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The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

Ryde, Ulf LU (1996) In European Biophysics Journal 24(4). p.213-221
Abstract

The coordination chemistry of the structural zinc ion in horse liver alcohol dehydrogenase has been examined by quantum chemical geometry optimisations. It is shown that all four cysteine ligands are deprotonated in the enzyme, not only two of them as has been suggested. The Zn-S bond lengths are very sensitive to the theoretical treatment; in vacuum they are predicted to be 15 pm longer than in the crystal structure. Half of this discrepancy is due to electronic correlation, the rest can be attributed to screening of the negative sulphide charges by the enzyme, in particular by N-H ··· S hydrogen bonds. The potential surface is rather flat, so the large difference in geometry between the crystal and the vacuum structure corresponds to... (More)

The coordination chemistry of the structural zinc ion in horse liver alcohol dehydrogenase has been examined by quantum chemical geometry optimisations. It is shown that all four cysteine ligands are deprotonated in the enzyme, not only two of them as has been suggested. The Zn-S bond lengths are very sensitive to the theoretical treatment; in vacuum they are predicted to be 15 pm longer than in the crystal structure. Half of this discrepancy is due to electronic correlation, the rest can be attributed to screening of the negative sulphide charges by the enzyme, in particular by N-H ··· S hydrogen bonds. The potential surface is rather flat, so the large difference in geometry between the crystal and the vacuum structure corresponds to an energy change of less than 35 kJ/mol. The experimental bond lengths can be reproduced only with methods that account explicitly for the enzyme. A dielectric continuum model gives bond lengths which are too long, indicating that the enzyme solvates the coordination sphere better than water. Thus, the structural zinc ion can be used as a sensitive test of methods which try to model the surrounding medium in quantum chemical computations.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
combined quantum chemical and molecular geometry optimisations, protein strain, solvent cavity models
in
European Biophysics Journal
volume
24
issue
4
pages
9 pages
publisher
Springer
external identifiers
  • scopus:0029919895
ISSN
0175-7571
DOI
10.1007/BF00205102
language
English
LU publication?
yes
id
aa69339c-a7b3-4f58-97f5-6322c937a236
date added to LUP
2017-02-04 11:33:00
date last changed
2017-07-30 05:21:06
@article{aa69339c-a7b3-4f58-97f5-6322c937a236,
  abstract     = {<p>The coordination chemistry of the structural zinc ion in horse liver alcohol dehydrogenase has been examined by quantum chemical geometry optimisations. It is shown that all four cysteine ligands are deprotonated in the enzyme, not only two of them as has been suggested. The Zn-S bond lengths are very sensitive to the theoretical treatment; in vacuum they are predicted to be 15 pm longer than in the crystal structure. Half of this discrepancy is due to electronic correlation, the rest can be attributed to screening of the negative sulphide charges by the enzyme, in particular by N-H ··· S hydrogen bonds. The potential surface is rather flat, so the large difference in geometry between the crystal and the vacuum structure corresponds to an energy change of less than 35 kJ/mol. The experimental bond lengths can be reproduced only with methods that account explicitly for the enzyme. A dielectric continuum model gives bond lengths which are too long, indicating that the enzyme solvates the coordination sphere better than water. Thus, the structural zinc ion can be used as a sensitive test of methods which try to model the surrounding medium in quantum chemical computations.</p>},
  author       = {Ryde, Ulf},
  issn         = {0175-7571},
  keyword      = {combined quantum chemical and molecular geometry optimisations,protein strain,solvent cavity models},
  language     = {eng},
  number       = {4},
  pages        = {213--221},
  publisher    = {Springer},
  series       = {European Biophysics Journal},
  title        = {The coordination chemistry of the structural zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations},
  url          = {http://dx.doi.org/10.1007/BF00205102},
  volume       = {24},
  year         = {1996},
}