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Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements

Ryde, Ulf LU ; Hsiao, Ya-Wen LU ; Rulisek, Lubomir LU and Solomon, Edward I. (2007) In Journal of the American Chemical Society 129(4). p.726-727
Abstract
We have developed a computational method that combines extended X-ray absorption fine structure (EXAFS) refinements with the integrated quantum mechanical and molecular mechanics (QM/MM) method. This method allows us to obtain a structure of a metal site inside a protein that is compatible with both EXAFS data and QM calculations (i.e., that is chemically reasonable). Thereby, the QM/MM calculations play the same role as MM in nearly all NMR and crystallographic refinements-EXAFS ensures that the metal-ligand distances are accurate and QM/MM fills in all the other structural data. We have used this method to show that a structure with a peroxide ion in the center of the trinuclear cluster fits experimental EXAFS data better than a... (More)
We have developed a computational method that combines extended X-ray absorption fine structure (EXAFS) refinements with the integrated quantum mechanical and molecular mechanics (QM/MM) method. This method allows us to obtain a structure of a metal site inside a protein that is compatible with both EXAFS data and QM calculations (i.e., that is chemically reasonable). Thereby, the QM/MM calculations play the same role as MM in nearly all NMR and crystallographic refinements-EXAFS ensures that the metal-ligand distances are accurate and QM/MM fills in all the other structural data. We have used this method to show that a structure with a peroxide ion in the center of the trinuclear cluster fits experimental EXAFS data better than a structure with the peroxide ion on the side of the cluster for the peroxide adduct of multicopper oxidases. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of the American Chemical Society
volume
129
issue
4
pages
726 - 727
publisher
The American Chemical Society
external identifiers
  • wos:000243683800001
  • scopus:33846561241
ISSN
1520-5126
DOI
10.1021/ja062954g
language
English
LU publication?
yes
id
22abf3fc-1827-41c2-b8dc-3ecd42934a78 (old id 676572)
date added to LUP
2007-12-21 14:05:09
date last changed
2017-07-30 04:31:51
@article{22abf3fc-1827-41c2-b8dc-3ecd42934a78,
  abstract     = {We have developed a computational method that combines extended X-ray absorption fine structure (EXAFS) refinements with the integrated quantum mechanical and molecular mechanics (QM/MM) method. This method allows us to obtain a structure of a metal site inside a protein that is compatible with both EXAFS data and QM calculations (i.e., that is chemically reasonable). Thereby, the QM/MM calculations play the same role as MM in nearly all NMR and crystallographic refinements-EXAFS ensures that the metal-ligand distances are accurate and QM/MM fills in all the other structural data. We have used this method to show that a structure with a peroxide ion in the center of the trinuclear cluster fits experimental EXAFS data better than a structure with the peroxide ion on the side of the cluster for the peroxide adduct of multicopper oxidases.},
  author       = {Ryde, Ulf and Hsiao, Ya-Wen and Rulisek, Lubomir and Solomon, Edward I.},
  issn         = {1520-5126},
  language     = {eng},
  number       = {4},
  pages        = {726--727},
  publisher    = {The American Chemical Society},
  series       = {Journal of the American Chemical Society},
  title        = {Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements},
  url          = {http://dx.doi.org/10.1021/ja062954g},
  volume       = {129},
  year         = {2007},
}