title: A Molecular Dynamics Simulation of the Binding Modes of d-Glutamate and d-Glutamine to Glutamate Racemase.
abstract: Classical molecular dynamics simulations of the d-Gln/Aquifex pyrophilus MurI and d-Glu/Aquifex pyrophilus MurI complexes have been carried out. Since the active site of the enzyme contains many charged and polar residues, several binding modes are possible. Thus, three very different stable conformations of the substrate analogue d-Gln have been found, and at least three binding modes are possible for the substrate d-Glu. These qualitative results give an explanation for the apparent disagreement between the d-Gln bound MurI X-ray crystal structure and the expected position and orientation of the substrate d-Glu in order to make it possible the assumed Cα deprotonation (by Cys70)/reprotonation (by Cys178) racemization mechanism.
authors.affiliation: Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Eduard
authors.initials: E
authors.lastname: Puig
authors.affiliation: Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Mireia
authors.initials: M
authors.lastname: Garcia-Viloca
authors.affiliation: Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Àngels
authors.initials: À
authors.lastname: González-Lafont
authors.affiliation: Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Inés
authors.initials: I
authors.lastname: López
authors.affiliation: Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Xavier
authors.initials: X
authors.lastname: Daura
authors.affiliation: Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: José M
authors.initials: JM
authors.lastname: Lluch