| 1. |
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
- Cryan, J P, et al.
(author)
-
Molecular frame Auger electron energy spectrum from N2
- 2012
-
In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 45:5, s. 055601-
-
Journal article (peer-reviewed)abstract
- Here we present the first angle-resolved, non-resonant (normal) Auger spectra for impulsively aligned nitrogen molecules. We have measured the angular pattern of Auger electron emission following K -shell photoionization by 1.1 keV photons from the Linac Coherent Light Source (LCLS). Using strong-field-induced molecular alignment to make molecular frame measurements is equally effective for both repulsive and quasi-bound final states. The capability to resolve Auger emission angular distributions in the molecular frame of reference provides a new tool for spectral assignments in congested Auger electron spectra that takes advantage of the symmetries of the final diction states. Based on our experimental results and theoretical predictions, we propose the assignment of the spectral features in the Auger electron spectrum.
|
|
| 5. |
- Fuchs, M.a b, et al.
(author)
-
Nonlinear X-ray compton scattering
- 2014
-
Conference paper (other academic/artistic)abstract
- We use XFEL pulses to observe the most fundamental nonlinear X-ray-matter interaction: nonlinear Compton scattering. In contrast to theoretical predictions, we measure an anonymous and yet to be explained red-shift in the observed photon energy.
|
|
| 6. |
- Nass, K., et al.
(author)
-
In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors
- 2020
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
-
Journal article (peer-reviewed)abstract
- Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5'-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 angstrom resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds. Trypanosoma brucei inosine-5 '-monophosphate dehydrogenase (IMPDH) is an enzyme in the guanine nucleotide biosynthesis pathway and of interest as a drug target. Here the authors present the 2.8 angstrom room temperature structure of TbIMPDH determined by utilizing X-ray free-electron laser radiation and crystals that were grown in insect cells and find that ATP and GMP are bound at the canonical sites of the Bateman domains.
|
|
| 7. |
- Hajkova, V., et al.
(author)
-
X-ray laser-induced ablation of lead compounds
- 2011
-
In: DAMAGE TO VUV, EUV, AND X-RAY OPTICS III. - : SPIE.
-
Conference paper (peer-reviewed)abstract
- The recent commissioning of a X-ray free-electron laser triggered an extensive research in the area of X-ray ablation of high-Z, high-density materials. Such compounds should be used to shorten an effective attenuation length for obtaining clean ablation imprints required for the focused beam analysis. Compounds of lead (Z=82) represent the materials of first choice. In this contribution, single-shot ablation thresholds are reported for PbWO(4) and PbI(2) exposed to ultra-short pulses of extreme ultraviolet radiation and X-rays at FLASH and LCLS facilities, respectively. Interestingly, the threshold reaches only 0.11 J/cm(2) at 1.55 nm in lead tungstate although a value of 0.4 J/cm(2) is expected according to the wavelength dependence of an attenuation length and the threshold value determined in the XUV spectral region, i.e., 79 mJ/cm(2) at a FEL wavelength of 13.5 nm. Mechanisms of ablation processes are discussed to explain this discrepancy. Lead iodide shows at 1.55 nm significantly lower ablation threshold than tungstate although an attenuation length of the radiation is in both materials quite the same. Lower thermal and radiation stability of PbI(2) is responsible for this finding.
|
|
| 8. |
- Echelmeier, A., et al.
(author)
-
Segmented flow generator for serial crystallography at the European X-ray free electron laser
- 2020
-
In: Nature Communications. - : Nature Research. - 2041-1723. ; 11:1
-
Journal article (peer-reviewed)abstract
- Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.
|
|
| 9. |
- Rolles, D., et al.
(author)
-
Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules
- 2014
-
In: Journal of Physics B: Atomic, Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 47:12
-
Journal article (peer-reviewed)abstract
- We present time-resolved femtosecond photoelectron momentum images and angular distributions of dissociating, laser-aligned 1,4-dibromobenzene (C6H4Br2) molecules measured in a near-infrared pump, soft-x-ray probe experiment performed at an x-ray free-electron laser. The observed alignment dependence of the bromine 2p photoelectron angular distributions is compared to density functional theory calculations and interpreted in terms of photoelectron diffraction. While no clear time-dependent effects are observed in the angular distribution of the Br(2p) photoelectrons, other, low-energy electrons show a pronounced dependence on the time delay between the near-infrared laser and the x-ray pulse.
|
|
| 10. |
- Frasinski, L. J., et al.
(author)
-
Dynamics of Hollow Atom Formation in Intense X-Ray Pulses Probed by Partial Covariance Mapping
- 2013
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 111:7, s. 073002-
-
Journal article (peer-reviewed)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.
|
|
| 11. |
- Mucke, Melanie, et al.
(author)
-
Covariance mapping of two-photon double core hole states in C2H2 and C2H6 produced by an x-ray free electron laser
- 2015
-
In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 17
-
Journal article (peer-reviewed)abstract
- Few-photon ionization and relaxation processes in acetylene (C2H2) and ethane (C2H6) were investigated at the linac coherent light source x-ray free electron laser (FEL) at SLAC, Stanford using a highly efficient multi-particle correlation spectroscopy technique based on a magnetic bottle. The analysis method of covariance mapping has been applied and enhanced, allowing us to identify electron pairs associated with double core hole (DCH) production and competing multiple ionization processes including Auger decay sequences. The experimental technique and the analysis procedure are discussed in the light of earlier investigations of DCH studies carried out at the same FEL and at third generation synchrotron radiation sources. In particular, we demonstrate the capability of the covariance mapping technique to disentangle the formation of molecular DCH states which is barely feasible with conventional electron spectroscopy methods.
|
|
| 12. |
|
|
| 13. |
- Thomas, H., et al.
(author)
-
Explosions of Xenon Clusters in Ultraintense Femtosecond X-Ray Pulses from the LCLS Free Electron Laser
- 2012
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 108:13
-
Journal article (peer-reviewed)abstract
- Explosions of large Xe clusters (< N > similar to 11 000) irradiated by femtosecond pulses of 850 eV x-ray photons focused to an intensity of up to 1017 W/cm(2) from the Linac Coherent Light Source were investigated experimentally. Measurements of ion charge-state distributions and energy spectra exhibit strong evidence for the formation of a Xe nanoplasma in the intense x-ray pulse. This x-ray produced Xe nanoplasma is accompanied by a three-body recombination and hydrodynamic expansion. These experimental results appear to be consistent with a model in which a spherically exploding nanoplasma is formed inside the Xe cluster and where the plasma temperature is determined by photoionization heating.
|
|
| 14. |
- Zhaunerchyk, Vitali, et al.
(author)
-
Using covariance mapping to investigate the dynamics of multi-photon ionization processes of Ne atoms exposed to X-FEL pulses
- 2013
-
In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 46:16, s. 164034-
-
Journal article (peer-reviewed)abstract
- We report on a detailed investigation into the electron emission processes of Ne atoms exposed to intense femtosecond x-ray pulses, provided by the Linac Coherent Light Source Free Electron Laser (FEL) at Stanford. The covariance mapping technique is applied to analyse the data, and the capability of this approach to disentangle both linear and nonlinear correlation features which may be hidden on coincidence maps of the same data set is demonstrated. Different correction techniques which enable improvements on the quality of the spectral features extracted from the covariance maps are explored. Finally, a method for deriving characteristics of the x-ray FEL pulses based on covariance mapping in combination with model simulations is presented.
|
|
| 15. |
|
|
| 16. |
- Frank, Matthias, et al.
(author)
-
Femtosecond X-ray diffraction from two-dimensional protein crystals
- 2014
-
In: IUCrJ. - 2052-2525. ; 1:2, s. 95-100
-
Journal article (peer-reviewed)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.
|
|
| 17. |
- Laksmono, Hartawan, et al.
(author)
-
Anomalous Behavior of the Homogeneous Ice Nucleation Rate in No-Man's Land
- 2015
-
In: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 6:14, s. 2826-2832
-
Journal article (peer-reviewed)abstract
- We present an analysis of ice nucleation kinetics from near-ambient pressure water as temperature decreases below the homogeneous limit T-H by cooling micrometer-sized droplets (microdroplets) evaporatively at 10(3)-10(4) K/s and probing the structure ultrafast using femtosecond pulses from the Linac Coherent Light Source (LCLS) free-electron X-ray laser. Below 232 K, we observed a slower nucleation rate increase with decreasing temperature than anticipated from previous measurements, which we suggest is due to the rapid decrease in water's diffusivity. This is consistent with earlier findings that microdroplets do not crystallize at <227 K, but vitrify at cooling rates of 10(6)-10(7) K/s. We also hypothesize that the slower increase in the nucleation rate is connected with the proposed fragile-to-strong transition anomaly in water.
|
|
| 18. |
- Milathianaki, D., et al.
(author)
-
Femtosecond Visualization of Lattice Dynamics in Shock-Compressed Matter
- 2013
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 342:6155, s. 220-223
-
Journal article (peer-reviewed)abstract
- The ultrafast evolution of microstructure is key to understanding high-pressure and strain-rate phenomena. However, the visualization of lattice dynamics at scales commensurate with those of atomistic simulations has been challenging. Here, we report femtosecond x-ray diffraction measurements unveiling the response of copper to laser shock-compression at peak normal elastic stresses of similar to 73 gigapascals (GPa) and strain rates of 10(9) per second. We capture the evolution of the lattice from a one-dimensional (1D) elastic to a 3D plastically relaxed state within a few tens of picoseconds, after reaching shear stresses of 18 GPa. Our in situ high-precision measurement of material strength at spatial (<1 micrometer) and temporal (<50 picoseconds) scales provides a direct comparison with multimillion-atom molecular dynamics simulations.
|
|
| 19. |
- Ryan, Rebecca A., et al.
(author)
-
Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene
- 2017
-
In: Journal of Visualized Experiments. - : MyJove Corporation. - 1940-087X. ; :126
-
Journal article (peer-reviewed)abstract
- The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C-60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C-60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.
|
|
| 20. |
- Aricescu, A R, et al.
(author)
-
Eukaryotic expression: developments for structural proteomics.
- 2006
-
In: Acta Crystallographica Section D: Biological Crystallography. - 1399-0047 .- 0907-4449. ; 62, s. 1114-1124
-
Journal article (peer-reviewed)abstract
- The production of sufficient quantities of protein is an essential prelude to a structure determination, but for many viral and human proteins this cannot be achieved using prokaryotic expression systems. Groups in the Structural Proteomics In Europe (SPINE) consortium have developed and implemented high-throughput (HTP) methodologies for cloning, expression screening and protein production in eukaryotic systems. Studies focused on three systems: yeast (Pichia pastoris and Saccharomyces cerevisiae), baculovirus-infected insect cells and transient expression in mammalian cells. Suitable vectors for HTP cloning are described and results from their use in expression screening and protein-production pipelines are reported. Strategies for co-expression, selenomethionine labelling (in all three eukaryotic systems) and control of glycosylation (for secreted proteins in mammalian cells) are assessed.
|
|
| 21. |
- Boll, Rebecca, et al.
(author)
-
Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules
- 2014
-
In: Faraday Discussions. - : Royal Society of Chemistry (RSC). - 1364-5498. ; 171, s. 57-80
-
Journal article (peer-reviewed)abstract
- This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C8H5F) and dissociating, laser-aligned 1,4-dibromobenzene (C6H4Br2) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.
|
|
| 22. |
- Brändén, Gisela, 1975, et al.
(author)
-
Coherent diffractive imaging of microtubules using an X-ray laser.
- 2019
-
In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
-
Journal article (peer-reviewed)abstract
- X-ray free electron lasers (XFELs) create new possibilities for structural studies of biological objects that extend beyond what is possible with synchrotron radiation. Serial femtosecond crystallography has allowed high-resolution structures to be determined from micro-meter sized crystals, whereas single particle coherent X-ray imaging requires development to extend the resolution beyond a few tens of nanometers. Here we describe an intermediate approach: the XFEL imaging of biological assemblies with helical symmetry. We collected X-ray scattering images from samples of microtubules injected across an XFEL beam using a liquid microjet, sorted these images into class averages, merged these data into a diffraction pattern extending to 2nm resolution, and reconstructed these data into a projection image of the microtubule. Details such as the 4nm tubulin monomer became visible in this reconstruction. These results illustrate the potential of single-molecule X-ray imaging of biological assembles with helical symmetry at room temperature.
|
|
| 23. |
- Ekeberg, Tomas, et al.
(author)
-
Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
- 2016
-
In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
-
Journal article (peer-reviewed)abstract
- Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.
|
|
| 24. |
- 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.
|
|
| 25. |
- 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.
|
|
| 26. |
- Hunter, Mark S, et al.
(author)
-
Fixed-target protein serial microcrystallography with an x-ray free electron laser.
- 2014
-
In: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4, s. 6026-
-
Journal article (peer-reviewed)abstract
- We present results from experiments at the Linac Coherent Light Source (LCLS) demonstrating that serial femtosecond crystallography (SFX) can be performed to high resolution (~2.5 Å) using protein microcrystals deposited on an ultra-thin silicon nitride membrane and embedded in a preservation medium at room temperature. Data can be acquired at a high acquisition rate using x-ray free electron laser sources to overcome radiation damage, while sample consumption is dramatically reduced compared to flowing jet methods. We achieved a peak data acquisition rate of 10 Hz with a hit rate of ~38%, indicating that a complete data set could be acquired in about one 12-hour LCLS shift using the setup described here, or in even less time using hardware optimized for fixed target SFX. This demonstration opens the door to ultra low sample consumption SFX using the technique of diffraction-before-destruction on proteins that exist in only small quantities and/or do not produce the copious quantities of microcrystals required for flowing jet methods.
|
|
| 27. |
- 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.
|
|
| 28. |
- 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.
|
|
| 29. |
- 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.
|
|
| 30. |
- Liu, Wei, et al.
(author)
-
Serial Femtosecond Crystallography of G Protein-Coupled Receptors
- 2013
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 342:6165, s. 1521-1524
-
Journal article (peer-reviewed)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.
|
|
| 31. |
- Malkoch, Michael, et al.
(author)
-
Orthogonal approaches to the simultaneous and cascade functionalization of macromolecules using click chemistry
- 2005
-
In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 127:42, s. 14942-14949
-
Journal article (peer-reviewed)abstract
- The development of selective chemistries that are orthogonal to the diverse array of functional groups present in many polymeric systems is becoming an important tool for the synthesis and use of macromolecules in fields ranging from biomedical devices to nanotechnology. By combining copper-catalyzed cycloaddition chemistry with other synthetic transformations such as esterification, amidation, etc., highly efficient and modular simultaneous and cascade functionalization strategies have been developed. These single-step strategies for preparing multifunctional macromolecules represent a significant advance as compared to traditional multistep approaches, and the utility of these concepts is demonstrated by selective preparation of a diverse range of orthogonally functionalized vinyl polymers.
|
|
| 32. |
- Nass, Karol, et al.
(author)
-
Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
- 2015
-
In: Journal of Synchrotron Radiation. - 0909-0495 .- 1600-5775. ; 22:2, s. 225-238
-
Journal article (peer-reviewed)abstract
- 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.
|
|
| 33. |
- Popp, David, et al.
(author)
-
Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser
- 2017
-
In: CYTOSKELETON. - : WILEY. - 1949-3584 .- 1949-3592. ; 74:12, s. 472-481
-
Journal article (peer-reviewed)abstract
- A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked -strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual -synuclein amyloids.
|
|
| 34. |
- 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.
|
|
| 35. |
- Stern, S., et al.
(author)
-
Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers
- 2014
-
In: Faraday Discussions. - : Royal Society of Chemistry (RSC). - 1364-5498. ; 171, s. 393-418
-
Journal article (peer-reviewed)abstract
- We give a detailed account of the theoretical analysis and the experimental results of an X-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gasphase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Coherent Light Source [Phys. Rev. Lett. 112, 083002 (2014)]. This experiment is the first step toward coherent diffractive imaging of structures and structural dynamics of isolated molecules at atomic resolution, i.e., picometers and femtoseconds, using X-ray free-electron lasers.
|
|
| 36. |
- Weierstall, Uwe, et al.
(author)
-
Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography
- 2014
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 3309-
-
Journal article (peer-reviewed)abstract
- Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for serial femtosecond crystallography. Data collected from sub-10-mu m-sized crystals produced with less than 0.5 mg of purified protein yield structural insights regarding cyclopamine binding to the Smoothened receptor.
|
|
