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Quantum chemical geometry optimizations in proteins using crystallographic raw data.

Ryde, Ulf LU ; Olsen, Lars and Nilsson, Kristina LU (2002) In Journal of Computational Chemistry 23(11). p.1058-1070
Abstract
A method is developed for the combination of quantum chemical geometry optimizations and crystallographic structure refinement. The method is implemented by integrating the quantum chemical software Turbomole with the crystallographic software Crystallography and NMR System (CNS), using three small procedures transferring information between the two programs. The program (COMQUM-X)is used to study the binding of the inhibitor N-methylmesoporphyrin to ferrochelatase, and we show that the method behaves properly and leads to an improvement of the structure of the inhibitor. It allows us to directly quantify in energy terms how much the protein distort the structure of the bound inhibitor compared to the optimum vacuum structure (4-6 kJ/mol).... (More)
A method is developed for the combination of quantum chemical geometry optimizations and crystallographic structure refinement. The method is implemented by integrating the quantum chemical software Turbomole with the crystallographic software Crystallography and NMR System (CNS), using three small procedures transferring information between the two programs. The program (COMQUM-X)is used to study the binding of the inhibitor N-methylmesoporphyrin to ferrochelatase, and we show that the method behaves properly and leads to an improvement of the structure of the inhibitor. It allows us to directly quantify in energy terms how much the protein distort the structure of the bound inhibitor compared to the optimum vacuum structure (4-6 kJ/mol). The approach improves the standard combined quantum chemical and molecular mechanics (QC/MM) approach by guaranteeing that the final structure is in accordance with experimental data (the reflections) and avoiding the risk of propagating errors in the crystal coordinates. The program can also be seen as an improvement of standard crystallographic refinement, providing an accurate empirical potential function for any group of interest. The results can be directly interpreted in standard crystallographic terms (e.g., R factors or electron density maps). The method can be used to interpret crystal structures (e.g., the protonation status of metal-bound water molecules) and even to locally improve them. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Computational Chemistry
volume
23
issue
11
pages
1058 - 1070
publisher
John Wiley & Sons
external identifiers
  • pmid:12116392
  • wos:000176605400003
  • scopus:0036667496
ISSN
1096-987X
DOI
10.1002/jcc.10093
language
English
LU publication?
yes
id
88349453-677f-4eb7-9ed0-f293699ae81a (old id 109286)
date added to LUP
2007-07-17 13:55:04
date last changed
2017-09-24 04:30:55
@article{88349453-677f-4eb7-9ed0-f293699ae81a,
  abstract     = {A method is developed for the combination of quantum chemical geometry optimizations and crystallographic structure refinement. The method is implemented by integrating the quantum chemical software Turbomole with the crystallographic software Crystallography and NMR System (CNS), using three small procedures transferring information between the two programs. The program (COMQUM-X)is used to study the binding of the inhibitor N-methylmesoporphyrin to ferrochelatase, and we show that the method behaves properly and leads to an improvement of the structure of the inhibitor. It allows us to directly quantify in energy terms how much the protein distort the structure of the bound inhibitor compared to the optimum vacuum structure (4-6 kJ/mol). The approach improves the standard combined quantum chemical and molecular mechanics (QC/MM) approach by guaranteeing that the final structure is in accordance with experimental data (the reflections) and avoiding the risk of propagating errors in the crystal coordinates. The program can also be seen as an improvement of standard crystallographic refinement, providing an accurate empirical potential function for any group of interest. The results can be directly interpreted in standard crystallographic terms (e.g., R factors or electron density maps). The method can be used to interpret crystal structures (e.g., the protonation status of metal-bound water molecules) and even to locally improve them.},
  author       = {Ryde, Ulf and Olsen, Lars and Nilsson, Kristina},
  issn         = {1096-987X},
  language     = {eng},
  number       = {11},
  pages        = {1058--1070},
  publisher    = {John Wiley & Sons},
  series       = {Journal of Computational Chemistry},
  title        = {Quantum chemical geometry optimizations in proteins using crystallographic raw data.},
  url          = {http://dx.doi.org/10.1002/jcc.10093},
  volume       = {23},
  year         = {2002},
}