X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane

Francesc Sepulcre, Arnau Cordomí, M. Grazia Proietti, Juan J. Perez, Joaquin García, Enric Querol, Esteve Padrós

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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 Mn2+ 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. © 2007 Wiley-Liss, Inc.
Original languageEnglish
Pages (from-to)360-374
JournalProteins: Structure, Function and Genetics
Volume67
DOIs
Publication statusPublished - 1 May 2007

Keywords

  • Bacteriorhodopsin
  • Mn K-edge
  • Mn-EXAFS
  • Mn-XANES
  • Proton pumping
  • Quick EXAFS

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    Sepulcre, F., Cordomí, A., Proietti, M. G., Perez, J. J., García, J., Querol, E., & Padrós, E. (2007). X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane. Proteins: Structure, Function and Genetics, 67, 360-374. https://doi.org/10.1002/prot.21273