structural biology; electron diffraction; nano-crystallography
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Clabbers Max T. B., Abrahams Jan Pieter (2018), Electron diffraction and three-dimensional crystallography for structural biology, in
Crystallography Reviews, 24(3), 176-204.
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.
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.
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.
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.
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.
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.
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.
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.
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
|
|
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.