Online dynamic flat-field correction for MHz microscopy data at European XFEL.

The high pulse intensity and repetition rate of the European X-ray Free-Electron Laser (EuXFEL) provide superior temporal resolution compared with other X-ray sources. In combination with MHz X-ray microscopy techniques, it offers a unique opportunity to achieve superior contrast and spatial resolution in applications demanding high temporal resolution. In both live visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of X-ray free-electron laser sources hinders the use of standard flat-field normalization methods during MHz X-ray microscopy experiments. Here, an online (i.e. near real-time) dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images is presented. The method is used for the normalization of individual X-ray projections and has been implemented as a near real-time analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.

XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates.

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.

A multi-million image Serial Femtosecond Crystallography dataset collected at the European XFEL.

Serial femtosecond crystallography is a rapidly developing method for determining the structure of biomolecules for samples which have proven challenging with conventional X-ray crystallography, such as for membrane proteins and microcrystals, or for time-resolved studies. The European XFEL, the first high repetition rate hard X-ray free electron laser, provides the ability to record diffraction data at more than an order of magnitude faster than previously achievable, putting increased demand on sample delivery and data processing. This work describes a publicly available serial femtosecond crystallography dataset collected at the SPB/SFX instrument at the European XFEL. This dataset contains information suitable for algorithmic development for detector calibration, image classification and structure determination, as well as testing and training for future users of the European XFEL and other XFELs.

Hard x-ray single-shot spectrometer at the European X-ray Free-Electron Laser.

The European X-ray Free-Electron Laser Facility in Germany delivers x-ray pulses with femtosecond pulse duration at a repetition rate of up to 4.5 MHz. The free-electron laser radiation is created by the self-amplified spontaneous emission (SASE) process, whose stochastic nature gives rise to shot-to-shot fluctuations in most beam properties, including spectrum, pulse energy, spatial profile, wavefront, and temporal profile. Each spectrum consisting of many spikes varies in width and amplitude that appear differently within the envelope of the SASE spectrum. In order to measure and study the SASE spectrum, the HIgh REsolution hard X-ray single-shot (HIREX) spectrometer was installed in the photon tunnel of the SASE1 undulator beamline. It is based on diamond gratings, bent crystals as a dispersive element, and a MHz-repetition-rate strip detector. It covers a photon energy range of 3 keV-25 keV and a bandwidth of 0.5% of the SASE beam. The SASE spikes are resolved with 0.15 eV separation using the Si 440 reflection, providing a resolving power of 60 000 at a photon energy of 9.3 keV. The measured SASE bandwidth is 25 eV. In this paper, we discuss the design specifications, installation, and commissioning of the HIREX spectrometer. The spectral results using Si (110), Si (111), and C (110) crystals are presented.

SPADE web service for prediction of allergen IgE epitopes.

The specific interaction of allergens with IgE antibodies and the allergen mediated cross-linking of receptor-bound IgE are key events of allergic diseases. The elucidation of the IgE binding sites (the epitopes) on the allergen surface is an important goal of allergy research. Only few allergen-specific IgE epitopes have been determined experimentally to date. Epitope prediction methods represent a viable alternative to experimental methods and have worked well with linear epitopes. However, as most IgE epitopes are of conformational and/or discontinuous nature sequence based prediction methods have had limited success in these cases. Here, we present the web server of the program SPADE (https://spade.uni-graz.at), which is the server implementation of a previously published program (1). In this approach we utilize the structural homology of cross-reactive allergens combined with the immunological cross-reactivity data for the discrimination of putative IgE-binding sites from non-cross-reactive surface patches. The method, although predictive, does not rely on machine-learning algorithms and does not require training data. The SPADE server features an easy-to-use interface, an automated pipeline consisting of third-party, as well as own, newly developed routines and a comprehensive output page.

Identification of the point of diminishing returns in high-multiplicity data collection for sulfur SAD phasing.

High-quality high-multiplicity X-ray diffraction data were collected on five different crystals of thaumatin using a homogeneous-profile X-ray beam at E = 8 keV to investigate the counteracting effects of increased multiplicity and increased radiation damage on the quality of anomalous diffraction data collected on macromolecular crystals. By comparing sulfur substructures obtained from subsets of the data selected as a function of absorbed X-ray dose with sulfur positions in the respective refined reference structures, the doses at which the highest quality of anomalous differences could be obtained were identified for the five crystals. A statistic σ{ΔF}D, calculated as the width σ of the normalized distribution of a set {ΔF} of anomalous differences collected at a dose D, is suggested as a measure of anomalous data quality as a function of dose. An empirical rule is proposed to identify the dose at which the gains in data quality due to increased multiplicity are outbalanced by the losses due to decreases in signal-to-noise as a consequence of radiation damage. Identifying this point of diminishing returns allows the optimization of the choice of data collection parameters and the selection of data to be used in subsequent crystal structure determination steps.

Structure of allergens and structure based epitope predictions.

The structure determination of major allergens is a prerequisite for analyzing surface exposed areas of the allergen and for mapping conformational epitopes. These may be determined by experimental methods including crystallographic and NMR-based approaches or predicted by computational methods. In this review we summarize the existing structural information on allergens and their classification in protein fold families. The currently available allergen-antibody complexes are described and the experimentally obtained epitopes compared. Furthermore we discuss established methods for linear and conformational epitope mapping, putting special emphasis on a recently developed approach, which uses the structural similarity of proteins in combination with the experimental cross-reactivity data for epitope prediction.

Characterization of mutants of a highly cross-reactive calcium-binding protein from Brassica pollen for allergen-specific immunotherapy.

The major turnip (Brassica rapa) pollen allergen, belongs to a family of calcium-binding proteins (i.e., two EF-hand proteins), which occur as highly cross-reactive allergens in pollen of weeds, grasses and trees. In this study, the IgE binding capacity and allergenic activity of three recombinant allergen variants containing mutations in their calcium-binding sites were analyzed in sensitized patients with the aim to identify the most suitable hypoallergenic molecule for specific immunotherapy. Analysis of the wildtype allergen and the mutants regarding IgE reactivity and activation of basophils in allergic patients indicated that the allergen derivative mutated in both calcium-binding domains had the lowest allergenic activity. Gel filtration and circular dichroism experiments showed that both, the wildtype and the double mutant, occurred as dimers in solution and assumed alpha-helical fold, respectively. However, both fold and thermal stability were considerably reduced in the double mutant. The use of bioinformatic tools for evaluation of the solvent accessibility and charge distribution suggested that the reduced IgE reactivity and different structural properties of the double mutant may be due to a loss of negatively charged amino acids on the surface. Interestingly, immunization of rabbits showed that only the double mutant but not the wildtype allergen induced IgG antibodies which recognized the allergen and blocked binding of allergic patients IgE. Due to the extensive structural similarity and cross-reactivity between calcium-binding pollen allergens the hypoallergenic double mutant may be useful not only for immunotherapy of turnip pollen allergy, but also for the treatment of allergies to other two EF-hand pollen allergens.

Prediction of IgE-binding epitopes by means of allergen surface comparison and correlation to cross-reactivity.

BACKGROUND: The experimental determination of conformational allergen epitopes recognized by IgE is a difficult task because they often involve discontinuous amino acid residues, being separated in the primary allergen sequence, and require the correct allergen fold. OBJECTIVE: We sought to develop a computational tool for the localization of conformational IgE epitopes by using a structure-based comparison of allergen surfaces and IgE cross-reactivity data. METHODS: Our approach involves the quantitative analysis of geometric and physicochemical surface parameters and the subsequent correlation of surface similarity scores to immunologic data. The software tool Surface comparison-based Prediction of Allergenic Discontinuous Epitopes (SPADE) is able to predict the IgE epitopes of an allergen given the availability of at least 2 structural models and IgE reactivity data. RESULTS: We report on the application of our tool to 3 allergen families: the lipocalins, the group 10 pathogenesis-related proteins, and the group 2/3 grass pollen allergens. First, we succeeded in the partial relocalization of IgE epitopes of bovine ß-lactoglobulin and grass pollen Phl p 2 as known from the x-ray structures of their antibody complexes. Second, we measured the relative binding of anti-Bet v 1 IgE to 10 homologous proteins and correlated these data to surface comparison results involving Bet v 1, 5 of the homologs, and 2 hypoallergenic Bet v 1 isoforms. Thereby we predicted IgE-reactive surface portions in agreement with IgE epitope-mapping studies. CONCLUSION: Our approach is the first for the prediction of IgE epitopes by combining structural and IgE cross-reactivity data. It should be useful for the development of point-mutated or structurally disrupted allergen derivatives for allergen-specific immunotherapy.

Synthesis and characterization of alkynyl complexes of groups 1 and 2.

The synthesis of N-heterocyclic carbene adducts of alkynyl lithium and magnesium is achieved, and different degrees of association are observed. Reaction of strontium amide nacnacSrN(SiMe(3))(2)(thf) (nacnac = CH(CMe2,6-iPr(2)C(6)H(3)N)(2)) with PhC[triple bond]CH in THF yields the dimeric alkynyl complex [nacnacSr(thf)(mu-C[triple bond]CPh)](2) which shows an interesting coordination geometry around the metal center. The compound retains the THF molecules, unlike its lighter congener, even in hydrocarbon solvents.

Rhenium(V) oxo complexes with acetylacetone derived Schiff bases: structure and catalytic epoxidation.

Substitution reactions of rhenium(V) oxo precursors [ReOCl3(PPh3)2] or [NBu4][ReOCl4] with the bidentate acetylacetone-derived ketoamine ligands APOH = 4-anilino-3-penten-2-one, DPOH = 4-[2,6-dimethylanilino]-3-penten-2-one, and MTPOH = 4-[2-(methylthio)anilino]-3-penten-2-one gave the complexes [ReO(APO)Cl2(PPh3)] (1), [ReO(DPO)Cl2(PPh3)] (2), and [NBu4][ReOLCl3] (3, L = APO; 4, L = DPO; 5, L = MTPO), respectively. All complexes exhibit only one ketoamino chelate, independent of the amount of ligand added to the rhenium precursors. The complexes were characterized by 1H and 13C NMR spectroscopy. X-ray crystal structures of the complexes 1, 2, 4, and 5, including that of MTPOH, were determined, revealing the trans position of the two oxygen atoms and the trans-Cl,Cl conformation in 1 and 2, in contrast to most other rhenium complexes of this type where the cis-Cl,Cl conformation is observed. Coordination of the potentially tridentate ligand MTPOH in 5 is bidentate with a dangling thioether substituent. Compound 2 shows catalytic activity in the oxidation of cis-cyclooctene with tert-butylhydroperoxide.

Optimization of selenium substructures as obtained from SHELXD.

Using the signal of naturally inbuilt or artificially introduced anomalous scatterers to derive initial phases in a macromolecular crystal structure determination has become routine in recent years. In the context of high-throughput crystallography in particular, MAD and SAD (multiple- and single-wavelength anomalous dispersion) methods are central tools. For both techniques, a crucial step is the determination of the substructure of anomalous scatterers; subsequent phasing procedures will profit from a substructure model that is as accurate as possible. The choice of the subset of the diffraction data to be used for the substructure determination has a strong influence on the quality of the substructure and can make the difference between success and failure. The accuracy of selenium substructures obtained using F(A) values or various anomalous differences truncated to different resolutions has been investigated by comparing the sites determined by SHELXD with the selenium positions in the refined models. Based on the analysis, some recommendations for obtaining accurate and precise substructures are derived.

The first molybdenum dioxo compounds with eta 2-pyrazolate ligands: crystal structure and oxo transfer properties.

Molybdenum dioxo compounds [MoO2Cl(eta 2-pz)] and [MoO2(eta 2-pz)2] with pz = eta (2)-3,5-di-tert-butylpyrazolate have been synthesized; crystallographic data, catalytic activity, and oxo transfer properties are described.