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Quantum Chemical Interpretation of Protein Crystal Structure

Nilsson, Kristina LU (2003)
Abstract
An initial model in the crystallographic structure determination process, usually contains many errors. To produce an accurate model, one must carry out several cycles of crystallographic refinement. Because of the limited resolution typically obtained for biomolecules, the experimental data are usually supplemented by some sort of chemical information, typically in the form of a molecular-mechanics (MM) force field. The resulting model will strongly depend on the accuracy of this force field. For unusual molecules, such as metal centres, substrates, and inhibitors, i.e. hetero-compounds, force-field parameters are often lacking or are inaccurate.



This thesis describes two methods to improve the process of... (More)
An initial model in the crystallographic structure determination process, usually contains many errors. To produce an accurate model, one must carry out several cycles of crystallographic refinement. Because of the limited resolution typically obtained for biomolecules, the experimental data are usually supplemented by some sort of chemical information, typically in the form of a molecular-mechanics (MM) force field. The resulting model will strongly depend on the accuracy of this force field. For unusual molecules, such as metal centres, substrates, and inhibitors, i.e. hetero-compounds, force-field parameters are often lacking or are inaccurate.



This thesis describes two methods to improve the process of crystallographic refinement and address these problems.



First, Hess2FF, a method to automatically generate topology and parameter files for crystallographic refinement of hetero-compounds. We base the force field on a calculation of the Hessian matrix, which can easily be obtained with any modern theoretical chemistry software. We show that the force-field obtained in such a way may improve the crystal structure and that the interpretation of the final structure will be affected by the choice of the force field. Moreover, we test what level of theory is necessary to obtain a good force field and how the atom types are best selected.



Second, we show that it is possible to use a quantum-chemical method to locally improve protein crystal structures and to interpret them, e.g. by determining the protonation status of interesting molecules and the oxidation states of metal ions. The quantum refinement method, implemented in the software ComQum-X, gives accurate protein structures, which are in agreement with the crystallographic raw data. At the same time, the geometry of the quantum system is directly comparable to structures from quantum-chemical vacuum calculations.



Calculations have been performed on MMP (N-methylmesoporphyrin) bound to the enzyme ferrochelatase, the active site structure of cytochrome c553, an alcohol or a water molecule ligated to the active zinc ion in alcohol dehydrogenase, the iron-bound water molecule in iron superoxide dismutase, and a compound II structure in myoglobin. (Less)
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author
opponent
  • Prof. Morokuma, Keiji
organization
publishing date
type
Thesis
publication status
published
subject
keywords
structure, Theoretical chemistry, quantum chemistry, Teoretisk kemi, kvantkemi, protein, ComQum-X, Hess2FF, QM/MM, hetero-compound, metal, oxidation state, protonation, force field, quantum refinement, refinement
pages
202 pages
publisher
Theoretical Chemistry, Lund University
defense location
Room B Chemical Center, Lund
defense date
2003-12-12 10:15
ISBN
91-7422-040-3
language
English
LU publication?
yes
id
0286008e-98d5-4afc-8646-3533ec106524 (old id 466437)
date added to LUP
2007-10-14 14:25:39
date last changed
2016-09-19 08:45:09
@misc{0286008e-98d5-4afc-8646-3533ec106524,
  abstract     = {An initial model in the crystallographic structure determination process, usually contains many errors. To produce an accurate model, one must carry out several cycles of crystallographic refinement. Because of the limited resolution typically obtained for biomolecules, the experimental data are usually supplemented by some sort of chemical information, typically in the form of a molecular-mechanics (MM) force field. The resulting model will strongly depend on the accuracy of this force field. For unusual molecules, such as metal centres, substrates, and inhibitors, i.e. hetero-compounds, force-field parameters are often lacking or are inaccurate.<br/><br>
<br/><br>
This thesis describes two methods to improve the process of crystallographic refinement and address these problems.<br/><br>
<br/><br>
First, Hess2FF, a method to automatically generate topology and parameter files for crystallographic refinement of hetero-compounds. We base the force field on a calculation of the Hessian matrix, which can easily be obtained with any modern theoretical chemistry software. We show that the force-field obtained in such a way may improve the crystal structure and that the interpretation of the final structure will be affected by the choice of the force field. Moreover, we test what level of theory is necessary to obtain a good force field and how the atom types are best selected.<br/><br>
<br/><br>
Second, we show that it is possible to use a quantum-chemical method to locally improve protein crystal structures and to interpret them, e.g. by determining the protonation status of interesting molecules and the oxidation states of metal ions. The quantum refinement method, implemented in the software ComQum-X, gives accurate protein structures, which are in agreement with the crystallographic raw data. At the same time, the geometry of the quantum system is directly comparable to structures from quantum-chemical vacuum calculations.<br/><br>
<br/><br>
Calculations have been performed on MMP (N-methylmesoporphyrin) bound to the enzyme ferrochelatase, the active site structure of cytochrome c553, an alcohol or a water molecule ligated to the active zinc ion in alcohol dehydrogenase, the iron-bound water molecule in iron superoxide dismutase, and a compound II structure in myoglobin.},
  author       = {Nilsson, Kristina},
  isbn         = {91-7422-040-3},
  keyword      = {structure,Theoretical chemistry,quantum chemistry,Teoretisk kemi,kvantkemi,protein,ComQum-X,Hess2FF,QM/MM,hetero-compound,metal,oxidation state,protonation,force field,quantum refinement,refinement},
  language     = {eng},
  pages        = {202},
  publisher    = {ARRAY(0xbb9ab38)},
  title        = {Quantum Chemical Interpretation of Protein Crystal Structure},
  year         = {2003},
}