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Carboxylate binding modes in zinc proteins : A theoretical study

Ryde, Ulf LU (1999) In Biophysical Journal 77(5). p.2777-2787
Abstract

The relative energies of different coordination modes (bidentate, monodentate, syn, and anti) of a carboxylate group bound to a zinc ion have been studied by the density functional method B3LYP with large basis sets on realistic models of the active site of several zinc proteins. In positively charged four-coordinate complexes, the mono- and bidentate coordination modes have almost the same energy (within 10 kJ/mol). However, if there are negatively charged ligands other than the carboxylate group, the monodentate binding mode is favored. In general, the energy difference between monodentate and bidentate coordination is small, 4-24 kJ/mol, and it is determined more by hydrogen-bond interactions with other ligands or second- sphere... (More)

The relative energies of different coordination modes (bidentate, monodentate, syn, and anti) of a carboxylate group bound to a zinc ion have been studied by the density functional method B3LYP with large basis sets on realistic models of the active site of several zinc proteins. In positively charged four-coordinate complexes, the mono- and bidentate coordination modes have almost the same energy (within 10 kJ/mol). However, if there are negatively charged ligands other than the carboxylate group, the monodentate binding mode is favored. In general, the energy difference between monodentate and bidentate coordination is small, 4-24 kJ/mol, and it is determined more by hydrogen-bond interactions with other ligands or second- sphere groups than by the zinc-carboxylate interaction. Similarly, the activation energy for the conversion between the two coordination modes is small, ~6 kJ/mol, indicating a very flat Zn-O potential surface. The energy difference between syn and anti binding modes of the monodentate carboxylate group is larger, 70-100 kJ/mol, but this figure again strongly depends on interactions with second-sphere molecules. Our results also indicate that the pK(a) of the zinc-bound water ligand in carboxypeptidase and thermolysin is 8-9.

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publication status
published
subject
in
Biophysical Journal
volume
77
issue
5
pages
11 pages
publisher
Cell Press
external identifiers
  • scopus:0032708644
ISSN
0006-3495
DOI
10.1016/S0006-3495(99)77110-9
language
English
LU publication?
yes
id
82b03c52-b954-4c69-970f-15c846c118dd
date added to LUP
2017-02-04 11:41:23
date last changed
2017-06-11 05:13:08
@article{82b03c52-b954-4c69-970f-15c846c118dd,
  abstract     = {<p>The relative energies of different coordination modes (bidentate, monodentate, syn, and anti) of a carboxylate group bound to a zinc ion have been studied by the density functional method B3LYP with large basis sets on realistic models of the active site of several zinc proteins. In positively charged four-coordinate complexes, the mono- and bidentate coordination modes have almost the same energy (within 10 kJ/mol). However, if there are negatively charged ligands other than the carboxylate group, the monodentate binding mode is favored. In general, the energy difference between monodentate and bidentate coordination is small, 4-24 kJ/mol, and it is determined more by hydrogen-bond interactions with other ligands or second- sphere groups than by the zinc-carboxylate interaction. Similarly, the activation energy for the conversion between the two coordination modes is small, ~6 kJ/mol, indicating a very flat Zn-O potential surface. The energy difference between syn and anti binding modes of the monodentate carboxylate group is larger, 70-100 kJ/mol, but this figure again strongly depends on interactions with second-sphere molecules. Our results also indicate that the pK(a) of the zinc-bound water ligand in carboxypeptidase and thermolysin is 8-9.</p>},
  author       = {Ryde, Ulf},
  issn         = {0006-3495},
  language     = {eng},
  number       = {5},
  pages        = {2777--2787},
  publisher    = {Cell Press},
  series       = {Biophysical Journal},
  title        = {Carboxylate binding modes in zinc proteins : A theoretical study},
  url          = {http://dx.doi.org/10.1016/S0006-3495(99)77110-9},
  volume       = {77},
  year         = {1999},
}