bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of magnetic and crystal structure of FeTe doped with Cr and Ni
Authors: Zajdel Pawel , Liu I-Lin , Butch Nicholas , Kruk Izabela
Published: November 2015

Due to inherent phase separation, it has been so far impossible to grow ideally stoichiometric (1:1) tetragonal (P 4/n m m) iron telluride. The excess iron ions are located in the inter-planar positions and usually represented as a fraction x in a general formula Fe1+xTe [1], where x ranges from about 4% to 17%. The additional iron has been found to negatively correlate with the level of anion site doping and subsequently with hindering the superconductivity (SC), for example in the Fe(Te,Se,S) [2] series, where SC can be induced by doping with selenium or small amounts of sulfur. A binary Fe1+xTe orders magnetically into incommensurate magnetic structure with the transition temperature and crystal structure in the magnetic state depending on the excess iron. For x<0.12 a monoclinic (P 21/m) distortion was observed and for x>0.12 an orthorhombic one (P m m n). In our work, we attempted to create and investigate compounds electronically equivalent to variable iron stoichometry by substituting Fe with chromium (3d electron deficient) or nickel (3d electron rich). Single crystal samples several millimeter in size were grown by solidification from melt method in the substitution range 0.025 to 0.1 and only in the case of nickel the incorporation of dopant into host lattice was confirmed. Despite low effective Cr content in the single crystal form [3], neutron powder diffraction (NPD) of polycrystaline specimens revealed systematic decrease of long range magnetic moment and gradual suppression of monoclinic (M) distortion in both series. In the Cr doped series, the structure evolved through a mixed phase region into orthorhombic (O) one (Fig. 1), whereas in the nickel system a complete restoration of tetragonal symmetry was found. The suppression of magnetic ordering and lack of the structural distortion did not result in the SC. This work is supported by the Polish National Science Centre grant No 2011/01/B/ST3/00425
Phase separation in AyFe2-xSe2(A= K, Rb, Cs) superconductors
Authors: Pomjakushina Ekaterina , Krzton-Maziopa Anna , Pomjakushin Vladimir , Bosak Alexei , Chernyshov Dmitry , Svitlyk Volodymyr , Dmitriev Vladimir , Speller Susannah , Conder Kazimierz
Published: November 2015

The interplay between superconductivity, magnetism and crystal structure in iron-based superconductors has attracted a great interest in the recent years as it is considered to be the key for understanding the mechanisms responsible for high temperature superconductivity. Alkali metal intercalated iron chalcogenide superconductors (A122) exhibit unique behavior which is not observed in other iron-based superconducting materials such as antiferromagnetic ordering above room temperature and iron vacancies ordering. These materials have complex crystal structures with several phase transitions and are mixtures of phases even in the form usually described as a single crystal. A pronounced reversible phase separation revealed in A122 single crystals, as well as controversies regarding the origin of superconductivity and the stoichiometry and symmetry of the superconducting phase are still in the forefront of scientific activity. Here we will present a diffraction study of the crystal structures, antiferromagnetic ordering and intrinsic phase separation in alkali-metal iron chalcogenides [1]. The complementary scanning electron microscope study, including high-resolution electron back-scatter diffraction mapping will be also presented [2].
Polarized neutron diffraction and anisotropic exchange in pyrochlores
Authors: Gukasov Arsen
Published: November 2015

Rare earth frustrated pyrochlore magnets are among the materials that exhibit no long range order down to the lowest explored temperatures. To better understand the many complex phenomena observed in the pyrochlores, knowledge of the local interactions present in these materials is necessary. In the pyrochlore lattice, selection between Ising, Heisenberg, or XY types of the anisotropy cannot be based on the analysis of the macroscopic properties because of the presence of four equivalent local anisotropy (<111> -type) axes. Then only an average over the four axes can be measured by classical methods. Polarized neutron diffraction based on the `site susceptibility approach' (A Gukasov and P. J. Brown, J. Phys.: Cond. Matt., 14, 8831, 2002) allows to determine the local susceptibility tensor on the magnetic site. Its temperature dependence in the paramagnetic phase can be accounted for by the crystal field anisotropy and a molecular field tensor that encompasses exchange and dipolar interactions. It was found that for rare earth pyrochlores an isotropic exchange model is not suitable to explain their magnetic behavior and that, instead, the exchange interaction appear anisotropic to large extent (H. Cao et al., PRL 103, 056402, 2009). The experimental evaluation of the anisotropic exchange in pyrochlores can provide a clue to the richness of the phase diagram observed in rare earth frustrated magnets.
Magnetic pair distribution function analysis: introduction and applications
Authors: Frandsen Benjamin , Yang Xiaohao , Billinge Simon
Published: November 2015

Short-range magnetic correlations play a crucial role in a variety of condensed matter phenomena, yet they remain notoriously difficult to investigate experimentally. Quantitative analysis of the diffuse scattering of neutrons from local magnetic correlations represents a viable but challenging route toward revealing short-range magnetic order in complex materials. Reverse Monte Carlo techniques that iteratively fit randomly generated structural models in momentum space have been used successfully [1], demonstrating that diffuse magnetic scattering can be rich in information. Recently [2], we developed a real-space approach to investigating local magnetic correlations, which we call magnetic pair distribution function (mPDF) analysis in analogy to the more familiar atomic pair distribution function. This experimentally accessible quantity reveals magnetic correlations directly in real space and places diffuse and Bragg scattering on equal footing, thereby gaining sensitivity to both short- and long-range magnetic order. Here we present the basic theory behind mPDF analysis and provide several examples of its utility using both simulated and experimentally measured data on several interesting magnetic systems, including a canonical antiferromagnetic, a spin glass, and a spin ice. We discuss the potential impact that mPDF methods may have on current and future research interests in magnetism.
Multi-k magnetic order in Ca3CuNi2(PO4)4: irrep approach and Shubnikov symmetry
Authors: Pomjakushin Vladimir
Published: November 2015

The multi-k magnetic structures with propagation vectors k being the arms of the propagation vector star rarely can be justified experimentally. We show that the antiferromagnetic structure in the low dimensional quantum spin trimer system Ca3CuNi2(PO4)4 is based on the full star of propagation vector k=[1/2,1/2,0] of the paramagnetic space group C2/c. The relation between representation analysis in the propagation vector formalism and Shubnikov magnetic space group (MSG) symmetry is examined in details. A symmetry restrictive MSG that excellently fits the experimental data can be constructed only with the use of the full star. The magnetic structure is further supported by the calculations of the spin expectation values of the isolated Ni-Cu-Ni trimer with realistic Hamiltonian.
Magnetic structure and 5d-electronic state in a pyrochlore iridate Eu2Ir2O7
Authors: Sagayama Hajime , Uematsu Daisuke , Arima Taka-hisa , Ishikawa Jun , O'Farrell Eoin , Nakatsuji Satoru , Sugimoto Kunihisa , Takagi Hidenori , Yoshida Masahiro , Mizuki Jun'ichiro , Ishii Kenji
Published: November 2015

The pyrochlore-type iridium oxide Eu2Ir2O7 exhibits a metal-insulator transition at 120 K, accompanied by magnetic ordering. We performed resonant x-ray scattering (RXS) experiment with photon energies near the iridium absorption edge L3 to investigate the arrangement of Ir4+ magnetic moments. Magnetic RXS was observed in the insulating phase, providing direct evidence of long-range ordering of Ir4+ magnetic moments with a propagation vector of (4n+2 0 0) . Our single-crystal structure analysis revealed that the lattice retains its face-centered-cubic structure across the metal-insulator transition, indicating all-in-all-out magnetic order, where all the magnetic moments on the four vertices of each Ir4+ tetrahedron point inward or outward as shown in Fig. 1 [1]. To investigate the 5d-electronic state of Ir4+, we performed resonant inelastic x-ray scattering (RIXS) experiment near the L3 edge. Obtained RIXS spectra indicate that the 5d-electronic state is affected by not only the spin-orbit interaction but also trigonal distortion of IrO6 octahedron [2].
Lattice row distance
Authors: Wang Hejing , Li Ting , Wang Ling , Zhou Zhao , Yuan Lei
Published: November 2015

Lattice and diffraction are two relating aspects of a crystal. The former reflects the nature of a crystal and the latter describes the basic feature of a crystal. A lattice possesses points and rows two basic characteristics. Great attention has been paid to the points and their distances and directions (angles) they form since the early time of crystallography. Starting from lattice points people have already revealed and found so many regulations in crystals and made great progresses in crystallography. What about the lattice rows? Starting from the geometric relations of reciprocal lattice, we propose six general formulae [1] to describe the relationships between the lattice row distance, the Miller indices h, k, l and the lattice parameters for all crystal systems along any direction. This, like the lattice points, establishes the foundation of the row-indexing, row-refinement of lattice parameters and row-determination of incidence direction theoretically. It is a new method from the lattice row distance to the Miller indices, to the lattice parameters or to the incidence direction. Five steps are optimized for the procedure of "Row-indexing" or "Row-refinement". For example, the procedure of row-indexing is described as 1) measurement of row distance; 2) calculation of row distance; 3) comparison of the measured with the calculated row distances; 4) indexing, and 5) check according to the crystallographic regulations. In respect to diffraction patterns, a series of diffraction spots (points) comprise row(s) and arrange into a series of parallel "lines". When diffraction is strong, diffraction spots are isolated and sharp. However, when diffraction is weak, those spots are obscure or gloomy and often distorted into elongation, asymmetry, deformation, etc. This leads to the outstanding of the rowing "lines" relatively and hence, the row-distance formulae are able to be utilized to structure analysis for those "linear diffraction patterns".
Error estimation guided rebuilding of de novo models for ab initio phasing
Authors: Shrestha Rojan , Simoncini David , Zhang Kam
Published: November 2015

Recent advancement in computational methods for protein structure prediction has made it possible to generate high quality de novo models required for ab initio phasing of crystallographic diffraction data using molecular replacement. Despite those encouraging achievements in ab initio phasing using de novo models, its success is limited only to those targets for which high quality de novo models can be generated. Here, an approach is introduced that can identify and rebuild the residues with larger errors, which subsequently reduces the overall C-alpha root mean square deviations (CA-RMSD) to the native protein structure. The error in a predicted model is estimated by the average pairwise geometric distance per residue computed among selected lowest energy coarse-grained models. This score is subsequently employed to guide a rebuilding process that focuses on more error-prone residues in the coarse-grained models. These rebuilt coarse-grained models were then turned into all-atom models and refined to produce improved de novo models for molecular replacement. This rebuilding methodology has been tested on ten protein targets that were unsuccessful with the current state-of-the-art methods. Seven diffraction datasets were successfully phased using rebuilt de novo models indicating the improved quality of these rebuilt de novo models and the effectiveness of this rebuilding process.
Explicit and Implicit data merging in Crystallographic Least Squares
Authors: Rae Alan
Published: November 2015

For single crystals and twins the assumption that the background can be subtracted from an integrated intensity and the result regarded as a complete observation introduces a systematic error that is worst for the weakest reflections. Refinement and difference maps will be improved if the background is included in a model of peak-plus-background and the background and its associated error is known. A recent review [1] showed how an intensity associated with a sampling point in reciprocal space may be described in terms of partial observations that describe uncorrelated components of the intensity, one of which is the background. Thus Yo(h), the square root of the observed intensity, may be described as the vector sum of orthogonal components and the direction of Yo(h) is defined by an initial model that evolves with refinement. For any least squares refinement cycle the direction and magnitude of Yo(h) is assumed to be fixed by an initial model but Yo(h) does have a variance and the orthogonal components define partial observations. The variance of a residual |Yo(h)| - |Yc(h)| can also be subdivided into contributions that include the background. We can then can assess the fraction of a residual that is being refined and how much of that fraction is associated with individual parameters or combination of parameters. If we assume a variance for an unrefined parameter or combination of parameters we can evaluate what fraction of the total number of observations this is associated with. These ideas allow error distribution and the number of partial observations to be assessed for any feature of the model of the diffraction pattern. The refinement of partial observations of the integrated intensities can be separated from the refinement of the background and peak shapes. Information about the various integrated intensities is duplicated in different parts of the diffraction data. Proper notice should be taken of this duplication to obtain an integrated intensity and its associated partial observation.
ValiFrag: Evaluating fragment quality during automated protein model building
Authors: Pereira Joana , Wiegels Tim , Lamzin Victor
Published: November 2015

X-ray diffraction data from flexible macromolecules and their complexes can rarely be measured to a resolution better than 3 Å. Due to a loss of detectable atomic features, the determination of low-resolution structures is beyond the current operational range of crystallographic software and requires a large amount of manual intervention. ARP/wARP [1] v7.4 generates structures that are up to 80% complete at 3.0 Å, but the completeness drops sharply as the resolution gets worse. Reduction of the model completeness is accompanied with an increase in the number of fragments built, which become shorter. Such fragments are applicable for further model building if they are correct. Though, if they are wrong they may cause the formation of incorrectly built regions in the final model. Thus, there is a need to improve fragment quality before automated model completion is applied. We exploit the vast amount of structural information deposited in the Protein Data Bank (PDB) [2], to make use of it for structural validation of built fragments. Precisely, we evaluate the conformation of each fragment. If the conformation is present in several different protein models in the PDB, it is likely to be modelled correctly in the built model and is accepted. If, on the contrary, it cannot be found in any PDB model, it is probably incorrect. Here we present the software implementation of this validation, called ValiFrag, which checks the validity of automatically built protein chain fragments by evaluating their occurrence in the PDB. Protein models from the PDB were broken into dipeptides and conformational parameters for each of these were then stored in a database. For each automatically built fragment, ValiFrag computes the probability of it to be correct according to the conformation of all possible dipeptides. It can, therefore, assess which fragments are likely to be structurally incorrect and should possibly be modified, or even removed, to improve the final model.
DIALS – a toolbox for diffraction data analysis
Authors: Fuentes-Montero Luis , Parkhurst James , Winter Graeme , Waterman David , Gildea Richard , Brewster Aaron , Hattne Johan , Sauter Nicholas , Evans Gwyndaf
Published: November 2015

DIALS is a collaborative initiative to produce an open source software toolbox encompassing all aspects of diffraction data analysis, with an initial focus on X-ray diffraction data from synchrotrons and free-electron lasers for macromolecular crystallography. DIALS [1] has been developed as a modular plug-in framework that permits flexibility not only in the development of new methods and algorithms but also in the application of these methods to data analysis. DIALS builds on the cctbx [2] in addition to its own dedicated tool-kits. We will present the ideas behind DIALS and give examples of its versatility in permitting the use of several spot-finding and indexing schemes, global refinement and both two and three dimensional integration methods.
RigakuIntegrate : A New Single Crystal Integration Program
Authors: Pressprich Mark , Ferrara Joseph
Published: November 2015

RigakuIntegrate is a new single crystal integration program designed to increase integration accuracy by optimizing the reflection domain to exclude all but relevant elastic scattering. Instead of integrating over a shoebox domain, RigakuIntegrate sums over a tailored detector region that incorporates the known diffraction physics of each reflection as it passes through the Ewald sphere, combined with the known properties of the area detector. The reciprocal space reflections are modelled by ellipsoids that account for the crystal radius, beam crossfire, mosaicity, and wavelength dispersion. In case of laboratory sources separate ellipsoids are assigned to each of the Kα1 and Kα2 components. The passage of the reflection through the diffraction condition is modeled by the intersection of the ellipsoid(s) with the Ewald sphere, resulting in a set of ellipses. This set of intersection ellipses is then projected onto the detector plane along the scattered ray direction. Interaction with the detector sensor is modeled by appropriate convolution, resulting in reflection-specific integration domains over the surface of the detector. Results from crystals ranging in quality from exquisite (a charge density analysis of oxalic acid at 100K using a RAPID IP detector) to marginal (a highly mosaic and split crystal that refines to R1(all data) = 2.6% using a Pilatus detector) will be presented.
Nanostructure studies using complex modeling method
Authors: Juhas Pavol , McKerns Michael , Billinge Simon
Published: November 2015

Accurate characterization of nanostructures is an open difficult problem. Nanoparticle sizes are too small to form a sizable periodic order in atom positions that would give rise to resolved Bragg peaks. A significant number of atoms lie at the surface where their positions can relax and distort. Experimental data from nanoparticles are thus in general more noisy and less signal-rich than from crystals, but their structures have less symmetry and require more variables for their characterization. To overcome these difficulties, we have developed Complex Modeling (CM) approach, which combines multiple experimental and theoretical probes in a common structure optimization routine. The Complex Modeling method is based on the DiffPy software library of forward calculators for pair distribution function, bond valence sums, hard-sphere atom overlaps and third-party routines for small angle scattering simulations and structure restraints for bond lengths and bond angles. The top-level SrFit framework allows flexible setup of optimization schemes by tying available experimental inputs and theoretical and chemical constraints or restraints on the structure. The presentation will provide several examples of Complex Modeling studies of concrete nanostructure systems, such as determination of atomic structure and shape of CdSe quantum dots from PDF and SAXS, structure determination of Au nanoparticle from PDF data and surface optimization, and determination of molecule packing in organic crystals from PDF and chemical constraints.
Construction of quasiperiodic patterns in the Moroccan ornamental art
Authors: Thalal Abdelmalek , Aboufadil Youssef , Elidrissi My Ahmed
Published: November 2015

The similarity between the structure of Islamic decorative patterns and quasicrystal, aroused the interest of several crystallographers. They analyzed these patterns, by different approaches, various kinds of ornamental quasiperiodic patterns encountered in the Morocco and Alhambra (Andalusia) as well as in the eastern of Islamic world. In this work, we are interesting in the quasiperiodic patterns found in several Moroccan historical buildings constructed in the 14th century. We first describe the Zellige panels (fine mosaics) decorating the Madrasas (schools) Attarine and Bou Inania in Fez in term of Penrose tiling, to confirm that both panels have quasiperiodic structure (Makovicky et al, 1998). The panel Madrasas Attarine appears as a finite part of this quasiperiodic pattern (Figure 1-c). As already mentioned by several authors, we can notice the similarity of the decagonal pattern with the diffraction pattern of the quasicrystal Al Mn (Schechtman et al, 1984) (Figure 1-a and c). The multigrid method developed by De Bruijn (1981) and reformulated by Gratias (2002) to obtain a quasiperiodic paving, is used to construct known quasiperiodic patterns from periodic patterns extracted from the Madrasas Bou Inania and Ben Youssef (Marrakech). At last, we propose a method of construction of heptagonal, enneagonal, tetradecagonal and octadecagonal quasiperiodic patterns, not encountered in the Moroccan ornamental art. They are built from tiling (skeleton) generated by the multigrid method and decorated by motifs obtained by the craftsmen method.
Symmetry Groups Associated with Tilings of a Flat Torus
Authors: Loyola Mark , De Las Peñas Ma. Louise Antonette , Estrada Grace , Santoso Eko
Published: November 2015

A flat torus E^2/Λ is the quotient of the Euclidean plane E^2 with a full rank lattice Λ generated by two linearly independent vectors v_1 and v_2. A motif-transitive tiling T of the plane whose symmetry group G contains translations with vectors v_1 and v_2 induces a tiling T^* of the flat torus. Using a sequence of injective maps, we realize T^* as a tiling T-of a round torus (the surface of a doughnut) in the Euclidean space E^3. This realization is obtained by embedding T^* into the Clifford torus S^1 × S^1 ⊆ E^4 and then stereographically projecting its image to E^3. We then associate two groups of isometries with the tiling T^* – the symmetry group G^* of T^* itself and the symmetry group G-of its Euclidean realization T-. This work provides a method to compute for G^* and G-using results from the theory of space forms, abstract polytopes, and transformation geometry. Furthermore, we present results on the color symmetry properties of the toroidal tiling T^* in relation with the color symmetry properties of the planar tiling T. As an application, we construct toroidal polyhedra from T-and use these geometric structures to model carbon nanotori and their structural analogs.
Non-Perfect Colorings of Symmetrical Tilings with Color Groups of Index 4
Authors: Gozo, Jr. Beaunonie , De Las Peñas Ma. Louise Antonette , Felix Rene
Published: November 2015

In this work we present a method that will allow for the construction and enumeration of non-perfect colorings of symmetrical tilings. If G is the symmetry group of an uncolored symmetrical tiling, then a coloring of the symmetrical tiling is non-perfect if its associated color group is a proper subgroup of G. The process will facilitate a systematic construction of non-perfect colorings of a wider class of symmetrical tilings where the stabilizer of a tile in the symmetry group G of the uncolored symmetrical tiling is non-trivial and the set of tiles may not form a transitive set under the action of G. This poster discusses results on how to identify and characterize non-perfect colorings arising from the method with associated color groups of index 4. The approach obtained here provides an avenue to model and characterize various chemical structures with atoms of different proportions, and their symmetries. This is relevant particularly for understanding new and emerging structures, such as structural analogues of carbon nanotubes, where a lot of its physical and electronic properties depend on their symmetry.
Periodic cubic <110> six-way cylinder packing structures
Authors: Teshima Yoshinori , Matsumoto Takeo , Moore Moreton
Published: November 2015

Packing problems are an important aspect of crystallography. In particular, sphere packings have played an important role in improving our understanding of crystal structures. Cylinder packings are also important for the same reason and have been investigated in the fields of both science and engineering. In the field of science, the complex structure of garnet has been explained on the basis of cylinder packing to be a periodic structure with a cubic <111> four-way cylinder packing [1a]. In the field of engineering, cylinder packings are important for determining the fiber packings of composite materials. Some regular fiber packing structures have been designed. Motivated by structures of composite materials, periodic cubic <110> six-way cylinder packing structures have also been investigated [1b]. The known <110> six-way cylinder packings can be classified into three categories on the basis of packing density: (√2)π/9 ≍ 0.494 (Type-I), (√2)π/18 ≍ 0.247 (Type-II), and (351√2 + 108√6)π/1936 ≍ 0.376 (Type-III). Recently, Teshima and Matsumoto studied the space group of the Type-III structure [2]. And Moore reported another type of periodic cubic <110> six-way cylinder packing structure (packing density ≍ 0.133) [3a,b]. In this study, authors consider a general description of periodic cubic <110> six-way cylinder packing structures.
The 17,803 types of double antisymmetry space groups
Authors: VanLeeuwen Brian , Huang Mantao , Litvin Daniel , Gopalan Venkatraman
Published: November 2015

"Double antisymmetry, as a type of color symmetry, refers to the consideration of two independent color-reversing operations. We found that there are 17,803 types of double antisymmetry space groups. The ""types"" of double antisymmetry space groups being the proper affine equivalence classes thereof, i.e. if two groups differ only by changes in origin, lattice constants, and angles then they are considered the same type of group, just as with the 230 types of crystallographic space groups. The significance of listing the types of double antisymmetry space groups is that it gives all possible symmetries of a crystal when two independent antisymmetries are considered in conjunction with the conventional 3D Euclidean space symmetry. Examples from our listing of their properties and symmetry diagrams (available online) will be given."
Symmetry in plants: from Bravais' lattices to an explanation of Fibonacci phyllotaxis.
Authors: Gole Christophe
Published: November 2015

In 1837, fourteen years before publishing his seminal Etude sur la cristallographie Auguste Bravais and his brother Louis wrote an equally seminal work on the arrangement of leaves around the stem of a plant. In this paper, one of the very first truly bio-mathematical work, they introduce and analyze cylindrical lattices and conjecture that only those with the golden angle between successive leaves can exhibit the Fibonacci numbers of spirals predominant in plants. With the advent of the microscope, and following  observations of the plants growing tips by Hofmeister, botanists Schwendener and van Iterson  developed an accretion model of the plant structures. Their work use ideas of what we now would call renormalization of morphogenetic fronts to understand transitions between successive Fibonacci pairs. This gives rise to a  simple explanation of the omni-presence of Fibonacci numbers in plants, which can be verified on digitized plant samples and with systematic computer simulations. This could inform crystallographers in their study of dislocations.
Optical and structural characterization of antimony doped ZnO single crystal.
Authors: Juarez Diaz Gabriel , Martinez Juarez Javier , Peña Sierra Ramon , Lopez Salazar Primavera , Contreras Rascon Jorge , Diaz Reyes Joel
Published: November 2015

We present the optical and structural study of the antimony doped zinc oxide (ZnO) performed by atomic diffusion. Diffusion is carried out at a temperature of 10000C for periods of 1, 2 and 4 hrs from a solid source prepared by partial oxidation of antimony, characterizing each step of the process was performed by photoluminescence (PL) and x-ray diffraction (XRD). The characterization by photoluminescence shows the effect of doping with antimony in radiative transitions caused by the creation of impurity levels. Doped samples were analyzed by high resolution diffraction and reciprocal space mapping which revealed the structural modification of the quality of the single crystal produced by the introduction of antimony. The results indicate that the antimony is introduced fully the volume of ZnO and does not modify the quality of the crystal.
Structure and Functional Analysis of a Ribosomal Oxygenase
Authors: van Staalduinen Laura , Novakowski Stefanie , Jia Zongchao
Published: November 2015

The 2-oxoglutarate/Fe(II)-dependent oxygenases (2OG oxygenases) are a large family of proteins that share a similar overall three-dimensional structure and catalyze a diverse array of oxidation reactions. The Jumonji C (JmjC)-domain containing proteins represent an important subclass of the 2OG oxygenase family that typically catalyze protein hydroxylation; however, recently other reactions have been identified, such as tRNA modification. The E. coli gene, ycfD, was predicted to be a JmjC-domain containing protein of unknown function based on primary sequence. Recently YcfD was determined to act as a ribosomal oxygenase, hydroxylating an arginine residue on the 50S ribosomal protein L-16 (RL-16). We have determined the crystal structure of YcfD at 2.7 Å resolution, revealing that YcfD is structurally similar to known JmjC proteins and possesses the characteristic double stranded β-helix fold or cupin domain. Separate from the cupin domain, an additional globular module termed -helical arm mediates dimerization of YcfD. We further have shown that 2-oxoglutarate binds to YcfD using isothermal titration calorimetry and identified R140 and S116 as key 2OG binding residues using mutagenesis which, together with the iron location and structural similarity with other cupin family members, allowed identification of the active site. Structural homology to ribosomal assembly proteins combined with GST-YcfD pull-down of a ribosomal protein and docking of RL-16 to the YcfD active site support the role of YcfD in regulation of bacterial ribosome assembly. Furthermore, overexpression of YcfD is shown to inhibit cell growth signifying a toxic effect on ribosome assembly.
Crystal structures of GCN2 C-terminal domain: Insight into GCN2 regulation
Authors: Singh Isha , He Hongzhen , Wek Sheree , Dey Souvik , Baird Thomas , Wek Ronald , Georgiadis Millie
Published: November 2015

General control non-derepressible 2 kinase (GCN2) is a serine threonine kinase that curtails translation in response to diverse stress stimuli [1]. It is a primary sensor of amino acid starvation and mediates translation repression by phosphorylating eIF2 [2]. In addition to the kinase domain, GCN2 contains two regulatory regions; a histidyl-tRNA synthetase-like domain (HisRS) and a C-terminal domain (CTD), which function together to sense nutrient depletion. Both domains have been proposed to bind uncharged tRNA's that accumulate during amino acid starvation followed by dimerization of the kinase domain facilitating activation of GCN2 [3]. Thus, while the CTD plays an important regulatory role in activating GCN2, information on how the CTD facilitates dimerization and whether the CTD plays a similar role in murine GCN2 is limited. Moreover, the sequences of vertebrate CTDs share less than 10% sequence identity with their yeast counterpart; therefore, it is not known whether regulatory mechanisms in GCN2 are conserved across different species. We present here the experimentally phased crystal structures of murine CTD at 1.9 Å and yeast CTD at 1.95 Å. Both murine and yeast CTDs share a novel interdigitated dimeric organization, although the dimeric structures differ somewhat in overall shape and size. Additional biochemical analysis of the murine CTD confirms an important role for dimerization in its activation. Moreover, functional studies reveal that both yeast and murine GCN2 have similar nucleic acid binding properties, but mGCN2 does not appear to exhibit ribosomal association, a key feature in the model for regulation of yeast GCN2, suggesting that there are regulatory differences between the murine GCN2 and its yeast counterpart. Our data provides a basis for understanding the role of the CTD in regulation of GCN2 in both yeast and mammals.
Structural Insights into Regulation of Quinate Degradation in Bacteria
Authors: Prezioso Stephanie , Christendat Dinesh
Published: November 2015

The shikimate pathway is an essential metabolic pathway in bacteria, as well as plants and fungi, which ultimately leads to the synthesis of three aromatic amino acids among other important aromatic compounds. The fourth step in the pathway is the reduction of dehydroshikimate to shikimate, catalyzed by shikimate dehydrogenase (SDH/AroE). In addition to AroE, at least four functionally distinct SDH homologs exist in bacteria. The structure and catalytic residues of the SDH enzyme family are highly conserved, however the key residues for substrate binding vary among the different homologs. Together, these data suggest that the catalytic mechanism is maintained among homologs, yet each may bind a different substrate. The YdiB homolog catalyzes the first step in the quinate degradation pathway, which is a branch of the shikimate pathway. In various species, the operons containing the ydiB gene are predicted to be controlled by one of two different transcriptional regulators belonging to either the TetR or LysR family. In both cases, these regulators are predicted to be activated or repressed by intermediates of the quinate degradation pathway. We will be using structural biology to determine how these regulators recognize pathway intermediates, and to understand the structural basis of how two distinct regulators can control transcription of the equivalent operon in different species.
Structural and functional profiling of estrogen receptors environmental ligands
Authors: Delfosse Vanessa , Grimaldi Marina , Pons Jean-Luc , Cavaillès Vincent , Labesse Gilles , Balaguer Patrick , Bourguet William
Published: November 2015

Endocrine-disrupting chemicals (EDCs) are exogenous substances that interfere with the function of hormonal systems and cause deleterious effects on humans and wildlife. Many EDCs are man-made chemicals produced by industry and released into the environment. Some naturally occurring EDCs can also be found in plants or fungi. Epidemiological studies suggest a link between the exposure to these chemicals and the development of diseases like cancers, reproduction defects, or metabolic disorders. Endocrine disruption has raised considerable concern in recent years so that several countries have developed risk assessment programs aimed at evaluating the toxic potential of more than 100,000 chemicals. In this context, we have been using a battery of structural, biophysical and cell-based approaches to investigate the mechanisms by which a variety of environmental pollutants, including bisphenols [1], pesticides, phthalates, benzophenones, parabens, myco- and phytoestrogens or alkylphenols, bind to and modulate the activity of the estrogen receptors ERα and ERβ, two nuclear hormone receptors (NRs) that are primary targets of environmental contaminants. Crystallographic analysis reveals that these structurally and chemically diverse compounds bind to ERs via diverse sets of protein–ligand interactions reflecting their differential activities, binding affinities and specificities. A detailed analysis of the various binding/activation mechanisms will be presented. Based on these structural data, we are developing a protocol for in silico evaluation of the interaction between pollutants and ERs or other members of the NR family. The server which utilises crystal structures to model any NR/xenobiotics complexes and estimate binding affinities will also be presented. Overall, this study provides a wealth of tools and information that could be used for the development of safer chemicals devoid of NR-mediated activity and more generally for environmental risk assessment.
Structural basis for post-transcriptional gene silencing by human Argonaute-2
Authors: MacRae Ian
Published: November 2015

Argonaute proteins are a unique class of RNases that degrade substrate RNAs in a sequence-specific manner. Argonaute proteins acquire substrate specificity by binding to a small RNA (21 nucleotide), termed the guide RNA, and use the encoded sequence to locate target message RNAs (mRNAs) through base-pairing complementarity. We have determined crystal structures of human Argonaute-2 (Ago2) bound a guide RNA and a variety of complementary target RNAs. The structures reveal how Ago2 uses discrete regions of the guide to scan for targets and the conformational changes associated with target recognition. Using free phenol as a probe, we also identified a constellation of hydrophobic cavities on the surface of Ago2 that we suggest are involved in the recruitment of additional protein factors to target mRNAs upon recognition by Ago2.
Structures of human m6A RNA demethylases: FTO and ALKBH5
Authors: Aik Wei Shen , Demetriades Marina , Schofield Christopher , McDonough Michael
Published: November 2015

Methylation at the N6 position of adenosine in mRNA (m6A) was first observed around 40 years ago but little was known about the function of this modification at the time of discovery. Research over the last ten years has led to the identification of methyltransferases that produce or `write' the m6A RNA mark and recently demethylases that remove or `erase' m6A marks, thus indicating that the m6A modification is reversible. Recent analyses have identified the motif and regions where m6A marks are present within RNA transcripts as well as m6A binding protein `readers'. These studies have revealed a role for m6A methylation in mRNA stability and demonstrated that sequence specific subsets of transcripts can be regulated in this manner. Like the histone lysine JmjC demethylases, nucleic acid demethylases are members of the 2-oxoglutarate and iron dependent oxygenase superfamily. The human nucleic acid oxygenases (NAOXs) with known structures include the TET enzyme that produces 5-hydroxymethylcytosine in DNA, ALKBH2 and 3 that demethylate 3-methylcytosine and 1-methyladenine in DNA, and ALKBH8 that modifies tRNA. We identified the fat mass and obesity associated protein, FTO, as a NAOX1and m6A in RNA was recently reported to be a bona-fide substrate of FTO in in-vivo. Subsequently, ALKBH5 was also shown to be an m6A demethylase. Here we present structural studies of FTO2and ALKBH53as well as biochemical work that has led to structurally informed inhibitor design of the m6A demethylases for the development of small molecules to probe biological function and for potential use as therapeutics.
Crystal structure of RNA polymerase I
Authors: Fernández-Tornero Carlos
Published: November 2015

In eukaryotes ribosome biosynthesis starts with ribosomal RNA production by RNA polymerase I (Pol I), a process that is critical to regulate cell growth and proliferation. We were able to obtain the crystal structure of yeast Pol I, a 14-subunit complex with a total mass of 590 kDa, at 3.0 Å resolution [1]. The current communication deals with the functional implications of this beautiful structure, while details on structure determination will be presented by Tim Gruene at this meeting. The structure represents the latent state of the enzyme, characterized by three major features. First, it forms dimers that involve the C-terminal tail of the stalk subunit A43. Second, the two enzyme halves pivot along the DNA-binding cleft to produce an open cleft and an unfolded bridge helix. Third, an extended loop in subunit A190 mimics the DNA backbone along the cleft, hampering nucleic acid binding. All three features must be resolved during enzyme activation. The Pol I crystal structure also reveals intrinsic modules that only bind transiently in other RNA polymerases. Subunit A12.2 inserts a TFIIS-like zinc ribbon into the active site, providing insight into its role in RNA cleavage and Pol I insensitivity to α-amanitin. The A49-A34.5 heterodimer binds the outer side of subunit A135 through a TFIIF-like dimerization module, suggesting how it may function during transcriptional initiation and elongation.
Structural insight into the eIF2-eIF2B interaction
Authors: Kashiwagi Kazuhiro , Ito Takuhiro , Yokoyama Shigeyuki
Published: November 2015

eIF2B (eukaryotic initiation factor 2B) is a key regulator of translation initiation. It catalyzes guanine nucleotide exchange on eIF2, which delivers the methionylated initiator tRNA to the 40S ribosomal subunit. This exchange reaction is inhibited by the stress-induced phosphorylation of the eIF2 alpha subunit, which leads to global repression of cellular protein synthesis. eIF2B is composed of five subunits. The catalytic gamma/epsilon subcomplex is responsible for nucleotide exchange, while the regulatory alpha/beta/delta subcomplex discriminates the phosphorylation status of the eIF2 alpha subunit. We established a bacterial expression system for eIF2B, and determined its crystal structure at 3.2 Å resolution. The crystal structure revealed that eIF2B is a decamer containing two molecules of each subunit. The hexameric regulatory subcomplex is formed by the trimerization of one alpha-alpha homodimer unit and two beta-delta heterodimer units, and two catalytic subcomplexes are individually connected to the regulatory subcomplex through two beta-delta heterodimer units. Photo-cross-linking analyses showed that the N-terminal domain of the eIF2 alpha subunit, which bears the phosphorylation site, is recognized by a composite surface formed by the eIF2B alpha, beta, and delta subunits. Based on these results, we report structural insights into the interaction between eIF2 and eIF2B.
Different teaching way to space group and symmetry operation: polyhedral vs ball
Authors: Zhou Jian , Wang Hejing
Published: November 2015

To introduce the regulations of space group combining with a symmetry operation, put an orientation ball at a position shift away from the lattice tops is a good way [1]. However, based on the fundamental knowledge of "lattice", it often occurs that the tops of a lattice "should be" the positions of "atom balls" thought by most beginnings in teaching practice. This "thought" leads them never deduce out those regulations in symmetry operations and often misleads a wrong conclusion. As a beginning one wishes watching movies and pictures instead of mathematical deduction or vector calculation. It easily arises that a lattice has eight tops with atom balls. This "idea" lets the orientation balls shifting away from the lattice tops become difficult to understand. Nevertheless, the balls with a sign of "comma" in the middle are also difficult to understand that they can stand for a certain orientation because ball is circle. "Tops" and "directions" are two troubles in learning crystallographic symmetry and symmetry operations for those beginnings. How to guide them to overcome the two fences is an important step that will lead those beginnings to a never understanding status, on one hand, or let them understand throughout all regulations of space group(s) combining with a symmetry operation on the other. From teaching practice, a polyhedral at lattice tops could overcome both difficulties at position and in orientation. First, a polyhedral is always in orientation, even it is a cubic. This is easily understood. Secondly the centre of a polyhedral could easily meet with the tops of a lattice; it lets students easily understand "a lattice has eight tops occupied – a natural thought by beginnings". This way let them easily understand and deduce all regulations in crystallographic symmetry operations, such as a body-centred lattice combining with a symmetry plane (m) produces n symmetry operation at 1/4t, etc. see figures below.
Polymorphism, what it is and how to identify it
Authors: Brog Jean-Pierre , Chanez Claire-Lise , Crochet Aurelien , Fromm Katharina
Published: November 2015

Polymorphism is a very important phenomenon not only in basic research, but certainly in pharmaceutical industry and materials science. Polymorphs possess different properties, for instance the solubility or the mechanical resistance can differ dramatically from one polymorph to the other – properties which can be crucial for their application. Hence, it is important to be able to control the formation of polymorphs and to understand their formation. We here gave some insights into the basic knowledge of polymorph formation and their identification and characterization in order to give an overview on the current state of the art. In order to give interested peoples a tool in hand to test their compounds for polymorphism, we established a series of flow sheets to follow, depending on the class of compounds, hoping that they are useful for many scientists who are not so well acquainted with polymorphism. The presented schemes resume thus the identification steps for polymorphs. It should also help to use the term polymorph correctly in order to reduce the number of publications in which this term is not used in a correct way.
Holistic Integration of Crystallography in Undergraduate Chemistry
Authors: Dawe Louise
Published: November 2015

One of the criteria for the evaluation of undergraduate instructors by their students is often "Did the instructor stimulate my interest in the subject matter of the course?" Instillation of passion in science for undergraduates can start with passionate instructors. It was with this reasoning, and the impetus of the International Year of Crystallography, that I undertook the holistic redesign of a required third year Honours course on Chemical Literature and Scientific Communication at Wilfrid Laurier University, in Waterloo, ON, Canada. The course outcomes were based on recommendations for information literacy [1], and included the analysis of complex ethical problems, understanding the organization of the library, and the demonstration of critical thinking by evaluation of information from literature, and with help from university librarians and learning services, the broad exploration of crystallography was integrated throughout. The students were then tasked to share their new skills in communication, and knowledge of crystallography, in a public poster conference, attended by 400 first year science undergraduates. This talk will highlight the impact of peer-share crystallographic education, as well as other integral activities in first year introductory and senior inorganic chemistry courses.