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Structure, strain, and reorganization energy of blue copper models in the protein

Ryde, Ulf LU and Olsson, Mats H. M. (2001) In International Journal of Quantum Chemistry 81(5). p.335-347
Abstract
The copper coordination geometry in the blue copper proteins plastocyanin, nitrite reductase, cucumber basic protein, and azurin has been studied by combined density functional (B3LYP) and molecular mechanical methods. Compared to quantum chemical vacuum calculations, a significant improvement of the geometry is seen (toward the experimental structures) not only for the dihedral angles of the ligands but also for the bond lengths and angles around the copper ion. The flexible Cu–SMet bond is well reproduced in the oxidized structures, whereas it is too long in some of the reduced complexes (too short in vacuum). The change in the geometry compared to the vacuum state costs 33–66 kJ/mol. If the covalent bonds between the ligands and the... (More)
The copper coordination geometry in the blue copper proteins plastocyanin, nitrite reductase, cucumber basic protein, and azurin has been studied by combined density functional (B3LYP) and molecular mechanical methods. Compared to quantum chemical vacuum calculations, a significant improvement of the geometry is seen (toward the experimental structures) not only for the dihedral angles of the ligands but also for the bond lengths and angles around the copper ion. The flexible Cu–SMet bond is well reproduced in the oxidized structures, whereas it is too long in some of the reduced complexes (too short in vacuum). The change in the geometry compared to the vacuum state costs 33–66 kJ/mol. If the covalent bonds between the ligands and the protein are broken, this energy decreases by ∼25 kJ/mol, which is an estimate of the covalent strain. This is similar to what is found for other proteins, so the blue copper proteins are not more strained than other metalloproteins. The inner-sphere self-exchange reorganization energy of all four proteins are ∼30 kJ/mol. This is 30–50 kJ/mol lower than in vacuum. The decrease is caused by dielectric and electrostatic effects in the protein, especially the hydrogen bond(s) to the cysteine copper ligands and not by covalent strain. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
blue copper proteins, entatic state theory, protein strain, QM/MM method, reorganization energy
in
International Journal of Quantum Chemistry
volume
81
issue
5
pages
335 - 347
publisher
John Wiley & Sons
external identifiers
  • scopus:0035252132
ISSN
0020-7608
DOI
10.1002/1097-461X(2001)81:5<335::AID-QUA1003>3.0.CO;2-Q
language
English
LU publication?
yes
id
ad5a67da-29cc-4acd-9884-bae407f41b34 (old id 2275891)
date added to LUP
2012-01-04 11:57:30
date last changed
2018-04-08 03:40:20
@article{ad5a67da-29cc-4acd-9884-bae407f41b34,
  abstract     = {The copper coordination geometry in the blue copper proteins plastocyanin, nitrite reductase, cucumber basic protein, and azurin has been studied by combined density functional (B3LYP) and molecular mechanical methods. Compared to quantum chemical vacuum calculations, a significant improvement of the geometry is seen (toward the experimental structures) not only for the dihedral angles of the ligands but also for the bond lengths and angles around the copper ion. The flexible Cu–SMet bond is well reproduced in the oxidized structures, whereas it is too long in some of the reduced complexes (too short in vacuum). The change in the geometry compared to the vacuum state costs 33–66 kJ/mol. If the covalent bonds between the ligands and the protein are broken, this energy decreases by ∼25 kJ/mol, which is an estimate of the covalent strain. This is similar to what is found for other proteins, so the blue copper proteins are not more strained than other metalloproteins. The inner-sphere self-exchange reorganization energy of all four proteins are ∼30 kJ/mol. This is 30–50 kJ/mol lower than in vacuum. The decrease is caused by dielectric and electrostatic effects in the protein, especially the hydrogen bond(s) to the cysteine copper ligands and not by covalent strain.},
  author       = {Ryde, Ulf and Olsson, Mats H. M.},
  issn         = {0020-7608},
  keyword      = {blue copper proteins,entatic state theory,protein strain,QM/MM method,reorganization energy},
  language     = {eng},
  number       = {5},
  pages        = {335--347},
  publisher    = {John Wiley & Sons},
  series       = {International Journal of Quantum Chemistry},
  title        = {Structure, strain, and reorganization energy of blue copper models in the protein},
  url          = {http://dx.doi.org/10.1002/1097-461X(2001)81:5<335::AID-QUA1003>3.0.CO;2-Q},
  volume       = {81},
  year         = {2001},
}