Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway.

Contact sensitizer 2,4-dinitrochlorobenzene is a highly potent human TRPA1 agonist

2,4-Dinitrochlorobenzene (DNCB) is widely used in human clinical studies and in experimental animal studies to evoke allergic contact dermatitis. 2,4-Dinitrochlorobenzene is a potent immunogen capable of inducing contact sensitization in all humans exposed. However, the mechanism by which DNCB evokes such symptoms is presently unknown. TRPA1 is a nonselective cation channel that is expressed in peptidergic sensory neurons and fibroblasts. TRPA1 activation was recently implicated in the pathophysiology of atopic dermatitis especially in transducing cutaneous itch signals. Here, we test the hypothesis that DNCB acts as a TRPA1 agonist and thereby evokes allergic symptoms. We found that DNCB activates human TRPA1 dose dependently in FLIPR experiments with an EC50 of 167 nM, an effect that was fully blocked by selective TRPA1 antagonists Chembridge-5861528 and A-967079. Similarly, DNCB activated nonselective TRPA1 current in patch clamp studies. Neutralization of 3 critical cysteines in TRPA1 resulted in a loss of DNCB agonism.

Serial Femtosecond Crystallography user's consortium apparatus at European XFEL

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

Serial femtosecond X-ray diffraction of in vivo crystals in intact yeast cells

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.

Serial crystallography using synchrotron radiation - novel strategies for microcrystallography

Protein crystallography continues to be one of the most frequently used techniques to obtain structural information of biomacromolecules to atomic resolution. Since protein crystals of delicate target systems are often limited in size, one of the main goals in the design of modern beamlines is the construction of highly intense X-ray beams with small focal size to obtain high resolution diffraction images of microcrystals. However, this development has led to the situation, that the full intensity of the beam can destroy a protein crystal within fractions of a second. Therefore often only a small number of diffraction patterns can be obtained from one single crystal. Here we describe the adaptation of the serial crystallography approach, which has first been developed at X-ray Free-Electron Lasers (Chapman et al. 2011) to the usage of a microfocus synchrotron beamline, using a standard cryogenic loop for sample delivery. We proved this concept with in vivo grown cathepsinB microcrystals (TbCatB, Koopmann et al. 2012, Redecke et al. 2013) (average of 9 μm3), a medically and pharmaceutically relevant protein, involved in the life cycle of T. brucei. In these experiments it was possible to show that serial crystallography enables the utilization and outcome of the above described bottlenecks and features of modern 3rd generation synchrotron microfocus beamlines. Our strategy exploits the combination of a micron-sized X-ray beam, high precision diffractometry and shutterless data acquisition with a pixel-array detector. By combining the data of 80 TbCatB crystals, it was possible to assemble a dataset to 3.0 Å resolution. The data allow the refinement of a structural model that is consistent with that previously obtained using FEL radiation, providing mutual validation.

AGIPD detector for Serial Femtosecond Crystallography Apparatus at European XFEL

The European X-ray Free-Electron Laser (XFEL.EU) [1] will provide ultra-short, highly-intense, coherent x-ray pulses at an unprecedented repetition rate, transforming experiments in many scientific areas, including serial femtosecond crystallography (SFX). For the purpose of SFX experiments at the XFEL.EU, a dedicated endstation is being developed to be installed within the Single Particles, Clusters and Biomolecules (SPB) instrument [2]. The setup will refocus the beam spent by SPB into a second interaction region, thereby enabling two parallel experiments. In order to overcome various challenges in XFEL crystallography, and to optimize the output for SFX experiments at XFEL.EU, the Adaptive Gain Integrating Pixel Detector (AGIPD) [3] is currently under development and is to be implemented in the SPB instrument, including a 4 Megapixel version for the SFX apparatus. The AGIPD is a hybrid-pixel detector with pixels of 200 x 200 micron^2 each. The gain of each single pixel dynamically and independently adapts to the incoming signal. Thus, diffraction patterns of high dynamic range can be recorded, with the measured signal within a single data frame ranging from single photons and up to 1e+4 photons at 12 keV. Moreover, the AGIPD is designed to store over 350 data frames from successive pulses prior to digitization and read-out, thereby enabling operation at the European XFEL with its challenging repetition rate with 10 Hz pulse trains and a 4.5 MHz intra-train repetition rate. Furthermore, the incorporation of a veto system in AGIPD will allow one to potentially store only the frames that contain diffraction data from actual crystal hits, which ultimately increases the efficiency of the detector and DAQ systems dramatically. In the present work, we will review the design of the 4Mpix AGIPD for the SFX apparatus and discuss simulations and tests of its expected performance under the conditions foreseen for SFX experiments at the XFEL.EU.

Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data

The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.

Source apportionment of heavy metals and ionic contaminants in rainwater tanks in a subtropical urban area in Australia

Due to prolonged droughts in recent years, the use of rainwater tanks in urban areas has increased in Australia. In order to apportion sources of contribution to heavy metal and ionic contaminants in rainwater tanks in Brisbane, a subtropical urban area in Australia, monthly tank water samples (24 sites, 31 tanks) and concurrent bulk deposition samples (18 sites) were collected during mainly April 2007-March 2008. The samples were analysed for acid-soluble metals, soluble anions, total inorganic carbon and total organic carbon, and characteristics such as total solid and pH. The Positive Matrix Factorisation model, EPA PMF 3.0, was used to apportion sources of contribution to the contaminants. Four source factors were identified for the bulk deposition samples, including 'crustal matter/sea salt', 'car exhausts/road side dust', 'industrial dust' and 'aged sea salt/secondary aerosols'. For the tank water samples, apart from these atmospheric deposition related factors which contributed in total to 65% of the total contaminant concentration on average, another six rainwater collection system related factors were identified, including 'plumbing', 'building material', 'galvanizing', 'roofing', 'steel' and 'lead flashing/paint' (contributing in total to 35% of the total concentration on average). The Australian Drinking Water Guideline for lead was exceeded in 15% of the tank water samples. The collection system related factors, in particular the 'lead flashing/paint' factor, contributed to 79% of the lead in the tank water samples on average. The concentration of lead in tank water was found to vary with various environmental and collection system factors, in particular the presence of lead flashing on the roof. The results also indicated the important role of sludge dynamics inside the tank on the quality of tank water.

Short-pulse Laser Induced Transient Structure Formation and Ablation Studied with Time-resolved Coherent XUV-scattering

The structural dynamics of short-pulse laser irradiated surfaces and nano-structures has been studied with nm spatial and ultrafast temporal resolution by means of single-shot coherent XUV-scattering techniques. The experiments allowed us to time-resolve the formation of laser-induced periodic surface structures, and to follow the expansion and disintegration of nano-objects during laser ablation.

Soft x-ray free electron laser microfocus for exploring matter under extreme conditions

We have focused a beam (BL3) of FLASH (Free-electron LASer in Hamburg: lambda = 13.5 nm, pulse length 15 fs, pulse energy 10-40 microJ, 5 Hz) using a fine polished off-axis parabola having a focal length of 270 mm and coated with a Mo/Si multilayer with an initial reflectivity of 67% at 13.5 nm. The OAP was mounted and aligned with a picomotor controlled six-axis gimbal. Beam imprints on poly(methyl methacrylate) - PMMA were used to measure focus and the focused beam was used to create isochoric heating of various slab targets. Results show the focal spot has a diameter of < or =1 microm. Observations were correlated with simulations of best focus to provide further relevant information.