Molecular simulations of DD-peptidase,a model ß-lactam-binding protein: Synergy between X-ray crystallography and computational chemistry

Using computer model building, the three-dimensional structure of an enzyme from Streptomyces R61 that is inhibited by ß-lactam antibiotics has been constructed starting from incomplete X-ray crystallographic data for this 37.4 kDa protein. The so-called DD-peptidase catalyzes transpeptidation and hydrolysis of peptides terminating in D-Ala-D-Ala and is a model for bacterial transpeptidases and carboxypeptidases essential in the biosynthesis of the peptidoglycan layer of the cell wall. The structure, which was completed with the SYBYL molecular modeling package, has been refined by energy minimization and molecular dynamics using Quanta/CHARMm software. A simulation of 105 ps was run with waters of solvation in the active site. From these computations, the interatomic distances between the active serine and key residues around the active site were determined. Inadequacies at reproducing geometric details of the ß-lactam ring of a cephalosporin are pointed out which are typical of most commercially available force fields.