title: Hybrid Potential Simulation of the Acylation of Enterococcus faecium l,d-Transpeptidase by Carbapenems.
abstract: The l,d-transpeptidases, Ldts, catalyze peptidoglycan cross-linking in β-lactam-resistant mutant strains of several bacteria, including Enterococcus faecium and Mycobacterium tuberculosis. Although unrelated to the essential d,d-transpeptidases, which are inactivated by the β-lactam antibiotics, they are nevertheless inhibited by the carbapenem antibiotics, making them potentially useful targets in the treatment of some important diseases. In this work, we have investigated the acylation mechanism of the Ldt from E. faecium by the carbapenem, ertapenem, using computational techniques. We have employed molecular dynamics simulations in conjunction with QC/MM hybrid potential calculations to map out possible reaction paths. We have focused on determining the following: (i) the protonation state of the nucleophilic cysteine of the enzyme when it attacks; (ii) whether nucleophilic attack and β-lactam ring-opening are concerted or stepwise, the latter occurring via an oxyanion intermediate; and (iii) the identities of the proton acceptors at the beginning and end of the reaction. Overall, we note that there is considerable plasticity in the mechanisms, owing to the significant flexibility of the enzyme, but find that the preferred pathways are ones in which nucleophilic attack of cysteine thiolate is concerted with β-lactam ring-opening.
authors.affiliation: DYNAMO/DYNAMOP, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.
authors.forename: Nicholus
authors.initials: N
authors.lastname: Bhattacharjee
authors.affiliation: DYNAMO/DYNAMOP, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Field
authors.affiliation: RMN, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Simorre
authors.affiliation: Centre de Recherche des Cordeliers, Equipe 12, UMR S 872, Université Pierre et Marie Curie-Paris 6, INSERM, Université Paris Descartes, Sorbonne Paris Cité, 15 rue de l'Ecole de Médecine, 75006 Paris, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Arthur
authors.affiliation: RMN, UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Bougault
mesh_terms: D000215:Acylation; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D015780:Carbapenems / Q000737:chemistry / Q000378:metabolism*; D016984:Enterococcus faecium / Q000201:enzymology*; D056004:Molecular Dynamics Simulation; D010458:Peptidyl Transferases / Q000737:chemistry / Q000378:metabolism*; D011789:Quantum Theory
chemical_list: D001426:Bacterial Proteins; D015780:Carbapenems; D010458:Peptidyl Transferases