title: GRID/tetrahedral intermediate computational approach to the study of selectivity of penicillin G acylase in amide bond synthesis.
abstract: Molecular modelling was used to investigate the catalytic site of penicillin G acylase (PGA) by building up a simple enzyme-ligand model able to describe and predict the enzyme selectivity. The investigation was based on a double computational approach: first, the GRID computational procedure was applied to gain a qualitative description of the chemical features of the PGA active site; second, a classical "transition state approach" was used to simulate the tetrahedral intermediates and to evaluate their energies. GRID calculations employed different probes which gave a complete description of the chemical interactions occurring upon binding of different ligands, thus indicating those structures having good affinity with the active site of the enzyme. Tetrahedral intermediates were constructed on the basis of GRID results and provided both geometrical features and energies of enzyme-substrate interaction. Such energies were compared to experimental kinetic data obtained in the enzymatic acylation of L-phenylglycine methyl ester using various methyl phenylacetate derivatives. The good agreement of computational results with experimental evidence demonstrates the validity of the model as a rapid and flexible tool to describe and predict the enzyme selectivity.
authors.affiliation: Dipartimento di Scienze Farmaceutiche, Università degli Studi, Piazzale Europa 1, 34127 Trieste, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Basso
authors.forename: Paolo
authors.initials: P
authors.lastname: Braiuca
authors.forename: Cynthia
authors.initials: C
authors.lastname: Ebert
authors.forename: Lucia
authors.initials: L
authors.lastname: Gardossi
authors.forename: Paolo
authors.initials: P
authors.lastname: Linda
authors.forename: Fabio
authors.initials: F
authors.lastname: Benedetti
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D008958:Models, Molecular; D010399:Penicillin Amidase / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D013379:Substrate Specificity
chemical_list: D010399:Penicillin Amidase