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  • 1.
    Brodmerkel, Maxim N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    De Santis, Emiliano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Uetrecht, Charlotte
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany.
    Marklund, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins2022In: Current Research in Structural Biology, E-ISSN 2665-928X, Vol. 4, p. 338-348Article in journal (Refereed)
    Abstract [en]

    Proteins are innately dynamic, which is important for their functions, but which also poses significant challenges when studying their structures. Gas-phase techniques can utilise separation and a range of sample manipulations to transcend some of the limitations of conventional techniques for structural biology in crystalline or solution phase, and isolate different states for separate interrogation. However, the transfer from solution to the gas phase risks affecting the structures, and it is unclear to what extent different conformations remain distinct in the gas phase, and if resolution in silico can recover the native conformations and their differences. Here, we use extensive molecular dynamics simulations to study the two distinct conformations of dimeric capsid protein of the MS2 bacteriophage. The protein undergoes notable restructuring of its peripheral parts in the gas phase, but subsequent simulation in solvent largely recovers the native structure. Our results suggest that despite some structural loss due to the experimental conditions, gas-phase structural biology techniques provide meaningful data that inform not only about the structures but also conformational dynamics of proteins.

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  • 2.
    Duelfer, Jasmin
    et al.
    Leibniz Inst Expt Virol, Heinrich Pette Inst, D-20251 Hamburg, Germany.
    Yan, Hao
    Leibniz Inst Expt Virol, Heinrich Pette Inst, D-20251 Hamburg, Germany.
    Brodmerkel, Maxim N.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Creutznacher, Robert
    Univ Lubeck, Inst Chem & Metabol, D-23562 Lübeck, Germany.
    Mallagaray, Alvaro
    Univ Lubeck, Inst Chem & Metabol, D-23562 Lübeck, Germany.
    Peters, Thomas
    Univ Lubeck, Inst Chem & Metabol, D-23562 Lübeck, Germany.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany.
    Marklund, Erik G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Uetrecht, Charlotte
    Leibniz Inst Expt Virol, Heinrich Pette Inst, D-20251 Hamburg, Germany; European XFEL GmbH, D-22869 Schenefeld, Germany.
    Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status2021In: Molecules, ISSN 1431-5157, E-ISSN 1420-3049, Vol. 26, no 8, article id 2125Article in journal (Refereed)
    Abstract [en]

    Noroviruses are the major cause of viral gastroenteritis and re-emerge worldwide every year, with GII.4 currently being the most frequent human genotype. The norovirus capsid protein VP1 is essential for host immune response. The P domain mediates cell attachment via histo blood-group antigens (HBGAs) in a strain-dependent manner but how these glycan-interactions actually relate to cell entry remains unclear. Here, hydrogen/deuterium exchange mass spectrometry (HDX-MS) is used to investigate glycan-induced protein dynamics in P dimers of different strains, which exhibit high structural similarity but different prevalence in humans. While the almost identical strains GII.4 Saga and GII.4 MI001 share glycan-induced dynamics, the dynamics differ in the emerging GII.17 Kawasaki 308 and rare GII.10 Vietnam 026 strain. The structural aspects of glycan binding to fully deamidated GII.4 P dimers have been investigated before. However, considering the high specificity and half-life of N373D under physiological conditions, large fractions of partially deamidated virions with potentially altered dynamics in their P domains are likely to occur. Therefore, we also examined glycan binding to partially deamidated GII.4 Saga and GII.4 MI001 P dimers. Such mixed species exhibit increased exposure to solvent in the P dimer upon glycan binding as opposed to pure wildtype. Furthermore, deamidated P dimers display increased flexibility and a monomeric subpopulation. Our results indicate that glycan binding induces strain-dependent structural dynamics, which are further altered by N373 deamidation, and hence hint at a complex role of deamidation in modulating glycan-mediated cell attachment in GII.4 strains.

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  • 3. Kierspel, Thomas
    et al.
    Kadek, Alan
    Barran, Perdita
    Bellina, Bruno
    Bijedic N, Adi
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Brodmerkel, Maxim N.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Commandeur, Jan
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Centre for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, E22607, Hamburg, Germany.
    Damjanović, Tomislav
    Dawod, Ibrahim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany.
    De Santis, Emiliano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Lekkas, Alexandros
    Lorenzen, Kristina
    López Morillo, Luis
    Mandl, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. University of Applied Sciences Technikum Wien, Höchstädtpl. 6, 1200, Vienna, Austria.
    Marklund, Erik G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Papanastasiou, Dimitris
    Ramakers, Lennart A. I.
    Schweikhard, Lutz
    Simke, Florian
    Sinelnikova, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Smyrnakis, Athanasios
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Uetrecht, Charlotte
    Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC2023In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 415, no 18 SI, p. 4209-4220Article in journal (Refereed)
    Abstract [en]

    MS SPIDOC is a novel sample delivery system designed for single (isolated) particle imaging at X-ray Free-Electron Lasers that is adaptable towards most large-scale facility beamlines. Biological samples can range from small proteins to MDa particles. Following nano-electrospray ionization, ionic samples can be m/z-filtered and structurally separated before being oriented at the interaction zone. Here, we present the simulation package developed alongside this prototype. The first part describes how the front-to-end ion trajectory simulations have been conducted. Highlighted is a quadrant lens; a simple but efficient device that steers the ion beam within the vicinity of the strong DC orientation field in the interaction zone to ensure spatial overlap with the X-rays. The second part focuses on protein orientation and discusses its potential with respect to diffractive imaging methods. Last, coherent diffractive imaging of prototypical T = 1 and T = 3 norovirus capsids is shown. We use realistic experimental parameters from the SPB/SFX instrument at the European XFEL to demonstrate that low-resolution diffractive imaging data (q < 0.3 nm−1) can be collected with only a few X-ray pulses. Such low-resolution data are sufficient to distinguish between both symmetries of the capsids, allowing to probe low abundant species in a beam if MS SPIDOC is used as sample delivery.

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  • 4.
    Sobolev, Egor
    et al.
    DESY, European Mol Biol Lab, Notkestr 85, D-22607 Hamburg, Germany..
    Zolotarev, Serguey
    NRC Kurchatov Inst, Pl Akad Kurchatova 1, Moscow 123098, Russia..
    Giewekemeyer, Klaus
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Bielecki, Johan
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Okamoto, Kenta
    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.
    Andreasson, Jakob
    Acad Sci Czech Republ, ELI Beamlines, Inst Phys, Slovance 2, CZ-18221 Prague, Czech Republic..
    Ayyer, Kartik
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Struct & Dynam Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Barak, Imrich
    SAS, Inst Mol Biol, Dubravska Cesta 21, Bratislava 84551, Slovakia..
    Bari, Sadia
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Barty, Anton
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Bean, Richard
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Bobkov, Sergey
    NRC Kurchatov Inst, Pl Akad Kurchatova 1, Moscow 123098, Russia..
    Chapman, Henry N.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany.;Univ Hamburg, Dept Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Chojnowski, Grzegorz
    DESY, European Mol Biol Lab, Notkestr 85, D-22607 Hamburg, Germany..
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Natl Univ Singapore, Ctr Biolmaging Sci, Dept Biol Sci, 14 Sci Dr 4, Singapore 117557, Singapore..
    Doerner, Katerina
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Flueckiger, Leonie
    La Trobe Univ, ARC Ctr Adv Mol Imaging, Dept Chem & Phys, Melbourne, Vic 3086, Australia..
    Galzitskaya, Oxana
    Russian Acad Sci, Inst Prot Res, Lab Bioinformat & Prote, Pushchino 142290, Moscow Region, Russia.;Russian Acad Sci, Inst Theoret & Expt Biophys, Pushchino 142290, Moscow Region, Russia..
    Gelisio, Luca
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Hauf, Steffen
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Hogue, Brenda G.
    Arizona State Univ, Sch Life Sci SOLS, Tempe, AZ 85287 USA..
    Horke, Daniel A.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Hosseinizadeh, Ahmad
    Univ Wisconsin, Dept Phys, KIRC, 3135 N Maryland Ave, Milwaukee, WI 53211 USA..
    Ilyin, Vyacheslav
    NRC Kurchatov Inst, Pl Akad Kurchatova 1, Moscow 123098, Russia..
    Jung, Chulho
    Pohang Univ Sci & Technol, Dept Phys, Pohang 37673, South Korea..
    Kim, Chan
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Kim, Yoonhee
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Kirian, Richard A.
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Kirkwood, Henry
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Kulyk, Olena
    Acad Sci Czech Republ, ELI Beamlines, Inst Phys, Slovance 2, CZ-18221 Prague, Czech Republic..
    Kuepper, Jochen
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany.;Univ Hamburg, Dept Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Letrun, Romain
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Loh, N. Duane
    Natl Univ Singapore, Ctr Biolmaging Sci, Dept Biol Sci, 14 Sci Dr 4, Singapore 117557, Singapore..
    Lorenzen, Kristina
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Messerschmidt, Marc
    Arizona State Univ, Biodesign Inst, Tempe, AZ 85287 USA..
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ourmazd, Abbas
    Univ Wisconsin, Dept Phys, KIRC, 3135 N Maryland Ave, Milwaukee, WI 53211 USA..
    Raab, Natascha
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Rode, Andrei, V
    Australian Natl Univ, Laser Phys Ctr, Res Sch Phys, Canberra, ACT 2601, Australia..
    Rose, Max
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Round, Adam
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Sato, Takushi
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Schubert, Robin
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Schwander, Peter
    Univ Wisconsin, Dept Phys, KIRC, 3135 N Maryland Ave, Milwaukee, WI 53211 USA..
    Sellberg, Jonas A.
    KTH Royal Inst Technol, AlbaNova Univ Ctr, Dept Appl Phys, Biomed & Xray Phys, SE-10691 Stockholm, Sweden..
    Sikorski, Marcin
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Silenzi, Alessandro
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Song, Changyong
    Pohang Univ Sci & Technol, Dept Phys, Pohang 37673, South Korea..
    Spence, John C. H.
    Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Stern, Stephan
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Sztuk-Dambietz, Jolanta
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Teslyuk, Anthon
    NRC Kurchatov Inst, Pl Akad Kurchatova 1, Moscow 123098, Russia..
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Trebbin, Martin
    SUNY Buffalo, Dept Chem, Nat Sci Complex,Room 760, Buffalo, NY 14260 USA..
    Uetrecht, Charlotte
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany.;Leibniz Inst Expt Virol, Heinrich Pette Inst, Martinistr 52, D-20251 Hamburg, Germany..
    Weinhausen, Britta
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Williams, Garth J.
    Brookhaven Natl Lab, NSLS 2, Upton, NY 11772 USA..
    Xavier, P. Lourdu
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Max Planck Inst Struct & Dynam Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Xu, Chen
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Vartanyants, Ivan A.
    DESY, Notkestr 85, D-22607 Hamburg, Germany.;Natl Res Nucl Univ, MEPhI Moscow Engn Phys Inst, Kashirskoe Shosse 31, Moscow 115409, Russia..
    Lamzin, Victor S.
    DESY, European Mol Biol Lab, Notkestr 85, D-22607 Hamburg, Germany..
    Mancuso, Adrian
    European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Maia, Filipe R.N.C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Lawrence Berkeley Natl Lab, NERSC, Berkeley, CA 94720 USA..
    Megahertz single-particle imaging at the European XFEL2020In: Communications Physics, E-ISSN 2399-3650, Vol. 3, no 1, article id 97Article in journal (Refereed)
    Abstract [en]

    The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is expected to provide 27,000 pulses per second, over two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The results obtained pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.

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