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  • 151.
    Pabis, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Risso, Valeria A.
    Univ Granada, Fac Ciencias, Dept Quim Fis, E-18071 Granada, Spain..
    Sanchez-Ruiz, Jose M.
    Univ Granada, Fac Ciencias, Dept Quim Fis, E-18071 Granada, Spain..
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Biology.
    Cooperativity and flexibility in enzyme evolution2018In: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 48, p. 83-92Article in journal (Refereed)
    Abstract [en]

    Enzymes are flexible catalysts, and there has been substantial discussion about the extent to which this flexibility contributes to their catalytic efficiency. What has been significantly less discussed is the extent to which this flexibility contributes to their evolvability. Despite this, recent years have seen an increasing number of both experimental and computational studies that demonstrate that cooperativity and flexibility play significant roles in enzyme innovation. This review covers key developments in the field that emphasize the importance of enzyme dynamics not just to the evolution of new enzyme function(s), but also as a property that can be harnessed in the design of new artificial enzymes.

  • 152. Park, Hyung Joo
    et al.
    Loh, N. Duane
    Sierra, Raymond G.
    Hampton, Christina Y.
    Starodub, Dmitri
    Martin, Andrew V.
    Barty, Anton
    Aquila, Andrew
    Schulz, Joachim
    Steinbrener, Jan
    Shoeman, Robert L.
    Lomb, Lukas
    Kassemeyer, Stephan
    Bostedt, Christoph
    Bozek, John
    Epp, Sascha W.
    Erk, Benjamin
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Rudek, Benedikt
    Foucar, Lutz
    Kimmel, Nils
    Weidenspointner, Georg
    Hauser, Guenter
    Holl, Peter
    Pedersoli, Emanuele
    Liang, Mengning
    Hunter, Mark S.
    Gumprecht, Lars
    Coppola, Nicola
    Wunderer, Cornelia
    Graafsma, Heinz
    Maia, Filipe R. N. C.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fleckenstein, Holger
    Hirsemann, Helmut
    Nass, Karol
    Tobias, Herbert J.
    Farquar, George R.
    Benner, W. Henry
    Hau-Riege, Stefan
    Reich, Christian
    Hartmann, Andreas
    Soltau, Heike
    Marchesini, Stefano
    Bajt, Sasa
    Barthelmess, Miriam
    Strueder, Lothar
    Ullrich, Joachim
    Bucksbaum, Philip
    Frank, Matthias
    Schlichting, Ilme
    Chapman, Henry N.
    Bogan, Michael J.
    Elser, Veit
    Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers2013In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 21, no 23, p. 28729-28742Article in journal (Refereed)
    Abstract [en]

    Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.

  • 153.
    Parkinson, Dilworth Y.
    et al.
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Beattie, Keith
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Chen, Xian
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Correa, Joaquin
    Natl Energy Res Sci Comp Ctr, Berkeley, CA 94720 USA..
    Dart, Eli
    Energy Sci Network, Berkeley, CA 94720 USA..
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Deslippe, Jack R.
    Natl Energy Res Sci Comp Ctr, Berkeley, CA 94720 USA..
    Hexemer, Alexander
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Krishnan, Harinarayan
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    MacDowell, Alastair A.
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marchesini, Stefano
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA.;Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Padmore, Howard A.
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Patton, Simon J.
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Perciano, Talita
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Sethian, James A.
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Math, Berkeley, CA 94720 USA..
    Shapiro, David
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Stromsness, Rune
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Tamura, Nobumichi
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Tierney, Brian L.
    Energy Sci Network, Berkeley, CA 94720 USA..
    Tull, Craig E.
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Ushizima, Daniela
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Real-Time Data-Intensive Computing2016In: Proceedings Of The 12Th International Conference On Synchrotron Radiation Instrumentation (SRI2015), 2016, article id 050001Conference paper (Refereed)
    Abstract [en]

    Today users visit synchrotrons as sources of understanding and discovery-not as sources of just light, and not as sources of data. To achieve this, the synchrotron facilities frequently provide not just light but often the entire end station and increasingly, advanced computational facilities that can reduce terabytes of data into a form that can reveal a new key insight. The Advanced Light Source (ALS) has partnered with high performance computing, fast networking, and applied mathematics groups to create a "super-facility", giving users simultaneous access to the experimental, computational, and algorithmic resources to make this possible. This combination forms an efficient closed loop, where data-despite its high rate and volume-is transferred and processed immediately and automatically on appropriate computing resources, and results are extracted, visualized, and presented to users or to the experimental control system, both to provide immediate insight and to guide decisions about subsequent experiments during beamtime. We will describe our work at the ALS ptychography, scattering, micro-diffraction, and micro-tomography beamlines.

  • 154.
    Passoni, Matteo
    et al.
    Politecnico di Milano.
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Politecnico di Milano.
    Sgattoni, Andrea
    Politecnico di Milano.
    Dellasega, David
    Politecnico di Milano.
    Macchi, Andrea
    Università di Pisa.
    Prencipe, Irene
    Politecnico di Milano.
    Floquet, Vincent
    CEA Saclay.
    Martin, Philippe
    CEA Saclay.
    Liseykina, Tatiana
    Universität Rostock.
    Ceccotti, Tiberio
    CEA Saclay.
    Energetic ions at moderate laser intensities using foam-based multi-layered targets2014In: Plasma Physics and Controlled Fusion, ISSN 0741-3335, E-ISSN 1361-6587, Vol. 56, no 4, p. 045001-Article in journal (Refereed)
    Abstract [en]

    The experimental feasibility of the laser-driven ion acceleration concept with multi-layered,foam-based targets has been investigated. Targets with the required features have beenproduced and characterized, exploiting the potential of the pulsed laser deposition technique.In the intensity range 1016–1017 Wcm−2, they allow us to obtain maximum proton energies2–3 times higher compared to bare solid targets, able to reach and surpass the MeV range withboth low and ultrahigh contrast pulses. The results of two-dimensional particle-in-cellsimulations, supporting the interpretation of the experimental results, and directions to exploitthe concept also at ultrahigh intensities, are presented.

  • 155.
    Patriksson, Alexandra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    A temperature predictor for parallel tempering simulations2008In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, no 15, p. 2073-2077Article in journal (Other (popular science, discussion, etc.))
    Abstract [en]

    An algorithm is proposed that generates a set of temperatures for use in parallel tempering simulations ( also known as temperature- replica exchange molecular dynamics simulations) of proteins to obtain a desired exchange probability P-des. The input consists of the number of protein atoms and water molecules in the system, information about the use of constraints and virtual sites and the lower temperature limits. The temperatures generated yield probabilities which are very close to Pdes ( correlation 97%), independent of force. field and over a wide temperature range.

  • 156. Pedersoli, E.
    et al.
    Loh, N. D.
    Capotondi, F.
    Hampton, C. Y.
    Sierra, R. G.
    Starodub, D.
    Bostedt, C.
    Bozek, J.
    Nelson, A. J.
    Aslam, M.
    Li, S.
    Dravid, V. P.
    Martin, A. V.
    Aquila, A.
    Barty, A.
    Fleckenstein, H.
    Gumprecht, L.
    Liang, M.
    Nass, K.
    Schulz, J.
    White, T. A.
    Coppola, N.
    Bajt, S.
    Barthelmess, M.
    Graafsma, H.
    Hirsemann, H.
    Wunderer, C.
    Epp, S. W.
    Erk, B.
    Rudek, B.
    Rudenko, A.
    Foucar, L.
    Kassemeyer, S.
    Lomb, L.
    Rolles, D.
    Shoeman, R. L.
    Steinbrener, J.
    Hartmann, R.
    Hartmann, A.
    Hauser, G.
    Holl, P.
    Kimmel, N.
    Reich, C.
    Soltau, H.
    Weidenspointner, G.
    Benner, W. H.
    Farquar, G. R.
    Hau-Riege, S. P.
    Hunter, M. S.
    Ekeberg, Tomas
    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.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Tobias, H. J.
    Marchesini, S.
    Frank, M.
    Strueder, L.
    Schlichting, I.
    Ullrich, J.
    Chapman, H. N.
    Bucksbaum, P. H.
    Kiskinova, M.
    Bogan, M. J.
    Mesoscale morphology of airborne core-shell nanoparticle clusters: x-ray laser coherent diffraction imaging2013In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 46, no 16 SI, p. 164033-Article in journal (Refereed)
    Abstract [en]

    Unraveling the complex morphology of functional materials like core-shell nanoparticles and its evolution in different environments is still a challenge. Only recently has the single-particle coherent diffraction imaging (CDI), enabled by the ultrabright femtosecond free-electron laser pulses, provided breakthroughs in understanding mesoscopic morphology of nanoparticulate matter. Here, we report the first CDI results for Co@SiO2 core-shell nanoparticles randomly clustered in large airborne aggregates, obtained using the x-ray free-electron laser at the Linac Coherent Light Source. Our experimental results compare favourably with simulated diffraction patterns for clustered Co@SiO2 nanoparticles with similar to 10 nm core diameter and similar to 30 nm shell outer diameter, which confirms the ability to resolve the mesoscale morphology of complex metastable structures. The findings in this first morphological study of core-shell nanomaterials are a solid base for future time-resolved studies of dynamic phenomena in complex nanoparticulate matter using x-ray lasers.

  • 157. Pedersoli, Emanuele
    et al.
    Capotondi, Flavio
    Cocco, Daniele
    Zangrando, Marco
    Kaulich, Burkhard
    Menk, Ralf H.
    Locatelli, Andrea
    Mentes, Tevfik O.
    Spezzani, Carlo
    Sandrin, Gilio
    Bacescu, Daniel M.
    Kiskinova, Maya
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Schulz, Joachim
    Gumprecht, Lars
    Chapman, Henry N.
    Nelson, A. J.
    Frank, Matthias
    Pivovaroff, Michael J.
    Woods, Bruce W.
    Bogan, Michael J.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Multipurpose modular experimental station for the DiProI beamline of Fermi@Elettra free electron laser2011In: Review of Scientific Instruments, ISSN 0034-6748, E-ISSN 1089-7623, Vol. 82, no 4, p. 043711-Article in journal (Refereed)
    Abstract [en]

    We present a compact modular apparatus with a flexible design that will be operated at the DiProI beamline of the Fermi@Elettra free electron laser (FEL) for performing static and time-resolved coherent diffraction imaging experiments, taking advantage of the full coherence and variable polarization of the short seeded FEL pulses. The apparatus has been assembled and the potential of the experimental setup is demonstrated by commissioning tests with coherent synchrotron radiation. This multipurpose experimental station will be open to general users after installation at the Fermi@Elettra free electron laser in 2011.

  • 158.
    Philippe, Nadege
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Legendre, Matthieu
    Doutre, Gabriel
    Coute, Yohann
    Poirot, Olivier
    Lescot, Magali
    Arslan, Defne
    Seltzer, Virginie
    Bertaux, Lionel
    Bruley, Christophe
    Garin, Jerome
    Claverie, Jean-Michel
    Abergel, Chantal
    Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes2013In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 341, no 6143, p. 281-286Article in journal (Refereed)
    Abstract [en]

    Ten years ago, the discovery of Mimivirus, a virus infecting Acanthamoeba, initiated a reappraisal of the upper limits of the viral world, both in terms of particle size (>0.7 micrometers) and genome complexity (>1000 genes), dimensions typical of parasitic bacteria. The diversity of these giant viruses (the Megaviridae) was assessed by sampling a variety of aquatic environments and their associated sediments worldwide. We report the isolation of two giant viruses, one off the coast of central Chile, the other from a freshwater pond near Melbourne (Australia), without morphological or genomic resemblance to any previously defined virus families. Their micrometer-sized ovoid particles contain DNA genomes of at least 2.5 and 1.9 megabases, respectively. These viruses are the first members of the proposed "Pandoravirus" genus, a term reflecting their lack of similarity with previously described microorganisms and the surprises expected from their future study.

  • 159.
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Statistical processing of Flash X-ray Imaging of protein complexes2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Flash X-ray Imaging (FXI) at X-ray Free Electron Lasers (XFELs) is a promising technique that permits the investigation of the 3D structure of molecules without the need for crystallization, by diffracting on single individual sample particles.

    In the past few years, some success has been achieved by using FXI on quite large biological complexes (40 nm-1 μm in diameter size). Still, the desired dream-goal of imaging a single individual of a molecule or a protein complex (<15 nm in diameter size) has not been reached yet. The main issue that prevented us from a complete success has been the low signal strength, almost comparable to background noise. That is particularly true for experiments performed at the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS).

    In this thesis, we provide a brief review of the CXI instrument (focusing on experiments there performed) and present a statistical method to deal with low signal-to-noise ratios. We take into account a variety of biological particles, showing the benefits of estimating a background model from sample data and using that for processing said data. Moreover, we present the results of some computer simulations in order to explore the limits and potentials of the proposed approach.

    Last, we show another method (named COACS) that, being fed with the previous findings from the background model, helps obtaining clearer results in the phase retrieval problem.

    List of papers
    1. Artifact reduction in the CSPAD detectors used for LCLS experiments
    Open this publication in new window or tab >>Artifact reduction in the CSPAD detectors used for LCLS experiments
    2017 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 24, p. 1092-1097Article in journal (Refereed) Published
    National Category
    Biophysics
    Identifiers
    urn:nbn:se:uu:diva-328543 (URN)10.1107/S160057751701058X (DOI)000408902800025 ()28862634 (PubMedID)
    Projects
    eSSENCE
    Available from: 2017-07-18 Created: 2017-08-25 Last updated: 2019-01-14Bibliographically approved
    2. A statistical approach to detect protein complexes at X-ray free electron laser facilities
    Open this publication in new window or tab >>A statistical approach to detect protein complexes at X-ray free electron laser facilities
    Show others...
    2018 (English)In: Communications Physics, E-ISSN 2399-3650, Vol. 1, p. 92:1-11, article id 92Article in journal (Refereed) Published
    National Category
    Biophysics
    Identifiers
    urn:nbn:se:uu:diva-369876 (URN)10.1038/s42005-018-0092-6 (DOI)000452676300003 ()
    Projects
    eSSENCE
    Available from: 2018-12-07 Created: 2018-12-17 Last updated: 2019-05-06Bibliographically approved
    3. Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy
    Open this publication in new window or tab >>Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy
    2018 (English)In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 26, p. 24422-24443Article in journal (Refereed) Published
    National Category
    Computational Mathematics Biophysics
    Identifiers
    urn:nbn:se:uu:diva-360037 (URN)10.1364/OE.26.024422 (DOI)000444705000012 ()30469561 (PubMedID)
    Projects
    eSSENCE
    Available from: 2018-09-05 Created: 2018-09-09 Last updated: 2019-01-14Bibliographically approved
  • 160.
    Pietrini, Alberto
    et al.
    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.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Hantke, Max F.
    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.
    Loh, N. Duane
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sébastien
    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.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A statistical approach to detect protein complexes at X-ray free electron laser facilities2018In: Communications Physics, E-ISSN 2399-3650, Vol. 1, p. 92:1-11, article id 92Article in journal (Refereed)
  • 161.
    Pietrini, Alberto
    et al.
    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, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Artifact reduction in the CSPAD detectors used for LCLS experiments2017In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 24, p. 1092-1097Article in journal (Refereed)
  • 162.
    Pietrini, Alberto
    et al.
    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, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy2018In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 26, p. 24422-24443Article in journal (Refereed)
  • 163.
    Popp, David
    et al.
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore..
    Loh, N. Duane
    Natl Univ Singapore, Dept Phys, Singapore 117557, Singapore.;Natl Univ Singapore, Ctr BioImaging Sci, Singapore 117546, Singapore..
    Zorgati, Habiba
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore.;Natl Univ Singapore, Dept Biochem, Singapore 117597, Singapore..
    Ghoshdastider, Umesh
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore..
    Liow, Lu Ting
    Natl Univ Singapore, Dept Med, Singapore 119074, Singapore..
    Ivanova, Magdalena I.
    Univ Michigan, Dept Neurol, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA..
    Larsson, Mårten
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore.
    DePonte, Daniel P.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bean, Richard
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;European XFEL GmbH, D-22761 Hamburg, Germany..
    Beyerlein, Kenneth R.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Gati, Cornelius
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Oberthuer, Dominik
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Inst Biochem & Mol Biol, D-22607 Hamburg, Germany..
    Arnlund, David
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Branden, Gisela
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Berntsen, Peter
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Cascio, Duilio
    Univ Calif Los Angeles, Howard Hughes Med Inst, Los Angeles, CA 90095 USA..
    Chavas, Leonard M. G.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chen, Joe P. J.
    Univ Canterbury, Computat Imaging Grp, Dept Elect & Comp Engn, Christchurch, New Zealand.;Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Ding, Ke
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore..
    Fleckenstein, Holger
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Gumprecht, Lars
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Harimoorthy, Rajiv
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Mossou, Estelle
    Inst Laue Langevin, F-38000 Grenoble, France.;Keele Univ, EPSAM ISTM, Keele ST5 5BG, Staffs, England..
    Sawaya, Michael R.
    Univ Calif Los Angeles, Howard Hughes Med Inst, Los Angeles, CA 90095 USA..
    Brewster, Aaron S.
    Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA..
    Hattne, Johan
    Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA.;Howard Hughes Med Inst, Janelia Res Campus,19700 Helix Dr, Ashburn, VA 20147 USA..
    Sauter, Nicholas K.
    Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA..
    Seibert, Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seuring, Carolin
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Stellato, Francesco
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Tilp, Thomas
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Eisenberg, David S.
    Univ Calif Los Angeles, Howard Hughes Med Inst, Los Angeles, CA 90095 USA..
    Messerschmidt, Marc
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Williams, Garth J.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Koglin, Jason E.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Makowski, Lee
    Northeastern Univ, Dept Bioengn, 360 Huntington Ave, Boston, MA 02115 USA..
    Millane, Rick P.
    Univ Canterbury, Computat Imaging Grp, Dept Elect & Comp Engn, Christchurch, New Zealand..
    Forsyth, Trevor
    Inst Laue Langevin, F-38000 Grenoble, France.;Keele Univ, EPSAM ISTM, Keele ST5 5BG, Staffs, England..
    Boutet, Sebastien
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    White, Thomas A.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Barty, Anton
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chapman, Henry
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, Luruper Chaussee 149, D-22607 Hamburg, Germany..
    Chen, Swaine L.
    Natl Univ Singapore, Dept Med, Singapore 119074, Singapore.;ASTAR, Biopolis, Genome Inst Singapore, Singapore 138672, Singapore..
    Liang, Mengning
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Neutze, Richard
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Robinson, Robert C.
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore.;Natl Univ Singapore, Dept Biochem, Singapore 117597, Singapore.;Okayama Univ, Res Inst Interdisciplinary Sci, Okayama 7008530, Japan..
    Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser2017In: CYTOSKELETON, ISSN 1949-3584, Vol. 74, no 12, p. 472-481Article in journal (Refereed)
    Abstract [en]

    A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked -strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual -synuclein amyloids.

  • 164.
    R. N. C. Maia, Filipe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ultrafast Coherent X-ray Diffractive Nanoimaging2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    X-ray lasers are creating unprecedented research opportunities in physics,chemistry and biology. The peak brightness of these lasers exceeds presentsynchrotrons by 1010, the coherence degeneracy parameters exceedsynchrotrons by 109, and the time resolution is 105 times better. In theduration of a single flash, the beam focused to a micron-sized spot has the samepower density as all the sunlight hitting the Earth, focused to a millimetresquare. Ultrafast coherent X-ray diffractive imaging (CXDI) with X-ray lasers exploitsthese unique properties of X-ray lasers to obtain high-resolution structures fornon-crystalline biological (and other) objects. In such an experiment, thesample is quickly vaporised, but not before sufficient scattered light can berecorded. The continuous diffraction pattern can then be phased and thestructure of a more or less undamaged sample recovered% (speed of light vs. speed of a shock wave).This thesis presents results from the first ultrafast X-ray diffractive imagingexperiments with linear accelerator-driven free-electron lasers and fromoptically-driven table-top X-ray lasers. It also explores the possibility ofinvestigating phase transitions in crystals by X-ray lasers. An important problem with ultrafast CXDI of small samples such as single proteinmolecules is that the signal from a single measurement will be small, requiringsignal enhancement by averaging over multiple equivalent samples. We present anumerical investigation of the problems, including the case where samplemolecules are not exactly identical, and propose tentative solutions. A new software package (Hawk) has been developed for data processing and imagereconstruction. Hawk is the first publicly available software package in thisarea, and it is released as an open source software with the aspiration offostering the development of this field.

    List of papers
    1. Femtosecond diffractive imaging with a soft-X-ray free-electron laser
    Open this publication in new window or tab >>Femtosecond diffractive imaging with a soft-X-ray free-electron laser
    Show others...
    2006 (English)In: Nature Physics, ISSN 1745-2473, E-ISSN 1745-2481, Vol. 2, no 12, p. 839-843Article in journal (Refereed) Published
    Abstract [en]

    Theory predicts(1-4) that, with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft-X-ray free-electron laser. An intense 25 fs, 4 x 10(13) W cm(-2) pulse, containing 10(12) photons at 32 nm wavelength, produced a coherent diffraction pattern from a nanostructured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single-photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling(5-9), shows no measurable damage, and is reconstructed at the diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one(10).

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-24416 (URN)10.1038/nphys461 (DOI)000242478000021 ()
    Available from: 2007-02-05 Created: 2007-02-05 Last updated: 2017-12-07Bibliographically approved
    2. Structural studies of melting on the picosecond time scale
    Open this publication in new window or tab >>Structural studies of melting on the picosecond time scale
    2008 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, no 42, p. 6344-6349Article, review/survey (Refereed) Published
    Abstract [en]

    Ultrafast structural studies of laser-induced melting have demonstrated that the solid-liquid phase transition can take place on a picosecond time scale in a variety of materials. Experimental studies using ångström wavelength X-rays from the sub-picosecond pulse source at Stanford (now retired) on non-thermal melting of semi-conductors, such as indium antimonide, employed the decay of a single Bragg-peak to measure the time component of the phase transition. These materials were found to start melting within one picosecond after the laser pulse. Recent computer simulations have described the thermal melting of ice induced by an infrared laser pulse. Here it was shown that melting can happen within a few picoseconds, somewhat slower than non-thermal melting in semi-conductors. These computer simulations are compatible with spectroscopy experiments on ice-melting, demonstrating that simulations form a very powerful complement to experiments targeting the process of phase-transitions. Here we present an overview of recent experimental and theoretical studies of melting, as well as new simulations of ice-melting where the effect of the size of the crystal on scattering is studied. Based on simulations of a near-macroscopic crystal, we predict the decay of the most intense Bragg peaks of ice following heating by laser pulse, by modeling the scattering from the melting sample in the simulations.

    National Category
    Physical Sciences Chemical Sciences Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121924 (URN)10.1039/b807550f (DOI)000260485600001 ()18972022 (PubMedID)
    Available from: 2010-03-31 Created: 2010-03-31 Last updated: 2017-12-12Bibliographically approved
    3. Single-Shot Diffractive Imaging with a Table-Top Femtosecond Soft X-Ray Laser-Harmonics Source
    Open this publication in new window or tab >>Single-Shot Diffractive Imaging with a Table-Top Femtosecond Soft X-Ray Laser-Harmonics Source
    Show others...
    2009 (English)In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 103, no 2, p. 028104-Article in journal (Refereed) Published
    Abstract [en]

    Coherent x-ray diffractive imaging is a powerful method for studies on   nonperiodic structures on the nanoscale. Access to femtosecond dynamics   in major physical, chemical, and biological processes requires   single-shot diffraction data. Up to now, this has been limited to   intense coherent pulses from a free electron laser. Here we show that   laser-driven ultrashort x-ray sources offer a comparatively inexpensive  alternative. We present measurements of single-shot diffraction patterns from isolated nano-objects with a single 20 fs pulse from a   table-top high-harmonic x-ray laser. Images were reconstructed with a   resolution of 119 nm from the single shot and 62 nm from multiple shots.

    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-121910 (URN)10.1103/PhysRevLett.103.028104 (DOI)000267887800065 ()
    Available from: 2010-03-31 Created: 2010-03-31 Last updated: 2017-12-12Bibliographically approved
    4. Structural variability and the incoherent addition of scattered intensities in single-particle diffraction
    Open this publication in new window or tab >>Structural variability and the incoherent addition of scattered intensities in single-particle diffraction
    Show others...
    2009 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 80, no 3, p. 031905-Article in journal (Refereed) Published
    Abstract [en]

    X-ray lasers may allow structural studies on single particles and biomolecules without crystalline periodicity in the samples. We examine here the effect of sample dynamics as a source of structural heterogeneity on the resolution of the reconstructed image of a small protein molecule. Structures from molecular-dynamics simulations of lysozyme were sampled and aligned. These structures were then used to calculate diffraction patterns corresponding to different dynamic states. The patterns were incoherently summed and the resulting data set was phased using the oversampling method. Reconstructed images of hydrated and dehydrated lysozyme gave resolutions of 3.7 angstrom and 7.6 angstrom, respectively. These are significantly worse than the root-mean-square deviation of the hydrated (2.7 angstrom for all atoms and 1.45 angstrom for C-alpha positions) or dehydrated (3.7 angstrom for all atoms and 2.5 angstrom for C-alpha positions) structures. The noise introduced by structural dynamics and incoherent addition of dissimilar structures restricts the maximum resolution to be expected from direct image reconstruction of dynamic systems. A way of potentially reducing this effect is by grouping dynamic structures into distinct structural substates and solving them separately.

    Keywords
    x-ray-diffraction, electron cascades, proteins, crystallography, resolution, pulses
    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-111993 (URN)10.1103/PhysRevE.80.031905 (DOI)000270383400104 ()1539-3755 (ISBN)
    Note

    Part 1 501LM Times Cited:0 Cited References Count:32

    Available from: 2010-01-05 Created: 2010-01-05 Last updated: 2017-12-12Bibliographically approved
    5. Hawk: the image reconstruction package for coherent X-ray diffractive imaging
    Open this publication in new window or tab >>Hawk: the image reconstruction package for coherent X-ray diffractive imaging
    2010 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 43, no 6, p. 1535-1539Article in journal (Other academic) Published
    Abstract [en]

    The past few years have seen a tremendous growth in the field of coherent X-ray diffractive imaging, in large part due to X-ray free-electron lasers which provide a peak brilliance billions of times higher than that of synchrotrons. However, this rapid development in terms of hardware has not been matched on the software side. The release of Hawk is intended to close this gap. To the authors knowledge Hawk is the first publicly available and fully open source software program for reconstructing images from continuous diffraction patterns. The software handles all steps leading from a raw diffraction pattern to a reconstructed two-dimensional image including geometry determination, background correction, masking and phasing. It also includes preliminary three-dimensional support and support for graphics processing units using the Compute Unified Device Architecture, which speeds up processing by orders of magnitude compared to a single central processing unit. Hawk implements numerous algorithms and is easily extended. This, in combination with its open-source licence, provides a platform for other groups to test, develop and distribute their own algorithms.

    Keywords
    computer programs, diffractive imaging, free-electron lasers, Hawk, open-source software, phasing, reconstruction
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121927 (URN)10.1107/S0021889810036083 (DOI)000284550900033 ()
    Available from: 2010-03-31 Created: 2010-03-31 Last updated: 2017-12-12Bibliographically approved
  • 165.
    Raber, Johan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Quantum Chemical Studies of Chemotherapeutic Drug Cisplatin: Activation and Binding to DNA2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The serendipitous discovery of the potent cytotoxic properties of cisplatin brought about a revolution in the treatment of certain types of cancer, but almost fifty years later, there still remain unknown areas in the chemistry of cisplatin. There are questions regarding which form of the drug reaches its DNA target, or why certain DNA sequences are more preferred than others for reaction with cisplatin. The work presented here aims to address some of these problems, using quantum chemical calculations to complement and interpret available experimental data.

    Cisplatin's activation reactions are explored by Density Functional Theory (DFT) on two model systems, one solely using a self-consistent reaction field (SCRF) for modeling bulk water, and one including an additional partial solvation shell of water molecules. It is concluded that adding explicit solvation provides a better picture than using SCRF solvation alone. The energy surface supports the view that the active form of cisplatin is the monoaquated form.

    The activation reactions of the cisplatin-derived drug, JM118, are investigated using DFT and SCRF calculations using three solvation model systems. The results show a slower rate of hydrolysis for the first reaction, and a faster rate for the second, suggesting diaquated JM118 as the main DNA binding form of the drug.

    Diaquated cisplatin's first and second reaction with guanine and adenine are studied using DFT and SCRF solvation. Cisplatin's propensity toward guanine in the first substitution is explained by larger stabilisation energy for the initially formed complex and by favoured kinetics. For the second substitution, higher stability in complexation with guanine over adenine is ascribed as the main factor favouring guanine over adenine substitution. This provides the first explanation for the predominance of 1,2-d(GpG) over 1,2-d(ApG) adducts, and the direction specificity of the 1,2-d(ApG) adducts.

    List of papers
    1. The Activation of Anti-Cancer Drug Cisplatin – is the Activated Complex Fully Aquated?
    Open this publication in new window or tab >>The Activation of Anti-Cancer Drug Cisplatin – is the Activated Complex Fully Aquated?
    2004 In: Molecular Physics, ISSN 0026–8976, Vol. 102, no 23-24, p. 2537-2544Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95773 (URN)
    Available from: 2007-04-20 Created: 2007-04-20Bibliographically approved
    2. Theoretical Study of Cisplatin Binding to DNA: The Importance of Initial Complex Stabilization
    Open this publication in new window or tab >>Theoretical Study of Cisplatin Binding to DNA: The Importance of Initial Complex Stabilization
    2005 In: The Journal of Physical Chemistry B, ISSN 1089-5647, Vol. 109, no 21, p. 11006-11015Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95774 (URN)
    Available from: 2007-04-20 Created: 2007-04-20Bibliographically approved
    3. Hydrolysis Process of the Second Generation Platinum-Based Anticancer Drug cis-Amminedichlorocyclohexylamineplatinum(II)
    Open this publication in new window or tab >>Hydrolysis Process of the Second Generation Platinum-Based Anticancer Drug cis-Amminedichlorocyclohexylamineplatinum(II)
    2005 In: The Journal of Physical Chemistry B, ISSN 1089-5647, Vol. 109, no 24, p. 12195-12205Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95775 (URN)
    Available from: 2007-04-20 Created: 2007-04-20Bibliographically approved
    4. Density-functional Theory in Drug Design – the Chemistry of the Anti-tumor Drug Cisplatin and Photoactive Psoralen Compounds
    Open this publication in new window or tab >>Density-functional Theory in Drug Design – the Chemistry of the Anti-tumor Drug Cisplatin and Photoactive Psoralen Compounds
    2003 In: Quantum Medicinal Chemistry, 2003, p. 113-153Chapter in book (Other academic) Published
    Identifiers
    urn:nbn:se:uu:diva-95776 (URN)3-527-30456-8 (ISBN)
    Available from: 2007-04-20 Created: 2007-04-20Bibliographically approved
  • 166.
    Raber, Johan
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Llano, Jorge
    Eriksson, Leif A.
    Density-functional Theory in Drug Design – the Chemistry of the Anti-tumor Drug Cisplatin and Photoactive Psoralen Compounds2003In: Quantum Medicinal Chemistry, 2003, p. 113-153Chapter in book (Other academic)
  • 167.
    Raber, Johan
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zhu, Chuanbao
    Eriksson, Leif A.
    The Activation of Anti-Cancer Drug Cisplatin – is the Activated Complex Fully Aquated?2004In: Molecular Physics, ISSN 0026–8976, Vol. 102, no 23-24, p. 2537-2544Article in journal (Refereed)
  • 168.
    Raber, Johan
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zhu, Chuanbao
    Eriksson, Leif A.
    Theoretical Study of Cisplatin Binding to DNA: The Importance of Initial Complex Stabilization2005In: The Journal of Physical Chemistry B, ISSN 1089-5647, Vol. 109, no 21, p. 11006-11015Article in journal (Refereed)
  • 169.
    Rath, Asawari D.
    et al.
    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.
    Maia, Filipe R. N. C.
    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.
    Fleckenstein, Holger
    Iwan, Bianca
    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.
    Hasse, Dirk
    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.
    Westphal, Daniel
    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.
    Hantke, Max
    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.
    Seibert, M. Marvin
    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.
    Liang, Mengning
    Stellato, Francesco
    Kirian, Richard
    Bean, Richard
    Barty, Anton
    Galli, Lorenzo
    Nass, Karol
    Barthelmess, Miriam
    Aquila, Andrew
    Toleikis, Sven
    Treusch, Rolf
    Roling, Sebastian
    Wöstmann, Michael
    Zacharias, Helmut
    Chapman, Henry N.
    Bajt, Saša
    DePonte, Daniel
    Hajdu, Janos
    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.
    Explosion dynamics of sucrose nanospheres monitored by time of flight spectrometry and coherent diffractive imaging at the split-and-delay beam line of the FLASH soft X-ray laser2014In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 22, no 23, p. 28914-28925Article in journal (Refereed)
    Abstract [en]

    We use a Mach-Zehnder type autocorrelator to split and delay XUV pulses from the FLASH soft X-ray laser for triggering and subsequently probing the explosion of aerosolised sugar balls. FLASH was running at 182 eV photon energy with pulses of 70 fs duration. The delay between the pump-probe pulses was varied between zero and 5 ps, and the pulses were focused to reach peak intensities above 1016 W/cm2 with an off-axis parabola. The direct pulse triggered the explosion of single aerosolised sucrose nano-particles, while the delayed pulse probed the exploding structure. The ejected ions were measured by ion time of flight spectrometry, and the particle sizes were measured by coherent diffractive imaging. The results show that sucrose particles of 560-1000 nm diameter retain their size for about 500 fs following the first exposure. Significant sample expansion happens between 500 fs and 1 ps. We present simulations to support these observations.

  • 170.
    Rawle, Robert J.
    et al.
    Univ Virginia, Dept Mol Physiol & Biol Phys, Charlottesville, VA 22908 USA;Univ Virginia, Dept Biomed Engn, Charlottesville, VA 22908 USA;Williams Coll, Dept Chem, Williamstown, MA 01267 USA.
    Giraldo, Ana M. Villamil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Boxer, Steven G.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    Kasson, Peter M.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Univ Virginia, Dept Mol Physiol & Biol Phys, Charlottesville, VA 22908 USA;Univ Virginia, Dept Biomed Engn, Charlottesville, VA 22908 USA.
    Detecting and Controlling Dye Effects in Single-Virus Fusion Experiments2019In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 117, no 3, p. 445-452Article in journal (Refereed)
    Abstract [en]

    Fluorescent dye-dequenching assays provide a powerful and versatile means to monitor membrane fusion events. They have been used in bulk assays, for measuring single events in live cells, and for detailed analysis of fusion kinetics for liposomal, viral, and cellular fusion processes; however, the dyes used also have the potential to perturb membrane fusion. Here, using single-virus measurements of influenza membrane fusion, we show that fluorescent membrane probes can alter both the efficiency and the kinetics of lipid mixing in a dye- and illumination-dependent manner. R18, a dye that is commonly used to monitor lipid mixing between membranes, is particularly prone to these effects, whereas Texas Red is somewhat less sensitive. R18 further undergoes photoconjugation to viral proteins in an illumination-dependent manner that correlates with its inactivation of viral fusion. These results demonstrate how fluorescent probes can perturb measurements of biological activity and provide both data and a method for determining minimally perturbative measurement conditions.

  • 171.
    Rawle, Robert J.
    et al.
    Univ Virginia, Dept Mol Physiol & Biol Phys, Charlottesville, VA 22908 USA;Univ Virginia, Dept Biomed Engn, Charlottesville, VA 22908 USA.
    Webster, Elizabeth R.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    Jelen, Marta
    Univ Virginia, Dept Mol Physiol & Biol Phys, Charlottesville, VA 22908 USA;Univ Virginia, Dept Biomed Engn, Charlottesville, VA 22908 USA.
    Kasson, Peter M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Univ Virginia, Dept Mol Physiol & Biol Phys, Charlottesville, VA 22908 USA;Univ Virginia, Dept Biomed Engn, Charlottesville, VA 22908 USA.
    Boxer, Steven G.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    pH Dependence of Zika Membrane Fusion Kinetics Reveals an Off-Pathway State2018In: ACS CENTRAL SCIENCE, ISSN 2374-7943, Vol. 4, no 11, p. 1503-1510Article in journal (Refereed)
    Abstract [en]

    The recent spread of Zika virus stimulated extensive research on its structure, pathogenesis, and immunology, but mechanistic study of entry has lagged behind, in part due to the lack of a defined reconstituted system. Here, we report Zika membrane fusion measured using a platform that bypasses these barriers, enabling observation of single-virus fusion kinetics without receptor reconstitution. Surprisingly, target membrane binding and low pH are sufficient to trigger viral hemifusion to liposomes containing only neutral lipids. Second, although the extent of hemifusion strongly depends on pH, hemifusion rates are relatively insensitive to pH. Kinetic analysis shows that an off-pathway state is required to capture this pH-dependence and suggests this may be related to viral inactivation. Our surrogate-receptor approach thus yields new understanding of flaviviral entry mechanisms and should be applicable to many emerging viruses.

  • 172.
    Reddy, Hemanth K. N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Yoon, Chun Hong
    Aquila, Andrew
    Awel, Salah
    Ayyer, Kartik
    Barty, Anton
    Berntsen, Peter
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bobkov, Sergey
    Bucher, Maximilian
    Carini, Gabriella A.
    Carron, Sebastian
    Chapman, Henry
    Daurer, Benedikt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    DeMirci, Hasan
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Fromme, Petra
    Hajdu, Janos
    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.
    Hart, Philip
    Hogue, Brenda G.
    Hosseinizadeh, Ahmad
    Kim, Yoonhee
    Kirian, Richard A.
    Kurta, Ruslan P.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mancuso, Adrian P.
    Mühlig, Kerstin
    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.
    Nam, Daewoong
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ourmazd, Abbas
    Rose, Max
    Schwander, Peter
    Seibert, Marvin
    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.
    Song, Changyong
    Spence, John C. H.
    Svenda, Martin
    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.
    Vartanyants, Ivan A.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source2017In: Scientific Data, E-ISSN 2052-4463, Vol. 4, article id 170079Article in journal (Refereed)
  • 173.
    Reddy, Hemanth K.N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carroni, Marta
    Stockholm Univ, Dept Biochem & Biophys, Stockholm, Sweden.
    Hajdu, J
    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.
    Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture2019In: eLIFE, E-ISSN 2050-084X, Vol. 8, article id e48496Article in journal (Refereed)
    Abstract [en]

    Bacteriophage PR772, a member of the Tectiviridae family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 angstrom, while the resolution of the protein capsid is 2.3 angstrom. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.

  • 174.
    Reddy, Hemanth K.N.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Marta, Carroni
    Hajdu, J
    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.
    CryoEM of coliphage PR772 reveals the composition & structure of the elusive vertex complex and the capsid architecture.In: eLIFE, E-ISSN 2050-084XArticle in journal (Refereed)
    Abstract [en]

    Bacteriophage PR772, a member of the Tectiviridae family, has a 70-nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T=25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.

  • 175. Redecke, Lars
    et al.
    Nass, Karol
    Deponte, Daniel P
    White, Thomas A