bluuebunny/crossref_metadata_2025 huggingface dataset:
Formation of nanostructures in Eu3+ doped glass–ceramics: an XAS study
Authors: Pellicer-Porres Julio , Segura Alfredo , Martínez-Criado Gema , Rodríguez-Mendoza Ulises , Lavín Víctor
Published: November 2015

Lead-aluminosilicate oxyfluoride transparent glass–ceramics doped with RE3+ ions have been revealed to be unique in the field of optical material engineering. This kind of material consists of a beta_x000C_-PbF2 fluoride nanocrystalline phase in an aluminosilicate glassy amorphous phase. In this way, the macroscopic properties of this material are characteristic of aluminosilicate glass, whereas the spectroscopic properties of the RE3+ ions remain those of low-phonon-energy fluoride crystals. The optical properties of the RE3+ ions, and therefore their interest for photonic applications, depend on the final environment of these ions in a host matrix. Exploration of the local structure of the Eu3+ ions as well as characterization of the amorphous matrix demands structural techniques that do not rely on long range order. Given the complexity of the system under study, chemical selectivity is also required. In this work [1], we describe the results of x-ray absorption experiments carried out to deduce structural and chemical information in Eu3+ doped, transparent, oxyfluoride glass and nanostructured glass–ceramic samples. The spectra were measured at the Pb and Eu–LIII edges. The Eu environment in the glass samples is observed to be similar to that of EuF3. Complementary x-ray diffraction experiments show that thermal annealing creates _x000C_beta-PbF2 type nanocrystals. X-ray absorption indicates that Eu ions act as seeds in the nanocrystal formation. There is evidence of interstitial fluorine atoms around Eu ions as well as Eu dimers. X-ray absorption at the Pb–LIII edge shows that after the thermal treatment most lead atoms form a PbO amorphous phase and that only 10% of the lead atoms remain available to form _x000C_beta-PbF2 type nanocrystals. Both x-ray diffraction and absorption point to a high Eu content in the nanocrystals. Our study suggests new approaches to the oxyfluoride glass–ceramic synthesis in order to further improve their properties.
Fast quantitative analysis of the amorphous content with the Rietveld method
Authors: Ibanez Jordi , Fernandez-Turiel Jose , Elvira Josep , Rejas Marta , Alvarez Soledad
Published: November 2015

The characterization of the mineralogy and chemical composition of multi-phase mixtures is of chief importance in many different contexts, from industry to basic research. In the case of industrial processes, it is often necessary to perform fast and reliable quantitative phase analyses (QPAs) in large amounts of samples that contain amorphous phases. Rietveld refinement from powder x-ray diffraction (XRD) data is widely employed for this purpose. The quantification of the amorphous content with the Rietveld method is usually performed by spiking the samples with an internal standard, and this implies increased processing times. Alternatively, in samples exhibiting the typical, broad XRD signal from the amorphous (glassy) matrix, a poorly-crystalline structure can be used to represent the amorphous phase during the Rietveld analysis [1]. This procedure provides highly consistent data, but is limited because the particular crystal structure used for the QPAs is strongly sample dependent. Recently, it has been shown that fast Rietveld QPAs of coal fly ashes can be carried out with no sample spiking by initially calibrating the XRD signal from the glass [2]. In this work, we evaluate the usefulness of the calibration Rietveld-based approach on two different types of samples: fly ashes from coal combustion plants, and volcanic ashes. While the mineralogy of the fly ashes considered here is relatively simple (they mainly contain quartz, mullite and glass), the volcanic ashes contain sizable amounts of crystalline compounds with both simple and complex structures, including quartz, feldspars, biotite, pyroxene or iron oxides. We show that the calibration approach provides a suitable method to assess in a fast and consistent manner the amount of crystalline and amorphous phases in both types of samples. This method may be extended to industrial characterization processes involving large numbers of complex samples, reducing considerably the analytical times.
In situ reduction study of cobalt model Fischer-Tropsch synthesis catalyst
Authors: du Plessis Hester , Forbes Roy , Barnard Werner , Ferreira Alta , Steuwer Axel
Published: November 2015

Fischer-Tropsch (FT) synthesis is an important process to manufacture hydrocarbons and oxygenated hydrocarbons from mixtures of carbon monoxide and hydrogen (syngas). The catalysis process occurs on for example cobalt metal surfaces at elevated temperatures and pressures. A fundamental understanding of the reduction pathway of supported cobalt oxides, and the intermediate species present during the activation, can assist in developing improved industrial supported cobalt catalysts. Measurements were done during in-situ hydrogen activation of a model Co/alumina catalyst using in-situ synchrotron X-ray powder diffraction and pair-distribution function (PDF) analysis. Strong metal-support interactions between the Co and the support1 can make the catalyst more stable towards sintering. The supported cobalt oxide catalyst precursors have to undergo reductive pre-treatments before their use as FT catalysts. During activation the cobalt oxides evolve, resulting in the formation of metallic cobalt depending on temperature, pressure of activation gases, concentration, time of exposure etc. The effect of hydrogen activation treatments on model catalysts were reported previously [1,2], however analysis of the alumina support phases was excluded from the interpretation by subtraction and normalisation. The PDF refinement accounted for all cobalt present in the catalyst sample and after reduction mainly Co(fcc) with a little Co(hcp) was found to be present. This is a novel approach to in situ PDF analysis of catalysts containing a mixture of phases [3].
Effect of Pressure Changes during Optical Floating Zone Crystal Growth
Authors: Munsie Timothy , Luke Graeme , Dabkowska Hanna
Published: November 2015

In the process of the growth of the magnetically frustrated pyrochlore holmium titanate, Ho2Ti2O7, fluctuations in the pressure of the optical floating zone image furnace were observed. Upon removal, banding from colour centres was noted. These bands were removed by annealing the material at 600 degrees Celsius for 12 hours. Based on this observation, a series of growths was performed to determine the effects of small pressure fluctuations on the lattice spacing of a material grown by the optical floating zone method. Multiple crystals of holmium titanate were prepared from the same precursor materials, pre-reacted in an identical way and grown under variable overpressures between 2 and 8 atmospheres in both argon and oxygen. Initial measurements using single crystal x-ray diffraction showed that there were differences in the crystallographic lattice spacings that were significantly outside of instrumental error. These differences generally corresponded to a correlation of decreased spacing with increase pressure. This talk will present our recent results of a significantly larger sample set of this material, analyzed using powder x-ray diffraction methods on ground up portions of the grown single crystal.
HR-TEM study of oxygen vacancy ordered Sr4+nMn4+nO10+3n compounds
Authors: Suescun Leopoldo , Hadermann Joke , Dabrowski Bogdan
Published: November 2015

The study of oxygen vacancy ordering in the LaxSr1-xMnOy system has shown a strong correlation between Mn formal valence and coordination to oxygen. The Mn2+ was found forming octahedra (Oc) and tetrahedra (Te), Mn3+ octahedra and pyramids (Py) and Mn4+ only octahedra. This tendency was derived from the presence of three kinds of vacancy orderings in the system. For y>2.5 and the average Mnm+ charge of 2<m<3 (x>0.5), brownmillerite-type structures are found with Mn2+/3+ Oc and Mn2+ Te. [1] For 3<m<4 (x<0.5) structures of the homologous Sr4+nMn4+nO10+3n –type series are found with Mn3+ Py and Mn3+/4+ Oc. [2] For y<2.5 and 2<m<3 (x<0.5) a complex layered structure with OcTeOcOcTe'Oc ordering and step defects of Mn3+ Py and Mn2+ Te [3] is observed. Brownmillerite-type structure is absent in the Sr-rich region since mostly Mn3+ is present, which does not show tendency to form Te. Compounds of the Sr4+nMn4+nO10+3n series have been described as arrangements of groups of four Py and n Oc in symmetrical patterns. [2] This description did not elucidate the crystal chemistry reasons for specific pattern (n=0, 1 and 3) since it neglected the coordination stabilization associated with oxygen vacancy, charge and orbital ordering observed in the structures.[2] Using high-resolution transmission electron microscopy (HR-TEM) for SrMnOy with y values located between corresponding n=0, 1 and 3 compositions, we have determined that the oxygen vacancy ordering directs the formation of these patterns. The structural patterns can be described as perovskites with lines of oxygen vacancies along [001] with nearest lines of vacancies in the cubic (310) plane. Successive (310) planes are n perovskite blocks (Oc) apart in the [010] direction. This ordering pattern allows the coherent growth of phases with different n at the sides of (310) plane as observed in grains of a sample of SrMnO2.668 where n=1 and n=3 phases grown coherently one at each side of the vacancy plane.
Two crystal forms of peptidylarginine deiminase typeIII (PAD3)
Authors: Akimoto Megumi , Ishihara Makiko , Kizawa Kenji , Takahara Hidenari , Unno Masaki
Published: November 2015

Peptidylarginine deiminase (PAD) is a Ca2+-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. Protein citrullination by PAD confers large structural and mechanical effects on the target proteins by altering intermolecular and intramolecular ionic or hydrophobic interactions. Five paralogous genes (PADI1 - 4 and 6) on human chromosome 1p35-36 encode the human PAD isozymes. Among the PADs, PAD3 shows the highest substrate specificity for synthetic and natural substrate. S100A3 is an EF-hand-type Ca2+-binding S100 protein family member that colocalizes with PAD3 in hair cuticular cells. PAD3 converts a symmetric pair of Arg51 residues on an S100A3 dimer surface to citrullines, causing assembly of a homotetramer, but does not convert other arginines. Although this specific citrullination is largely affected by the formation of two intramolecular disulfides in S100A3, it is not clear how the sheltered Arg51 residues is recognized by PAD3. We are aiming structural analysis of the substrate bound forms to elucidate structural factor that PAD3 recognize Arg51 residues only. Although X-ray crystal structures of the PAD4 isozyme and its complexes with substrate peptides have been reported, structural analysis of other PAD isozymes has not yet been conducted. To obtain the crystals of the substrate-complex, we prepared the C646A mutant and the other inactive mutants (D350A, H470A, D472A) of PAD3. We determined the crystal structures of wild-type PAD3, at first. Then, we have tried to determine the structure of the substrate complex with the mutants of PAD3. However, the solved structures did not contain the substrate at present stage. From our structural analysis, only the crystals of C646A were belonged to different crystal system from the others, and its difference didn't relate to their crystallization condition. In this conference, we discuss the origin(s) of the differences in the crystal system of C646 from the others.
Protein Crystallography: Getting in on the Ground Floor
Authors: Matthews Brian
Published: November 2015

The first diffraction pattern from crystals of a protein was obtained by Desmond Bernal and Dorothy Crowfoot Hodgkin in 1934. As early as 1939, Bernal described how such diffraction patterns might be used to determine the complete three-dimensional structure of a protein. It was not until 1954, however, that Max Perutz showed how isomorphous replacement could be used to determine the phases for crystalline hemoglobin. Using this approach, Kendrew and coworkers described the three-dimensional structure of myoglobin in 1960. In 1965, David Phillips' group determined the structure of hen egg-white lysozyme. Then, in 1967, three different protein crystal structures were reported. Macromolecular crystallography had come of age. The talk will touch on some of these early events and include reminiscences of work at the MRC Lab in David Blow's group leading up to the successful determination of the alpha-chymotrypsin structure.
Use of Precession Electron and X Powder for solution and refinement of materials
Authors: Colmont Marie , Palatinus Lukas , Huvé Marielle , Mentré Olivier , Roussel Pascal
Published: November 2015

This communication will present the case study of ALa5O5(VO4)2 (A= Li, Na, K, Rb), example of the use of a combination of Precession Electron and X-ray Powder Data for the solution and the refinement of new materials. Indeed, an original structural type has been evidenced in the system (A, La, V, O) with A=Li, Na, K, Rb. Attempts to solve the structure ab initio on X-ray powder data were unsuccessful (more particularly because the powder was a mixture of the title compound and of unreacted precursors). The structure was finally solved by charge flipping using Precession Electron Data (3D tomography) on a nanocrystal, enabling a posteriori the good formulation of a pure powder. This powder was then classically refined by Rietveld method showing the correctness of the electron-solved structure. It crystallizes in a monoclinic unit cell with space group C2/m and a=20.2282(14) b=5.8639(4) c=12.6060(9) Å and β=117.64(1)0. The ALa5O5(VO4)2 structure is built of (OLa4) tetrahedral units creating Crenel-like 2D ribbons. These ribbons, surrounded by four isolated VO4 tetrahedra, are creating channels parallel to b axis in which A+ ions are located.
Probing Chemical Catalysts – How Can Advanced Crystallography Help?
Authors: Zheng Shao-Liang , Powers David , Nocera Daniel , Powers Tamara , Betley Theodore , Chen Yu-Sheng
Published: November 2015

Crystallography can directly provide ultimate three-dimensional structural information in a way that other science difficult to approach. We will discuss how we have used photocrystallography studies and anomalous scattering analysis to probe chemical catalysts: 1) Photochemical HCl splitting provides an opportunity to store solar energy as a chemical fuel, and is mechanistically simpler than water splitting chemistry. Families of binuclear transition metal complexes have been developed for photochemical HX-splitting but the bottle-neck to development of second generation catalysts is the challenge of halogen elimination chemistry. Current photocrystallography experiments have allowed direct observation of metastable intermediates in the photochemical manifolds of both Rh2 and Pt2 complexes, which has led to the design on new families of halide-bridged Rh2 catalysts for HX splitting. 2) Metal atom substitution within homotrinuclear clusters of Co, Mn, and Fe can have dramatic effects in the local electronic structure, which results in the changes in observed reactivity, substrate binding affinities, and catalytic function. Anomalous scattering measurements are critical for the unambiguous assignment of the trinuclear core composition, which has allowed us to investigate changes in both ensemble electronic structures and reactivity profiles.
Responsive magnetic coordination polymers: effects of gas sorption
Authors: Mínguez Espallargas Guillermo , Giménez-Marqués Mónica , Calvo Galve Néstor , Coronado Eugenio
Published: November 2015

Responsive materials for which physical or chemical properties can be tuned by applying an external stimulus are attracting considerable interest in view of their potential applications as chemical switches or molecular sensors [1]. A major source of such materials is provided by the so-called metal-organic frameworks (MOFs), in which physisorption of guest molecules, located in the pores, can cause subtle changes which affect the magnetic properties. Here we present two different approaches to modify the magnetic properties through gas sorption. First, we show that the chemisorption of gaseous HCl molecules by a non-porous one-dimensional coordination polymer instigates drastic modifications in the magnetic properties of the material, switching from strong antiferromagnets to ferromagnets upon gas sorption [2]. These conversions result from profound structural changes, involving cleavage and formation of covalent bonds caused by the removal/addition of ligands from the framework itself, but with no disruption of crystallinity. In a different approach, we present a family of FeII coordination polymers which shows spin-crossover behaviour and selectively sorbs CO2 over N2 [3]. Despite the lack of permanent channels, these non-porous coordination polymers trap CO2 gas molecules into the internal cavities due to the flexible and dynamic nature of the framework. One CO2 molecule is incorporated in each internal cavity of the crystalline material, as unequivocally demonstrated by structural determination after CO2 loading. This physisorption shifts the spin transition producing an increase in the transition temperature of 9 K (see Figure).
Phase transitions and critical phenomena of ice under high pressure
Authors: Matsumoto Masakazu , Himoto Kazuhiro , Mochizuki Kenji , Tanaka Hideki
Published: November 2015

Water distributes ubiquitously among the solar system and outer space in a wide variety of solid forms, i.e. more than ten kinds of crystalline ice, two types of amorphous ice, and clathrate hydrates. These polymorphs often play crucial roles in the planetary geology. Diversity of the stable ices and hydrates also suggests the existence of the various kinds of stable and metastable phases yet to be discovered [1]. Computer simulations and the theoretical treatments are useful to explore them. In this talk, we introduce the phase transitions of ice VII, which is one of the highest-pressure ice phases. The melting curve of ice VII to high-pressure liquid water has not been settled by experiments. We have proposed the intervention of a plastic phase of ice (plastic ice) between ice VII and liquid water, based on molecular dynamics (MD) simulations and the free energy calculations [2], which enables to account for large gaps among the various experimental curves of ice VII. In plastic ice, the water molecules are fixed at the lattice points, while they rotate freely. Interestingly, our additional survey by large-scale MD simulations elucidates that the phase transition between ice VII and plastic ice is first-order at low pressure as it was already predicted, while it is found to be second-order at higher pressures, where a tricritical point joins these phase boundaries together [3]. The critical fluctuations may give a clue for determining the phase boundary experimentally. We also argue about the phase transition dynamics of liquid water to ice VII at their direct phase boundary where metastable plastic ice phase plays an important role.
Soft quasicrystals with 12- and 18-fold rotatonial symmetry
Authors: Dulle Martin , Exner Alexander , Karg Matthias , Lindner Peter , Foerster Stephan
Published: November 2015

Over the past decade quasicrystalline order has been reported in many soft-matter systems. We have found quasicrystals with 12- and 18-fold rotational symmetry (Q12, Q18) in aqueous solutions of polymer micelles, which are particularly soft systems. [1] Transitions from an FCC phase to Q12 and subsequently to Q18 upon cooling could be followed by time-resolved small-angle X-ray and neutron scattering. Recent investigations using cryo-scanning electron microscopy indicate that the micelles are arranged in the form of mosaic two-length scale quasicrystals, which have recently been identified by Dotera et al. using Monte-Carlo simulations of particles with square-shoulder repulsion. The results indicate that these soft systems are special types of quasicrystals having a direct relation to the hexatic phase observed in liquid crystals.
Latest Hybrid Pixel Detectors for increased q/t-resolution in SAXS
Authors: Donath Tilman , Lüthi Benjamin , Schulze-Briese Clemens
Published: November 2015

The PILATUS was the first Hybrid Pixel Detector available for SAXS. It has transformed data collection by its photon-counting technology, which enables noise-free X-ray detection with high dynamic range and excellent stability at high frame rates. These properties are essential for superior data quality in all scattering experiments, especially for optimal background correction when studying low-concentration samples. Besides optimal data quality at each sampling point, highest resolution is desired in most SAXS experiments both in q-range and in time. The newly developed EIGER pixel detector more than doubles the q-resolution that can be achieved when compared with PILATUS3 for the same sample-to-detector distance. EIGER features a pixel size of only 75 µm (in comparison: PILATUS3 has 172 µm). To characterize the spatial resolution of these detectors, point-spread functions were measured at the PTB laboratory at BESSY II, which show that the resolution is directly proportional to the pixel size with minimal cross talk between neighboring pixels. The EIGER 1M detector allows data acquisition at up to 3'000 frames per second. This enables unprecedented temporal resolution in time-resolved SAXS measurements and increases the speed of novel imaging techniques such as scanning SAXS/WAXS and coherent diffractive imaging applications, allowing images to be recorded faster or with higher spatial resolution. The design of the EIGER detector makes it vacuum compatible. Operation at low X-ray energies and correspondingly large scattering angles is another way of increasing q-resolution and also gives access to the lowest q data near the beam stop. In-vacuum detectors enable measurements with ultra-soft x-rays and thus high q-resolution. Moreover they optimize the data quality in scattering experiments by removing absorption and scatter caused from air and windows. An in-vacuum PILATUS 1M detector has been installed at the BESSY-2 FCM beamline and is applied for SAXS/GI-SAXS measurements at energies from 1.75 to 10 keV. For simultaneous SAXS/WAXS applications covering an even wider q-range, in-vacuum detectors with L-shaped detection surface are under development. These will detect the WAXS signal, while a clearance in the detector permits the direct beam to pass on to a SAXS detector placed at larger distance. These latest detector developments will be presented along with corresponding experimental results.
Recrystallization behavior of amorphous and crystalline lactose from TSPDF
Authors: Cheung Eugene , Terban Maxwell , Billinge Simon , Krolikowski Paul , Hollis Steve
Published: November 2015

Lactose is a disaccharide sugar of galactose and glucose that is most commonly associated with milk. Its importance to the food and animal product industry cannot be overstated, as it is involved in aspects as diverse as baking, confectionary, and infant products. The other major use of lactose is in the pharmaceutical industry. The mildly sweet and loosely bland flavor of lactose has lent to its use as a stabilizer and excipient in pharmaceutical products. Despite the wide range of applications for this material, there is still much to be studied. While it is known to exist in several crystalline forms and as two anomers, α and β, characterized by the flipping of a hydroxide group on the glucose ring, the amorphous form of lactose is less understood. Yet it is this amorphous form which may play a crucial role in the physicochemical stability of amorphous drug dispersions. In order to fully understand the structural changes which lactose undergoes when converted from a crystalline to amorphous material, total scattering experiments coupled with PDF analysis for structural identification of amorphous lactose of different origins were undertaken with the goal of understanding the recrystallization behavior of this versatile material. Samples measured included commercial forms of lactose, crystalline and amorphous, and amorphous forms obtained by melt quenching and lyophilization. Recrystallization was followed for the amorphous forms by measuring characteristic samples aged at 400C/75% RH, which is a standard condition for stressing pharmaceutical materials to extrapolate shelf-life. By fitting the PDF curves to a structural model of lactose, and refining with the characteristic function for a sphere of radius r, an estimate of the coherence length of atom-atom correlations for a give sample provides a measure of the growth progression, from single molecule to crystallite for the lactose samples. Coupled with data from NMR spectroscopy, TSPDF analysis is teasing out the nuances of the recrystallization behavior of lactose.
Analysis of archaeological samples using XRPD-PDF and Raman spectroscopy
Authors: Cersoy Sophie , Martinetto Pauline , Bordet Pierre , Hodeau Jean-Louis , Walter Philippe , Van Elslande Elsa
Published: November 2015

Carbon black materials have been frequently used from prehistory as pigments for drawings and paintings and also as dyes, inks and cosmetics. If these material are easy to make by burning organic matter from animal or vegetal origin (e.g. peach black), they form carbonaceous phases, often ill-ordered, that can hardly be characterized [1]. This project is part of studies on archaeological cosmetics, shedding light on ancient manufacturing in physical-chemistry. Six black Roman micro samples found in vessels in Pompeii Houses were studied. To understand the composition of these complex, heterogeneous (mixture of organic/mineral, crystallized/amorphous phases) and precious black powders, a new methodology had to be developed. X-ray powder diffraction tomography enabled to locate the various phases (either crystallized or not) in virtual slices among which ill-ordered materials were analyzed using the Pair Distribution Function (PDF) [2]. X-ray diffraction data were recorded on D2AM beamline at ESRF on the samples and on reference modern carbon black powders purchased from pigments suppliers to help the interpretation of the diffuse signal. High Q data were acquired by scanning the 2D detector and using 25 keV X-rays. This enabled us to obtain well-resolved PDFs to study the amorphous carbonaceous phases contained in our samples (see figure). A comparison between archaeological samples and pure carbon black references was carried out after identification and quantitative analysis of the crystallized phases using Rietveld refinement. The proportion of crystallized phases versus ill-ordered carbonaceous ones was estimated on the PDFs using the maximization of Pearson product-moment correlation coefficients [3]. Results were confronted with those from Raman spectroscopy, known to account for the degree of disorder of non-graphitic carbons. The combination of both methods also provided specific information about the origin (plant, animal or mineral) of carbon black pigments.
Covalent host-targeting by thioester domains of Gram-positive pathogens
Authors: Walden Miriam , Edwards John , Dziewulska Aleksandra , Schwarz-Linek Uli , Banfield Mark
Published: November 2015

Gram-positive pathogens are a major concern to global health, with increasing resistance to antimicrobials and the lack of preventative therapeutics. Understanding how these bacteria interact with host cells is vital for the development of novel strategies to combat disease. One of the most crucial steps in infection is adhesion to the host cell. The discovery of complex cell-surface associated proteins, such as pili, has advanced our knowledge of this interaction, however the precise molecular mechanisms underlying this process remain unclear. Structural studies of pili revealed the presence of highly unusual intramolecular covalent bonds between amino acid side chains. These include isopeptide bonds between Lys and Asp/Asn residues, conferring mechanical strength, thermal stability and resistance to proteases [1,2]. In Streptococcus pyogenes pili, the adhesin Spy0125 (or Cpa) interacts with the host cell. It comprises three domains, two of which contain stabilising isopeptide bonds [2,3]. Intriguingly, the third domain contains an extremely rare thioester bond, between a Cys and a Gln residue. A Cys to Ala mutation results in a 75% reduction in adhesion, suggesting that this internal linkage may mediate direct attachment [3]. We have now discovered putative thioester domains (TEDs) in cell-surface proteins of several clinically important pathogens. The only other example of an internal thioester is found in complement proteins, where the reactive bond enables the formation of covalent attachment to pathogens. The presence of these bonds in bacterial proteins suggests the possibility of an as-yet uncharacterised, conserved mechanism of covalent host cell attachment. For a selection of pathogens, we have used mass spectrometry and crystallography to confirm the presence of the covalent link between the Cys and Gln residues within the TEDs. Furthermore, we have identified putative host cell targets of TEDs and confirmed covalent linkages between the TED and the target.
Structural characterization of Asparagine Synthase A from Trypanosoma cruzi
Authors: Weiler Ana Valéria , Santana Aline , Krieger Marco Aurélio , Zanchin Nilson , Murakami Mario , Souza Tatiana
Published: November 2015

In the Americas, 7.6 million people are infected with Trypanosoma cruzi, causative agent of Chagas disease. Although the parasite life cycle was determined in 1909, the drugs developed to eliminate T. cruzi have low efficacy and high toxicity, especially when the disease is in the chronic phase. Extracellular proteins secreted by protozoan parasites are key mediators in host-parasite interactions. Proteomic approaches have been used to investigate protein secreted by parasites intra-and extra-cellular and these studies led to the identification of a large number of proteins directly involved in fundamental processes of host-parasite interactions. There is evidence that the enzyme Asparagine synthase A from Trypanosoma cruzi is secreted during parasite invasion. This enzyme produces asparagine, glutamate, AMP and pyrophosphate in the presence of aspartate, ATP and glutamine or NH3. Although asparagine is of vital importance for the correct synthesis of proteins and post-translational modifications such as N-glycosylation, there is no structural characterization of this enzyme. In this work, the protein asparagine synthase A of T. cruzi was recombinantly-produced and purified. SAXS and DLS indicate changes in quaternary structure dependent on pH. Those modifications influence protein thermal stability. Structural analysis indicates the determinants of oligomerization and indicate potential sites of inhibition of this protein.
Deciphering the activation of the E3 ubiquitin ligase parkin
Authors: Sauvé Véronique , Gehring Kalle
Published: November 2015

Parkin is an E3 ubiquitin ligase responsible for some autosomal recessive forms of Parkinson's disease. Even though parkin is a RING-type E3 ligase, it uses a hybrid RING/HECT mechanism for its activity. The crystal structures of full-length and the RING0-RING1-In-Between-RING-RING2 module of parkin reveal a conformation of parkin in which its E2 binding site is too far from its catalytic cysteine for the transfer of ubiquitin [1]. Many intramolecular interactions occur between the different RING domains, as well as with a repressor element, which, with RING0, are unique to parkin. Mutations of residues involved in those interactions lead to an increase of parkin activity. This suggests that parkin adopts an auto-inhibited state in basal conditions. Therefore, under stress-response conditions, parkin needs to undergo molecular rearrangements, modulated by post-translational modification and/or interactions with other proteins, to become active. The phosphorylation of serine 65 in the Ubl domain of parkin by Pink1, a kinase also found mutated in some Parkinson's patient, was shown to increase the activity of parkin. Recent publications have demonstrated that ubiquitin is also phosphorylated by Pink1 and, furthermore, that phosphorylated ubiquitin could activate parkin [2,3]. We have used different techniques of structural biology and protein-protein interactions to further characterize the interaction of phosphorylated ubiquitin with parkin. This work provides insight into the mechanism of activation of parkin and that causes Parkinson's disease.
Crystal structure of PhoU from Pseudomonas aeruginosa
Authors: Lee Sang Jae , Ma Chao , Lee Bong-Jin , Suh Se Won
Published: November 2015

The PhoU protein in bacteria plays a role in maintaining phosphate homeostasis by regulating the Pho regulon. Recent studies showed that PhoU is essential for normal growth and is also involved in persister formation. PhoU is a potential target for overcoming drug tolerance of pathogenic bacteria. However, the exact mechanism of PhoU functions is still unknown. Here we have determined the crystal structure of PhoU from Pseudomonas aeruginosa at 2.28 Å resolution by Se SAD method. P. aeruginosa PhoU exists as a dimer in the crystals. A monomer of P. aeruginosa PhoU consists of six alpha-helices, which form two similar helical bundles. P. aeruginosa PhoU shares four conserved sequence motifs. Interestingly, P. aeruginosa PhoU has distinct features in some loops and the surface charge distribution. Two monomers of P. aeruginosa PhoU dimerize in a slightly different manner to those of other PhoU proteins. The present structure of PhoU from a bacterial pathogen may be useful for the antibacterial drug discovery.
Species-dependent variation in the structure of the CK2α-apigenin complex
Authors: Kinoshita Takayoshi , Sekiguchi Yusuke , Nakaniwa Tetsuko , Sogabe Yuri , Tanaka Mai , Sakurai Atsushi , Nakamura Shinya , Nakanishi Isao
Published: November 2015

Ser/Thr kinase CK2, consisting of two catalytic α subunits and two regulatory β subunits, represents various cell fates such as proliferation and is a crucial target for cancer and glomerulonephritis therapies. To date, several planar compounds have been identified as ATP-competitive CK2-inhibitors including apigenin, a flavonoid inhibitor. We here determined the crystal structures of human CK2α complexed with apigenin and an ATP analogue (AMPPNP) at 2.3 and 2.5 Å resolution, respectively and investigated the species specificity in the molecular recognition by the structural comparisons of these complexes with each maize equivalent. The pairs of the superimposed structures reveal that apigenin binds to human and maize CK2α in the quite distinct manners. while AMPPNP binds to the both species in a similar manner. Together with the chemical calculations, we deduce that the alternation at the Leu45/Val45 position of CK2α largely contributes to the species-dependent variation in the apigenin binding mode although the discrepancy is unrelated to the structural conservation in the ATP binding mode.
Structural Basis of Prion Protein Conformation Conversion Inhibition
Authors: Baral Pravas , Swayampakula Mridula , Rout Manoj , Spyracopoulos Leo , Aguzzi Adriano , James Michael
Published: November 2015

Prion diseases are fatal neurodegenerative diseases that affect humans and other animals. A conformational transition of the cellular prion protein, PrPC, into an infectious isoform, PrPSc, is the central event leading to aggregation and the fatal progression of these diseases. One of the therapeutic approaches for the prion diseases is the use of pharmacological chaperones. These molecules can stabilize the prion protein in its native conformation and can arrest the disease progression. Tricyclic phenothiazine compounds exhibit anti-prion activity; however, the underlying molecular mechanism of PrPSc inhibition remains elusive. We have determined the molecular structures of promazine and chlorpromazine bound to the mouse prion protein (moPrP) by forming crystals of the ternary complexes of the POM1 Fab:moPrP:promazine and the POM1 Fab:moPrP:chlorpromazine. The structures were solved by X-ray crystallography to resolutions of 1.9 Å and 2.2 Å, respectively. The small molecules are bound in a novel binding pocket formed at the intersection of the structured and the unstructured domains of the moPrP. Promazine binding induces a structural rearrangement of a portion of the unstructured region proximal to the first β-strand, β1, through the formation of a "hydrophobic anchor". We demonstrate that these molecules, promazine in particular, allosterically stabilize the misfolding initiator-motifs such as C-terminus of helix, α2, the α2-α3 loop as well as the polymorphic β2-α2 loop. Hence, the stabilization effects of the phenothiazine derivatives on initiator-motifs, induce a PrPC isoform that potentially resists oligomerization. Subtle structural differences are observed in the so-called initiator-motifs of the prion proteins that belong to many different mammalian species, and these diversities may possibly explain the generation of wide variety of scrapie strains in prion diseases.
Structural Studies on the SARAH Domain from MST and RASSF Family Proteins
Authors: Hwang Eunha , Cheong Hae-Kap , Hwang Kwang Yeon , Cheong Chaejoon
Published: November 2015

Although the recent progress towards the molecular biology of the Hippo signaling pathway, the mechanistic and structural information in this area remains elusive. Intriguingly, RASSFs function both positively and negatively depending on the events in the diverse cellular signals, by the interaction with MSTs through their SARAH domains. The precise mechanism of these sophisticated regulations of cell growth and apoptosis is still largely unknown. Here, we determined the 3D structures of SARAH domains as MST1-RASSF5 heterodimer and MST2 homodimer by X-ray crystallography. Although the structure of MST2 homodimer showed very similar to the previously reported MST1 homodimer, MST1-RASSF5 showed a distinct feature with flexible N-terminal extension of MST1 SARAH domain and a hydrophobic core stabilized by the aromatic interactions. Comparison of the interfaces and computational alanine scanning indicates the more extensive interactions in the dimer interface in MST1-RASSF5 heterodimer than those of homodimer. Monitoring the structural stability by urea denaturation indicated MSTs-RASSFs heterodimers are substantially more stable than MSTs homodimer. These results provide a 3D structural explanation for the preferential binding of MSTs-RASSFs SARAH domains which is a key mechanism of regulation in the Hippo pathway.
Structural studies of a novel phosphatase-transpoter interaction
Authors: Gulerez Irina , Gehring Kalle
Published: November 2015

The Phosphatase of Regenerating Liver (PRL) family, a subgroup of the protein tyrosine phosphatases, comprises three highly oncogenic members, PRL-1, -2 and -3, implicated in the progression of numerous cancer types. PRL-2 is overexpressed in breast cancer and was shown to promote mammary tumour growth in mice, but its full role in these oncogenic effects remains elusive. Recently, PRL-2 was found to interact with cyclin M3 (CNNM3), a magnesium transporter. To characterize this novel interaction, I crystallized PRL-2 in complex with the cytosolic cystathionine-β-synthase (CBS) domain of CNNM3. The binding surface consists of an elongated loop from CBS that makes contact close to the catalytic site of PRL-2. Site-directed CBS mutants confirmed the loop residues important for binding. PRL-2 and CBS bind particularly tightly, as determined by isothermal titration calorimetry, and PRL-2 enzyme assays revealed that CBS binding reduces the phosphatase's catalytic activity in vitro. The novel role of oncogenic PRL-2 as modulator of intracellular magnesium levels may represent the link between its overexpression and its effects on tumour growth. Small-molecule inhibitors of the PRL-2/CNNM3 complex formation are a potentially valuable tool for exploring the physiological function of this new interaction and may be used as future drug leads for the treatment of breast cancer.
Structure basis of Leukotriene C4 Synthase and its isophtalate inhibitors
Authors: Ago Hideo , Okimoto Noriaki , Kanaoka Yoshihide , Morimoto Gentaro , Ukita Yoko , Saino Hiromichi , Taiji Makoto , Miyano Masashi
Published: November 2015

Leukotriene (LT) C4 synthase (LTC4S) is a key enzyme for the production of cysteinyl leukotrienes, LTC4, LTD4 and LTE4, which are relevance to asthma and allergy. LTC4S catalyzes the conjugation of glutathione (GSH) to LTA4. The crystal structure of LTC4S complex with GSH revealed the active sites locate at the interfaces of adjacent monomer in trans-membrane homo-trimer [1]. The unique U-shaped GSH binds the inner hydrophilic interface cavity and the amphiphilic LTA4 was proposed to bind in the hydrophobic V-shaped crevasse on the interface of the trimer hydrophobic surface. Two essential arginine residues was proved to exert as acid-base catalysis at the both sides of two substrates in highly regio- and stereo-selective manner enzymatically and crystallographically [2]. The architecture of the catalysis with Arg104 and Arg31 residues is the unique among various Glutathione-S-transferases. Arg104 activates and stabilizes the thiorate anaion of the bound GSH and Arg31 stabilize and activate epoxy of the other substrate LTA4, and each mutation causes not only reduction of activity but also each substrate binding affinity substantially. Furthermore, the putative LTA4 binding position was confirmed using the anomalous signal of selenium of the bound seleno-dodecylmaltoside (Se-DDM) at the V-shaped crevasse. To identify leads for novel therapeutics, we attempted to search competitive inhibitors against the unique shaped GSH binding site to discriminate the GSH binding sites of other GSTs that accommodate only its extending backbone conformer [3]. Hierarchical in silico screenings of 6 million compounds provided 300,000 dataset for docking, and after energy minimization based on the crystal structure of LTC4S, 111 compounds were selected as candidates for a competitive inhibitor to glutathione. 5-(5-Methylene-4-oxo-4,5-dihydrothiazol-2-ylamino) isophthalic acid moiety was identified to inhibit LTC4 formation both an enzyme assay and a whole-cell assay. Finally, 5-((Z)-5-((E)-2-methyl-3-phenylallylidene)-4-oxo-4,5-dihydrothiazol-2-ylamino) isophthalic acid was found to be the most potent inhibitor with 1.9 µM of IC50, and in the whole-cell assay to inhibit LTC4 synthesis with cell permeability in a concentration dependent manner.
AutoProcess:Automated strategy calculation, data processing & structure solution
Authors: Fodje Michel , Janzen Kathryn , Labiuk Shanunivan , Gorin James , Grochulski Pawel
Published: November 2015

Two critical aspect of macromolecular crystallography experiments are (1) Determining the optimal parameters and strategy for collecting good quality data and (2) Optimal processing of the collected data to obtain to facilitate structure determination. These tasks can be daunting to inexperienced crystallographers and often lead to inefficiencies as valuable beam-time is used up. To support automation, remote access and high-throughput crystallography, we have developed a software system for automation of all data processing tasks required at the synchrotron. AutoProcess, is layered on the XDS data processing package and makes use of other utilities such as BEST from the European Molecular Biology Laboratory (EMBL), CCP4 utilities and SHELX. The software can be used from the command line as a standalone application but can also be run as a service on a high-performance computing cluster, and integrated into beamline control and information management systems such as MxDC and MxLIVE to allows users to determine the optimal strategy for data collection, and/or process full datasets with the click of a button. Users are presented with a graphical data processing report as well as reflection output files in popular formats automatically. For small molecule and peptide structures, an unrefined initial structure with an electron density map is automatically generated using only the raw diffraction images and the chemical composition of the molecule. Future developments will include sub-structure solution for MAD/SAD/SIRAS data. The software is freely available under an open-source license from the authors. The Canadian Light Source is supported by the Natural Sciences and Engineering Research Council of Canada, the National Research Council Canada, the Canadian Institutes of Health Research, the Province of Saskatchewan, Western Economic Diversification Canada, and the University of Saskatchewan.
Synchrotron powder diffraction simplified; management of an APS mail-in program
Authors: Suchomel Matthew , Halder Gregory , Ribaud Lynn
Published: November 2015

Synchrotrons have revolutionized powder diffraction. They enable rapid collection of data with tremendous angular resolution and exceptional statistics. High resolution powder diffraction beamlines employing multiple single crystal analyzer detectors routinely reveal subtle crystallographic distortions undetectable on other powder instruments, and are an important tool at most modern synchrotrons for structural studies of a diverse range of materials. Beamline 11-BM at the Advanced Photon Source (APS) is a dedicated high resolution (ΔQ/Q ~2×10-4) powder diffraction instrument which uses vertical and horizontal beam focusing capabilities and a counting system consisting of twelve perfect crystal analyzers paired with scintillator detectors. This APS beamline supports both traditional on-site experiments and a highly successfully rapid access mail-in program mode. This mail-in program has greatly simplified access for a growing user community (> 250 in 2013) to world-class synchrotron quality powder data for their research and resulting publications (> 100 11-BM citations in 2013). The presentation will provide an overview of 11-BM's unique mail-in program. It will be presented both from the view of an external remote user, and will also highlight the numerous alignment, calibration, correction and merging software routines needed to efficiently and accurately reduce the numerous multi-bank detector datasets associated with a high throughput user program. An integrated web interface has been developed to serve as a user-friendly relational database interface for tracking of samples and datasets throughout all stages of the measurements; from the initial user request to sample disposal. The database and software tools critical for this high-throughput synchrotron powder diffraction program will be discussed in detail. More information about the 11-BM and its mail-in program can be found on the beamline webpage: http://11bm.xray.aps.anl.gov