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Title: X-ray absorption studies of zn2+ binding sites in bacterial, avianand bovine cytochrome bc1 complexes.

Abstract

No abstract prepared.

Authors:
; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
COLLABORATION - University ofBologna
OSTI Identifier:
927326
Report Number(s):
LBNL-62872
Journal ID: ISSN 0006-3495; BIOJAU; R&D Project: 864U1F; TRN: US200811%%97
DOE Contract Number:
DE-AC02-05CH11231
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biophysical Journal; Journal Volume: 93; Related Information: Journal Publication Date: Jun 15 2007
Country of Publication:
United States
Language:
English
Subject:
59; ABSORPTION; CATTLE; CYTOCHROMES; XAFS, cytochrome bc complex, zinc binding sites, metal ioninhibition, Rhodobacter capsulatus

Citation Formats

Giachini, L., Francia, F., Veronesi, G., Lee, D.W., Daldal, F., Huang, L.S., Berry, E.A., Cocco, T., Papa, S., Boscherini, F., and Venturoli,G. X-ray absorption studies of zn2+ binding sites in bacterial, avianand bovine cytochrome bc1 complexes.. United States: N. p., 2007. Web. doi:10.1529/biophysj.107.110957.
Giachini, L., Francia, F., Veronesi, G., Lee, D.W., Daldal, F., Huang, L.S., Berry, E.A., Cocco, T., Papa, S., Boscherini, F., & Venturoli,G. X-ray absorption studies of zn2+ binding sites in bacterial, avianand bovine cytochrome bc1 complexes.. United States. doi:10.1529/biophysj.107.110957.
Giachini, L., Francia, F., Veronesi, G., Lee, D.W., Daldal, F., Huang, L.S., Berry, E.A., Cocco, T., Papa, S., Boscherini, F., and Venturoli,G. Tue . "X-ray absorption studies of zn2+ binding sites in bacterial, avianand bovine cytochrome bc1 complexes.". United States. doi:10.1529/biophysj.107.110957.
@article{osti_927326,
title = {X-ray absorption studies of zn2+ binding sites in bacterial, avianand bovine cytochrome bc1 complexes.},
author = {Giachini, L. and Francia, F. and Veronesi, G. and Lee, D.W. and Daldal, F. and Huang, L.S. and Berry, E.A. and Cocco, T. and Papa, S. and Boscherini, F. and Venturoli,G.},
abstractNote = {No abstract prepared.},
doi = {10.1529/biophysj.107.110957},
journal = {Biophysical Journal},
number = ,
volume = 93,
place = {United States},
year = {Tue May 22 00:00:00 EDT 2007},
month = {Tue May 22 00:00:00 EDT 2007}
}
  • The chicken mitochondrial ubiquinol cytochrome c oxidoreductase (bc1 complex) is inhibited by Zn{sup 2+} ions, but with higher Ki ({approximately}3 {micro}M) than the corresponding bovine enzyme. When equilibrated with mother liquor containing 200 mM ZnCl{sub 2} for 7 days, the crystalline chicken bc1 complex specifically binds Zn{sup 2+} at 4 sites representing two sites on each monomer in the dimer. These two sites are close to the stigmatellin-binding site, taken to be center Qo of the Q-cycle mechanism, and are candidates for the inhibitory site. One binding site is actually in the hydrophobic channel between the Qo site and themore » bulk lipid phase, and may interfere with quinone binding. The other is in a hydrophilic area between cytochromes b and c1, and might interfere with the egress of protons from the Qo site to the intermembrane aqueous medium. No zinc was bound near the putative proteolytic active site of subunits 1 and 2 (homologous to mitochondrial processing peptidase) under these conditions.« less
  • In this study, the speciation of Zn{sup 2+}, Pb{sup 2+}, and Cu{sup 2+} ions sorbed at the calcite surface was monitored during a 2.5-year reaction period, using extended X-ray absorption spectroscopy to characterize metal speciation on the molecular scale. Experiments were performed using pre-equilibrated calcite-water suspensions of pH 8.3, at metal concentrations below the solubility of metal hydroxide and carbonate precipitates, and at constant metal surface loadings. The EXAFS results indicate that all three metals remained coordinated at the calcite surface as inner-sphere adsorption complexes during the 2.5-year ageing period, with no evidence to suggest slow formation of dilute metal-calcitemore » solid solutions under the reaction conditions employed. All three divalent metals were found to form non-octahedral complexes upon coordination to the calcite surface, with Zn{sup 2+} adsorbing as a tetrahedral complex, Cu{sup 2+} as a Jahn-Teller distorted octahedral complex, and Pb{sup 2+} coordinating as a trigonal- or square-pyramidal surface complex. The non-octahedral configurations of these surface complexes may have hindered metal transfer from the calcite surface into the bulk, where Ca{sup 2+} is in octahedral coordination with respect to first-shell O. The use of pre-equilibrated calcite suspensions, with no net calcite dissolution or precipitation, likely prevented metal incorporation into the lattice as a result of surface recrystallization. The results from this study imply that ageing alone does not increase the stability of Zn{sup 2+}, Pb{sup 2+}, and Cu{sup 2+} partitioning to calcite if equilibrium with the solution is maintained during reaction; under these conditions, these metals are likely to remain available for exchange even after extended sorption times.« less
  • We have investigated the binding environments of Cu{sup 2+} and Pb{sup 2+} complexed by soil humic substances using synchrotron-based X-ray absorption spectroscopy. With the assistance of bond network analysis, analysis of X-ray absorption near edge structure (XANES) and radial structure functions derived from extended X-ray absorption fine structure (EXAFS) spectra of Cu-humate at pH 4, 5, and 6 yielded a tetragonally-distorted octahedral binding environment for Cu with 4 O atoms at an average distance of 1.94 {angstrom}, 20 atoms at an average distance of 2.02 {angstrom}, and 4 C atoms at an average distance of 3.13 {angstrom}. Analysis of Pb-humatemore » samples at pH 4, 5, and 6 yielded 4 O atoms at average distances between 2.46 {angstrom} to 2.32 {angstrom} and 2 C atoms at an average distance of 3.26 {angstrom} for Pb. We interpret the presence of C atoms in the second atomic shell of the metal binding site as evidence that both C{sup 2+} and Pb{sup 2+} form innersphere complexes with soil humic substances. Within the pH range 4-6, there is no significant change in the structure of the binding sites for either Cu or Pb. 65 refs., 8 figs., 5 tabs.« less
  • The coordination environments of first row transition elements (Co, Ni, Cu, and Zn) complexed by aquatic and soil humic substances were studied using X-ray absorption spectroscopy (XAS). With the assistance of bond network analysis, analysis of X-ray absorption near edge structure (XANES) spectra and radial structure functions (RSF) derived from extended X-ray absorption fine structure (EXAFS) spectra of Co, Ni, Cu, and Zn in humic substances indicate an octahedral binding environment for Co, Ni, and Zn and a tetragonally-distorted octahedral binding environment for Cu. Analysis of EXAFS spectra of each element provides detailed information on the internuclear distances, bond angles,more » and Debye-Waller factors within the first two atomic shells surrounding Co, Ni, Cu, and Zn bound to humic substances. We interpret the presence of C atoms in the second atomic shell of the metal binding site as further evidence that Co, Ni, Cu, and Zn form innersphere complexes with humic substances. The number and type of ligands involved in the binding are different for different elements. 71 refs., 10 figs., 5 tabs.« less