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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/139570
- author
- Nilsson, Kristina
LU
; Hersleth, H P
; Rod, Thomas
LU
; Andersson, K K
and Ryde, Ulf
LU
- organization
- publishing date
- 2004
- 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
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)
- id
- 674cb06d-c378-47bf-b9a2-0f2e040f0e85 (old id 139570)
- date added to LUP
- 2016-04-01 11:35:43
- date last changed
- 2023-01-02 20:33:09
@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 = {{https://lup.lub.lu.se/search/files/2553653/624738.pdf}},
doi = {{10.1529/biophysj.104.041590}},
volume = {{87}},
year = {{2004}},
}