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Arnlund D, Johansson LC, Wickstrand C, Barty A, Williams GJ, Malmerberg E, Davidsson J, Milathianaki D, DePonte DP, Shoeman RL, Wang D, James D, Katona G, Westenhoff S, White TA, Aquila A, Bari S, Berntsen P, Bogan M, van Driel TB, Doak RB, Kjær KS, Frank M, Fromme R, Grotjohann I, Henning R, Hunter MS, Kirian RA, Kosheleva I, Kupitz C, Liang M, Martin AV, Nielsen MM, Messerschmidt M, Seibert MM, Sjöhamn J, Stellato F, Weierstall U, Zatsepin NA, Spence JCH, Fromme P, Schlichting I, Boutet S, Groenhof G, Chapman HN, Neutze R. Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser. Nat Methods 2014; 11:923-6. [PMID: 25108686 DOI: 10.1038/nmeth.3067] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 07/09/2014] [Indexed: 01/07/2023]
Abstract
We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.
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Siefermann KR, Pemmaraju CD, Neppl S, Shavorskiy A, Cordones AA, Vura-Weis J, Slaughter DS, Sturm FP, Weise F, Bluhm H, Strader ML, Cho H, Lin MF, Bacellar C, Khurmi C, Guo J, Coslovich G, Robinson JS, Kaindl RA, Schoenlein RW, Belkacem A, Neumark DM, Leone SR, Nordlund D, Ogasawara H, Krupin O, Turner JJ, Schlotter WF, Holmes MR, Messerschmidt M, Minitti MP, Gul S, Zhang JZ, Huse N, Prendergast D, Gessner O. Atomic-Scale Perspective of Ultrafast Charge Transfer at a Dye-Semiconductor Interface. J Phys Chem Lett 2014; 5:2753-9. [PMID: 26277975 DOI: 10.1021/jz501264x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Understanding interfacial charge-transfer processes on the atomic level is crucial to support the rational design of energy-challenge relevant systems such as solar cells, batteries, and photocatalysts. A femtosecond time-resolved core-level photoelectron spectroscopy study is performed that probes the electronic structure of the interface between ruthenium-based N3 dye molecules and ZnO nanocrystals within the first picosecond after photoexcitation and from the unique perspective of the Ru reporter atom at the center of the dye. A transient chemical shift of the Ru 3d inner-shell photolines by (2.3 ± 0.2) eV to higher binding energies is observed 500 fs after photoexcitation of the dye. The experimental results are interpreted with the aid of ab initio calculations using constrained density functional theory. Strong indications for the formation of an interfacial charge-transfer state are presented, providing direct insight into a transient electronic configuration that may limit the efficiency of photoinduced free charge-carrier generation.
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Messerschmidt M, Chavas L, Ananthaneni S, Dadgostar H, Graafsma H, Liang M, Mancuso A, Raabe S, Stern S, Vagovic P, Chapman H. Serial Femtosecond Crystallography user's consortium apparatus at European XFEL. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314082515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The Serial Femtosecond Crystallography (SFX) user's consortium apparatus is to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument of the European X-ray Free-Electron Laser facility (XFEL.EU) [1, 2]. The XFEL.EU will provide ultra-short, highly intense, coherent X-ray pulses at an unprecedented repetition rate. The experimental setup and methodological approaches of many scientific areas will be transformed, including structural biology that could potentially overcome common problems and bottlenecks encountered in crystallography, such as creating large crystals, dealing with radiation damage, or understanding sub-picosecond time-resolved phenomena. The key concept of the SFX method is based on the kinetic insertion of protein crystal samples in solution via a gas dynamic virtual nozzle jet and recording diffraction signals of individual, randomly oriented crystals passing through the XFEL beam, as first demonstrated by Chapman et al. [3]. The SFX-apparatus will refocus the beam spent by the SPB instrument into a second interaction region, in some cases enabling two parallel experiments. The planned photon energy range at the SPB instrument is from 3 to 16 keV. The Adaptive Gain Integrating Pixel Detector (AGIPD) is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX-apparatus. The AGIPD is designed to store over 350 data frames from successive pulses, and aims to collect more than 3,000 images per second. Together with the implementation of automated procedures for sample exchange and injection, high-throughput nanocrystallography experiments can be integrated at the SFX-apparatus. In this work, we review the overall design of the SFX-apparatus and discuss the main parameters and challenges
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Passon D, Jakobi A, Stellato F, Liang M, Knoops K, Komadina D, Williams C, White T, Bourenkov G, Messerschmidt M, van der Klei I, Chapman H, Wilmanns M. Serial femtosecond X-ray diffraction of in vivo crystals in intact yeast cells. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314094297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Peroxisomes are membrane-enclosed organelles in eukaryotic cells with important roles in lipid metabolism and the scavenging of reactive oxygen species. Peroxisomes are capable of carrying an unusually high load of proteins, which under appropriate nutrient conditions results in the in situ crystallization of peroxisomal proteins in several yeast species and vertebrate hepatocytes [1,2]. In the methylotrophic yeast H.polymorpha, the predominant peroxisomal protein alcohol/methanol oxidase (AO) oligomerizes into octameric assemblies with a molecular mass of 600 kDa that spontaneously form 200-500 nm crystallites within peroxisomes [1]. We exposed H.polymorpha cell suspensions containing peroxisome-confined AO crystallites to femtosecond X-ray pulses at the Coherent X-ray Imaging (CXI) experimental endstation at the Linac Coherent Light Source. Peak detection routines mining the resulting scattering profiles identified >5000 Bragg-sampled diffraction patterns, providing the proof of concept that background scattering from the cells does not deteriorate the signal-to-noise ratio to an extent precluding observation of diffraction from individual AO crystallites. Summation patterns assembled from the individual frames match low-resolution powder diffraction patterns from concentrated suspensions of purified peroxisomes collected at the P14 beamline at the PETRAIII synchrotron, confirming that the observed diffraction mainly results from Bragg scattering of peroxisomal crystallites. To the best of our knowledge our data are the first to report room temperature X-ray diffraction from functional protein crystals in their native cellular environment. Currently the maximum resolution achieved in the diffraction patterns is limited to 20-15 Å. Future work will need to address improved sample preparation protocols in order to assess whether diffraction to a resolution sufficient to permit structure solution can be obtained. Protein crystal formation in vivo has been observed under physiological or pathological conditions in a number of other systems [3]. We hope that our results will help to establish serial femtosecond X-ray diffraction (SFX) as a method for structural characterization of cellular structures with crystalline content and provide a proof of concept for using in situ crystallization of proteins as a means to generate nanocrystalline samples for SFX.
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Barends T, Foucar L, Botha S, Doak RB, Shoeman R, Nass K, Koglin J, Williams G, Boutet S, Messerschmidt M, Schlichting I. De novo phasing of protein crystallography data from a free-electron laser. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314094315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Free-electron lasers (FELs) are pushing back the limits of possibility in protein crystallography. Using the high-intensity, femtosecond duration pulses afforded by FELs allow data collection from micrometer-sized crystals while outrunning radiation damage. Moreover, FELs may be used for pump-probe experiments with unprecedented time resolution. However, the intricacies of FEL data collection pose specific challenges: as every FEL pulse destroys the sample, data are mostly collected from a stream of microcrystals and averaged to remove the variations in crystal size and quality as well as shot-to-shot variations in beam parameters. This technique is called serial femtosecond crystallography (SFX). In SFX, several tens of thousands of images typically need to be averaged to obtain reasonably accurate structure factor amplitudes. We previously showed that SFX yields structure factor amplitudes accurate enough to detect the weak anomalous signal of endogenous sulfur atoms. Now we show that SFX can be used to collect data accurate enough for de-novo phasing of a protein structure[1]. Using a model system (gadolinium-derivatized lysozyme) we collected ~60,000 diffraction images and obtained structure factor amplitudes that allowed phasing by single-wavelength anomalous diffraction. This first demonstration of de novo phasing from FEL data leads us to anticipate that FEL-based crystallography will become an important tool for the structure determination of proteins that are extremely radiation sensitive or that are difficult to crystallize, such as membrane proteins.
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Bionta MR, Hartmann N, Weaver M, French D, Nicholson DJ, Cryan JP, Glownia JM, Baker K, Bostedt C, Chollet M, Ding Y, Fritz DM, Fry AR, Kane DJ, Krzywinski J, Lemke HT, Messerschmidt M, Schorb S, Zhu D, White WE, Coffee RN. Spectral encoding method for measuring the relative arrival time between x-ray/optical pulses. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:083116. [PMID: 25173255 DOI: 10.1063/1.4893657] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The advent of few femtosecond x-ray light sources brings promise of x-ray/optical pump-probe experiments that can measure chemical and structural changes in the 10-100 fs time regime. Widely distributed timing systems used at x-ray Free-Electron Laser facilities are typically limited to above 50 fs fwhm jitter in active x-ray/optical synchronization. The approach of single-shot timing measurements is used to sort results in the event processing stage. This has seen wide use to accommodate the insufficient precision of active stabilization schemes. In this article, we review the current technique for "measure-and-sort" at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The relative arrival time between an x-ray pulse and an optical pulse is measured near the experimental interaction region as a spectrally encoded cross-correlation signal. The cross-correlation provides a time-stamp for filter-and-sort algorithms used for real-time sorting. Sub-10 fs rms resolution is common in this technique, placing timing precision at the same scale as the duration of the shortest achievable x-ray pulses.
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Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glöckner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat Commun 2014; 5:4371. [PMID: 25006873 PMCID: PMC4151126 DOI: 10.1038/ncomms5371] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/10/2014] [Indexed: 01/07/2023] Open
Abstract
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.
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Johansson LC, Arnlund D, Katona G, White TA, Barty A, DePonte DP, Shoeman RL, Wickstrand C, Sharma A, Williams GJ, Aquila A, Bogan MJ, Caleman C, Davidsson J, Doak RB, Frank M, Fromme R, Galli L, Grotjohann I, Hunter MS, Kassemeyer S, Kirian RA, Kupitz C, Liang M, Lomb L, Malmerberg E, Martin AV, Messerschmidt M, Nass K, Redecke L, Seibert MM, Sjöhamn J, Steinbrener J, Stellato F, Wang D, Wahlgren WY, Weierstall U, Westenhoff S, Zatsepin NA, Boutet S, Spence JCH, Schlichting I, Chapman HN, Fromme P, Neutze R. Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography. Nat Commun 2014; 4:2911. [PMID: 24352554 PMCID: PMC3905732 DOI: 10.1038/ncomms3911] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/08/2013] [Indexed: 11/22/2022] Open
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 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure. Serial femtosecond crystallography is an X-ray free-electron-laser-based method that uses X-ray bursts to determine protein structures. Here the authors present the structure of a photosynthetic reaction centre, an integral membrane protein, achieved with no sign of X-ray-induced radiation damage.
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Zhu D, Feng Y, Stoupin S, Terentyev SA, Lemke HT, Fritz DM, Chollet M, Glownia JM, Alonso-Mori R, Sikorski M, Song S, van Driel TB, Williams GJ, Messerschmidt M, Boutet S, Blank VD, Shvyd'ko YV, Robert A. Performance of a beam-multiplexing diamond crystal monochromator at the Linac Coherent Light Source. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:063106. [PMID: 24985798 DOI: 10.1063/1.4880724] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
A double-crystal diamond monochromator was recently implemented at the Linac Coherent Light Source. It enables splitting pulses generated by the free electron laser in the hard x-ray regime and thus allows the simultaneous operations of two instruments. Both monochromator crystals are High-Pressure High-Temperature grown type-IIa diamond crystal plates with the (111) orientation. The first crystal has a thickness of ~100 μm to allow high reflectivity within the Bragg bandwidth and good transmission for the other wavelengths for downstream use. The second crystal is about 300 μm thick and makes the exit beam of the monochromator parallel to the incoming beam with an offset of 600 mm. Here we present details on the monochromator design and its performance.
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Carini GA, Boutet S, Chollet M, Dragone A, Haller G, Hart PA, Herrmann SC, Kenney CJ, Koglin J, Messerschmidt M, Nelson S, Pines J, Robert A, Song S, Thayer JB, Williams GJ, Zhu D. Experience with the CSPAD during dedicated detector runs at LCLS. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/1742-6596/493/1/012011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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61
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Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams PD, Sauter NK. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nat Methods 2014; 11:545-8. [PMID: 24633409 DOI: 10.1038/nmeth.2887] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 02/04/2014] [Indexed: 01/19/2023]
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.
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Szlachetko J, Milne CJ, Hoszowska J, Dousse JC, Błachucki W, Sà J, Kayser Y, Messerschmidt M, Abela R, Boutet S, David C, Williams G, Pajek M, Patterson BD, Smolentsev G, van Bokhoven JA, Nachtegaal M. Communication: The electronic structure of matter probed with a single femtosecond hard x-ray pulse. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2014; 1:021101. [PMID: 26798772 PMCID: PMC4711597 DOI: 10.1063/1.4868260] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 02/28/2014] [Indexed: 05/11/2023]
Abstract
Physical, biological, and chemical transformations are initiated by changes in the electronic configuration of the species involved. These electronic changes occur on the timescales of attoseconds (10(-18) s) to femtoseconds (10(-15) s) and drive all subsequent electronic reorganization as the system moves to a new equilibrium or quasi-equilibrium state. The ability to detect the dynamics of these electronic changes is crucial for understanding the potential energy surfaces upon which chemical and biological reactions take place. Here, we report on the determination of the electronic structure of matter using a single self-seeded femtosecond x-ray pulse from the Linac Coherent Light Source hard x-ray free electron laser. By measuring the high energy resolution off-resonant spectrum (HEROS), we were able to obtain information about the electronic density of states with a single femtosecond x-ray pulse. We show that the unoccupied electronic states of the scattering atom may be determined on a shot-to-shot basis and that the measured spectral shape is independent of the large intensity fluctuations of the incoming x-ray beam. Moreover, we demonstrate the chemical sensitivity and single-shot capability and limitations of HEROS, which enables the technique to track the electronic structural dynamics in matter on femtosecond time scales, making it an ideal probe technique for time-resolved X-ray experiments.
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63
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Frank M, Carlson DB, Hunter MS, Williams GJ, Messerschmidt M, Zatsepin NA, Barty A, Benner WH, Chu K, Graf AT, Hau-Riege SP, Kirian RA, Padeste C, Pardini T, Pedrini B, Segelke B, Seibert MM, Spence JCH, Tsai CJ, Lane SM, Li XD, Schertler G, Boutet S, Coleman M, Evans JE. Femtosecond X-ray diffraction from two-dimensional protein crystals. IUCRJ 2014; 1:95-100. [PMID: 25075325 PMCID: PMC4062087 DOI: 10.1107/s2052252514001444] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/21/2014] [Indexed: 05/19/2023]
Abstract
X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.
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Liu W, Wacker D, Gati C, Han GW, James D, Wang D, Nelson G, Weierstall U, Katritch V, Barty A, Zatsepin NA, Li D, Messerschmidt M, Boutet S, Williams GJ, Koglin JE, Seibert MM, Wang C, Shah ST, Basu S, Fromme R, Kupitz C, Rendek KN, Grotjohann I, Fromme P, Kirian RA, Beyerlein KR, White TA, Chapman HN, Caffrey M, Spence JC, Stevens RC, Cherezov V. Serial femtosecond crystallography of G protein-coupled receptors. Science 2013; 342:1521-4. [PMID: 24357322 PMCID: PMC3902108 DOI: 10.1126/science.1244142] [Citation(s) in RCA: 331] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
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.
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Milathianaki D, Boutet S, Williams GJ, Higginbotham A, Ratner D, Gleason AE, Messerschmidt M, Seibert MM, Swift DC, Hering P, Robinson J, White WE, Wark JS. Femtosecond Visualization of Lattice Dynamics in Shock-Compressed Matter. Science 2013; 342:220-3. [DOI: 10.1126/science.1239566] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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66
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Demirci H, Sierra RG, Laksmono H, Shoeman RL, Botha S, Barends TRM, Nass K, Schlichting I, Doak RB, Gati C, Williams GJ, Boutet S, Messerschmidt M, Jogl G, Dahlberg AE, Gregory ST, Bogan MJ. Serial femtosecond X-ray diffraction of 30S ribosomal subunit microcrystals in liquid suspension at ambient temperature using an X-ray free-electron laser. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1066-9. [PMID: 23989164 PMCID: PMC3758164 DOI: 10.1107/s174430911302099x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/27/2013] [Indexed: 12/03/2022]
Abstract
High-resolution ribosome structures determined by X-ray crystallography have provided important insights into the mechanism of translation. Such studies have thus far relied on large ribosome crystals kept at cryogenic temperatures to reduce radiation damage. Here, the application of serial femtosecond X-ray crystallography (SFX) using an X-ray free-electron laser (XFEL) to obtain diffraction data from ribosome microcrystals in liquid suspension at ambient temperature is described. 30S ribosomal subunit microcrystals diffracted to beyond 6 Å resolution, demonstrating the feasibility of using SFX for ribosome structural studies. The ability to collect diffraction data at near-physiological temperatures promises to provide fundamental insights into the structural dynamics of the ribosome and its functional complexes.
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Frasinski LJ, Zhaunerchyk V, Mucke M, Squibb RJ, Siano M, Eland JHD, Linusson P, v d Meulen P, Salén P, Thomas RD, Larsson M, Foucar L, Ullrich J, Motomura K, Mondal S, Ueda K, Osipov T, Fang L, Murphy BF, Berrah N, Bostedt C, Bozek JD, Schorb S, Messerschmidt M, Glownia JM, Cryan JP, Coffee RN, Takahashi O, Wada S, Piancastelli MN, Richter R, Prince KC, Feifel R. Dynamics of hollow atom formation in intense x-ray pulses probed by partial covariance mapping. PHYSICAL REVIEW LETTERS 2013; 111:073002. [PMID: 23992061 DOI: 10.1103/physrevlett.111.073002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Indexed: 05/23/2023]
Abstract
When exposed to ultraintense x-radiation sources such as free electron lasers (FELs) the innermost electronic shell can efficiently be emptied, creating a transient hollow atom or molecule. Understanding the femtosecond dynamics of such systems is fundamental to achieving atomic resolution in flash diffraction imaging of noncrystallized complex biological samples. We demonstrate the capacity of a correlation method called "partial covariance mapping" to probe the electron dynamics of neon atoms exposed to intense 8 fs pulses of 1062 eV photons. A complete picture of ionization processes competing in hollow atom formation and decay is visualized with unprecedented ease and the map reveals hitherto unobserved nonlinear sequences of photoionization and Auger events. The technique is particularly well suited to the high counting rate inherent in FEL experiments.
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68
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Clark JN, Beitra L, Xiong G, Higginbotham A, Fritz DM, Lemke HT, Zhu D, Chollet M, Williams GJ, Messerschmidt M, Abbey B, Harder RJ, Korsunsky AM, Wark JS, Robinson IK. Ultrafast three-dimensional imaging of lattice dynamics in individual gold nanocrystals. Science 2013; 341:56-9. [PMID: 23704372 DOI: 10.1126/science.1236034] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Key insights into the behavior of materials can be gained by observing their structure as they undergo lattice distortion. Laser pulses on the femtosecond time scale can be used to induce disorder in a "pump-probe" experiment with the ensuing transients being probed stroboscopically with femtosecond pulses of visible light, x-rays, or electrons. Here we report three-dimensional imaging of the generation and subsequent evolution of coherent acoustic phonons on the picosecond time scale within a single gold nanocrystal by means of an x-ray free-electron laser, providing insights into the physics of this phenomenon. Our results allow comparison and confirmation of predictive models based on continuum elasticity theory and molecular dynamics simulations.
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Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J. Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science 2013; 340:491-5. [PMID: 23413188 PMCID: PMC3732582 DOI: 10.1126/science.1234273] [Citation(s) in RCA: 334] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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 (S1) and the first illuminated state (S2) 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.
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70
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Graves CE, Reid AH, Wang T, Wu B, de Jong S, Vahaplar K, Radu I, Bernstein DP, Messerschmidt M, Müller L, Coffee R, Bionta M, Epp SW, Hartmann R, Kimmel N, Hauser G, Hartmann A, Holl P, Gorke H, Mentink JH, Tsukamoto A, Fognini A, Turner JJ, Schlotter WF, Rolles D, Soltau H, Strüder L, Acremann Y, Kimel AV, Kirilyuk A, Rasing T, Stöhr J, Scherz AO, Dürr HA. Nanoscale spin reversal by non-local angular momentum transfer following ultrafast laser excitation in ferrimagnetic GdFeCo. NATURE MATERIALS 2013; 12:293-8. [PMID: 23503010 DOI: 10.1038/nmat3597] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 02/07/2012] [Indexed: 05/19/2023]
Abstract
Ultrafast laser techniques have revealed extraordinary spin dynamics in magnetic materials that equilibrium descriptions of magnetism cannot explain. Particularly important for future applications is understanding non-equilibrium spin dynamics following laser excitation on the nanoscale, yet the limited spatial resolution of optical laser techniques has impeded such nanoscale studies. Here we present ultrafast diffraction experiments with an X-ray laser that probes the nanoscale spin dynamics following optical laser excitation in the ferrimagnetic alloy GdFeCo, which exhibits macroscopic all-optical switching. Our study reveals that GdFeCo displays nanoscale chemical and magnetic inhomogeneities that affect the spin dynamics. In particular, we observe Gd spin reversal in Gd-rich nanoregions within the first picosecond driven by the non-local transfer of angular momentum from larger adjacent Fe-rich nanoregions. These results suggest that a magnetic material's microstructure can be engineered to control transient laser-excited spins, potentially allowing faster (~ 1 ps) spin reversal than in present technologies.
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71
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Lutman AA, Coffee R, Ding Y, Huang Z, Krzywinski J, Maxwell T, Messerschmidt M, Nuhn HD. Experimental demonstration of femtosecond two-color x-ray free-electron lasers. PHYSICAL REVIEW LETTERS 2013; 110:134801. [PMID: 23581326 DOI: 10.1103/physrevlett.110.134801] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Indexed: 05/23/2023]
Abstract
With an eye toward extending optical wave-mixing techniques to the x-ray regime, we present the first experimental demonstration of a two-color x-ray free-electron laser at the Linac Coherent Light Source. We combine the emittance-spoiler technique with a magnetic chicane in the undulator section to control the pulse duration and relative delay between two intense x-ray pulses and we use differently tuned canted pole undulators such that the two pulses have different wavelengths as well. Two schemes are shown to produce two-color soft x-ray pulses with a wavelength separation up to ∼1.9% and a controllable relative delay up to 40 fs.
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72
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Erk B, Rolles D, Foucar L, Rudek B, Epp SW, Cryle M, Bostedt C, Schorb S, Bozek J, Rouzee A, Hundertmark A, Marchenko T, Simon M, Filsinger F, Christensen L, De S, Trippel S, Küpper J, Stapelfeldt H, Wada S, Ueda K, Swiggers M, Messerschmidt M, Schröter CD, Moshammer R, Schlichting I, Ullrich J, Rudenko A. Ultrafast charge rearrangement and nuclear dynamics upon inner-shell multiple ionization of small polyatomic molecules. PHYSICAL REVIEW LETTERS 2013; 110:053003. [PMID: 23414017 DOI: 10.1088/0953-4075/46/16/164031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Indexed: 05/23/2023]
Abstract
Ionization and fragmentation of methylselenol (CH(3)SeH) molecules by intense (>10(17) W/cm(2)) 5 fs x-ray pulses (ħω=2 keV) are studied by coincident ion momentum spectroscopy. We contrast the measured charge state distribution with data on atomic Kr, determine kinetic energies of resulting ionic fragments, and compare them to the outcome of a Coulomb explosion model. We find signatures of ultrafast charge redistribution from the inner-shell ionized Se atom to its molecular partners, and observe significant displacement of the atomic constituents in the course of multiple ionization.
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73
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Erk B, Rolles D, Foucar L, Rudek B, Epp SW, Cryle M, Bostedt C, Schorb S, Bozek J, Rouzee A, Hundertmark A, Marchenko T, Simon M, Filsinger F, Christensen L, De S, Trippel S, Küpper J, Stapelfeldt H, Wada S, Ueda K, Swiggers M, Messerschmidt M, Schröter CD, Moshammer R, Schlichting I, Ullrich J, Rudenko A. Ultrafast charge rearrangement and nuclear dynamics upon inner-shell multiple ionization of small polyatomic molecules. PHYSICAL REVIEW LETTERS 2013; 110:053003. [PMID: 23414017 DOI: 10.1103/physrevlett.110.053003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Indexed: 05/11/2023]
Abstract
Ionization and fragmentation of methylselenol (CH(3)SeH) molecules by intense (>10(17) W/cm(2)) 5 fs x-ray pulses (ħω=2 keV) are studied by coincident ion momentum spectroscopy. We contrast the measured charge state distribution with data on atomic Kr, determine kinetic energies of resulting ionic fragments, and compare them to the outcome of a Coulomb explosion model. We find signatures of ultrafast charge redistribution from the inner-shell ionized Se atom to its molecular partners, and observe significant displacement of the atomic constituents in the course of multiple ionization.
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74
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Redecke L, Nass K, DePonte DP, White TA, Rehders D, Barty A, Stellato F, Liang M, Barends TR, Boutet S, Williams GJ, Messerschmidt M, Seibert MM, Aquila A, Arnlund D, Bajt S, Barth T, Bogan MJ, Caleman C, Chao TC, Doak RB, Fleckenstein H, Frank M, Fromme R, Galli L, Grotjohann I, Hunter MS, Johansson LC, Kassemeyer S, Katona G, Kirian RA, Koopmann R, Kupitz C, Lomb L, Martin AV, Mogk S, Neutze R, Shoeman RL, Steinbrener J, Timneanu N, Wang D, Weierstall U, Zatsepin NA, Spence JCH, Fromme P, Schlichting I, Duszenko M, Betzel C, Chapman HN. Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Science 2013; 339:227-230. [PMID: 23196907 PMCID: PMC3786669 DOI: 10.1126/science.1229663] [Citation(s) in RCA: 356] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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.
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Juhra C, Wieskötter B, Chu K, Trost L, Weiss U, Messerschmidt M, Malczyk A, Heckwolf M, Raschke M. Bicycle accidents - do we only see the tip of the iceberg? A prospective multi-centre study in a large German city combining medical and police data. Injury 2012; 43:2026-34. [PMID: 22105099 DOI: 10.1016/j.injury.2011.10.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 09/30/2011] [Accepted: 10/16/2011] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Bicycles are becoming increasingly popular. In Münster, a German town with a population of 273,000, bicycles were the main method of transportation in 2009, used more often (37.8%) than cars (36.4%). Each day in Münster, bicycles are used around 450,000 times. In 1982, they were only used around 270,000 times a day. However, the increased use of bicycles has also led to an increased number of bicycle accidents. METHODS Between February 2009 and January 2010, data on bicycle-accidents leading to injuries were collected by the Police of Münster and in all emergency units of the six hospitals in Münster. A systematic acquisition of technical data from the police and the medical data from the hospitals were combined anonymously. None of the forms contained personal data of patients involved, except for patient age and sex as well as time and place of bicycle accidents to match the questionnaires. The data were entered into a central database (MS Access for input/MySQL for data retrieval). RESULTS 2250 patients were included in this study. For each of these patients either a patient record or a hospital record or a police record or a combination of any of these different records existed in our database. In total, 1767 patients received medical treatment at a hospital and 484 people included in the study did not go to a hospital. Three fatalities occurred as a result of bicycle accidents. Considering reasons for hospital admission, traumatic brain injuries were the leading cause (25.7%). However, the largest resource consumption was attributed to fractures of the upper extremities (36.8%) and lower extremities (29.9%) with major surgery. DISCUSSION Bicycle accidents occur more frequently than indicated by police records. The results of the Münster Bicycle Study have shown that the actual number of bicycle accidents exceeds the officially reported number by nearly two times. Since bicycle helmets cannot prevent accidents it is recommended not only to focus on helmet use as the only injury prevention method. Other factors, such as weather, pavement and default of traffic, roadworthiness of the bicycles or alcohol/drug abuse also affect the accident rates.
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