Quantum refinement in real and reciprocal space
(2025)- Abstract
- In order to understand and manipulate biological function at the molecular level, access to high-resolution structures of biological macromolecules is essential, as structure is intimately linked to function. The two main experimental techniques that can achieve atomic, or near-atomic, resolution are crystallography and electron microscopy. Unfortunately, the experimental data alone is typically not sufficient to obtain an accurate atomic model, owing to a poor data-to-parameter ratio. Therefore, prior knowledge of the chemical nature of the system is supplemented during refinement in the form of restraints. Traditional restraints are accurate for standard amino acids and nucleic acids, less so for novel ligands and metal sites.... (More)
- In order to understand and manipulate biological function at the molecular level, access to high-resolution structures of biological macromolecules is essential, as structure is intimately linked to function. The two main experimental techniques that can achieve atomic, or near-atomic, resolution are crystallography and electron microscopy. Unfortunately, the experimental data alone is typically not sufficient to obtain an accurate atomic model, owing to a poor data-to-parameter ratio. Therefore, prior knowledge of the chemical nature of the system is supplemented during refinement in the form of restraints. Traditional restraints are accurate for standard amino acids and nucleic acids, less so for novel ligands and metal sites. Additionally, transferability of these restraints is commonly assumed, ignoring the specific chemical environment. A solution is to use in situ quantum mechanical calculations for small, but interesting, parts of the structure, during refinement. Such an approach, called quantum refinement, has been shown to improve structures locally, to allow determination of protonation and oxidation states of ligands and metals and discriminate between different interpretations of the structure.
Previous implementations of quantum refinement have been limited to either X-ray or neutron crystallography data, using low-level quantum mechanical methods or not being able to treat metal sites. In this thesis, we present a new implementation of quantum refinement, called QRef. QRef supports X-ray, neutron and electron diffraction data, as well as cryo-EM data, and can use a wide range of quantum mechanical methods, allowing treatment of metal sites. QRef is released under a permissive license.
We have subsequently applied QRef to a variety of challenging biological systems. For a recent crystal structure of Fe-nitrogenase, we determined the protonation state of the homocitrate ligand. We performed a critical evaluation of metal sites in three cryo-EM structures of particulate methane monooxygenase, showing that several sites were incorrectly interpreted. This was the first time that quantum refinement had been applied to metal sites in cryo-EM structures and we suggest that quantum refinement is the method of choice for such systems. Furthermore, we have applied quantum refinement to data from XFEL and electron diffraction experiments, showing that quantum refinement can improve structures and interpretations in these cases as well. Finally, we have applied QRef to data from neutron diffraction experiments of manganese superoxide dismutase, demonstrating the challenges associated with neutron data of limited resolution. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/8f0427ad-f184-4c03-a3cd-7daa868e4f47
- author
- Lundgren, Kristoffer LU
- supervisor
-
- Ulf Ryde LU
- Esko Oksanen LU
- opponent
-
- Professor Biczysko, Małgorzata, University of Wrocław.
- organization
- publishing date
- 2025
- type
- Thesis
- publication status
- published
- subject
- keywords
- quantum refinement, X-ray crystallography, neutron crystallography, electron crystallography, cryo-EM, nitrogenase, particulate methane monooxygenase, ribonucleotide reductase, manganese superoxide dismutase
- pages
- 222 pages
- publisher
- Lund University
- defense location
- Kemicentrum, sal A
- defense date
- 2025-12-12 13:00:00
- ISBN
- 978-91-8096-131-8
- 978-91-8096-130-1
- language
- English
- LU publication?
- yes
- id
- 8f0427ad-f184-4c03-a3cd-7daa868e4f47
- date added to LUP
- 2025-11-14 15:55:13
- date last changed
- 2025-11-17 15:14:59
@phdthesis{8f0427ad-f184-4c03-a3cd-7daa868e4f47,
abstract = {{In order to understand and manipulate biological function at the molecular level, access to high-resolution structures of biological macromolecules is essential, as structure is intimately linked to function. The two main experimental techniques that can achieve atomic, or near-atomic, resolution are crystallography and electron microscopy. Unfortunately, the experimental data alone is typically not sufficient to obtain an accurate atomic model, owing to a poor data-to-parameter ratio. Therefore, prior knowledge of the chemical nature of the system is supplemented during refinement in the form of restraints. Traditional restraints are accurate for standard amino acids and nucleic acids, less so for novel ligands and metal sites. Additionally, transferability of these restraints is commonly assumed, ignoring the specific chemical environment. A solution is to use in situ quantum mechanical calculations for small, but interesting, parts of the structure, during refinement. Such an approach, called quantum refinement, has been shown to improve structures locally, to allow determination of protonation and oxidation states of ligands and metals and discriminate between different interpretations of the structure.<br/><br/>Previous implementations of quantum refinement have been limited to either X-ray or neutron crystallography data, using low-level quantum mechanical methods or not being able to treat metal sites. In this thesis, we present a new implementation of quantum refinement, called QRef. QRef supports X-ray, neutron and electron diffraction data, as well as cryo-EM data, and can use a wide range of quantum mechanical methods, allowing treatment of metal sites. QRef is released under a permissive license.<br/><br/>We have subsequently applied QRef to a variety of challenging biological systems. For a recent crystal structure of Fe-nitrogenase, we determined the protonation state of the homocitrate ligand. We performed a critical evaluation of metal sites in three cryo-EM structures of particulate methane monooxygenase, showing that several sites were incorrectly interpreted. This was the first time that quantum refinement had been applied to metal sites in cryo-EM structures and we suggest that quantum refinement is the method of choice for such systems. Furthermore, we have applied quantum refinement to data from XFEL and electron diffraction experiments, showing that quantum refinement can improve structures and interpretations in these cases as well. Finally, we have applied QRef to data from neutron diffraction experiments of manganese superoxide dismutase, demonstrating the challenges associated with neutron data of limited resolution.}},
author = {{Lundgren, Kristoffer}},
isbn = {{978-91-8096-131-8}},
keywords = {{quantum refinement; X-ray crystallography; neutron crystallography; electron crystallography; cryo-EM; nitrogenase; particulate methane monooxygenase; ribonucleotide reductase; manganese superoxide dismutase}},
language = {{eng}},
publisher = {{Lund University}},
school = {{Lund University}},
title = {{Quantum refinement in real and reciprocal space}},
url = {{https://lup.lub.lu.se/search/files/233011227/Kristoffer_Lundgren_kappa.pdf}},
year = {{2025}},
}