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Push the limitations of crystal structure determination by 3D electron diffraction: From inorganic porous materials to biomolecules
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).ORCID iD: 0000-0001-8444-6883
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 [en]
electron crystallography, 3D electron diffraction, cryo-EM specimen preparation, structure determination, porous materials, biomolecules
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-192517ISBN: 978-91-7911-448-0 (print)ISBN: 978-91-7911-449-7 (electronic)OAI: oai:DiVA.org:su-192517DiVA, id: diva2:1546653
Public defence
2021-06-11, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 09:00 (English)
Opponent
Supervisors
Available from: 2021-05-19 Created: 2021-04-22 Last updated: 2022-02-25Bibliographically approved
List of papers
1. PST-24: A Zeolite with Varying Intracrystalline Channel Dimensionality
Open this publication in new window or tab >>PST-24: A Zeolite with Varying Intracrystalline Channel Dimensionality
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2020 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 59, no 40, p. 17691-17696Article in journal (Refereed) Published
Abstract [en]

Herein we report the synthesis, structure solution, and catalytic properties of PST-24, a novel channel-based medium-pore zeolite. This zeolite was synthesized via the excess fluoride approach. Electron diffraction shows that its structure is built by composite cas-zigzag (cas-zz) building chains, which are connected by double 5-ring (d5r) columns. While the cas-zz building chains are ordered in the PST-24 framework, the d5r columns adopt one of two possible arrangements; the two adjacent d5r columns are either at the same height or at different heights, denoted arrangements S and D, which can be regarded as open and closed valves that connect the channels, respectively. A framework with arrangement D only has a 2D 10-ring channel system, whereas that with arrangement S only contains 3D channels. In actual PST-24 crystals, the open and closed valves are almost randomly dispersed to yield a zeolite framework where the channel dimensionality varies locally from 2D to 3D.

Keywords
aluminosilicates, channel dimensionality, electron diffraction, structure elucidation, zeolites
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-185386 (URN)10.1002/anie.202007804 (DOI)000557829400001 ()32609403 (PubMedID)
Available from: 2020-11-26 Created: 2020-11-26 Last updated: 2023-09-13Bibliographically approved
2. A metal-organic framework for efficient water-based ultra-low-temperature-driven cooling
Open this publication in new window or tab >>A metal-organic framework for efficient water-based ultra-low-temperature-driven cooling
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2019 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 3025Article in journal (Refereed) Published
Abstract [en]

Efficient use of energy for cooling applications is a very important and challenging field in science. Ultra-low temperature actuated (T-driving< 80 degrees C) adsorption-driven chillers (ADCs) with water as the cooling agent are one environmentally benign option. The nanoscale metal-organic framework [Al(OH)(C6H2O4S)] denoted CAU-23 was discovered that possess favorable properties, including water adsorption capacity of 0.37 g(H2O)/g(sorbent) around p/p(0 )= 0.3 and cycling stability of at least 5000 cycles. Most importantly the material has a driving temperature down to 60 degrees C, which allows for the exploitation of yet mostly unused temperature sources and a more efficient use of energy. These exceptional properties are due to its unique crystal structure, which was unequivocally elucidated by single crystal electron diffraction. Monte Carlo simulations were performed to reveal the water adsorption mechanism at the atomic level. With its green synthesis, CAU-23 is an ideal material to realize ultra-low temperature driven ADC devices.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-171758 (URN)10.1038/s41467-019-10960-0 (DOI)000474506700011 ()31289274 (PubMedID)
Available from: 2019-09-04 Created: 2019-09-04 Last updated: 2023-03-28Bibliographically approved
3. A simple pressure-assisted method for MicroED specimen preparation
Open this publication in new window or tab >>A simple pressure-assisted method for MicroED specimen preparation
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal contents. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED. 

National Category
Structural Biology Physical Chemistry
Identifiers
urn:nbn:se:su:diva-192523 (URN)
Available from: 2021-04-22 Created: 2021-04-22 Last updated: 2022-02-25Bibliographically approved
4. Solving a new R2lox protein structure by microcrystal electron diffraction
Open this publication in new window or tab >>Solving a new R2lox protein structure by microcrystal electron diffraction
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2019 (English)In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 8, article id eaax4621Article in journal (Refereed) Published
Abstract [en]

Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure-an R2lox enzyme-solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-angstrom resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.

National Category
Physical Sciences Biological Sciences
Identifiers
urn:nbn:se:su:diva-173201 (URN)10.1126/sciadv.aax4621 (DOI)000481798400057 ()31457106 (PubMedID)
Available from: 2019-09-16 Created: 2019-09-16 Last updated: 2022-03-23Bibliographically approved
5. Limiting the Effects of Radiation Damage in MicroED through Dose Selection during Data Processing
Open this publication in new window or tab >>Limiting the Effects of Radiation Damage in MicroED through Dose Selection during Data Processing
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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
Microcrystal Electron Diffraction (MicroED), Data processing, macromolecular structure, global radiation damage, site-specific radiation damage
National Category
Structural Biology Physical Chemistry
Identifiers
urn:nbn:se:su:diva-192527 (URN)
Available from: 2021-04-22 Created: 2021-04-22 Last updated: 2022-02-25Bibliographically approved
6. Atomic Structure of Amyloid Crystals
Open this publication in new window or tab >>Atomic Structure of Amyloid Crystals
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

 

A deep understanding of the self-assembly and crystallization of biomolecules as highly ordered biomaterials is crucial to enable the design and the generation of complex functional systems for cutting-edge applications in nanotechnology and biomedicine. In this work, we determined the atomic structure of Aβ16-20 crystals, a fragment of amyloid-β which aberrant folding is linked to the etiology of Alzheimer’s disease, the most common cause of dementia. We detailed the hierarchical aggregation mechanism of Aβ16-20 into highly ordered crystals and revealed that the self-assembly is reversible, leading to the formation of oligomers as an intermediate. Our structural investigation combined with molecular dynamics simulations highlights how a combination of favorable non-covalent interactions drives the efficient fast self-assembly and enhanced stability. We studied the chemical and surface properties of amyloid crystals, including their mechanical properties and their capability to transmit light; the long-rang order of Aβ16-20 crystals enables them to be used as optical waveguide materials for biologically based modulation and sensing. Our results shed new light on pathogenic amyloid assembly at the atomic level and reveal the potential of amyloid crystals for applications in nanotechnology.

National Category
Biophysics Physical Chemistry Organic Chemistry
Identifiers
urn:nbn:se:su:diva-192532 (URN)
Available from: 2021-04-22 Created: 2021-04-22 Last updated: 2025-02-20Bibliographically approved

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