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Your search keyword '"Oberthuer, Dominik"' showing total 3 results
Start Over Author "Oberthuer, Dominik" Topic x-ray diffraction
3 results on '"Oberthuer, Dominik"'

1. Crystallization and preliminary X-ray diffraction data of an LNA 7-mer duplex derived from a ricin aptamer.

Author

Förster C, Oberthuer D, Gao J, Eichert A, Quast FG, Betzel C, Nitsche A, Erdmann VA, and Fürste JP

Subjects
Aptamers, Nucleotide genetics, Base Sequence, Carbohydrates chemistry, Crystallization, Crystallography, X-Ray, Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Denaturation, Oligonucleotides genetics, Aptamers, Nucleotide chemistry, Nucleic Acid Heteroduplexes chemistry, Oligonucleotides chemistry, Ricin chemistry, X-Ray Diffraction
Abstract

Locked nucleic acids (LNAs) are modified nucleic acids which contain a modified sugar such as beta-D-2'-O,4'-C methylene-bridged ribofuranose or other sugar derivatives in LNA analogues. The beta-D-2'-O,4'-C methylene ribofuranose LNAs in particular possess high stability and melting temperatures, which makes them of interest for stabilizing the structure of different nucleic acids. Aptamers, which are DNAs or RNAs targeted against specific ligands, are candidates for substitution with LNAs in order to increase their stability. A 7-mer helix derived from the terminal part of an aptamer that was targeted against ricin was chosen. The ricin aptamer originally consisted of natural RNA building blocks and showed high affinity in ricin binding. For future stabilization of the aptamer, the terminal helix has been constructed as an ;all-locked' LNA and was successfully crystallized in order to investigate its structural properties. Optimization of crystal growth succeeded by the use of different metal salts as additives, such as CuCl(2), MgCl(2), MnCl(2), CaCl(2), CoCl(2) and ZnSO(4). Preliminary X-ray diffraction data were collected and processed to 2.8 A resolution. The LNA crystallized in space group P6(5), with unit-cell parameters a = 50.11, b = 50.11, c = 40.72 A. The crystals contained one LNA helix per asymmetric unit with a Matthews coefficient of 3.17 A(3) Da(-1), which implies a solvent content of 70.15%.

Published
2009
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2. Ab initio phasing of the diffraction of crystals with translational disorder

Author

Morgan, Andrew, Ayyer, Kartik, Barty, Anton, Chen, Joe P. J., Ekeberg, Tomas, Oberthuer, Dominik, White, Thomas A., Yefanov, Oleksandr, and Chapman, Henry N.

Subjects
Condensed Matter::Quantum Gases, Models, Molecular, phase retrieval, Physics::Biological Physics, Quantitative Biology::Biomolecules, Protein Conformation, Proteins, Physics::Optics, Crystallography, X-Ray, Research Papers, X-ray diffraction, diffuse scattering, Models, Chemical, macromolecular crystallography, Structural Biology, Mathematics::Metric Geometry, ddc:530, Algorithms, Strukturbiologi
Abstract

Acta crystallographica / A 75(1), 25 - 40 (2019). doi:10.1107/S2053273318015395, To date X-ray protein crystallography is the most successful technique available for the determination of high-resolution 3D structures of biological molecules and their complexes. In X-ray protein crystallography the structure of a protein is refined against the set of observed Bragg reflections from a protein crystal. The resolution of the refined protein structure is limited by the highest angle at which Bragg reflections can be observed. In addition, the Bragg reflections alone are typically insufficient (by a factor of two) to determine the structure ab initio, and so prior information is required. Crystals formed from an imperfect packing of the protein molecules may also exhibit continuous diffraction between and beyond these Bragg reflections. When this is due to random displacements of the molecules from each crystal lattice site, the continuous diffraction provides the necessary information to determine the protein structure without prior knowledge, to a resolution that is not limited by the angular extent of the observed Bragg reflections but instead by that of the diffraction as a whole. This article presents an iterative projection algorithm that simultaneously uses the continuous diffraction as well as the Bragg reflections for the determination of protein structures. The viability of this method is demonstrated on simulated crystal diffraction., Published by Blackwell, Oxford [u.a.]

Published
2019

3. Double-flow focused liquid injector for efficient serial femtosecond crystallography

Author

Oberthuer, Dominik, Knoška, Juraj, Wiedorn, Max O., Beyerlein, Kenneth, Bushnell, David A., Kovaleva, Elena G., Heymann, Michael, Gumprecht, Lars, Kirian, Richard A., Barty, Anton, Mariani, Valerio, Tolstikova, Aleksandra, Adriano, Luigi, Awel, Salah, Barthelmess, Miriam, Doerner, Katerina, Xavier, P. Lourdu, Yefanov, Oleksandr, James, Daniel R., Nelson, Garrett, Wang, Dingjie, Calvey, George, Chen, Yujie, Schmidt, Andrea, Szczepek, Michael, Frielingsdorf, Stefan, Lenz, Oliver, Snell, Edward, Robinson, Philip J., Šarler, Božidar, Belšak, Grega, Maček, Marjan, Wilde, Fabian, Aquila, Andrew, Boutet, Sébastien, Liang, Mengning, Hunter, Mark S., Scheerer, Patrick, Lipscomb, John D., Weierstall, Uwe, Kornberg, Roger D., Spence, John C. H., Pollack, Lois, Chapman, Henry N., and Bajt, Saša

Subjects
Crystallography, Time Factors, X-Ray Diffraction, ddc:000, Temperature, Computer Simulation, RNA Polymerase II, Saccharomyces cerevisiae, Rheology, Corrigenda, Article
Abstract

Scientific reports 7, 44628 (2017). doi:10.1038/srep44628, Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices., Published by Springer Nature, London

Published
2017

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