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Quantum refinement - a combination of quantum chemistry and protein crystallography.

Ryde, Ulf LU and Nilsson, Kristina LU (2003) In Journal of molecular structure. Theochem 632(1-3). p.259-275
Abstract
The combination of quantum mechanics and molecular mechanics (QM/MM) is one of the most promising approaches to study the structure, function, and properties of proteins. We here review our applications of QM/MM methods to alcohol dehydrogenase, blue copper proteins, iron–sulphur clusters, ferrochelatase, and myoglobin. We also describe our new quantum refinement method, which is a combination of quantum chemistry and protein crystallography. It has been shown to work properly and it can be used to improve the structure of protein metal centres in terms of the crystallographic Rfree factor and electron-density maps. It can be used to determine the protonation status of metal-bound solvent molecules in proteins by refining the various... (More)
The combination of quantum mechanics and molecular mechanics (QM/MM) is one of the most promising approaches to study the structure, function, and properties of proteins. We here review our applications of QM/MM methods to alcohol dehydrogenase, blue copper proteins, iron–sulphur clusters, ferrochelatase, and myoglobin. We also describe our new quantum refinement method, which is a combination of quantum chemistry and protein crystallography. It has been shown to work properly and it can be used to improve the structure of protein metal centres in terms of the crystallographic Rfree factor and electron-density maps. It can be used to determine the protonation status of metal-bound solvent molecules in proteins by refining the various possible states and see which fits the crystallographic raw data best. Applications to ferrochelatase, cytochrome c553, alcohol dehydrogenase, myoglobin, and methylmalonyl coenzyme A mutase are described. (Less)
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type
Contribution to journal
publication status
published
subject
keywords
Combined quantum mechanics and molecular mechanics, Crystallographic refinement, Metalloproteins, Density functional theory, Protonation status
in
Journal of molecular structure. Theochem
volume
632
issue
1-3
pages
259 - 275
publisher
Elsevier
external identifiers
  • wos:000185399100021
  • scopus:0345227309
ISSN
0166-1280
DOI
10.1016/S0166-1280(03)00304-X
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
af855daf-fd14-401c-acb2-ea9ece644d5d (old id 128839)
date added to LUP
2016-04-01 16:10:23
date last changed
2020-06-03 02:46:00
@article{af855daf-fd14-401c-acb2-ea9ece644d5d,
  abstract     = {The combination of quantum mechanics and molecular mechanics (QM/MM) is one of the most promising approaches to study the structure, function, and properties of proteins. We here review our applications of QM/MM methods to alcohol dehydrogenase, blue copper proteins, iron–sulphur clusters, ferrochelatase, and myoglobin. We also describe our new quantum refinement method, which is a combination of quantum chemistry and protein crystallography. It has been shown to work properly and it can be used to improve the structure of protein metal centres in terms of the crystallographic Rfree factor and electron-density maps. It can be used to determine the protonation status of metal-bound solvent molecules in proteins by refining the various possible states and see which fits the crystallographic raw data best. Applications to ferrochelatase, cytochrome c553, alcohol dehydrogenase, myoglobin, and methylmalonyl coenzyme A mutase are described.},
  author       = {Ryde, Ulf and Nilsson, Kristina},
  issn         = {0166-1280},
  language     = {eng},
  number       = {1-3},
  pages        = {259--275},
  publisher    = {Elsevier},
  series       = {Journal of molecular structure. Theochem},
  title        = {Quantum refinement - a combination of quantum chemistry and protein crystallography.},
  url          = {http://dx.doi.org/10.1016/S0166-1280(03)00304-X},
  doi          = {10.1016/S0166-1280(03)00304-X},
  volume       = {632},
  year         = {2003},
}