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  • 1.
    Andersson, Inger
    et al.
    Department of Molecular Biology, Swedish University of Agricultural Sciences.
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Structure and function of Rubisco2008In: Plant physiology and biochemistry (Paris), ISSN 0981-9428, E-ISSN 1873-2690, Vol. 46, no 3, p. 275-291Article in journal (Refereed)
    Abstract [en]

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating CO2 into the biosphere. At the same time Rubisco is an extremely inefficient catalyst and its carboxylase activity is compromised by an opposing oxygenase activity involving atmospheric O2. The shortcomings of Rubisco have implications for crop yield, nitrogen and water usage, and for the global carbon cycle. Numerous high-resolution crystal structures of different forms of Rubisco are now available, including structures of mutant enzymes. This review uses the information provided in these structures in a structure-based sequence alignment and discusses Rubisco function in the context of structural variations at all levels – amino acid sequence, fold, tertiary and quaternary structure – with an evolutionary perspective and an emphasis on the structural features of the enzyme that may determine its function as a carboxylase.

  • 2.
    Bielecki, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Reddy, Hemanth K. N.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gunn, Laura H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Munke, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Flueckiger, Leonie
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Lundholm, Ida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kulyk, Olena
    Higashiura, Akifumi
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, Ne-Te Duane
    Wysong, Taylor E.
    Bostedt, Christoph
    Gorkhover, Tais
    Iwan, Bianca
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Osipov, Timur
    Walter, Peter
    Hart, Philip
    Bucher, Maximilian
    Ulmer, Anatoli
    Ray, Dipanwita
    Carini, Gabriella
    Ferguson, Ken R.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Electrospray sample injection for single-particle imaging with x-ray lasers2019In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 5, article id eaav8801Article in journal (Refereed)
  • 3.
    Carlsson, Gunilla H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Cardinale, Francesca
    Univ Turin, Dept Agr Forestry & Food Sci, Largo Paolo Braccini 2, I-10095 Grugliasco 2, Italy.
    Prandi, Cristina
    Univ Turin, Dept Chem, Via P Giuria 7, I-10125 Turin, Italy.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    The elusive ligand complexes of the DWARF14 strigolactone receptor2018In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 69, no 9, p. 2345-2354Article in journal (Refereed)
    Abstract [en]

    Strigolactones, a group of terpenoid lactones, control many aspects of plant growth and development, but the active forms of these plant hormones and their mode of action at the molecular level are still unknown. The strigolactone protein receptor is unusual because it has been shown to cleave the hormone and supposedly forms a covalent bond with the cleaved hormone fragment. This interaction is suggested to induce a conformational change in the receptor that primes it for subsequent interaction with partners in the signalling pathway. Substantial efforts have been invested into describing the interaction of synthetic strigolactone analogues with the receptor, resulting in a number of crystal structures. This investigation combines a re-evaluation of models in the Protein Data Bank with a search for new conditions that may permit the capture of a receptor-ligand complex. While weak difference density is frequently observed in the binding cavity, possibly due to a low-occupancy compound, the models often contain features not supported by the X-ray data. Thus, at this stage, we do not believe that any detailed deductions about the nature, conformation, or binding mode of the ligand can be made with any confidence.

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  • 4. Chapman, Henry N.
    et al.
    Fromme, Petra
    Barty, Anton
    White, Thomas A.
    Kirian, Richard A.
    Aquila, Andrew
    Hunter, Mark S.
    Schulz, Joachim
    DePonte, Daniel P.
    Weierstall, Uwe
    Doak, R. Bruce
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    Schlichting, Ilme
    Lomb, Lukas
    Coppola, Nicola
    Shoeman, Robert L.
    Epp, Sascha W.
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Kimmel, Nils
    Weidenspointner, Georg
    Holl, Peter
    Liang, Mengning
    Barthelmess, Miriam
    Caleman, Carl
    Boutet, Sebastien
    Bogan, Michael J.
    Krzywinski, Jacek
    Bostedt, Christoph
    Bajt, Sasa
    Gumprecht, Lars
    Rudek, Benedikt
    Erk, Benjamin
    Schmidt, Carlo
    Hoemke, Andre
    Reich, Christian
    Pietschner, Daniel
    Strueder, Lothar
    Hauser, Guenter
    Gorke, Hubert
    Ullrich, Joachim
    Herrmann, Sven
    Schaller, Gerhard
    Schopper, Florian
    Soltau, Heike
    Kuehnel, Kai-Uwe
    Messerschmidt, Marc
    Bozek, John D.
    Hau-Riege, Stefan P.
    Frank, Matthias
    Hampton, Christina Y.
    Sierra, Raymond G.
    Starodub, Dmitri
    Williams, Garth J.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rocker, Andrea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Stern, Stephan
    Nass, Karol
    Andritschke, Robert
    Schroeter, Claus-Dieter
    Krasniqi, Faton
    Bott, Mario
    Schmidt, Kevin E.
    Wang, Xiaoyu
    Grotjohann, Ingo
    Holton, James M.
    Barends, Thomas R. M.
    Neutze, Richard
    Marchesini, Stefano
    Fromme, Raimund
    Schorb, Sebastian
    Rupp, Daniela
    Adolph, Marcus
    Gorkhover, Tais
    Andersson, Inger
    SLU.
    Hirsemann, Helmut
    Potdevin, Guillaume
    Graafsma, Heinz
    Nilsson, Björn
    Spence, John C. H.
    Femtosecond X-ray protein nanocrystallography2011In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 470, no 7332, p. 73-77Article in journal (Refereed)
    Abstract [en]

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded(1-3). It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source(4). We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes(5). More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (similar to 200 nm to 2 mm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes(6). This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

  • 5.
    Chaudhari, Aditya S.
    et al.
    Czech Acad Sci, Inst Biotechnol, Prague, Czech Republic.;Charles Univ Prague, Fac Sci, Prague, Czech Republic..
    Chatterjee, Aditi
    Czech Acad Sci, Inst Biotechnol, Prague, Czech Republic.;Charles Univ Prague, Fac Sci, Prague, Czech Republic..
    Domingos, Catarina A. O.
    Czech Acad Sci, Inst Biotechnol, Prague, Czech Republic.;Inst Politecn Setubal, Escola Super Tecnol Barreiro, Setubal, Portugal..
    Andrikopoulos, Prokopis C.
    Czech Acad Sci, Inst Biotechnol, Prague, Czech Republic..
    Liu, Yingliang
    Czech Acad Sci, Inst Biotechnol, Prague, Czech Republic..
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Czech Acad Sci, Inst Biotechnol, Prague, Czech Republic.
    Schneider, Bohdan
    Czech Acad Sci, Inst Biotechnol, Prague, Czech Republic..
    Lórenz-Fonfría, Víctor A.
    Univ Valencia, Inst Mol Sci, Paterna, Spain.;Univ Valencia, Inst Mol Sci, Carrer Catedrat Jose Beltran Martinez 2, Paterna 46980, Spain..
    Fuertes, Gustavo
    Czech Acad Sci, Inst Biotechnol, Prague, Czech Republic.;Czech Acad Sci, Inst Biotechnol, Prumyslova 595, Vestec 25250, Czech Republic..
    Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side-chains in EL2222023In: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 32, no 4, article id e4590Article in journal (Refereed)
    Abstract [en]

    Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at 45 positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A'α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A'α extension of the LOV domain in controlling EL222 photocycle length.

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  • 6.
    Daurer, Benedikt J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nettelblad, Carl
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Benner, W. Henry
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Tîmneanu, Nicuşor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ekeberg, Tomas
    Loh, N. Duane
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rath, Asawari D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kirian, Richard A.
    Awel, Salah
    Wiedorn, Max O.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sebastian
    Williams, Garth
    Koglin, Jason
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses2017In: IUCrJ, E-ISSN 2052-2525, Vol. 4, p. 251-262Article in journal (Refereed)
  • 7.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    Claverie, Jean-Michel
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    DePonte, Daniel P.
    Barty, Anton
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Martin, Andrew V.
    Chapman, Henry
    Bostedt, Christoph
    Bozek, John D.
    Ferguson, Ken R.
    Krzywinski, Jacek
    Epp, Sascha W.
    Rolles, Daniel
    Rudenko, Artem
    Hartmann, Robert
    Kimmel, Nils
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser2015In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 114, no 9, p. 098102:1-6, article id 098102Article in journal (Refereed)
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  • 8.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    DePonte, Daniel P.
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Aquila, Andrew
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;European XFEL, Albert Einstein Ring 19, D-22761 Hamburg, Germany..
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Ctr Etud Saclay, Commissariat Energie Atom & Energies Alternat, F-91191 Gif Sur Yvette, France..
    Jönsson, H. Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Odic, Dusko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Liang, Meng
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Martin, Andrew V.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Melbourne, 161 Barry St, Melbourne, Vic 3010, Australia..
    Gumprecht, Lars
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Fleckenstein, Holger
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Bajt, Sasa
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Barthelmess, Miriam
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Coppola, Nicola
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Claverie, Jean-Michel
    CNRS, Informat Genom & Struct UMR7256, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France.;Aix Marseille Univ, Inst Microbiol Mediterranee FR3479, Parc Sci Luminy,Case 934, F-13288 Marseille 9, France..
    Loh, N. Duane
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;Natl Univ Singapore, Ctr BioImaging Sci, 14 Sci Dr 4 Blk S1 A, Singapore 117546, Singapore..
    Bostedt, Christoph
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bozek, John D.
    Synchrotron SOLEIL, Lorme Merisiers Roundabout St Aubin, F-91190 St Aubin, France..
    Krzywinski, Jacek
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Messerschmidt, Marc
    SLAC Natl Accelerator Lab, LCLS, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bogan, Michael J.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Hampton, Christina Y.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Sierra, Raymond G.
    SLAC Natl Accelerator Lab, Stanford PULSE Inst, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Frank, Matthias
    Lawrence Livermore Natl Lab, 7000 East Ave,Mail Stop L-211, Livermore, CA 94551 USA..
    Shoeman, Robert L.
    Lomb, Lukas
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany..
    Foucar, Lutz
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Epp, Sascha W.
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Rolles, Daniel
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Kansas State Univ, Dept Phys, JR Macdonald Lab, 116 Cardwell Hall, Manhattan, KS 66506 USA..
    Rudenko, Artem
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany.;Kansas State Univ, Dept Phys, JR Macdonald Lab, 116 Cardwell Hall, Manhattan, KS 66506 USA..
    Hartmann, Robert
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Hartmann, Andreas
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Kimmel, Nils
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Holl, Peter
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Weidenspointner, Georg
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Rudek, Benedikt
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Erk, Benjamin
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Kassemeyer, Stephan
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany..
    Schlichting, Ilme
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Strueder, Lothar
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany.;Univ Siegen, Emmy Noether Campus,Walter Flex Str 3, D-57068 Siegen, Germany..
    Ullrich, Joachim
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany.;Phys Tech Bundesanstalt, Bundesallee 100, D-38116 Braunschweig, Germany..
    Schmidt, Carlo
    Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Kernphys, Saupfercheckweg 1, D-69117 Heidelberg, Germany..
    Krasniqi, Faton
    Max Planck Inst Med Res, Jahnstr 29, D-69120 Heidelberg, Germany.;Max Planck Adv Study Grp, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Hauser, Guenter
    Max Planck Inst Halbleiterlabor, Otto Hahn Ring 6, D-81739 Munich, Germany.;Max Planck Inst Extraterr Phys, Giessenbachstr, D-85741 Garching, Germany..
    Reich, Christian
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Soltau, Heike
    PNSensor GmbH, Otto Hahn Ring 6, D-81739 Munich, Germany..
    Schorb, Sebastian
    Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany..
    Hirsemann, Helmut
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Wunderer, Cornelia
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Graafsma, Heinz
    DESY, Photon Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chapman, Henry
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Notkestr 85, D-22607 Hamburg, Germany..
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. European XFEL, Albert Einstein Ring 19, D-22761 Hamburg, Germany..
    Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id UNSP 160060Article in journal (Refereed)
    Abstract [en]

    Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.

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  • 9.
    Gunn, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Valegard, K
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    A unique structural domain in Methanococcoides burtonii ribulose-1,5-bisphosphatecarboxylase/oxygenase (Rubisco) acts as a small subunit mimic2017In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 292, no 16, p. 6838-6850, article id jbc.M116.767145Article in journal (Refereed)
    Abstract [en]

    The catalytic inefficiencies of the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) often limit plant productivity. Strategies to engineer more efficient plant Rubiscos have been hampered by evolutionary constraints, prompting interest in Rubisco isoforms from non-photosynthetic organisms. The methanogenic archaeon Methanococcoides burtonii contains a Rubisco isoform that functions to scavenge the ribulose-1,5-bisphosphate (RuBP) byproduct of purine/pyrimidine metabolism. The crystal structure of M. burtonii Rubisco (MbR) presented here at 2.6 Å resolution is composed of catalytic large subunits (LSu) assembled into pentamers of dimers, (L2)5 and differs from Rubiscos from higher plants where LSus are glued together by small subunits (SSu) into hexadecameric L8S8 enzymes. MbR contains a unique 29-amino-acid insertion near the C-terminus, which folds as a separate domain in the structure. This domain, which is visualized for the first time in this study, is located in a similar position to SSus in L8S8 enzymes between LSus of adjacent L2 dimers, where negatively charged residues co-ordinate around a Mg2+ ion in a fashion that suggests this domain may be important for the assembly process. The Rubisco assembly domain is thus an inbuilt SSu mimic that concentrates L2 dimers. MbR assembly is ligand-stimulated and we show that only 6-carbon molecules with a particular stereochemistry at the C3 carbon can induce oligomerization. Based on MbR structure, subunit arrangement, sequence, phylogenetic distribution and function, MbR and a subset of Rubiscos from the Methanosarcinales order are proposed to belong to a new Rubisco sub-group, named form IIIB.

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    fulltext
  • 10.
    Hantke, Max F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    John, Katja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, Duane
    Martin, Andrew V.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ingelman, Margareta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Uetrecht, Charlotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    Stellato, Francesco
    DePonte, Daniel P.
    Bari, Sadia
    Hartmann, Robert
    Kimmel, Nils
    Kirian, Richard A.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Ferguson, Ken
    Bostedt, Christoph
    Carron, Sebastian
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Foucar, Lutz
    Epp, Sascha W.
    Chapman, Henry N.
    Barty, Anton
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    A data set from flash X-ray imaging of carboxysomes2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160061Article in journal (Refereed)
    Abstract [en]

    Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

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  • 11.
    Hantke, Max F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    John, Katja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Martin, Andrew V.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gijs, van der Schot
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ingelman, Margareta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    Stellato, Francesco
    DePonte, Daniel P.
    Hartmann, Robert
    Kimmel, Nils
    Kirian, Richard A.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Schorb, Sebastian
    Ferguson, Ken
    Bostedt, Christoph
    Carron, Sebastian
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Epp, Sascha
    Chapman, Henry N.
    Barty, Anton
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    High-throughput imaging of heterogeneous cell organelles with an X-ray laser2014In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 8, no 12, p. 943-949Article in journal (Refereed)
    Abstract [en]

    We overcome two of the most daunting challenges in single-particle diffractive imaging: collecting many high-quality diffraction patterns on a small amount of sample and separating components from mixed samples. We demonstrate this on carboxysomes, which are polyhedral cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min with the Linac Coherent Light Source running at 120 Hz. We separate different structures directly from the diffraction data and show that the size distribution is preserved during sample delivery. We automate phase retrieval and avoid reconstruction artefacts caused by missing modes. We attain the highest-resolution reconstructions on the smallest single biological objects imaged with an X-ray laser to date. These advances lay the foundations for accurate, high-throughput structure determination by flash-diffractive imaging and offer a means to study structure and structural heterogeneity in biology and elsewhere.

  • 12.
    Hasse, Dirk
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Evalena
    Carlsson, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Masloboy, Axel
    Hagemann, Martin
    Bauwe, Hermann
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Structure of the Homodimeric Glycine Decarboxylase P-protein from Synechocystis sp PCC 6803 Suggests a Mechanism for Redox Regulation2013In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 288, no 49, p. 35333-35345Article in journal (Refereed)
    Abstract [en]

    Glycine decarboxylase, or P-protein, is a pyridoxal 5-phosphate (PLP)-dependent enzyme in one-carbon metabolism of all organisms, in the glycine and serine catabolism of vertebrates, and in the photorespiratory pathway of oxygenic phototrophs. P-protein from the cyanobacterium Synechocystis sp. PCC 6803 is an (2) homodimer with high homology to eukaryotic P-proteins. The crystal structure of the apoenzyme shows the C terminus locked in a closed conformation by a disulfide bond between Cys(972) in the C terminus and Cys(353) located in the active site. The presence of the disulfide bridge isolates the active site from solvent and hinders the binding of PLP and glycine in the active site. Variants produced by substitution of Cys(972) and Cys(353) by Ser using site-directed mutagenesis have distinctly lower specific activities, supporting the crucial role of these highly conserved redox-sensitive amino acid residues for P-protein activity. Reduction of the 353-972 disulfide releases the C terminus and allows access to the active site. PLP and the substrate glycine bind in the active site of this reduced enzyme and appear to cause further conformational changes involving a flexible surface loop. The observation of the disulfide bond that acts to stabilize the closed form suggests a molecular mechanism for the redox-dependent activation of glycine decarboxylase observed earlier.

  • 13.
    Hasse, Dirk
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hülsemann, Janne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Valegård, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus2019In: Acta Crystallographica Section D: Structural Biology , E-ISSN 2059-7983, Vol. 75, p. 1107-1118Article in journal (Refereed)
    Abstract [en]

    The core of beta-lactam antibiotics originates from amino acids of primary metabolism in certain microorganisms. beta-Lactam-producing bacteria, including Streptomyces clavuligerus, synthesize the precursor of the amino acid alpha-aminoadipic acid by the catabolism of lysine in two steps. The second reaction, the oxidation of piperideine-6-carboxylate (or its open-chain form alpha-aminoadipate semialdehyde) to alpha-aminoadipic acid, is catalysed by the NAD(+)-dependent enzyme piperideine-6-carboxylate dehydrogenase (P6CDH). This structural study, focused on ligand binding and catalysis, presents structures of P6CDH from S. clavuligerus in its apo form and in complexes with the cofactor NAD(+), the product alpha-aminoadipic acid and a substrate analogue, picolinic acid. P6CDH adopts the common aldehyde dehydrogenase fold, consisting of NAD-binding, catalytic and oligomerization domains. The product binds in the oxyanion hole, close to the catalytic residue Cys299. Clear density is observed for the entire cofactor, including the nicotinamide riboside, in the binary complex. NAD(+) binds in an extended conformation with its nicotinamide ring overlapping with the binding site of the carboxylate group of the product, implying that the conformation of the cofactor may change during catalysis. The binding site of the substrate analogue overlaps with that of the product, suggesting that the cyclic form of the substrate, piperideine-6-carboxylate, may be accepted as a substrate by the enzyme. The catalytic mechanism and the roles of individual residues are discussed in light of these results.

  • 14.
    Hasse, Dirk
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Anna M
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Structure of Arabidopsis thaliana Rubisco activase2015In: Acta Crystallographica Section D: Biological Crystallography, ISSN 0907-4449, E-ISSN 1399-0047, Vol. 71, no Pt 4, p. 800-808Article in journal (Refereed)
    Abstract [en]

    The CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is inactivated by the formation of dead-end complexes with inhibitory sugar phosphates. In plants and green algae, the ATP-dependent motor protein Rubisco activase restores catalytic competence by facilitating conformational changes in Rubisco that promote the release of the inhibitory compounds from the active site. Here, the crystal structure of Rubisco activase from Arabidopsis thaliana is presented at 2.9 Å resolution. The structure reveals an AAA+ two-domain structure. More than 100 residues in the protein were not visible in the electron-density map owing to conformational disorder, but were verified to be present in the crystal by mass spectrometry. Two sulfate ions were found in the structure. One was bound in the loop formed by the Walker A motif at the interface of the domains. A second sulfate ion was bound at the N-terminal end of the first helix of the C-terminal domain. The protein packs in a helical fashion in the crystal, as observed previously for Rubisco activase, but differences in the helical pitch indicate flexibility in the packing of the protein.

  • 15.
    Larsson, Anna M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Valegård, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Crystal structures of β-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 14, p. 3857-3867Article in journal (Refereed)
    Abstract [en]

    Cyanobacterial CO2 fixation is promoted by encapsulating and co-localizing the CO2-fixing enzymes within a protein shell, the carboxysome. A key feature of the carboxysome is its ability to control selectively the flux of metabolites in and out of the shell. The beta-carboxysome shell protein CcmP has been shown to form a double layer of pseudohexamers with a relatively large central pore (similar to 13 angstrom diameter), which may allow passage of larger metabolites such as the substrate for CO2 fixation, ribulose 1,5-bisphosphate, through the shell. Here we describe two crystal structures, at 1.45 angstrom and 1.65 angstrom resolution, of CcmP from Synechococcus elongatus PCC7942 (SeCcmP). The central pore of CcmP is open or closed at its ends, depending on the conformation of two conserved residues, Glu69 and Arg70. The presence of glycerol resulted in a pore that is open at one end and closed at the opposite end. When glycerol was omitted, both ends of the barrel became closed. A binding pocket at the interior of the barrel featured residual density with distinct differences in size and shape depending on the conformation, open or closed, of the central pore of SeCcmP, suggestive of a metabolite-driven mechanism for the gating of the pore.

  • 16.
    Seibert, M. Marvin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sebastien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bogan, Michael J.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Hau-Riege, Stefan
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Frank, Matthias
    Benner, Henry
    Lee, Joanna Y.
    Marchesini, Stefano
    Shaevitz, Joshua W.
    Fletcher, Daniel A.
    Bajt, Sasa
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Chapman, Henry N.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Femtosecond diffractive imaging of biological cells2010In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 43, no 19, p. 194015-Article in journal (Refereed)
    Abstract [en]

    In a flash diffraction experiment, a short and extremely intense x-ray pulse illuminates the sample to obtain a diffraction pattern before the onset of significant radiation damage. The over-sampled diffraction pattern permits phase retrieval by iterative phasing methods. Flash diffractive imaging was first demonstrated on an inorganic test object (Chapman et al 2006 Nat. Phys. 2 839-43). We report here experiments on biological systems where individual cells were imaged, using single, 10-15 fs soft x-ray pulses at 13.5 nm wavelength from the FLASH free-electron laser in Hamburg. Simulations show that the pulse heated the sample to about 160 000 K but not before an interpretable diffraction pattern could be obtained. The reconstructed projection images return the structures of the intact cells. The simulations suggest that the average displacement of ions and atoms in the hottest surface layers remained below 3 angstrom during the pulse.

  • 17.
    Seibert, M. Marvin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Joensson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Odic, Dusko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rocker, Andrea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DePonte, Daniel P.
    Barty, Anton
    Schulz, Joachim
    Gumprecht, Lars
    Coppola, Nicola
    Aquila, Andrew
    Liang, Mengning
    White, Thomas A.
    Martin, Andrew
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Stern, Stephan
    Abergel, Chantal
    Seltzer, Virginie
    Claverie, Jean-Michel
    Bostedt, Christoph
    Bozek, John D.
    Boutet, Sebastien
    Miahnahri, A. Alan
    Messerschmidt, Marc
    Krzywinski, Jacek
    Williams, Garth
    Hodgson, Keith O.
    Bogan, Michael J.
    Hampton, Christina Y.
    Sierra, Raymond G.
    Starodub, Dmitri
    Andersson, Inger
    Bajt, Sasa
    Barthelmess, Miriam
    Spence, John C. H.
    Fromme, Petra
    Weierstall, Uwe
    Kirian, Richard
    Hunter, Mark
    Doak, R. Bruce
    Marchesini, Stefano
    Hau-Riege, Stefan P.
    Frank, Matthias
    Shoeman, Robert L.
    Lomb, Lukas
    Epp, Sascha W.
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Schmidt, Carlo
    Foucar, Lutz
    Kimmel, Nils
    Holl, Peter
    Rudek, Benedikt
    Erk, Benjamin
    Hoemke, Andre
    Reich, Christian
    Pietschner, Daniel
    Weidenspointner, Georg
    Strueder, Lothar
    Hauser, Guenter
    Gorke, Hubert
    Ullrich, Joachim
    Schlichting, Ilme
    Herrmann, Sven
    Schaller, Gerhard
    Schopper, Florian
    Soltau, Heike
    Kuehnel, Kai-Uwe
    Andritschke, Robert
    Schroeter, Claus-Dieter
    Krasniqi, Faton
    Bott, Mario
    Schorb, Sebastian
    Rupp, Daniela
    Adolph, Marcus
    Gorkhover, Tais
    Hirsemann, Helmut
    Potdevin, Guillaume
    Graafsma, Heinz
    Nilsson, Björn
    Chapman, Henry N.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Single mimivirus particles intercepted and imaged with an X-ray laser2011In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 470, no 7332, p. 78-81Article in journal (Refereed)
    Abstract [en]

    X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions(1-4). Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma(1). The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval(2). Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a noncrystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source(5). Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.

  • 18.
    Valegård, Karin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Andralojc, P. John
    Rothamsted Res, Dept Plant Sci, Harpenden AL5 2JQ, Herts, England.
    Haslam, Richard P.
    Rothamsted Res, Dept Plant Sci, Harpenden AL5 2JQ, Herts, England.
    Pearce, F. Grant
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Univ Canterbury, Sch Biol Sci, Private Bag 4800, Christchurch 8140, New Zealand.
    Eriksen, Gunilla K.
    Arctic Univ Norway, Norwegian Coll Fisheries Sci, N-9037 Tromso, Norway.
    Madgwickn, Pippa J.
    Rothamsted Res, Dept Plant Sci, Harpenden AL5 2JQ, Herts, England.
    Kristoffersen, Anne K.
    Univ Oslo, Dept Biosci, POB 1066, N-0316 Oslo, Norway;Univ Oslo, Fac Dent, Dept Oral Biol, POB 1052, N-0316 Oslo, Norway.
    van Lun, Michiel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Klein, Uwe
    Univ Oslo, Dept Biosci, POB 1066, N-0316 Oslo, Norway.
    Eilertsen, Hans C.
    Arctic Univ Norway, Norwegian Coll Fisheries Sci, N-9037 Tromso, Norway.
    Parry, Martin A. J.
    Rothamsted Res, Dept Plant Sci, Harpenden AL5 2JQ, Herts, England;Univ Lancaster, Lancaster Environm Ctr, Lancaster LA1 4YQ, England.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications2018In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 293, no 34, p. 13033-13043Article in journal (Refereed)
    Abstract [en]

    The catalytic performance of the major CO2-assimilating enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), restricts photosynthetic productivity. Natural diversity in the catalytic properties of Rubisco indicates possibilities for improvement. Oceanic phytoplankton contain some of the most efficient Rubisco enzymes, and diatoms in particular are responsible for a significant proportion of total marine primary production as well as being a major source of CO2 sequestration in polar cold waters. Until now, the biochemical properties and three-dimensional structures of Rubisco from diatoms were unknown. Here, diatoms from arctic waters were collected, cultivated, and analyzed for their CO2-fixing capability. We characterized the kinetic properties of five and determined the crystal structures of four Rubiscos selected for their high CO2-fixing efficiency. The DNA sequences of the rbcL, and rbcS genes of the selected diatoms were similar, reflecting their close phylogenetic relationship. The V-max and K-m for the oxygenase and carboxylase activities at 25 degrees C and the specificity factors (S-c/o) at 15, 25, and 35 degrees C were determined. The S-c/o values were high, approaching those of mono- and dicot plants, thus exhibiting good selectivity for CO(2 )relative to O-2. Structurally, diatom Rubiscos belong to form I C/D, containing small subunits characterized by a short beta A-beta B loop and a C-terminal extension that forms a beta-hairpin structure (beta E-beta F loop). Of note, the diatom Rubiscos featured a number of posttranslational modifications of the large subunit, including 4-hydroxyproline, beta-hydroxyleucine, hydroxylated and nitrosylated cysteine, mono- and dihydroxylated lysine, and trimethylated lysine. Our studies suggest adaptation toward achieving efficient CO2 fixation in arctic diatom Rubiscos.

  • 19.
    Valegård, Karin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Gunn, Laura H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bis­phosphate2018In: Acta Crystallographica Section D: Structural Biology , E-ISSN 2059-7983, Vol. 74, no 1, p. 1-9Article in journal (Refereed)
    Abstract [en]

    The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Arabidopsis thaliana is reported at 1.5 Å resolution. In light of the importance of A. thaliana as a model organism for understanding higher plant biology, and the pivotal role of Rubisco in photosynthetic carbon assimilation, there has been a notable absence of an A. thaliana Rubisco crystal structure. A. thaliana Rubisco is an L8S8 hexadecamer comprising eight plastome-encoded catalytic large (L) subunits and eight nuclear-encoded small (S) subunits. A. thaliana produces four distinct small-subunit isoforms (RbcS1A, RbcS1B, RbcS2B and RbcS3B), and this crystal structure provides a snapshot of A. thaliana Rubisco containing the low-abundance RbcS3B small-subunit isoform. Crystals were obtained in the presence of the transition-state analogue 2-carboxy-D-arabinitol-1,5-bisphosphate. A. thaliana Rubisco shares the overall fold characteristic of higher plant Rubiscos, but exhibits an interesting disparity between sequence and structural relatedness to other Rubisco isoforms. These results provide the structural framework to understand A. thaliana Rubisco and the potential catalytic differences that could be conferred by alternative A. thaliana Rubisco small-subunit isoforms.

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  • 20.
    Valegård, Karin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Iqbal, Aman
    Kershaw, Nadia J.
    Ivison, David
    Genereux, Catherine
    Dubus, Alain
    Blikstad, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Demetriades, Marina
    Hopkinson, Richard J.
    Lloyd, Adrian J.
    Roper, David I.
    Schofield, Christopher J.
    Andersson, Inger
    Department of Molecular Biology, Swedish University of Agricultural Sciences.
    McDonough, Michael A.
    Structural and mechanistic studies of the orf12 gene product from the clavulanic acid biosynthesis pathway2013In: Acta Crystallographica Section D: Biological Crystallography, ISSN 0907-4449, E-ISSN 1399-0047, Vol. 69, p. 1567-1579Article in journal (Refereed)
    Abstract [en]

    Structural and biochemical studies of the orf12 gene product (ORF12) from the clavulanic acid (CA) biosynthesis gene cluster are described. Sequence and crystallographic analyses reveal two domains: a C-terminal penicillin-binding protein (PBP)/beta-lactamase-type fold with highest structural similarity to the class A beta-lactamases fused to an N-terminal domain with a fold similar to steroid isomerases and polyketide cyclases. The C-terminal domain of ORF12 did not show beta-lactamase or PBP activity for the substrates tested, but did show low-level esterase activity towards 3'-O-acetyl cephalosporins and a thioester substrate. Mutagenesis studies imply that Ser173, which is present in a conserved SXXK motif, acts as a nucleophile in catalysis, consistent with studies of related esterases, beta-lactamases and d-Ala carboxypeptidases. Structures of wild-type ORF12 and of catalytic residue variants were obtained in complex with and in the absence of clavulanic acid. The role of ORF12 in clavulanic acid biosynthesis is unknown, but it may be involved in the epimerization of (3S,5S)-clavaminic acid to (3R,5R)-clavulanic acid.

  • 21.
    van der Schot, Gijs
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DePonte, Daniel P.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Schulz, Joachim
    Kirian, Richard
    Liang, Mengning
    Stellato, Francesco
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Almeida, F. Nunes
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Odic, Dusko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Martin, Andrew V.
    Schorb, Sebastian
    Bostedt, Christoph
    Bozek, John D.
    Rolles, Daniel
    Rudenko, Artem
    Epp, Sascha
    Foucar, Lutz
    Rudek, Benedikt
    Hartmann, Robert
    Kimmel, Nils
    Holl, Peter
    Englert, Lars
    Duane Loh, Ne-Te
    Chapman, Henry N.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Imaging single cells in a beam of live cyanobacteria with an X-ray laser2015In: Nature Communications, E-ISSN 2041-1723, Vol. 6, article id 5704Article in journal (Refereed)
    Abstract [en]

    There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.

  • 22.
    van der Schot, Gijs
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DePonte, Daniel P.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Aquila, Andrew
    Schulz, Joachim
    Kirian, Richard A.
    Liang, Mengning
    Stellato, Francesco
    Bari, Sadia
    Iwan, Bianca
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Nunes de Almeida, Francisca
    Odić, Duško
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S.D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Martin, Andrew V.
    Schorb, Sebastian
    Bostedt, Christoph
    Bozek, John D.
    Carron, Sebastian
    Ferguson, Ken
    Rolles, Daniel
    Rudenko, Artem
    Epp, Sascha W.
    Foucar, Lutz
    Rudek, Benedikt
    Erk, Benjamin
    Hartmann, Robert
    Kimmel, Nils
    Holl, Peter
    Englert, Lars
    Loh, N. Duane
    Chapman, Henry N.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Open data set of live cyanobacterial cells imaged using an X-ray laser2016In: Scientific Data, E-ISSN 2052-4463, Vol. 3, article id 160058Article in journal (Refereed)
    Abstract [en]

    Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

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  • 23. van Lun, Michiel
    et al.
    Hub, Jochen S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    CO2 and O-2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir2014In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 136, no 8, p. 3165-3171Article in journal (Refereed)
    Abstract [en]

    Protein gas interactions are important in biology. The enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes two competing reactions involving CO2 and O-2 as substrates. Carboxylation of the common substrate ribulose-1,5-bisphosphate leads to photosynthetic carbon assimilation, while the oxygenation reaction competes with carboxylation and reduces photosynthetic productivity. The migration of the two gases in and around Rubisco was investigated using molecular dynamics simulations. The results indicate that at equal concentrations of the gases, Rubisco binds CO2 stronger than it does O-2. Amino acids with small hydrophobic side chains are the most proficient in attracting CO2, indicating a significant contribution of the hydrophobic effect in the interaction. On average, residues in the small subunit bind approximately twice as much CO2 as do residues in the large subunit. We did not detect any cavities that would provide a route to the active site for the gases. Instead, CO2 appears to be guided toward the active site through a CO2 binding region around the active site opening that extends to the closest neighboring small subunits. Taken together, these results suggest the small subunit may function as a "reservoir" for CO2 storage.

  • 24. van Lun, Michiel
    et al.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Andersson, Inger
    Sveriges lantbruksuniversitet.
    Subunit Interface Dynamics in Hexadecameric Rubisco2011In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 411, no 5, p. 1083-1098Article in journal (Refereed)
    Abstract [en]

    Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) plays an important role in the global carbon cycle as a hub for biomass. Rubisco catalyzes not only the carboxylation of RuBP with carbon dioxide but also a competing oxygenation reaction of RuBP with a negative impact on photosynthetic yield. The functional active site is built from two large (L) subunits that form a dimer. The octameric core of four L(2) dimers is held at each end by a cluster of four small (S) subunits, forming a hexadecamer. Each large subunit contacts more than one S subunit. These interactions exploit the dynamic flexibility of Rubisco, which we address in this study. Here, we describe seven different types of interfaces of hexadecameric Rubisco. We have analyzed these interfaces with respect to the size of the interface area and the number of polar interactions, including salt bridges and hydrogen bonds in a variety of Rubisco enzymes from different organisms and different kingdoms of life, including the Rubisco-like proteins. We have also performed molecular dynamics simulations of Rubisco from Chlamydomonas reinhardtii and mutants thereof. From our computational analyses, we propose structural checkpoints of the S subunit to ensure the functionality and/or assembly of the Rubisco holoenzyme. These checkpoints appear to fine-tune the dynamics of the enzyme in a way that could influence enzyme performance.

  • 25.
    Zhou, Yu
    et al.
    Australian Natl Univ, Res Sch Biol, Plant Sci Div, Canberra, ACT, Australia..
    Gunn, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Birch, Rosemary
    Australian Natl Univ, Res Sch Biol, Plant Sci Div, Canberra, ACT, Australia..
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. UiT Arctic Univ Norway, Norwegian Coll Fisheries Sci, Tromso, Norway.;Acad Sci Czech Republ, Inst Biotechnol, Biocev, Vestec, Czech Republic..
    Whitney, Spencer M.
    Australian Natl Univ, Res Sch Biol, Plant Sci Div, Canberra, ACT, Australia..
    Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth2023In: NATURE PLANTS, E-ISSN 2055-0278, Vol. 9, p. 978-986Article in journal (Refereed)
    Abstract [en]

    Improving the carboxylation properties of Rubisco has primarily arisen from unforeseen amino acid substitutions remote from the catalytic site. The unpredictability has frustrated rational design efforts to enhance plant Rubisco towards the prized growth-enhancing carboxylation properties of red algae Griffithsia monilis GmRubisco. To address this, we determined the crystal structure of GmRubisco to 1.7 angstrom. Three structurally divergent domains were identified relative to the red-type bacterial Rhodobacter sphaeroides RsRubisco that, unlike GmRubisco, are expressed in Escherichia coli and plants. Kinetic comparison of 11 RsRubisco chimaeras revealed that incorporating C329A and A332V substitutions from GmRubisco Loop 6 (corresponding to plant residues 328 and 331) into RsRubisco increased the carboxylation rate (kcatc) by 60%, the carboxylation efficiency in air by 22% and the CO2/O-2 specificity (Sc/o) by 7%. Plastome transformation of this RsRubisco Loop 6 mutant into tobacco enhanced photosynthesis and growth up to twofold over tobacco producing wild-type RsRubisco. Our findings demonstrate the utility of RsRubisco for the identification and in planta testing of amino acid grafts from algal Rubisco that can enhance the enzyme's carboxylase potential.

1 - 25 of 25
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