Quantum refinement - a combination of quantum chemistry and protein crystallography.
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/128839
- author
- Ryde, Ulf LU and Nilsson, Kristina LU
- organization
- publishing date
- 2003
- 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
- 2023-01-24 02:30:34
@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}}, keywords = {{Combined quantum mechanics and molecular mechanics; Crystallographic refinement; Metalloproteins; Density functional theory; Protonation status}}, 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 = {{https://lup.lub.lu.se/search/files/135492048/58_cqrev.pdf}}, doi = {{10.1016/S0166-1280(03)00304-X}}, volume = {{632}}, year = {{2003}}, }