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SwissFEDI - a Free Electron Diffraction Instrument for nano-diffraction of biological specimens

Applicant Abrahams Jan Pieter
Number 165669
Funding scheme Project funding (Div. I-III)
Research institution Paul Scherrer Institut
Institution of higher education Paul Scherrer Institute - PSI
Main discipline Technical Physics
Start/End 01.02.2017 - 31.01.2020
Approved amount 740'977.00
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All Disciplines (5)

Discipline
Technical Physics
Microelectronics. Optoelectronics
Other disciplines of Physics
Biophysics
Material Sciences

Keywords (3)

structural biology; electron diffraction; nano-crystallography

Lay Summary (German)

Lead
Das Sichtbarmachen der Vorgänge in unserem Koerper auf kleinster Ebene istwichtig zum Verstaendnis biologischer Vorgaenge und der Entwicklung vonMedikamenten. Mit SwissFEDI baut das PSI ein Instrument, mit dem man invoellig neue Dimensionen der Visualisierung lebenswichtiger Molekuele vordringenwird.
Lay summary

Inhalt und Ziel des Forschungsprojekts 

Dieses Forschungsprojekt fuehrt Pilotexperimente und Pilotentwicklungen durch, die auf die Konstruktion des Instruments "SwissFEDI" hinauslaufen. SwissFEDI wird mittels Elektronenbeugung die biologische Maschinerie bei ihrer Arbeit in der Zelle visualisieren. Das neue an diesem Ansatz ist die Kombination der Genauigkeit von Elektronen als Messsonden mit dem schonenden Eingriff der Beugung, die die Probe erheblich weniger versehrt als die direkte Bildgebung. SwissFEDI wird Messungen von Enzymen und sogar in ganzen Zellen ermöglichen, aus denen sich ein Bild der durchleuchteten Probe rekonstruieren laesst. Konkret adressiert dieses Projekt einen Probenhalter, der die Messung von allen Seiten ermoeglicht - derzeitige Probenhalter haben einen zu grossen "toten Winkel" als dass man vollstaendige Daten messen koennte.  Desweiteren benoetigt man bei der Bildrekonstruktion Informationen, die sich nicht direkt aus der Messung ablesen lassen. Wir werden Instrumente und Methoden entwickeln, mit denen sich die
fehlende Information indirekt wiedergewinnen laesst, so dass der Bildrekonstruktion nichts mehr im Wege steht.

 

Direct link to Lay Summary Last update: 12.01.2017

Responsible applicant and co-applicants

Employees

Publications

Publication
2D Crystal Engineering of Nanosheets Assembled from Helical Peptide Building Blocks
Merg Andrea D., Touponse Gavin, van\hspace0.25emGenderen Eric, Zuo Xiaobing, Bazrafshan Alisina, Blum Thorsten, Hughes Spencer, Salaita Khalid, Abrahams Jan Pieter, Conticello Vincent P. (2019), 2D Crystal Engineering of Nanosheets Assembled from Helical Peptide Building Blocks, in Angewandte Chemie International Edition, 58(38), 13507-13512.
3D Electron Diffraction: The Nanocrystallography Revolution.
M Gemmi, E Mugnaioli, TE Gorelik, U Kolb, L Palatinus, P Boullay, S Hovmöller, JP Abrahams (2019), 3D Electron Diffraction: The Nanocrystallography Revolution., in ACS central science, 1315.
Inelastic scattering and solvent scattering reduce dynamical diffraction in biological crystals
Latychevskaia T., Abrahams J.P. (2019), Inelastic scattering and solvent scattering reduce dynamical diffraction in biological crystals, in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 75, 523-531.
Longitudinal cell division is associated with single mutations in the FtsZ-recruiting SsgB in Streptomyces
Xiao Xiansha, Willemse Joost, Voskamp Patrick, Li Xinmeng, Lamers Meindert H, Abrahams Jan Pieter, Pannu Navraj, van Wezel Gilles P (2019), Longitudinal cell division is associated with single mutations in the FtsZ-recruiting SsgB in Streptomyces, in BioRxiv, 860916.
Reducing dynamical electron scattering reveals hydrogen atoms
Clabbers Max T. B., Gruene Tim, van Genderen Eric, Abrahams Jan Pieter (2019), Reducing dynamical electron scattering reveals hydrogen atoms, in Acta Crystallographica Section A Foundations and Advances, 75(1), 82-93.
Seeded Heteroepitaxial Growth of Crystallizable Collagen Triple Helices: Engineering Multifunctional Two-Dimensional Core-Shell Nanostructures.
AD Merg, van Genderen E, A Bazrafshan, H Su, X Zuo, G Touponse, TB Blum, K Salaita, JP Abrahams, VP Conticello (2019), Seeded Heteroepitaxial Growth of Crystallizable Collagen Triple Helices: Engineering Multifunctional Two-Dimensional Core-Shell Nanostructures., in Journal of the American Chemical Society, 20107.
Supramolecular architectures of molecularly thin yet robust free-standing layers.
M Moradi, NL Opara, LG Tulli, C Wäckerlin, SJ Dalgarno, SJ Teat, M Baljozovic, O Popova, van Genderen E, A Kleibert, H Stahlberg, JP Abrahams, P Shahgaldian (2019), Supramolecular architectures of molecularly thin yet robust free-standing layers., in Science advances, eaav4489.
The wild-type flagellar filament of the Firmicute Kurthia at 2.8 Å resolution in vivo.
TB Blum, S Filippidou, M Fatton, P Junier, JP Abrahams (2019), The wild-type flagellar filament of the Firmicute Kurthia at 2.8 Å resolution in vivo., in Scientific reports, 14948.
A Molecular Level Approach To Elucidate the Supramolecular Packing of Light-Harvesting Antenna Systems.
B Thomas, RK Dubey, MTB Clabbers, KBSS Gupta, van Genderen E, WF Jager, JP Abrahams, EJR Sudholter, de Groot HJM (2018), A Molecular Level Approach To Elucidate the Supramolecular Packing of Light-Harvesting Antenna Systems., in Chemistry (Weinheim an der Bergstrasse, Germany), 14989.
Electron crystallography with the EIGER detector.
G Tinti, E Fröjdh, van Genderen E, T Gruene, B Schmitt, de Winter DAM, BM Weckhuysen, JP Abrahams (2018), Electron crystallography with the EIGER detector., in IUCrJ, 190.
Electron diffraction and three-dimensional crystallography for structural biology
Clabbers Max T. B., Abrahams Jan Pieter (2018), Electron diffraction and three-dimensional crystallography for structural biology, in Crystallography Reviews, 24(3), 176-204.
Electron diffraction data processing with DIALS
Clabbers Max T. B., Gruene Tim, Parkhurst James M., Abrahams Jan Pieter, Waterman David G. (2018), Electron diffraction data processing with DIALS, in Acta Crystallographica Section D Structural Biology, 74(6), 506-518.
Lattice filter for processing image data of three-dimensional protein nanocrystals
van Genderen E., Li Y.-W., Nederlof I., Abrahams J.P. (2018), Lattice filter for processing image data of three-dimensional protein nanocrystals, in International Journal of Dermatology, 57(1), 34-39.
The Neuronal Tau Protein Blocks in Vitro Fibrillation of the Amyloid-β (Aβ) Peptide at the Oligomeric Stage.
C Wallin, Y Hiruma, SKTS Wärmländer, I Huvent, J Jarvet, JP Abrahams, A Gräslund, G Lippens, J Luo (2018), The Neuronal Tau Protein Blocks in Vitro Fibrillation of the Amyloid-β (Aβ) Peptide at the Oligomeric Stage., in Journal of the American Chemical Society, 8138.
A Novel Capturing Method for Quantification of Extra-Cellular Nanovesicles.
Q Yin, Z Liu, F Laroche, X Zhou, N Shao, B Lin, Wang, N Yuan, J Ding, JP Abrahams (2017), A Novel Capturing Method for Quantification of Extra-Cellular Nanovesicles., in Journal of nanoscience and nanotechnology, 908.
Neutravidin-mediated extraction of isolated small diameter single walled carbon nanotubes for bio-recognition
Su J., Wang H., Wu K., Liu Z., Yin Q., Wang R., Lv W., Yin S., Liu Z., Abrahams J.P. (2017), Neutravidin-mediated extraction of isolated small diameter single walled carbon nanotubes for bio-recognition, in Journal of Nanoscience and Nanotechnology, 17(5), 3588-3596.
Protein structure determination by electron diffraction using a single three-dimensional nanocrystal.
MTB Clabbers, van Genderen E, W Wan, EL Wiegers, T Gruene, JP Abrahams (2017), Protein structure determination by electron diffraction using a single three-dimensional nanocrystal., in Acta crystallographica. Section D, Structural biology, 738.
Purification of Biotinylated Proteins Using Single Walled Carbon Nanotube-Streptavidin Complexes.
R Wang, M Boleij, Q Yin, N Galjart, B Lin, N Yuan, X Zhou, M Tan, J Ding, Z Liu, JP Abrahams (2017), Purification of Biotinylated Proteins Using Single Walled Carbon Nanotube-Streptavidin Complexes., in Journal of nanoscience and nanotechnology, 926.
Testing and Comparison of Imaging Detectors for Electrons in the Energy Range 10-20 keV
Matheson J., Moldovan G., Kirkland A., Allinson N., Abrahams J.P. (2017), Testing and Comparison of Imaging Detectors for Electrons in the Energy Range 10-20 keV, in Journal of Instrumentation, 12(11), C11016.

Datasets

Cryo-EM structure of the wild-type flagellar filament of the Firmicute Kurthia

Author Abrahams, Jan Pieter; Blum, Thorsten
Publication date 30.10.2019
Persistent Identifier (PID) 10.2210/pdb6T17/pdb
Repository 6T17.pdb
Abstract
Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which switches the handedness of the filament's supercoil. So far, all studied functional filaments are composed of a mixture of L- and R-state flagellin monomers. Here we show in a study of the wild type Firmicute Kurthia sp., that curved, functional filaments can adopt a conformation in vivo that is closely related to a uniform, all-L-state. This sheds additional light on transitions of the flagellar supercoil and uniquely reveals the atomic structure of a wild-type flagellar filament in vivo, including six residues showing clearly densities of O-linked glycosylation.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

Author Abrahams, Jan Pieter
Publication date 23.08.2017
Persistent Identifier (PID) 5O4W.pdb
Repository 5O4W.pdb
Abstract
Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm 3 , i.e. no more than 6 × 10 5 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

Author Abrahams, Jan Pieter
Publication date 23.08.2017
Persistent Identifier (PID) 5O4X
Repository 5O4X
Abstract
Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm 3 , i.e. no more than 6 × 10 5 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

BISGAO

Author Abrahams, Jan Pieter
Publication date 14.11.2018
Persistent Identifier (PID) BISGAO
Repository BISGAO


IRELOH01

Author Abrahams, Jan Pieter
Publication date 14.11.2018
Persistent Identifier (PID) IRELOH01
Repository IRELOH01


Collaboration

Group / person Country
Types of collaboration
Braun/Abela, SwissFEL, PSI Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Dunin, Ernst Ruska Center Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Stahlberg, C-CINA, Biozentrum Basel Uni Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Ravelli, Maastricht University Netherlands (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Ischebeck, accelerator technology, PSI Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Tsujino, PSI Laboratory for Micro- and Nanotechnology Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Schmitt, Detector Group PSI Lab for Macromolecules and Bioimaging Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Housset, IBS France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
van Wezel Netherlands (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Conticello, Emory University United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Structural Biology enabled by XFELs and Cryo-EM Talk given at a conference Electron diffraction for structural biology 25.06.2019 PSI, Villigen, Switzerland Abrahams Jan Pieter;
Novel Accelerators for Electron Diffraction Talk given at a conference Application of electron diffraction in biology 17.06.2019 PSI, Villigen, Switzerland Abrahams Jan Pieter;
Pico 2019 Talk given at a conference How human lon protease clears the mitochondrial matrix of damaged protein 06.05.2019 Vaalsbroek, Netherlands Abrahams Jan Pieter; Borsa Christopher John; Blum Thorsten;
INTERNATIONAL SCHOOL of CRYSTALLOGRAPHY: ELECTRON CRYSTALLOGRAPHY Talk given at a conference General theory of diffraction 02.06.2018 Erice, Italy Abrahams Jan Pieter;
Ringberg meeting cryo-EM Talk given at a conference Electron diffraction 01.11.2017 Tegernsee, Germany Abrahams Jan Pieter;
Gordon Conference on Opening New Frontiers with Cryo-Electron Microscopy Talk given at a conference Electron Diffraction and Crystallography for Structural Biology - A Quantitive Analysis of Recent Results 11.06.2017 Les Diablerets, Switzerland Abrahams Jan Pieter;


Self-organised

Title Date Place
3D Electron Crystallography for Macromolecular Compounds 18.09.2017 PSI, Villigen, Switzerland

Associated projects

Number Title Start Funding scheme
177020 Probe corrected TEM/STEM for high resolution STEM imaging in materials science 01.09.2018 R'EQUIP
170802 Direct electron detector for cryo-EM single particle analysis, electron tomography and protein nanocrystallography 01.11.2017 R'EQUIP

Abstract

Cryo-electron microscopy allows visualizing structures of biomolecular complexes in almost atomic detail. But inside cells, or when the complexes are smaller than 300 kD, or when we need true atomic resolution, cryo-EM does not work. At high resolution, cryo-EM images of such samples are indistinguishable from random noise. Switching from cryo-EM to free electron diffraction at cryogenic temperatures (cryo-ED) can enhance high-resolution contrast of biological samples by two orders of magnitude. But cryo-ED loses essential phase information. Here, I propose optimizing cryo-ED of biological samples and new ways of retrieving the missing phase information of electron diffraction data of crystalline and non-crystalline samples. It combines adapting current designs of electron microscopes with novel data collection methods and algorithms for extracting phase information. These innovations will be evaluated and optimized with existing top-end electron microscopes. The project will also produce a quantitative model for a free electron diffraction instrument (SwissFEDI) for more challenging non-crystalline samples, like small protein complexes, and larger complexes in their cellular context.The project is also of major importance for optimizing the output of SwissFEL, as it will allow straightforward pre-screening of nano-crystalline samples.
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