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1.	Alonso-Mori, Roberto, et al. (author) Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode 2012 In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:47, s. 19103-19107 Journal article (peer-reviewed)abstract The ultrabright femtosecond X-ray pulses provided by X-ray free-electron lasers open capabilities for studying the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. Recently, this probe-before-destroy approach has been demonstrated for atomic structure determination by serial X-ray diffraction of microcrystals. There has been the question whether a similar approach can be extended to probe the local electronic structure by X-ray spectroscopy. To address this, we have carried out femtosecond X-ray emission spectroscopy (XES) at the Linac Coherent Light Source using redox-active Mn complexes. XES probes the charge and spin states as well as the ligand environment, critical for understanding the functional role of redox-active metal sites. K beta(1,3) XES spectra of Mn-II and Mn-2(III,IV) complexes at room temperature were collected using a wavelength dispersive spectrometer and femtosecond X-ray pulses with an individual dose of up to > 100 MGy. The spectra were found in agreement with undamaged spectra collected at low dose using synchrotron radiation. Our results demonstrate that the intact electronic structure of redox active transition metal compounds in different oxidation states can be characterized with this shot-by-shot method. This opens the door for studying the chemical dynamics of metal catalytic sites by following reactions under functional conditions. The technique can be combined with X-ray diffraction to simultaneously obtain the geometric structure of the overall protein and the local chemistry of active metal sites and is expected to prove valuable for understanding the mechanism of important metalloproteins, such as photosystem II.
2.	Hattne, Johan, et al. (author) Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers 2014 In: Nature Methods. - 1548-7091 .- 1548-7105. ; 11:5, s. 545-548 Journal article (peer-reviewed)abstract X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
3.	Hattne, Johan, et al. (author) Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers 2014 In: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 11:5, s. 545-548 Journal article (peer-reviewed)abstract X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
4.	Kern, Jan, et al. (author) Room temperature femtosecond X-ray diffraction of photosystem II microcrystals 2012 In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:25, s. 9721-9726 Journal article (peer-reviewed)abstract Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This lightdriven, four-photon reaction is catalyzed by the Mn4CaO5 cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (<50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the probe before destroy approach using an X-ray free electron laser works even for the highly-sensitive Mn4CaO5 cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn4CaO5 cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.
5.	Kern, Jan, et al. (author) Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature 2013 In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 340:6131, s. 491-495 Journal article (peer-reviewed)abstract Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S-1) and the first illuminated state (S-2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.
6.	Pedersoli, Emanuele, et al. (author) Multipurpose modular experimental station for the DiProI beamline of Fermi@Elettra free electron laser 2011 In: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 82:4, s. 043711- Journal article (peer-reviewed)abstract 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.
7.	Kern, Jan, et al. (author) Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy 2014 In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4371- Journal article (peer-reviewed)abstract The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O-2 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 mu s 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 mu s 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 angstrom. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.
8.	Koopmann, Rudolf, et al. (author) In vivo protein crystallization opens new routes in structural biology 2012 In: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 9:3, s. 259-262 Journal article (peer-reviewed)abstract 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.
9.	Kupitz, Christopher, et al. (author) Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser 2014 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 513:7517, s. 261-265 Journal article (peer-reviewed)abstract 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.
10.	Mitzner, Rolf, et al. (author) L-Edge X-ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X-ray Free-Electron Laser 2013 In: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 4:21, s. 3641-3647 Journal article (peer-reviewed)abstract L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming 0 K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.
11.	Redecke, Lars, et al. (author) Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. 2013 In: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 339:6116, s. 227-30 Journal article (peer-reviewed)abstract The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.
12.	Sierra, Raymond G., et al. (author) Nanoflow electrospinning serial femtosecond crystallography 2012 In: Acta Crystallographica Section D. - : Wiley-Blackwell. - 0907-4449 .- 1399-0047. ; 68, s. 1584-1587 Journal article (peer-reviewed)abstract An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14-3.1 mu l min(-1) to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 mu l min(-1) and diffracted to beyond 4 angstrom resolution, producing 14 000 indexable diffraction patterns, or four per second, from 140 mu g of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.
13.	Aquila, Andrew, et al. (author) Time-resolved protein nanocrystallography using an X-ray free-electron laser 2012 In: Optics Express. - 1094-4087. ; 20:3, s. 2706-2716 Journal article (peer-reviewed)abstract We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
14.	Chapman, Henry N, et al. (author) Femtosecond X-ray protein nanocrystallography. 2011 In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 470:7332, s. 73-7 Journal article (peer-reviewed)abstract X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200nm to 2μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
15.	Johansson, Linda C, 1983, et al. (author) Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. 2013 In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4 Journal article (peer-reviewed)abstract Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8Å resolution and determine its serial femtosecond crystallography structure to 3.5Å resolution. Although every microcrystal is exposed to a dose of 33MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.
16.	Loh, N. Duane, et al. (author) Sensing the wavefront of x-ray free-electron lasers using aerosol spheres 2013 In: Optics Express. - 1094-4087. ; 21:10, s. 12385-12394 Journal article (peer-reviewed)abstract 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.
17.	Park, Hyung Joo, et al. (author) Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers 2013 In: Optics Express. - 1094-4087. ; 21:23, s. 28729-28742 Journal article (peer-reviewed)abstract 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.
18.	Bogan, Michael J., et al. (author) Aerosol Imaging with a Soft X-Ray Free Electron Laser 2010 In: Aerosol Science and Technology. - : Informa UK Limited. - 0278-6826 .- 1521-7388. ; 44:3, s. I-VI Journal article (peer-reviewed)abstract Lasers have long played a critical role in the advancement of aerosol science. A new regime of ultrafast laser technology has recently be realized, the world's first soft x-ray free electron laser. The Free electron LASer in Hamburg, FLASH, user facility produces a steady source of 10 femtosecond pulses of 7–32 nm x-rays with 1012 photons per pulse. The high brightness, short wavelength, and high repetition rate (> 500 pulses per second) of this laser offers unique capabilities for aerosol characterization. Here we use FLASH to perform the highest resolution imaging of single PM2.5 aerosol particles in flight to date. We resolve to 35 nm the morphology of fibrous and aggregated spherical carbonaceous nanoparticles that existed for less than two milliseconds in vacuum. Our result opens the possibility for high spatial- and time-resolved single particle aerosol dynamics studies, filling a critical technological need in aerosol science.
19.	Hau-Riege, Stefan P., et al. (author) Sacrificial Tamper Slows Down Sample Explosion in FLASH Diffraction Experiments 2010 In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 104:6, s. 064801- Journal article (peer-reviewed)abstract Intense and ultrashort x-ray pulses from free-electron lasers open up the possibility for near-atomic resolution imaging without the need for crystallization. Such experiments require high photon fluences and pulses shorter than the time to destroy the sample. We describe results with a new femtosecond pump-probe diffraction technique employing coherent 0.1 keV x rays from the FLASH soft x-ray free-electron laser. We show that the lifetime of a nanostructured sample can be extended to several picoseconds by a tamper layer to dampen and quench the sample explosion, making <1 nm resolution imaging feasible.
20.	Johansson, Linda C, 1983, et al. (author) Lipidic phase membrane protein serial femtosecond crystallography. 2012 In: Nature methods. - : Springer Science and Business Media LLC. - 1548-7105 .- 1548-7091. ; 9:3, s. 263-265 Journal article (peer-reviewed)abstract X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.
21.	Kassemeyer, Stephan, et al. (author) Femtosecond free-electron laser x-ray diffraction data sets for algorithm development 2012 In: Optics Express. - 1094-4087. ; 20:4, s. 4149-4158 Journal article (peer-reviewed)abstract 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.
22.	Lomb, Lukas, et al. (author) Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser 2011 In: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 84:21, s. 214111-1-214111-6 Journal article (peer-reviewed)abstract X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.
23.	Schreck, Simon, et al. (author) Reabsorption of Soft X-Ray Emission at High X-Ray Free-Electron Laser Fluences 2014 In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 113:15, s. 153002- Journal article (peer-reviewed)abstract We report on oxygen K-edge soft x-ray emission spectroscopy from a liquid water jet at the Linac Coherent Light Source. We observe significant changes in the spectral content when tuning over a wide range of incident x-ray fluences. In addition the total emission yield decreases at high fluences. These modifications result from reabsorption of x-ray emission by valence-excited molecules generated by the Auger cascade. Our observations have major implications for future x-ray emission studies at intense x-ray sources. We highlight the importance of the x-ray pulse length with respect to the core-hole lifetime.
24.	Seibert, M. Marvin, et al. (author) Femtosecond diffractive imaging of biological cells 2010 In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 43:19, s. 194015- Journal article (peer-reviewed)abstract In a flash diffraction experiment, a short and extremely intense x-ray pulse illuminates the sample to obtain a diffraction pattern before the onset of significant radiation damage. The over-sampled diffraction pattern permits phase retrieval by iterative phasing methods. Flash diffractive imaging was first demonstrated on an inorganic test object (Chapman et al 2006 Nat. Phys. 2 839-43). We report here experiments on biological systems where individual cells were imaged, using single, 10-15 fs soft x-ray pulses at 13.5 nm wavelength from the FLASH free-electron laser in Hamburg. Simulations show that the pulse heated the sample to about 160 000 K but not before an interpretable diffraction pattern could be obtained. The reconstructed projection images return the structures of the intact cells. The simulations suggest that the average displacement of ions and atoms in the hottest surface layers remained below 3 angstrom during the pulse.
25.	Seibert, M. Marvin, et al. (author) Single mimivirus particles intercepted and imaged with an X-ray laser 2011 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 470:7332, s. 78-81 Journal article (peer-reviewed)abstract X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions(1-4). Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma(1). The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval(2). Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a noncrystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source(5). Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.

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