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The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: Quantum refinement

Nilsson, Kristina LU ; Hersleth, H P; Rod, Thomas LU ; Andersson, K K and Ryde, Ulf LU (2004) In Biophysical Journal 87(5). p.3437-3447
Abstract
Treatment of met-myoglobin (Fe-III) with H2O2 gives rise to ferryl myoglobin, which is closely related to compound II in peroxidases. Experimental studies have given conflicting results for this species. In particular, crystallographic and extended x-ray absorption fine-structure data have shown either a short (similar to170 pm) or a longer (similar to190 pm) Fe-O bond, indicating either a double or a single bond. We here present a combined experimental and theoretical investigation of this species. In particular, we use quantum refinement to re-refine a crystal structure with a long bond, using 12 possible states of the active site. The states differ in the formal oxidation state of the iron ion and in the protonation of the oxygen ligand... (More)
Treatment of met-myoglobin (Fe-III) with H2O2 gives rise to ferryl myoglobin, which is closely related to compound II in peroxidases. Experimental studies have given conflicting results for this species. In particular, crystallographic and extended x-ray absorption fine-structure data have shown either a short (similar to170 pm) or a longer (similar to190 pm) Fe-O bond, indicating either a double or a single bond. We here present a combined experimental and theoretical investigation of this species. In particular, we use quantum refinement to re-refine a crystal structure with a long bond, using 12 possible states of the active site. The states differ in the formal oxidation state of the iron ion and in the protonation of the oxygen ligand (O2-, OH-, or H2O) and the distal histidine residue (with a proton on N-delta1, N-epsilon2, or on both atoms). Quantum refinement is essentially standard crystallographic refinement, where the molecular-mechanics potential, normally used to supplement the experimental data, is replaced by a quantum chemical calculation. Thereby, we obtain an accurate description of the active site in all the different protonation and oxidation states, and we can determine which of the 12 structures fit the experimental data best by comparing the crystallographic R-factors, electron-density maps, strain energies, and deviation from the ideal structure. The results indicate that Fe-III OH- and Fe-IV OH- fit the experimental data almost equally well. These two states are appreciably better than the standard model of compound II, Fe-IV O2-. Combined with the available spectroscopic data, this indicates that compound II in myoglobin is protonated and is best described as Fe-IV OH-. It accepts a hydrogen bond from the distal His, which may be protonated at low pH. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Biophysical Journal
volume
87
issue
5
pages
3437 - 3447
publisher
Cell Press
external identifiers
  • wos:000224732500045
  • pmid:15339813
  • scopus:13844270250
ISSN
1542-0086
DOI
10.1529/biophysj.104.041590
language
English
LU publication?
yes
id
674cb06d-c378-47bf-b9a2-0f2e040f0e85 (old id 139570)
date added to LUP
2007-07-17 12:12:25
date last changed
2017-09-24 03:27:50
@article{674cb06d-c378-47bf-b9a2-0f2e040f0e85,
  abstract     = {Treatment of met-myoglobin (Fe-III) with H2O2 gives rise to ferryl myoglobin, which is closely related to compound II in peroxidases. Experimental studies have given conflicting results for this species. In particular, crystallographic and extended x-ray absorption fine-structure data have shown either a short (similar to170 pm) or a longer (similar to190 pm) Fe-O bond, indicating either a double or a single bond. We here present a combined experimental and theoretical investigation of this species. In particular, we use quantum refinement to re-refine a crystal structure with a long bond, using 12 possible states of the active site. The states differ in the formal oxidation state of the iron ion and in the protonation of the oxygen ligand (O2-, OH-, or H2O) and the distal histidine residue (with a proton on N-delta1, N-epsilon2, or on both atoms). Quantum refinement is essentially standard crystallographic refinement, where the molecular-mechanics potential, normally used to supplement the experimental data, is replaced by a quantum chemical calculation. Thereby, we obtain an accurate description of the active site in all the different protonation and oxidation states, and we can determine which of the 12 structures fit the experimental data best by comparing the crystallographic R-factors, electron-density maps, strain energies, and deviation from the ideal structure. The results indicate that Fe-III OH- and Fe-IV OH- fit the experimental data almost equally well. These two states are appreciably better than the standard model of compound II, Fe-IV O2-. Combined with the available spectroscopic data, this indicates that compound II in myoglobin is protonated and is best described as Fe-IV OH-. It accepts a hydrogen bond from the distal His, which may be protonated at low pH.},
  author       = {Nilsson, Kristina and Hersleth, H P and Rod, Thomas and Andersson, K K and Ryde, Ulf},
  issn         = {1542-0086},
  language     = {eng},
  number       = {5},
  pages        = {3437--3447},
  publisher    = {Cell Press},
  series       = {Biophysical Journal},
  title        = {The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: Quantum refinement},
  url          = {http://dx.doi.org/10.1529/biophysj.104.041590},
  volume       = {87},
  year         = {2004},
}