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Limiting the Effects of Radiation Damage in MicroED through Dose Selection during Data Processing
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).ORCID iD: 0000-0001-8444-6883
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Microcrystal electron diffraction (MicroED), also known as three-dimensional electron diffraction (3D ED), allows collection of diffraction data from submicron-sized crystals under low electron dose conditions, typically around 5-6 e-Å-2 in total. Despite having several advantages of MicroED over most conventional X-ray crystallographic techniques, susceptibility to radiation damage is a big problem that remains to be solved. Similar to X-ray crystallography, radiation damage to the macromolecular crystal structures in MicroED manifests in two forms, the global damage that affects the overall crystal lattice order and the site-specific damage that affects highly sensitive residues and moieties in macromolecules. In this study, we investigated data processing strategies that could be used to limit the effects of radiation damage to the crystal even when data collection is performed at high electron doses. During MicroED data collection, radiation damage increases with the number of acquired ED frames because the accumulated electron dose increases. To limit the damage, we propose to process only the first few frames of a dataset with a certain low dose cutoff. Data collected from several crystals and processed in this way can be merged to increase completeness and subsequently be used for structure refinement. According to our results, this approach improves the resolution of the data, the data statistics, the structure determination, and the quality of the final structure. The suggested approach could be especially useful in MicroED structure-based drug discovery where atomic resolution structures will provide detailed information about ligand-protein binding properties, which are essential during library screening and hit identification. 

Keywords [en]
Microcrystal Electron Diffraction (MicroED), Data processing, macromolecular structure, global radiation damage, site-specific radiation damage
National Category
Structural Biology Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-192527OAI: oai:DiVA.org:su-192527DiVA, id: diva2:1546585
Available from: 2021-04-22 Created: 2021-04-22 Last updated: 2022-02-25Bibliographically approved
In thesis
1. Push the limitations of crystal structure determination by 3D electron diffraction: From inorganic porous materials to biomolecules
Open this publication in new window or tab >>Push the limitations of crystal structure determination by 3D electron diffraction: From inorganic porous materials to biomolecules
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Structure elucidation is fundamental to understanding the chemical and physical properties of a material. Three-dimensional electron diffraction (3D ED) has shown great power for structure determination of nanometer- or submicrometer-sized crystals that are either too small or too complex for X-ray diffraction. 3D ED can be applied to a wide range of crystalline materials from inorganic materials, small organic molecules, to macromolecules. In this thesis, continuous rotation electron diffraction (cRED), also known as micro-crystal electron diffraction (MicroED) in macromolecular crystallography, has been applied for the determination of interesting novel crystal structures. New methods and protocols have been developed to push the current limitations of crystal structure determination by 3D ED.

The structure of silicate zeolite PST-24 is highly disordered. A combination of cRED with high-resolution transmission electron microscopy (HRTEM) revealed its unique channel system with varying dimensionality from 2D to 3D. The aluminum metal-organic framework CAU-23 nanocrystals form aggregates and are very beam sensitive. Its structure, as determined by cRED, is built by twisted helical Al-O chains connected by TDC2- linkers, forming a chiral structure with square channels. The unique structure of CAU-23 provides high stability and high water adsorption capacity, making it an ideal material for ultra-low temperature adsorption driven chillers.

A simple pressure-assisted specimen preparation method, denoted Preassis, has been developed to overcome the challenges in the application of MicroED on biological samples with high viscosity and low crystal concentration. It has been successfully applied for the specimen preparation of several bio-molecular crystals including a novel R2lox metalloenzyme, which was crucial for its structure determination. Furthermore, an investigation of the influence of radiation damage on lysozyme crystals was performed to improve the data quality and final structural model. Finally, the crystal structure of acetylated amyloid-β fragment Ac-Aβ16-20, related to Alzheimer’s disease, has been studied. The crystal has an active optical wave-guiding property with an excitation wavenumber of 488 nm due to its unique packing of Ac-KLVFF β–sheets.

Place, publisher, year, edition, pages
Stockholm: Department of Materials and Environmental Chemistry (MMK), Stockholm University, 2021. p. 82
Keywords
electron crystallography, 3D electron diffraction, cryo-EM specimen preparation, structure determination, porous materials, biomolecules
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-192517 (URN)978-91-7911-448-0 (ISBN)978-91-7911-449-7 (ISBN)
Public defence
2021-06-11, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 09:00 (English)
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Available from: 2021-05-19 Created: 2021-04-22 Last updated: 2022-02-25Bibliographically approved

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Zhao, JingjingHofer, GerhardXu, Hongyi

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