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  • 101.
    Jönsson, Olof
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses2017Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Investigations of soft matter using ultrashort high intensity pulses have been made possible through the advent of X-ray free-electrons lasers. The last decade has seen the development of a new type of protein crystallography where femtosecond dynamics can be studied, and single particle imaging with atomic resolution is on the horizon. The pulses are so intense that any sample quickly turns into a plasma. This thesis studies the ultrafast transition from soft matter to warm dense matter, and the implications for structural determination of proteins.                   

    We use non-thermal plasma simulations to predict ultrafast structural and electron dynamics. Changes in atomic form factors due to the electronic state, and displacement as a function of temperature, are used to predict Bragg signal intensity in protein nanocrystals. The damage processes started by the pulse will gate the diffracted signal within the pulse duration, suggesting that long pulses are useful to study protein structure. This illustrates diffraction-before-destruction in crystallography.

    The effect from a varying temporal photon distribution within a pulse is also investigated. A well-defined initial front determines the quality of the diffracted signal. At lower intensities, the temporal shape of the X-ray pulse will affect the overall signal strength; at high intensities the signal level will be strongly dependent on the resolution.

    Water is routinely used to deliver biological samples into the X-ray beam. Structural dynamics in water exposed to intense X-rays were investigated with simulations and experiments. Using pulses of different duration, we found that non-thermal heating will affect the water structure on a time scale longer than 25 fs but shorter than 75 fs. Modeling suggests that a loss of long-range coordination of the solvation shells accounts for the observed decrease in scattering signal.

    The feasibility of using X-ray emission from plasma as an indicator for hits in serial diffraction experiments is studied. Specific line emission from sulfur at high X-ray energies is suitable for distinguishing spectral features from proteins, compared to emission from delivery liquids. We find that plasma emission continues long after the femtosecond pulse has ended, suggesting that spectrum-during-destruction could reveal information complementary to diffraction.

    Delarbeten
    1. Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
    Öppna denna publikation i ny flik eller fönster >>Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
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    2015 (Engelska)Ingår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 23, nr 2, s. 1213-1231Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.

    Nyckelord
    Ultrafast lasers, UV, EUV, and X-ray lasers, X-ray imaging, Diffraction theory, Ultrafast phenomena
    Nationell ämneskategori
    Atom- och molekylfysik och optik
    Identifikatorer
    urn:nbn:se:uu:diva-242136 (URN)10.1364/OE.23.001213 (DOI)000349166100061 ()
    Anmärkning

    De två första författarna delar förstaförfattarskapet.

    Tillgänglig från: 2015-01-21 Skapad: 2015-01-21 Senast uppdaterad: 2017-12-05Bibliografiskt granskad
    2. Simulations of Radiation Damage as a Function of the Temporal Pulse Profile in Femtosecond X-ray Protein Crystallography
    Öppna denna publikation i ny flik eller fönster >>Simulations of Radiation Damage as a Function of the Temporal Pulse Profile in Femtosecond X-ray Protein Crystallography
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    2015 (Engelska)Ingår i: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, nr 2, s. 256-266Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10$\sp 4$ to 10$\sp 7$Jcm$\sp $-$2$ with photon energies from 2 to 12keV, up to 100fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.

    Nyckelord
    X-ray free-electron laser, serial femtosecond crystallography, radiation damage, plasma simulations
    Nationell ämneskategori
    Atom- och molekylfysik och optik
    Identifikatorer
    urn:nbn:se:uu:diva-245210 (URN)10.1107/S1600577515002878 (DOI)000350641100007 ()
    Tillgänglig från: 2015-02-25 Skapad: 2015-02-25 Senast uppdaterad: 2019-04-28
    3. FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
    Öppna denna publikation i ny flik eller fönster >>FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
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    2018 (Engelska)Ingår i: High Energy Density Physics, ISSN 1574-1818, Vol. 26, s. 93-98Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Over the last decade X-ray free-electron laser (XFEL) sources have been made available to the scientific community. One of the most successful uses of these new machines has been protein crystallography. When samples are exposed to the intense short X-ray pulses provided by the XFELs, the sample quickly becomes highly ionized and the atomic structure is affected. Here we present a webtool dubbed FreeDam based on non-thermal plasma simulations, for estimation of radiation damage in free-electron laser experiments in terms of ionization, temperatures and atomic displacements. The aim is to make this tool easily accessible to scientists who are planning and performing experiments at XFELs.

    Nyckelord
    FreeDam, non-local thermodynamic equilibrium, x-ray free-electron laser, radiation damage, serial femtosecond x-ray crystallography, Cretin, simulation, database
    Nationell ämneskategori
    Atom- och molekylfysik och optik
    Identifikatorer
    urn:nbn:se:uu:diva-329499 (URN)
    Tillgänglig från: 2017-09-17 Skapad: 2017-09-17 Senast uppdaterad: 2019-04-28
    4. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
    Öppna denna publikation i ny flik eller fönster >>Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
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    2015 (Engelska)Ingår i: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, nr 2, s. 225-238Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe–4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe–4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.

    Nyckelord
    free-electron laser, SFX, serial femtosecond crystallography, radiation damage, protein crystallography, metalloprotein
    Nationell ämneskategori
    Strukturbiologi
    Identifikatorer
    urn:nbn:se:uu:diva-245011 (URN)10.1107/S1600577515002349 (DOI)000350641100004 ()
    Tillgänglig från: 2015-02-23 Skapad: 2015-02-23 Senast uppdaterad: 2017-12-04Bibliografiskt granskad
    5. Ultrafast non-thermal heating of water initiated by an X-ray laser
    Öppna denna publikation i ny flik eller fönster >>Ultrafast non-thermal heating of water initiated by an X-ray laser
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    2018 (Engelska)Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, nr 22, s. 5652-5657Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    X-ray Free-Electron Lasers have opened the door to a new era in structural biology, enabling imaging of biomolecules and dynamics that were impossible to access with conventional methods. A vast majority of imaging experiments, including Serial Femtosecond Crystallography, use a liquid jet to deliver the sample into the interaction region. We have observed structural changes in the carrying water during X-ray exposure, showing how it transforms from the liquid phase to a plasma. This ultrafast phase transition observed in water provides evidence that any biological structure exposed to these X-ray pulses is destroyed during the X-ray exposure.The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2. These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.

    Nationell ämneskategori
    Atom- och molekylfysik och optik
    Identifikatorer
    urn:nbn:se:uu:diva-294554 (URN)10.1073/pnas.1711220115 (DOI)000433283700046 ()29760050 (PubMedID)
    Forskningsfinansiär
    Stiftelsen för strategisk forskning (SSF)Vetenskapsrådet, 2013-3940Stiftelsen för internationalisering av högre utbildning och forskning (STINT)Swedish National Infrastructure for Computing (SNIC)Carl Tryggers stiftelse för vetenskaplig forskning
    Anmärkning

    De två första författarna delar förstaförfattarskapet

    Tillgänglig från: 2016-05-24 Skapad: 2016-05-24 Senast uppdaterad: 2018-08-20Bibliografiskt granskad
    6. Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
    Öppna denna publikation i ny flik eller fönster >>Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
    2017 (Engelska)Ingår i: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, nr 6, s. 778-784Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

    Nyckelord
    hit detection, plasma emission spectra, serial femtosecond crystallography, protein structure
    Nationell ämneskategori
    Biofysik
    Forskningsämne
    Fysik med inriktning mot biofysik
    Identifikatorer
    urn:nbn:se:uu:diva-331934 (URN)10.1107/S2052252517014154 (DOI)000414266200011 ()29123680 (PubMedID)
    Forskningsfinansiär
    VetenskapsrådetSwedish National Infrastructure for Computing (SNIC), 2016-7-61Stiftelsen för strategisk forskning (SSF)Stiftelsen för internationalisering av högre utbildning och forskning (STINT)ÅForsk (Ångpanneföreningens Forskningsstiftelse)
    Tillgänglig från: 2017-10-25 Skapad: 2017-10-25 Senast uppdaterad: 2018-02-05Bibliografiskt granskad
  • 102.
    Jönsson, Olof
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    Östlin, Christofer
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    Scott, Howard A.
    Lawrence Livermore Natl Lab, Livermore, CA 94550 USA.
    Chapman, Henry
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik. DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany;Univ Hamburg, Dept Phys, Luruper Chaussee 149, DE-22761 Hamburg, Germany;Univ Hamburg, Ctr Ultrafast Imaging, Luruper Chaussee 149, DE-22761 Hamburg, Germany.
    Aplin, Steve J.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany.
    Timneanu, Nicusor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    Caleman, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik. DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany.
    FreeDam: A webtool for free-electron laser-induced damage in femtosecond X-ray crystallography2018Ingår i: HIGH ENERGY DENSITY PHYSICS, ISSN 1574-1818, Vol. 26, s. 93-98Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Over the last decade X-ray free-electron laser (XFEL) sources have been made available to the scientific community. One of the most successful uses of these new machines has been protein crystallography. When samples are exposed to the intense short X-ray pulses provided by the XFELs, the sample quickly becomes highly ionized and the atomic structure is affected. Here we present a webtool dubbed FreeDam based on non-thermal plasma simulations, for estimation of radiation damage in free-electron laser experiments in terms of ionization, temperatures and atomic displacements. The aim is to make this tool easily accessible to scientists who are planning and performing experiments at XFELs.

  • 103.
    Kaltenbach, Miriam
    et al.
    Weizmann Inst Sci, Dept Biol Chem, Rehovot, Israel.
    Burke, Jason R.
    Salk Inst Biol Studies, Howard Hughes Med Inst, Jack H Skirball Ctr Chem Biol & Prote, La Jolla, CA 92037 USA.
    Dindo, Mirco
    Weizmann Inst Sci, Dept Biol Chem, Rehovot, Israel;Univ Verona, Biol Chem Sect, Dept Neurosci Biomed & Movement Sci, Verona, Italy.
    Pabis, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Steffen-Munsberg, Fabian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Rabin, Avigayel
    Weizmann Inst Sci, Dept Biol Chem, Rehovot, Israel;Hebrew Univ Jerusalem, Alexander Silberman Inst Life Sci, Dept Biol Chem, Edmond J Safra Campus, Jerusalem, Israel.
    Kamerlin, Shina C. Lynn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Strukturbiologi.
    Noel, Joseph P.
    Salk Inst Biol Studies, Howard Hughes Med Inst, Jack H Skirball Ctr Chem Biol & Prote, La Jolla, CA 92037 USA.
    Tawfik, Dan S.
    Weizmann Inst Sci, Dept Biol Chem, Rehovot, Israel.
    Evolution of chalcone isomerase from a noncatalytic ancestor2018Ingår i: Nature Chemical Biology, ISSN 1552-4450, E-ISSN 1552-4469, Vol. 14, nr 6, s. 548-555Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The emergence of catalysis in a noncatalytic protein scaffold is a rare, unexplored event. Chalcone isomerase (CHI), a key enzyme in plant flavonoid biosynthesis, is presumed to have evolved from a nonenzymatic ancestor related to the widely distributed fatty-acid binding proteins (FAPs) and a plant protein family with no isomerase activity (CHILs). Ancestral inference supported the evolution of CHI from a protein lacking isomerase activity. Further, we identified four alternative founder mutations, i.e., mutations that individually instated activity, including a mutation that is not phylogenetically traceable. Despite strong epistasis in other cases of protein evolution, CHI's laboratory reconstructed mutational trajectory shows weak epistasis. Thus, enantioselective CHI activity could readily emerge despite a catalytically inactive starting point. Accordingly, X-ray crystallography, NMR, and molecular dynamics simulations reveal reshaping of the active site toward a productive substratebinding mode and repositioning of the catalytic arginine that was inherited from the ancestral fatty-acid binding proteins.

  • 104.
    Karlsson, Johan
    et al.
    Chalmers, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    Martinelli, Anna
    Chalmers, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    Fathali, Hoda M.
    Chalmers, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    Bielecki, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Andersson, Martin
    Chalmers, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    The effect of alendronate on biomineralization at the bone/implant interface2016Ingår i: Journal of Biomedical Materials Research. Part A, ISSN 1549-3296, E-ISSN 1552-4965, Vol. 104, nr 3, s. 620-629Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A recent approach to improve the osseointegration of implants is to utilize local drug administration. The presence of an osteoporosis drug may influence both bone quantity and quality at the bone/implant interface. Despite this, the performance of bone-anchoring implants is traditionally evaluated only by quantitative measurements. In the present study, the osteoporosis drug alendronate (ALN) was administrated from mesoporous titania thin films that were coated onto titanium implants. The effect that the drug had on biomineralization was explored both in vitro using simulated body fluid (SBF) and in vivo in a rat tibia model. The SBF study showed that the apatite formation was completely hindered at a high concentration of ALN (0.1 mg/mL). However, when ALN was administrated from the mesoporous coating the surface became completely covered with apatite. Ex vivo characterization of the bone/implant interface using Raman spectroscopy demonstrated that the presence of ALN enhanced the bone mineralization, and that the chemical signature of newly formed bone in the presence of ALN had a higher resemblance to the pre-existing mature bone than to the bone formed without drug. Taken together, this study demonstrates the importance of evaluating the quality of the formed bone to better understand the performance of implants.

  • 105. Kassemeyer, Stephan
    et al.
    Steinbrener, Jan
    Lomb, Lukas
    Hartmann, Elisabeth
    Aquila, Andrew
    Barty, Anton
    Martin, Andrew V
    Hampton, Christina Y
    Bajt, Saša
    Barthelmess, Miriam
    Barends, Thomas R M
    Bostedt, Christoph
    Bott, Mario
    Bozek, John D
    Coppola, Nicola
    Cryle, Max
    Deponte, Daniel P
    Doak, R Bruce
    Epp, Sascha W
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hartmann, Andreas
    Hartmann, Robert
    Hauser, Günter
    Hirsemann, Helmut
    Hömke, André
    Holl, Peter
    Jönsson, Olof
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Kimmel, Nils
    Krasniqi, Faton
    Liang, Mengning
    Maia, Filipe R N C
    Marchesini, Stefano
    Nass, Karol
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schmidt, Carlo
    Schulz, Joachim
    Shoeman, Robert L
    Sierra, Raymond G
    Soltau, Heike
    Spence, John C H
    Starodub, Dmitri
    Stellato, Francesco
    Stern, Stephan
    Stier, Gunter
    Svenda, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Weidenspointner, Georg
    Weierstall, Uwe
    White, Thomas A
    Wunderer, Cornelia
    Frank, Matthias
    Chapman, Henry N
    Ullrich, Joachim
    Strüder, Lothar
    Bogan, Michael J
    Schlichting, Ilme
    Femtosecond free-electron laser x-ray diffraction data sets for algorithm development2012Ingår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 20, nr 4, s. 4149-4158Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.

  • 106.
    Kasson, Peter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Univ Virginia, Uppsala, Sweden..
    Simulations and Experiments Show a Mechanistic Role for Influenza Fusion Peptides in Membrane Bending and Fusion Stoichiometry2018Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, nr 3, s. 605A-605AArtikel i tidskrift (Övrigt vetenskapligt)
  • 107.
    Kasson, Peter
    et al.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Univ Virginia, Mol Physiol & Biomed Engn, Charlottesville, VA USA..
    Cortina, George
    Univ Virginia, Mol Physiol & Biomed Engn, Charlottesville, VA USA..
    Latallo, Malgorzata
    Univ Virginia, Mol Physiol & Biomed Engn, Charlottesville, VA USA..
    Understanding allosteric modulation of beta lactamase function and bacterial drug resistance2017Ingår i: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 254Artikel i tidskrift (Övrigt vetenskapligt)
  • 108.
    Kasson, Peter
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Uppsala universitet, Science for Life Laboratory, SciLifeLab. University of Virginia, Charlottesville, United States.
    Jha, Shantenu
    Rutgers University, Piscataway, United States.
    Adaptive ensemble simulations of biomolecules2018Ingår i: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 52, s. 87-94Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of individual simulation trajectories and analyze statistics across them. Adaptive ensemble simulations offer a further level of sophistication and flexibility by enabling high-level algorithms to control simulations-based on intermediate results. We review some of the adaptive ensemble algorithms and software infrastructure currently in use and outline where the complexities of implementing adaptive simulation have limited algorithmic innovation to date. We describe an adaptive ensemble API to overcome some of these barriers and more flexibly and simply express adaptive simulation algorithms to help realize the power of this type of simulation.

  • 109. Kern, Jan
    et al.
    Tran, Rosalie
    Alonso-Mori, Roberto
    Koroidov, Sergey
    Echols, Nathaniel
    Hattne, Johan
    Ibrahim, Mohamed
    Gul, Sheraz
    Laksmono, Hartawan
    Sierra, Raymond G
    Gildea, Richard J
    Han, Guangye
    Hellmich, Julia
    Lassalle-Kaiser, Benedikt
    Chatterjee, Ruchira
    Brewster, Aaron S
    Stan, Claudiu A
    Glöckner, Carina
    Lampe, Alyssa
    DiFiore, Dörte
    Milathianaki, Despina
    Fry, Alan R
    Seibert, M Marvin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Koglin, Jason E
    Gallo, Erik
    Uhlig, Jens
    Sokaras, Dimosthenis
    Weng, Tsu-Chien
    Zwart, Petrus H
    Skinner, David E
    Bogan, Michael J
    Messerschmidt, Marc
    Glatzel, Pieter
    Williams, Garth J
    Boutet, Sébastien
    Adams, Paul D
    Zouni, Athina
    Messinger, Johannes
    Sauter, Nicholas K
    Bergmann, Uwe
    Yano, Junko
    Yachandra, Vittal K
    Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy2014Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, s. 4371-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.

  • 110. Kirian, Richard A.
    et al.
    White, Thomas A.
    Holton, James M.
    Chapman, Henry N.
    Fromme, Petra
    Barty, Anton
    Lomb, Lukas
    Aquila, Andrew
    Maia, Filipe R. N. C.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Martin, Andrew V.
    Fromme, Raimund
    Wang, Xiaoyu
    Hunter, Mark S.
    Schmidt, Kevin E.
    Spence, John C. H.
    Structure-factor analysis of femtosecond micro-diffraction patterns from protein nanocrystals2011Ingår i: Acta Crystallographica Section A: Foundations of Crystallography, ISSN 0108-7673, E-ISSN 1600-5724, Vol. 67, nr 2, s. 131-140Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A complete set of structure factors has been extracted from hundreds of thousands of femtosecond single-shot X-ray microdiffraction patterns taken from randomly oriented nanocrystals. The method of Monte Carlo integration over crystallite size and orientation was applied to experimental data from Photosystem I nanocrystals. This arrives at structure factors from many partial reflections without prior knowledge of the particle-size distribution. The data were collected at the Linac Coherent Light Source (the first hard-X-ray laser user facility), to which was fitted a hydrated protein nanocrystal injector jet, according to the method of serial crystallography. The data are single 'still' diffraction snapshots, each from a different nanocrystal with sizes ranging between 100 nm and 2 mu m, so the angular width of Bragg peaks was dominated by crystal-size effects. These results were compared with single-crystal data recorded from large crystals of Photosystem I at the Advanced Light Source and the quality of the data was found to be similar. The implications for improving the efficiency of data collection by allowing the use of very small crystals, for radiation-damage reduction and for time-resolved diffraction studies at room temperature are discussed.

  • 111.
    Klimesova, Eva
    et al.
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic.
    Kulyk, Olena
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic.
    Gu, Yanjun
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic.
    Dittrich, Laura
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic;Tech Univ Berlin, Inst Opt & Atomare Phys, ER 1-1,Str 17 Juni 135, D-10623 Berlin, Germany.
    Korn, Georg
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic.
    Hajdu, Janos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic.
    Krikunova, Maria
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic;Tech Univ Berlin, Inst Opt & Atomare Phys, ER 1-1,Str 17 Juni 135, D-10623 Berlin, Germany.
    Andreasson, Jakob
    ELI Beamlines, Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic;Chalmers Univ Technol, Dept Phys, Gothenburg, Sweden.
    Plasma channel formation in NIR laser-irradiated carrier gas from an aerosol nanoparticle injector2019Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, artikel-id 8851Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Aerosol nanoparticle injectors are fundamentally important for experiments where container-free sample handling is needed to study isolated nanoparticles. The injector consists of a nebuliser, a differential pumping unit, and an aerodynamic lens to create and deliver a focused particle beam to the interaction point inside a vacuum chamber. The tightest focus of the particle beam is close to the injector tip. The density of the focusing carrier gas is high at this point. We show here how this gas interacts with a near infrared laser pulse (800 nm wavelength, 120 fs pulse duration) at intensities approaching 10(16) Wcm(-2). We observe acceleration of gas ions to kinetic energies of 100s eV and study their energies as a function of the carrier gas density. Our results indicate that field ionisation by the intense near-infrared laser pulse opens up a plasma channel behind the laser pulse. The observations can be understood in terms of a Coulomb explosion of the created underdense plasma channel. The results can be used to estimate gas background in experiments with the injector and they open up opportunities for a new class of studies on electron and ion dynamics in nanoparticles surrounded by a low-density gas.

  • 112. Koopmann, Rudolf
    et al.
    Cupelli, Karolina
    Redecke, Lars
    Nass, Karol
    DePonte, Daniel P
    White, Thomas A
    Stellato, Francesco
    Rehders, Dirk
    Liang, Mengning
    Andreasson, Jakob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Aquila, Andrew
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J
    Bostedt, Christoph
    Boutet, Sebastien
    Bozek, John D
    Caleman, Carl
    Coppola, Nicola
    Davidsson, Jan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi.
    Doak, R Bruce
    Ekeberg, Tomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Epp, Sascha W
    Erk, Benjamin
    Fleckenstein, Holger
    Foucar, Lutz
    Graafsma, Heinz
    Gumprecht, Lars
    Hajdu, Janos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Hampton, Christina Y
    Hartmann, Andreas
    Hartmann, Robert
    Hauser, Gunter
    Hirsemann, Helmut
    Holl, Peter
    Hunter, Mark S
    Kassemeyer, Stephan
    Kirian, Richard A
    Lomb, Lukas
    Maia, Filipe R N C
    Kimmel, Nils
    Martin, Andrew V
    Messerschmidt, Marc
    Reich, Christian
    Rolles, Daniel
    Rudek, Benedikt
    Rudenko, Artem
    Schlichting, Ilme
    Schulz, Joachim
    Seibert, M Marvin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Shoeman, Robert L
    Sierra, Raymond G
    Soltau, Heike
    Stern, Stephan
    Struder, Lothar
    Timneanu, Nicusor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Ullrich, Joachim
    Wang, Xiaoyu
    Weidenspointner, Georg
    Weierstall, Uwe
    Williams, Garth J
    Wunderer, Cornelia B
    Fromme, Petra
    Spence, John C H
    Stehle, Thilo
    Chapman, Henry N
    Betzel, Christian
    Duszenko, Michael
    In vivo protein crystallization opens new routes in structural biology2012Ingår i: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 9, nr 3, s. 259-262Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.

  • 113.
    Krikunova, Maria
    et al.
    Tech Univ Berlin, Inst Opt & Atomare Phys, Str 17 Juni 135,ER 1-1, D-10623 Berlin, Germany..
    Timneanu, Nicusor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    Andreasson, Jakob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Acad Sci Czech Republic, Inst Phys, ELI Beamlines, Na Slovance 2, Prague 18221, Czech Republic.
    Atomic and molecular systems under intense X-ray radiation2016Ingår i: Ultrafast Dynamics Driven by Intense Light Pulses: From Atoms to Solids, from Lasers to Intense X-rays, Switzerland: Springer, 2016, 86, Vol. 86, s. 319-339Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    The review covers recent progress in the development of X-ray pulse metrology essential for experiments at Free Electron Lasers. The scientific section is focused on time-resolved studies of ionization dynamics of atoms, molecules and (bio-)nanoparticles. We discuss the role of ionization dynamics for high resolution imaging of bio-and bio-like nanoparticles and illustrate the potential for multidirectional imaging of unique non-reproducible samples.

  • 114. Kupitz, Christopher
    et al.
    Basu, Shibom
    Grotjohann, Ingo
    Fromme, Raimund
    Zatsepin, Nadia A
    Rendek, Kimberly N
    Hunter, Mark S
    Shoeman, Robert L
    White, Thomas A
    Wang, Dingjie
    James, Daniel
    Yang, Jay-How
    Cobb, Danielle E
    Reeder, Brenda
    Sierra, Raymond G
    Liu, Haiguang
    Barty, Anton
    Aquila, Andrew L
    Deponte, Daniel
    Kirian, Richard A
    Bari, Sadia
    Bergkamp, Jesse J
    Beyerlein, Kenneth R
    Bogan, Michael J
    Caleman, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    Chao, Tzu-Chiao
    Conrad, Chelsie E
    Davis, Katherine M
    Fleckenstein, Holger
    Galli, Lorenzo
    Hau-Riege, Stefan P
    Kassemeyer, Stephan
    Laksmono, Hartawan
    Liang, Mengning
    Lomb, Lukas
    Marchesini, Stefano
    Martin, Andrew V
    Messerschmidt, Marc
    Milathianaki, Despina
    Nass, Karol
    Ros, Alexandra
    Roy-Chowdhury, Shatabdi
    Schmidt, Kevin
    Seibert, Marvin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Steinbrener, Jan
    Stellato, Francesco
    Yan, Lifen
    Yoon, Chunhong
    Moore, Thomas A
    Moore, Ana L
    Pushkar, Yulia
    Williams, Garth J
    Boutet, Sébastien
    Doak, R Bruce
    Weierstall, Uwe
    Frank, Matthias
    Chapman, Henry N
    Spence, John C H
    Fromme, Petra
    Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser2014Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 513, nr 7517, s. 261-265Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.

  • 115.
    Kurimoto, Eiji
    et al.
    Meijo Univ, Fac Pharm, Tempaku Ku, 150 Yagotoyama, Nagoya, Aichi 4688503, Japan..
    Satoh, Tadashi
    Nagoya City Univ, Grad Sch Pharmaceut Sci, Mizuho Ku, Nagoya, Aichi 4678603, Japan.;JST, PRESTO, Mizuho Ku, Nagoya, Aichi 4678603, Japan..
    Ito, Yuri
    Meijo Univ, Fac Pharm, Tempaku Ku, 150 Yagotoyama, Nagoya, Aichi 4688503, Japan..
    Ishihara, Eri
    Meijo Univ, Fac Pharm, Tempaku Ku, 150 Yagotoyama, Nagoya, Aichi 4688503, Japan..
    Okamoto, Kenta
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Nagoya City Univ, Grad Sch Pharmaceut Sci, Mizuho Ku, Nagoya, Aichi 4678603, Japan.
    Yagi-Utsumi, Maho
    Nagoya City Univ, Grad Sch Pharmaceut Sci, Mizuho Ku, Nagoya, Aichi 4678603, Japan.;Natl Inst Nat Sci, Okazaki Inst Integrat Biosci, 5-1 Higashiyama, Okazaki, Aichi 4448787, Japan.;Natl Inst Nat Sci, Inst Mol Sci, 5-1 Higashiyama, Okazaki, Aichi 4448787, Japan..
    Tanaka, Keiji
    Tokyo Metropolitan Inst Med Sci, Lab Prot Metab, Setagaya Ku, Tokyo 1568506, Japan..
    Kato, Koichi
    Nagoya City Univ, Grad Sch Pharmaceut Sci, Mizuho Ku, Nagoya, Aichi 4678603, Japan.;Natl Inst Nat Sci, Okazaki Inst Integrat Biosci, 5-1 Higashiyama, Okazaki, Aichi 4448787, Japan.;Natl Inst Nat Sci, Inst Mol Sci, 5-1 Higashiyama, Okazaki, Aichi 4448787, Japan..
    Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation2017Ingår i: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 26, nr 5, s. 1080-1085Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The 26S proteasome is a large protein complex, responsible for degradation of ubiquinated proteins in eukaryotic cells. Eukaryotic proteasome formation is a highly ordered process that is assisted by several assembly chaperones. The assembly of its catalytic 20S core particle depends on at least five proteasome-specific chaperones, i.e., proteasome-assembling chaperons 1-4 (PAC1-4) and proteasome maturation protein (POMP). The orthologues of yeast assembly chaperones have been structurally characterized, whereas most mammalian assembly chaperones are not. In the present study, we determined a crystal structure of human PAC4 at 1.90-angstrom resolution. Our crystallographic data identify a hydrophobic surface that is surrounded by charged residues. The hydrophobic surface is complementary to that of its binding partner, PAC3. The surface also exhibits charge complementarity with the proteasomal 4-5 subunits. This will provide insights into human proteasome-assembling chaperones as potential anticancer drug targets.

  • 116. Kurta, Ruslan P.
    et al.
    Donatelli, Jeffrey J.
    Yoon, Chun Hong
    Berntsen, Peter
    Bielecki, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Daurer, Benedikt J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    DeMirci, Hasan
    Fromme, Petra
    Hantke, Max Felix
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Maia, Filipe R. N. C.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Munke, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Nettelblad, Carl
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Pande, Kanupriya
    Reddy, Hemanth K. N.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Sellberg, Jonas A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Sierra, Raymond G.
    Svenda, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    van der Schot, Gijs
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Vartanyants, Ivan A.
    Williams, Garth J.
    Xavier Paulraj, Lourdu
    Aquila, Andrew
    Zwart, Peter H.
    Mancuso, Adrian P.
    Correlations in scattered X-ray laser pulses reveal nanoscale structural features of viruses2017Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 119, nr 15, s. 158102:1-7, artikel-id 158102Artikel i tidskrift (Refereegranskat)
  • 117.
    Larsson, Anna M.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Hasse, Dirk
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Valegård, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Andersson, Inger
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Crystal structures of β-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore2017Ingår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, nr 14, s. 3857-3867Artikel i tidskrift (Refereegranskat)
    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.

  • 118.
    Lejon, Sara
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Ellis, Jacqueline
    Valegård, Karin
    The last step in cephalosporin C formation revealed: Crystal Structures of Deacetylcephalosporin C Acetyltransferase from Acremonium chrysogenum in Complexes with Reaction Intermediates2008Ingår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 377, nr 3, s. 935-944Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Deacetylcephalosporin C acetyltransferase (DAC-AT) catalyses the last step in the biosynthesis of cephalosporin C, a broad-spectrum beta-lactam antibiotic of large clinical importance. The acetyl transfer step has been suggested to be limiting for cephalosporin C biosynthesis, but has so far escaped detailed structural analysis. We present here the crystal structures of DAC-AT in complexes with reaction intermediates, providing crystallographic snapshots of the reaction mechanism. The enzyme is found to belong to the alpha/beta hydrolase class of acetyltransferases, and the structures support previous observations of a double displacement mechanism for the acetyl transfer reaction in other members of this class of enzymes. The structures of DAC-AT reported here provide evidence of a stable acyl - enzyme complex, thus underpinning a mechanism involving acetylation of a catalytic serine residue by acetyl coenzyme A, followed by transfer of the acetyl group to deacetylcephalosporin C through a suggested tetrahedral transition state.

  • 119.
    Lejon, Sara
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Ellis, Jacqueline
    Valegård, Karin
    The last step in cephalosporin C formation revealed: Crystal Structures of Deacetylcephalosporin C Acetyltransferase from Acremonium chrysogenum in Complexes with Reaction Intermediates2008Ingår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 377, nr 3, s. 935-944Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Deacetylcephalosporin C acetyltransferase (DAC-AT) catalyses the last step in the biosynthesis of cephalosporin C, a broad-spectrum beta-lactam antibiotic of large clinical importance. The acetyl transfer step has been suggested to be limiting for cephalosporin C biosynthesis, but has so far escaped detailed structural analysis. We present here the crystal structures of DAC-AT in complexes with reaction intermediates, providing crystallographic snapshots of the reaction mechanism. The enzyme is found to belong to the alpha/beta hydrolase class of acetyltransferases, and the structures support previous observations of a double displacement mechanism for the acetyl transfer reaction in other members of this class of enzymes. The structures of DAC-AT reported here provide evidence of a stable acyl - enzyme complex, thus underpinning a mechanism involving acetylation of a catalytic serine residue by acetyl coenzyme A, followed by transfer of the acetyl group to deacetylcephalosporin C through a suggested tetrahedral transition state.

  • 120.
    Lemmens, Liesbeth
    et al.
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Brussels, Belgium.
    Tilleman, Laurentijn
    Univ Ghent, Fac Pharmaceut Sci, Lab Pharmaceut Biotechnol, Ghent, Belgium.
    De Koning, Ezra
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Brussels, Belgium.
    Valegård, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Lindås, Ann-Christin
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, Stockholm, Sweden.
    Van Nieuwerburgh, Filip
    Univ Ghent, Fac Pharmaceut Sci, Lab Pharmaceut Biotechnol, Ghent, Belgium.
    Maes, Dominique
    Vrije Univ Brussel, Dept Bioengn Sci, Struct Biol Brussels, Brussels, Belgium.
    Peeters, Eveline
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Brussels, Belgium.
    YtrASa, a GntR-Family Transcription Factor, Represses Two Genetic Loci Encoding Membrane Proteins in Sulfolobus acidocaldarius2019Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 10, artikel-id 2084Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In bacteria, the GntR family is a widespread family of transcription factors responsible for the regulation of a myriad of biological processes. In contrast, despite their occurrence in archaea only a little information is available on the function of GntR-like transcription factors in this domain of life. The thermoacidophilic crenarchaeon Sulfolobus acidocaldarius harbors a GntR-like regulator belonging to the YtrA subfamily, encoded as the first gene in an operon with a second gene encoding a putative membrane protein. Here, we present a detailed characterization of this regulator, named YtrA(Sa), with a focus on regulon determination and mechanistic analysis with regards to DNA binding. Genome-wide chromatin immunoprecipitation and transcriptome experiments, the latter employing a ytrA(Sa) overexpression strain, demonstrate that the regulator acts as a repressor on a very restricted regulon, consisting of only two targets including the operon encoding its own gene and a distinct genetic locus encoding another putative membrane protein. For both targets, a conserved 14-bp semi-palindromic binding motif was delineated that covers the transcriptional start site and that is surrounded by additional half-site motifs. The crystallographic structure of YtrA(Sa) was determined, revealing a compact dimeric structure in which the DNA-binding motifs are oriented ideally to enable a specific high-affinity interaction with the core binding motif. This study provides new insights into the functioning of a YtrA-like regulator in the archaeal domain of life.

  • 121. Leontowich, Adam F. G.
    et al.
    Aquila, Andrew
    Stellato, Francesco
    Bean, Richard
    Fleckenstein, Holger
    Prasciolu, Mauro
    Liang, Mengning
    DePonte, Daniel P.
    Barty, Anton
    Wang, Fenglin
    Andreasson, Jakob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Hajdu, Janos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Chapman, Henry N.
    Bajt, Sasa
    Characterizing the focus of a multilayer coated off-axis parabola for FLASH beam at lambda = 4.3 nm2013Konferensbidrag (Refereegranskat)
    Abstract [en]

    A super-polished substrate with an off-axis parabola figure was coated with a Sc/B4C/Cr multilayer. This optic was used to focus pulses of 4.3 nm photons from the Free-electron LASer in Hamburg (FLASH) at normal incidence. Beam imprints were made in poly(methyl methacrylate) to align the optic and to measure the beam profile at the focal plane. The intense interaction resulted in imprints with raised perimeters, surrounded by ablated material extending out several micrometres. These features interfere with the beam profile measurement. The effect of a post-exposure development step on the beam imprints was investigated.

  • 122.
    Liao, Qinghua
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Strukturbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Pabis, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Strodel, Birgit
    Forschungszentrum Julich, Julich, Germany; Heinrich Heine Univ Dusseldorf, Dusseldorf, Germany.
    Kamerlin, Shina Caroline Lynn
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Strukturbiologi.
    Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions2017Ingår i: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 8, nr 21, s. 5408-5414Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Modeling metalloproteins often requires classical molecular dynamics (MD) simulations in order to capture their relevant motions, which in turn necessitates reliable descriptions of the metal centers involved. One of the most successful approaches to date is provided by the "cationic dummy model", where the positive charge of the metal ion is transferred toward dummy particles that are bonded to the central metal ion in a predefined coordination geometry. While this approach allows for ligand exchange, and captures the correct electrostatics as demonstrated for different divalent metal ions, current dummy models neglect ion-induced dipole interactions. In the present work, we resolve this weakness by taking advantage of the recently introduced 12-6-4 type Lennard-Jones potential to include ion-induced dipole interactions. We revise our previous dummy model for Mg2+ and demonstrate that the resulting model can simultaneously reproduce the experimental solvation free energy and metal ligand distances without the need for artificial restraints or bonds. As ion-induced dipole interactions become particularly important for highly charged metal ions, we develop dummy models for the biologically relevant ions Al3+, Fe3+, and Cr3+. Finally, the effectiveness of our new models is demonstrated in MD simulations of several diverse (and highly challenging to simulate) metalloproteins.

  • 123. Lindas, Ann-Christin
    et al.
    Chruszcz, Maksymilian
    Bernander, Rolf
    Valegård, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Structure of crenactin, an archaeal actin homologue active at 90 degrees C2014Ingår i: Acta Crystallographica Section D: Biological Crystallography, ISSN 0907-4449, E-ISSN 1399-0047, Vol. 70, s. 492-500Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The crystal structure of the archaeal actin, crenactin, from the rod-shaped hyperthermophilic (optimal growth at 90 degrees C) crenarchaeon Pyrobaculum calidifontis is reported at 3.35 angstrom resolution. Despite low amino-acid sequence identity, the three-dimensional structure of the protein monomer is highly similar to those of eukaryotic actin and the bacterial MreB protein. Crenactin-specific features are also evident, as well as elements that are shared between crenactin and eukaryotic actin but are not found in MreB. In the crystal, crenactin monomers form right-handed helices, demonstrating that the protein is capable of forming filament-like structures. Monomer interactions in the helix, as well as interactions between crenactin and ADP in the nucleotide-binding pocket, are resolved at the atomic level and compared with those of actin and MreB. The results provide insights into the structural and functional properties of a heat-stable archaeal actin and contribute to the understanding of the evolution of actin-family proteins in the three domains of life.

  • 124. Liu, Wei
    et al.
    Wacker, Daniel
    Gati, Cornelius
    Han, Gye Won
    James, Daniel
    Wang, Dingjie
    Nelson, Garrett
    Weierstall, Uwe
    Katritch, Vsevolod
    Barty, Anton
    Zatsepin, Nadia A.
    Li, Dianfan
    Messerschmidt, Marc
    Boutet, Sebastien
    Williams, Garth J.
    Koglin, Jason E.
    Seibert, M. Marvin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Wang, Chong
    Shah, Syed T. A.
    Basu, Shibom
    Fromme, Raimund
    Kupitz, Christopher
    Rendek, Kimberley N.
    Grotjohann, Ingo
    Fromme, Petra
    Kirian, Richard A.
    Beyerlein, Kenneth R.
    White, Thomas A.
    Chapman, Henry N.
    Caffrey, Martin
    Spence, John C. H.
    Stevens, Raymond C.
    Cherezov, Vadim
    Serial Femtosecond Crystallography of G Protein-Coupled Receptors2013Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 342, nr 6165, s. 1521-1524Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    X-ray crystallography of G protein-coupled receptors and other membrane proteins is hampered by difficulties associated with growing sufficiently large crystals that withstand radiation damage and yield high-resolution data at synchrotron sources. We used an x-ray free-electron laser (XFEL) with individual 50-femtosecond-duration x-ray pulses to minimize radiation damage and obtained a high-resolution room-temperature structure of a human serotonin receptor using sub-10-micrometer microcrystals grown in a membrane mimetic matrix known as lipidic cubic phase. Compared with the structure solved by using traditional microcrystallography from cryo-cooled crystals of about two orders of magnitude larger volume, the room-temperature XFEL structure displays a distinct distribution of thermal motions and conformations of residues that likely more accurately represent the receptor structure and dynamics in a cellular environment.

  • 125. Loh, N. D.
    et al.
    Bogan, M. J.
    Elser, V.
    Barty, A.
    Boutet, S.
    Bajt, S.
    Hajdu, Janos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Ekeberg, Tomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Maia, Filipe R. N. C.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Schulz, J.
    Seibert, Marvin Marvin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Iwan, Bianca
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Timneanu, Nicusor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Marchesini, S.
    Schlichting, I.
    Shoeman, R. L.
    Lomb, L.
    Frank, M.
    Liang, M.
    Chapman, H. N.
    Cryptotomography: Reconstructing 3D Fourier Intensities from Randomly Oriented Single-Shot Diffraction Patterns2010Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 104, nr 22, s. 225501-1-225501-5Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We reconstructed the 3D Fourier intensity distribution of monodisperse prolate nanoparticles using single-shot 2D coherent diffraction patterns collected at DESY's FLASH facility when a bright, coherent, ultrafast x-ray pulse intercepted individual particles of random, unmeasured orientations. This first experimental demonstration of cryptotomography extended the expansion-maximization-compression framework to accommodate unmeasured fluctuations in photon fluence and loss of data due to saturation or background scatter. This work is an important step towards realizing single-shot diffraction imaging of single biomolecules.

  • 126. Loh, N. D.
    et al.
    Hampton, C. Y.
    Martin, A. V.
    Starodub, D.
    Sierra, R. G.
    Barty, A.
    Aquila, A.
    Schulz, J.
    Lomb, L.
    Steinbrener, J.
    Shoeman, R. L.
    Kassemeyer, S.
    Bostedt, C.
    Bozek, J.
    Epp, S. W.
    Erk, B.
    Hartmann, R.
    Rolles, D.
    Rudenko, A.
    Rudek, B.
    Foucar, L.
    Kimmel, N.
    Weidenspointner, G.
    Hauser, G.
    Holl, P.
    Pedersoli, E.
    Liang, M.
    Hunter, M. M.
    Gumprecht, L.
    Coppola, N.
    Wunderer, C.
    Graafsma, H.
    Maia, F. R. N. C.
    Ekeberg, Tomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Hantke, Max
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Fleckenstein, H.
    Hirsemann, H.
    Nass, K.
    White, T. A.
    Tobias, H. J.
    Farquar, G. R.
    Benner, W. H.
    Hau-Riege, S. P.
    Reich, C.
    Hartmann, A.
    Soltau, H.
    Marchesini, S.
    Bajt, S.
    Barthelmess, M.
    Bucksbaum, P.
    Hodgson, K. O.
    Strueder, L.
    Ullrich, J.
    Frank, M.
    Schlichting, I.
    Chapman, H. N.
    Bogan, M. J.
    Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight2012Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 486, nr 7404, s. 513-517Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology(1) to climate science(2), yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate(3); visible light scattering provides insufficient resolution(4); and X-ray synchrotron studies have been limited to ensembles of particles(5). Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source(6) free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins(7), vibrational energy transfer by the hydrodynamic interaction of amino acids(8), and large-scale production of nanoscale structures by flame synthesis(9).

  • 127. Loh, N. Duane
    et al.
    Starodub, Dmitri
    Lomb, Lukas
    Hampton, Christina Y.
    Martin, Andrew V.
    Sierra, Raymond G.
    Barty, Anton
    Aquila, Andrew
    Schulz, Joachim
    Steinbrener, Jan
    Shoeman, Robert L.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Hantke, Max Felix
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Fleckenstein, Holger
    Hirsemann, Helmut
    Nass, Karol
    White, Thomas A.
    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.
    Sensing the wavefront of x-ray free-electron lasers using aerosol spheres2013Ingår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 21, nr 10, s. 12385-12394Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 1021 W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.

  • 128. Lomb, Lukas
    et al.
    Barends, Thomas R. M.
    Kassemeyer, Stephan
    Aquila, Andrew
    Epp, Sascha W.
    Erk, Benjamin
    Foucar, Lutz
    Hartmann, Robert
    Rudek, Benedikt
    Rolles, Daniel
    Rudenko, Artem
    Shoeman, Robert L.
    Andreasson, Jakob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Bogan, Michael J.
    Bostedt, Christoph
    Bozek, John D.
    Caleman, Carl
    Coffee, Ryan
    Coppola, Nicola
    DePonte, Daniel P.
    Doak, R. Bruce
    Ekeberg, Tomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Fleckenstein, Holger
    Fromme, Petra
    Gebhardt, Maike
    Graafsma, Heinz
    Gumprecht, Lars
    Hampton, Christina Y.
    Hartmann, Andreas
    Hauser, Guenter