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Start Over Author "Robert Dods" Topic 030104 developmental biology
5 results on '"Robert Dods"'

1. Ultrafast structural changes within a photosynthetic reaction centre

Author

Rebecka Andersson, Gisela Brändén, Gergely Katona, Michał Maj, Antoine Royant, David Arnlund, Hoi Ling Luk, Oleksandr Yefanov, Despina Milathianaki, Sergio Carbajo, Robert Bosman, Greger Hammarin, Linda C. Johansson, Adams Vallejos, Elin Claesson, Joseph Robinson, Cecilia Wickstrand, Erik Malmerberg, Cecilia Safari, Garth J. Williams, Chelsie E. Conrad, Kenneth R. Beyerlein, Richard Neutze, Anton Barty, Chufeng Li, Rajiv Harimoorthy, Daniel P. DePonte, Amit Sharma, Mark S. Hunter, Sébastien Boutet, Viktor Ahlberg Gagnér, Garrett Nelson, Dmitry Morozov, Stella Lisova, Jan Davidsson, Joachim Kübel, Petra Båth, Robert Dods, Mengning Liang, Sebastian Westenhoff, Peter Dahl, Peter Berntsen, Gerrit Groenhof, Department of Chemistry and Molecular Biology [Gothenburg], University of Gothenburg (GU), Department of Chemistry [Jyväskylä Univ] (JYU), University of Jyväskylä (JYU), Nanoscience Center [Jyväskylä Univ] (NSC@JYU), Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron [Hamburg] (DESY), Department of Physics, Arizona State University (ASU), Arizona State University [Tempe] (ASU), Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Australian Research Council Centre of Excellence in Advanced Molecular Imaging [Victoria, Australia], Molecular Biophysics and Integrated Bioimaging Division [Berkeley, CA, USA], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), University of Southern California (USC), Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85282, U.S.A., Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), European Synchrotron Radiation Facility (ESRF), Department of Chemistry – Ångström Laboratory, UPPSALA University, Box 538, 75120, Uppsala, Sweden, and Uppsala University

Subjects
0301 basic medicine, Photosynthetic reaction centre, Chlorophyll, Models, Molecular, klorofylli, Cytoplasm, Ubiquinone, Photosynthetic Reaction Center Complex Proteins, Electrons, 02 engineering and technology, Photochemistry, medicine.disease_cause, yhteyttäminen, bakteerit, Electron Transport, 03 medical and health sciences, Electron transfer, medicine, Molecule, ddc:530, Bacteriochlorophylls, bioenergetiikka, ComputingMilieux_MISCELLANEOUS, Hyphomicrobiaceae, Multidisciplinary, Binding Sites, Crystallography, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Blastochloris viridis, Lasers, kalvot (biologia), Pheophytins, Biological membrane, Vitamin K 2, 021001 nanoscience & nanotechnology, Acceptor, 030104 developmental biology, Picosecond, Femtosecond, sense organs, Protons, 0210 nano-technology, Oxidation-Reduction, röntgenkristallografia
Abstract

Nature / Physical science 589, 310 - 314 (2021). doi:10.1038/s41586-020-3000-7, Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions., Published by Macmillan Publishers Limited, part of Springer Nature, London

Published
2021

2. From Macrocrystals to Microcrystals: A Strategy for Membrane Protein Serial Crystallography

Author

Despina Milathianaki, Robert Bosman, Stella Lisova, David Arnlund, Jan Davidsson, Mark S. Hunter, Mengling Liang, Peter Dahl, Gisela Brändén, Chufeng Li, Linda C. Johansson, Garrett Nelson, Sergio Carbajo, Rebecka Andersson, Rajiv Harimoorthy, Peter Berntsen, Erik Malmerberg, Anton Barty, Kenneth R. Beyerlein, Robert Dods, Daniel P. DePonte, Amit Sharma, Cecilia Wickstrand, Chelsie E. Conrad, Richard Neutze, Elin Claesson, Cecilia Safari, Oleksandr Yefanov, Petra Båth, Garth J. Williams, Joseph Robinson, and Greger Hammarin

Subjects
0301 basic medicine, Models, Molecular, Hyphomicrobiaceae, Chemistry, Protein Conformation, Resolution (electron density), Membrane Proteins, Nanotechnology, 02 engineering and technology, 021001 nanoscience & nanotechnology, Crystallography, X-Ray, 03 medical and health sciences, Crystallography, 030104 developmental biology, Bacterial Proteins, Structural Biology, Homogeneous, X-ray crystallography, Femtosecond, Photosynthesis, 0210 nano-technology, Molecular Biology
Abstract

Summary Serial protein crystallography was developed at X-ray free-electron lasers (XFELs) and is now also being applied at storage ring facilities. Robust strategies for the growth and optimization of microcrystals are needed to advance the field. Here we illustrate a generic strategy for recovering high-density homogeneous samples of microcrystals starting from conditions known to yield large (macro) crystals of the photosynthetic reaction center of Blastochloris viridis (RC vir ). We first crushed these crystals prior to multiple rounds of microseeding. Each cycle of microseeding facilitated improvements in the RC vir serial femtosecond crystallography (SFX) structure from 3.3-A to 2.4-A resolution. This approach may allow known crystallization conditions for other proteins to be adapted to exploit novel scientific opportunities created by serial crystallography.

Published
2017

3. Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature

Author

Osamu Nureki, Robert Bosman, Rebecka Andersson, Petra Båth, Gisela Brändén, Rie Tanaka, Richard Neutze, Yasumasa Joti, Eriko Nango, Robert Dods, Takanori Nakane, So Iwata, Cecilia Safari, Kensuke Tono, Elin Dunevall, and Ayumi Yamashita

Subjects
0301 basic medicine, Models, Molecular, Protein Conformation, Science, Crystallography, X-Ray, Ligands, Article, Electron Transport Complex IV, 03 medical and health sciences, Structure-Activity Relationship, Oxidoreductase, Catalytic Domain, Molecule, Cytochrome c oxidase, X-ray crystallography, chemistry.chemical_classification, Multidisciplinary, Binding Sites, 030102 biochemistry & molecular biology, biology, Cytochrome c, Thermus thermophilus, Resolution (electron density), Temperature, Active site, biology.organism_classification, Crystallography, 030104 developmental biology, chemistry, Enzyme mechanisms, biology.protein, Medicine, Protons, Protein Binding
Abstract

Cytochrome c oxidase catalyses the reduction of molecular oxygen to water while the energy released in this process is used to pump protons across a biological membrane. Although an extremely well-studied biological system, the molecular mechanism of proton pumping by cytochrome c oxidase is still not understood. Here we report a method to produce large quantities of highly diffracting microcrystals of ba3-type cytochrome c oxidase from Thermus thermophilus suitable for serial femtosecond crystallography. The room-temperature structure of cytochrome c oxidase is solved to 2.3 Å resolution from data collected at an X-ray Free Electron Laser. We find overall agreement with earlier X-ray structures solved from diffraction data collected at cryogenic temperature. Previous structures solved from synchrotron radiation data, however, have shown conflicting results regarding the identity of the active-site ligand. Our room-temperature structure, which is free from the effects of radiation damage, reveals that a single-oxygen species in the form of a water molecule or hydroxide ion is bound in the active site. Structural differences between the ba3-type and aa3-type cytochrome c oxidases around the proton-loading site are also described.

Published
2017

4. A three-dimensional movie of structural changes in bacteriorhodopsin

Author

Eriko Nango, Jörg Standfuss, Shigeki Owada, Takanori Nakane, Petra Båth, Robert Dods, Ayumi Yamashita, Byeonghyun Jeon, Minoru Kubo, Takaaki Fujiwara, Jan Davidsson, Rebecka Andersson, Dohyun Im, Michihiro Sugahara, Yasuaki Yamanaka, Kazumasa Oda, Makina Yabashi, Osamu Nureki, Takaki Hatsui, Kensuke Tono, Tomoyuki Tanaka, Michio Murata, Gebhard F. X. Schertler, Antoine Royant, Daewoong Nam, Takashi Nomura, Eiichi Mizohata, Satoshi Kawatake, Tetsunari Kimura, So Iwata, Przemyslaw Nogly, Tatsuro Shimamura, Takashi Kameshima, Changyong Song, Masahiro Fukuda, Jun Kobayashi, Shigeru Matsuoka, Yasumasa Joti, Ana-Nicoleta Bondar, Richard Neutze, Cecilia Wickstrand, Toshiaki Hosaka, Rie Tanaka, Toshi Arima, Tomohiro Nishizawa, RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), European Synchrotron Radiation Facility (ESRF), Department of Biological Sciences, The University of Tokyo (UTokyo), Department of Chemistry and Molecular Biology [Gothenburg], University of Gothenburg (GU), Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN)-RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Department of Applied Chemistry, Osaka University [Osaka], Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute (PSI), Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), Department of Physics, Pohang University of Science and Technology (POSTECH), Department of Cell Biology, Graduate School of Medicine, Kyoto University [Kyoto], Angström Laboratory, Uppsala University, JST-Exploratory Research for Advanced Technology (ERATO), Japan Synchrotron Radiation Research Institute [Hyogo] (JASRI), Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, ANR-11-JSV5-0009,SOxygen,Oxygène singulet : du dégât sur les protéines vers le développement de bio-détecteurs et générateurs(2011), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Kyoto University

Subjects
Protein Conformation, alpha-Helical, 0301 basic medicine, Cytoplasm, Proton, Motion Pictures, Biophysics, 02 engineering and technology, 03 medical and health sciences, Imaging, Three-Dimensional, Nuclear magnetic resonance, Proton transport, Molecule, fluorescent protein, Branchiostoma lanceolatum, Crystallography, Multidisciplinary, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Membrane transport protein, Chemistry, Lasers, Spectrum Analysis, Biochemistry and Molecular Biology, Bacteriorhodopsin, specific radiation damage, 021001 nanoscience & nanotechnology, Transmembrane protein, Biofysik, Time resolved crystallography, Transmembrane domain, 030104 developmental biology, in crystallo optical spectroscopy, Bacteriorhodopsins, Retinaldehyde, biology.protein, Protons, online Raman spectroscopy, 0210 nano-technology, Biokemi och molekylärbiologi
Abstract

Snapshots of bacteriorhodopsin Bacteriorhodopsin is a membrane protein that harvests the energy content from light to transport protons out of the cell against a transmembrane potential. Nango et al. used timeresolved serial femtosecond crystallography at an x-ray free electron laser to provide 13 structural snapshots of the conformational changes that occur in the nanoseconds to milliseconds after photoactivation. These changes begin at the active site, propagate toward the extracellular side of the protein, and mediate internal protonation exchanges that achieve proton transport. Science , this issue p. 1552

Published
2016

5. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

Author

Chufeng Li, Petra Båth, Jesse Coe, Rafael Abela, Peter Berntsen, Tetsunari Kimura, Christopher J. Milne, Henry N. Chapman, Cornelius Gati, Matthias Frank, Jörg Standfuss, Jan Rheinberger, Valerie Panneels, Thomas A. White, Wenting Wu, Przemyslaw Nogly, Minoru Kubo, Robert Dods, Eriko Nango, Mark S. Hunter, Sébastien Boutet, Garrett Nelson, Garth J. Williams, Petra Fromme, Gebhard F. X. Schertler, Kenneth R. Beyerlein, Uwe Weierstall, Leonardo Sala, So Iwata, Yun Zhao, Chelsie E. Conrad, Richard Neutze, Despina Milathianaki, Daniel P. DePonte, Daniel James, Jason E. Koglin, Rajiv Harimoorthy, John C. H. Spence, Richard Bean, and Anton Barty

Subjects
0301 basic medicine, Time Factors, Protein Conformation, Physics::Optics, General Physics and Astronomy, 02 engineering and technology, Crystal structure, Crystallography, X-Ray, 01 natural sciences, Biochemistry, Crystal, Structural Biology, Proton transport, Nanotechnology, General Materials Science, Physics::Biological Physics, Quantitative Biology::Biomolecules, Multidisciplinary, Crystallography, biology, Viscosity, Resolution (electron density), 021001 nanoscience & nanotechnology, Condensed Matter Physics, Lipids, Time resolved crystallography, X-Ray Absorption Spectroscopy, Bacteriorhodopsins, Femtosecond, ddc:500, 0210 nano-technology, Materials science, Absorption spectroscopy, Science, Bioengineering, 010402 general chemistry, Article, General Biochemistry, Genetics and Molecular Biology, Inorganic Chemistry, 03 medical and health sciences, Physical and Theoretical Chemistry, Lasers, Bacteriorhodopsin, General Chemistry, 0104 chemical sciences, 030104 developmental biology, biology.protein, X-Ray, Feasibility Studies, Synchrotrons
Abstract

Nature Communications 7, 12314(2016). doi:10.1038/ncomms12314, Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX., Published by Nature Publishing Group, London

Published
2016

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