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Protein strain in blue copper proteins studied by free energy perturbations

De Kerpel, Jan O A and Ryde, Ulf LU orcid (1999) In Proteins: Structure, Function and Genetics 36(2). p.157-174
Abstract

Free energy perturbations have been performed on two blue copper proteins, plastocyanin and nitrite reductase. By changing the copper coordination geometry, force constants, and charges, we have estimated the maximum energy with which the proteins may distort the copper coordination sphere. By comparing this energy with the quantum chemical energy cost for the same perturbation on the isolated copper complex, various hypotheses about protein strain have been tested. The calculations show that the protein can only modify the copper-methionine bond length by a modest amount of energy -- <5 kJ/mol--and they lend no support to the suggestion that the quite appreciable difference in the copper coordination geometry encountered in the two... (More)

Free energy perturbations have been performed on two blue copper proteins, plastocyanin and nitrite reductase. By changing the copper coordination geometry, force constants, and charges, we have estimated the maximum energy with which the proteins may distort the copper coordination sphere. By comparing this energy with the quantum chemical energy cost for the same perturbation on the isolated copper complex, various hypotheses about protein strain have been tested. The calculations show that the protein can only modify the copper-methionine bond length by a modest amount of energy -- <5 kJ/mol--and they lend no support to the suggestion that the quite appreciable difference in the copper coordination geometry encountered in the two proteins is a result of the proteins enforcing different Cu- methionine bond lengths. On the contrary, this bond is very flexible, and neither the geometry nor the electronic structure change appreciably when the bond length is changed. Moreover, the proteins are rather indifferent to the length of this bond. Instead, the Cu(II) coordination geometries in the two proteins represent two distinct minima on the potential surface of the copper ligand sphere, characterized by different electronic structures, a tetragonal, mainly or-bonded, structure in nitrite reductase and a trigonal, π-bonded, structure in plastocyanin. In vacuum, the structures have almost the same energy, and they are stabilized in the proteins by a combination of geometric and electrostatic interactions. Plastocyanin favors the bond lengths and electrostatics of the trigonal structure, whereas in nitrite reductase, the angles are the main discriminating factor.

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author
and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Entatic state theory, Induced-rack theory, Molecular dynamics, Nitrite reductase, Plastocyanin
in
Proteins: Structure, Function and Genetics
volume
36
issue
2
pages
18 pages
publisher
John Wiley & Sons Inc.
external identifiers
  • pmid:10398364
  • scopus:0033180952
ISSN
0887-3585
DOI
10.1002/(SICI)1097-0134(19990801)36:2<157::AID-PROT3>3.0.CO;2-Y
language
English
LU publication?
yes
id
3070384e-0534-4580-aa7f-0da5c79f6594
date added to LUP
2017-02-04 11:41:42
date last changed
2024-01-13 13:08:37
@article{3070384e-0534-4580-aa7f-0da5c79f6594,
  abstract     = {{<p>Free energy perturbations have been performed on two blue copper proteins, plastocyanin and nitrite reductase. By changing the copper coordination geometry, force constants, and charges, we have estimated the maximum energy with which the proteins may distort the copper coordination sphere. By comparing this energy with the quantum chemical energy cost for the same perturbation on the isolated copper complex, various hypotheses about protein strain have been tested. The calculations show that the protein can only modify the copper-methionine bond length by a modest amount of energy -- &lt;5 kJ/mol--and they lend no support to the suggestion that the quite appreciable difference in the copper coordination geometry encountered in the two proteins is a result of the proteins enforcing different Cu- methionine bond lengths. On the contrary, this bond is very flexible, and neither the geometry nor the electronic structure change appreciably when the bond length is changed. Moreover, the proteins are rather indifferent to the length of this bond. Instead, the Cu(II) coordination geometries in the two proteins represent two distinct minima on the potential surface of the copper ligand sphere, characterized by different electronic structures, a tetragonal, mainly or-bonded, structure in nitrite reductase and a trigonal, π-bonded, structure in plastocyanin. In vacuum, the structures have almost the same energy, and they are stabilized in the proteins by a combination of geometric and electrostatic interactions. Plastocyanin favors the bond lengths and electrostatics of the trigonal structure, whereas in nitrite reductase, the angles are the main discriminating factor.</p>}},
  author       = {{De Kerpel, Jan O A and Ryde, Ulf}},
  issn         = {{0887-3585}},
  keywords     = {{Entatic state theory; Induced-rack theory; Molecular dynamics; Nitrite reductase; Plastocyanin}},
  language     = {{eng}},
  month        = {{08}},
  number       = {{2}},
  pages        = {{157--174}},
  publisher    = {{John Wiley & Sons Inc.}},
  series       = {{Proteins: Structure, Function and Genetics}},
  title        = {{Protein strain in blue copper proteins studied by free energy perturbations}},
  url          = {{http://dx.doi.org/10.1002/(SICI)1097-0134(19990801)36:2<157::AID-PROT3>3.0.CO;2-Y}},
  doi          = {{10.1002/(SICI)1097-0134(19990801)36:2<157::AID-PROT3>3.0.CO;2-Y}},
  volume       = {{36}},
  year         = {{1999}},
}