lactam nitrogen through Ser‐130 hydroxyl. This proton is transferred from Oγ of the catalytic Ser‐70 through the bridging hydrolytic water to Glu‐166 Oε. Then the hydrogen is simultaneously passed through SN2 inversion mechanism at Lys‐73 Nζ to Ser‐130 Oγ, which loses its proton to the β‐lactam nitrogen. The protonation of β‐lactam nitrogen proceeds with an immediate ring opening and collapse of the first tetrahedral species into an acyl‐enzyme intermediate. However, the studies that considered the effect of solvation lower the barrier for the pathway, which utilizes Lys‐73 as a general base, thus creating a possibility of multiple mechanisms for the acylation step in the class A β‐lactamases. These findings help explain the exceptional efficiency of these enzymes. They emphasize an important role of Glu‐166, Lys‐73, and Ser‐130 for enzymatic catalysis and shed light on details of the acylation step of class A β‐lactamase mechanism. The acylation step for class C β‐lactamases and six classes of PBPs were also considered with continuum solvent models and MD simulations. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1559–1576, 2002