title: X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane.
abstract: The present work describes the results of a study aimed at identifying candidate cation binding sites on the extracellular region of bacteriorhodopsin, including a site near the retinal pocket. The approach used is a combined effort involving computational chemistry methods (computation of cation affinity maps and molecular dynamics) together with the Extended X-Ray Absorption Fine Structure (EXAFS) technique to obtain relevant information about the local structure of the protein in the neighborhood of Mn(2+) ions in different affinity binding sites. The results permit the identification of a high-affinity binding site where the ion is coordinated simultaneously to Asp212(-) and Asp85(-). Comparison of EXAFS data of the wild type protein with the quadruple mutant E9Q/E74Q/E194Q/E204Q at pH 7.0 and 10.0 demonstrate that extracellular glutamic acid residues are involved in cation binding.
authors.affiliation: Departament d'Enginyeria Agroalimentària i Biotecnologia, Escola Superior d'Agricultura de Barcelona, Universitat Politècnica de Catalunya, Barcelona, Spain. francesc.sepulcre@upc.edu
authors.forename: Francesc
authors.initials: F
authors.lastname: Sepulcre
authors.forename: Arnau
authors.initials: A
authors.lastname: Cordomí
authors.forename: M Grazia
authors.initials: MG
authors.lastname: Proietti
authors.forename: Juan J
authors.initials: JJ
authors.lastname: Perez
authors.forename: Joaquin
authors.initials: J
authors.lastname: García
authors.forename: Enric
authors.initials: E
authors.lastname: Querol
authors.forename: Esteve
authors.initials: E
authors.lastname: Padrós
mesh_terms: D001436:Bacteriorhodopsins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D002412:Cations; D018698:Glutamic Acid / Q000737:chemistry; D006217:Halobacterium; D006863:Hydrogen-Ion Concentration; D008345:Manganese / Q000737:chemistry*; D008958:Models, Molecular; D009038:Motion; D018717:Purple Membrane / Q000737:chemistry* / Q000378:metabolism; D013057:Spectrum Analysis; D014965:X-Rays
chemical_list: D002412:Cations; D018698:Glutamic Acid; D008345:Manganese; D001436:Bacteriorhodopsins