bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural Study of Thioesterase Domains in Complex with Covalent Inhibitors
Authors: Bergeret Fabien , Argyropoulos Panos , Reimer Janice , Boddy Christopher , Schmeing Martin
Published: November 2015

Polyketide synthases (PKS) are large multifunctional enzymes that are responsible for the biosynthesis of a wide array of secondary metabolites that are of great interest for medical applications. PKS catalyze carbon-carbon bond formations by successive Claisen condensations of small thioesters. All PKS are organized in modules where each module is composed of catalytic domains that add a single ketide unit to the growing chain and optionally reduce the beta-keto function. The Thioesterase (TE) domain is responsible for the released of the final polyketide chain. Two ways are used by the TE domains: hydrolysis to form a linear chain or cyclization to form a macrolide. The molecular mechanism which controls the cyclization versus hydrolysis decision is not fully understood and a better understanding of this mechanism could be a great interest for generating new pharmaceutical compounds. To answer this question, we are studying the structure and function of PKS TE domains in collaboration with the group of Dr. Boddy (University of Ottawa). Recent results about the biochemical study in complex with inhibitors, crystallization and structures of one of these TE domains will be presented.
Exploration of strategies to altering thermal properties of industrial enzymes
Authors: Baltulionis Gediminas , O'Neill Maeve , Gallagher Denise , Ellis Andrew , Charalampapolous Dimitrios , Watson Kimberly
Published: November 2015

Endoproteases and exopeptidases occupy a pivotal position with respect to their commercial applications in food (e.g. as additives in whey protein processing) and, as additives in detergent, textile and a number of other industries. Food processing at low temperatures by cold-active enzymes has many advantages as it minimises undesirable chemical reactions as well as the risk of microbial contamination. Cold-active enzymes were found to display higher specific activity and catalytic efficiency resulting in lower quantities of enzyme required and significantly shortened processing times. On the other hand, industrial hydrolysis typically occur at elevated temperatures due to the faster reaction rates, increased substrate solubility and thermophilic biocatalysts are required to maintain reactions at very high temperatures. The aim of our work is to exploit structure-function relationships of extremophilic enzymes that give rise to novel industrially useful proteases. We are using the high-throughput capability of the Oxford Protein Purification Facility (OPPF) to study a number of structural modifications leading to protein extremophilic functional behaviour. Several strategies to effectively alter the thermal properties of commercial serine endoproteases and aminopeptidases are being tested including; i) site directed mutagenesis targeted to reduce quantity of prolines, salt bridges, S-S bridges, and hydrophobic clusters, and ii) iterative saturation mutagenesis relying on residues with low B-factors (local rigidity) according to available 3D structures are currently being implemented. Our recent results reveal the potential for an emerging universal mechanism to modify the thermostability of any given enzyme.
Structure of B. cereus Class Ib Ribonucleotide Reductase NrdI-Fe2-NrdF Complex
Authors: Hammerstad Marta , Hersleth Hans-Petter , Tomter Ane , Røhr Åsmund , Andersson K. Kristoffer
Published: November 2015

Class Ib ribonucleotide reductases (RNRs) use a dimetal-tyrosyl radical (Y·) cofactor in their NrdF (beta2) subunit to initiate ribonucleotide reduction in the NrdE (beta2) subunit. Contrary to the diferric tyrosyl radical (FeIII2-Y·) cofactor, which can self-assemble from FeII2-NrdF and O2, generation of the MnIII2-Y· cofactor requires the reduced form of a flavoprotein, NrdIhq, and O2 for its assembly. Here we report the 1.8 Å resolution crystal structure of Bacillus cereus Fe2-NrdF in complex with NrdI. Compared to the previously solved Escherichia coli NrdI-MnII2-NrdF structure, NrdI and NrdF binds similarly in Bacillus cereus through conserved core interactions. This protein-protein association seems to be unaffected by metal ion type bound in the NrdF subunit. The Bacillus cereus MnII2-NrdF and Fe2-NrdF structures, also presented here, show conformational flexibility of residues surrounding the NrdF metal ion site. The movement of one of the metal-coordinating carboxylates is linked to the metal type present at the di-metal site, and not associated with NrdI-NrdF binding. This carboxylate conformation seems to be vital for the water network connecting the NrdF di-metal site and the flavin in NrdI. From these observations, we suggest that metal-dependent variations in carboxylate coordination geometries are important for active Y· cofactor generation in class Ib RNRs. Additionally, we show that binding of NrdI to NrdF would structurally interfere with the suggested alfa2beta2 (NrdE-NrdF) holoenzyme formation, suggesting the potential requirement for NrdI dissociation before NrdE-NrdF assembly after NrdI-activation. The mode of interactions between the proteins involved in the class Ib RNR system is, however, not fully resolved. [1]
Towards the structure of an unusual nonribosomal peptide synthetase
Authors: Alonzo Diego , Reimer Janice , Magarvey Nathan , Schmeing T. Martin
Published: November 2015

Cereulide synthetase (Ces) is a macromolecular machine that produces a toxin involved in severe and lethal food poisoning. Ces belongs to the nonribosomal peptide synthetase (NRPS) family protein, and as such, it employs an assembly line mechanism to generate its cereulide product. The assembly line for cereulide differs from the canonical NRPS pathway because it adds hydroxy acids instead of amino acids at half of the positions in the molecule. To achieve this, the megaenzyme selects alpha keto acids through specialized adenylation domains and then reduces them to hydroxy acids in embedded ketoreductase domains, before adding them to the growing depsipeptide. Several details on the structural features of this unusual NRPS remain unknown. Here we report a full biochemical characterization of this highly complex megaenzyme. We obtained the kinetic constants of each of its four adenylation domains and probed the side chain selectivity for its alpha keto acid – recognizing adenylation domains. Also, we report that the activating protein MbtH is not required for full activity of the assembly line. Finally, we show that each of the modules can be inhibited through mechanism-based inhibitors, which can restrain the conformational flexibility paving the way for structural studies by X-ray crystallography.
Structures of the surface exposed proteins of Gram positive bacteria
Authors: Minasov George , Nocadello Salvatore , Filippova Ekaterina , Halavaty Andrei , Anderson Wayne
Published: November 2015

The Center for Structural Genomics for Infectious Diseases (CSGID) applies structural genomics approaches to biomedically important proteins from human pathogens. It also provides the infectious disease community with a high throughput pipeline for structure determination that carries out all steps of the process, from target selection through structure deposition. Target proteins include drug targets, essential enzymes, virulence factors and vaccine candidates. The CSGID has deposited over 680 structures in the Protein Data Bank. The proteins that are exposed on the surface of Gram positive bacterial pathogens (including Staphylococcus aureus, Bacillus anthracis, Listeria monocytogenes, Streptococcus species and Clostridium species) have been one focus area for the CSGID. So far, the structures of more than 55 of these proteins have been determined. The surface proteins are important in the interactions between the pathogen and its host, but many of them are as yet functionally uncharacterized. Among the examples that will be presented is the Bacillus anthracis SpoIID protein. SpoIID is part of a coordinated cell wall degradation machine that is essential for sporulation and the morphological changes involved. It represents a new family of lytic transglycosylases that degrade the glycan strands of the peptidoglycan cell wall. The two active site clefts in the dimeric enzyme include residues from both subunits, suggesting that the dimer is required for activity. This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contracts No. HHSN272200700058C and HHSN272201200026C.
AccD1 And AccA1 from M. tuberculosis form A dodecameric MCC-type holo complex
Authors: Ehebauer Matthias , Anandhakrishnan Madhan , Zimmermann Michael , Noens Elke , Jakobi Arjen , Sachse Carsten , Sauer Uwe , Wilmanns Matthias
Published: November 2015

Mycobacteria have an unusual redundancy of six putative carboxyltransferase genes that form high-molecular weight holo acyl coenzyme A carboxylase complexes with a complementary set of three biotin carboxylase genes. Most of these enzyme complexes use small fatty acid coenzyme A esters as substrate, to allow their extension by one methylene group via a carboxybiotin-mediated α-carboxylation reaction. Redundant occurrence of these complexes was assumed to be related to highly complex enzymatic requirements in lipid biosynthesis, as the mycobacterial thick cell wall comprises unusual very long chain fatty acids, including mycolic acid. We have solved two high-resolution crystal structures of the 350 kDa hexameric assemblies of two different acyl coenzyme A carboxylase hexameric assemblies, AccD5 and AccD6 [1; Anandhakrishnan et al., unpublished], and characterized these enzyme complexes functionally. In a second step we investigated the acyl coenzyme A carboxylase complex AccD1-AccA1 from Mycobacteria tuberculosis with hitherto unknown function. By using a metabolomics approach we found that AccD1-AccA1 is involved in branched amino acid catabolism, which was not investigated in mycobacteria before [Ehebauer et al, unpublished. Using an in vitro assay, we show that the enzyme complex uses methylcrotonyl coenzyme A as substrate]. We determined the overall architecture of the 700 kDa AccD1-AccA1 complex to be formed from three layers of a central AccD1 hexameric ring, flanked by two distal tiers composed of three AccA1 subunits each. Our electron microscopy data match the overall dimensions of a methylcrotonyl coenzyme A holo complex with known structure and thus support our functional findings. Our data suggest a unique functional role of the AccD1-AccA1 complex within the Mycobacterium tuberculosis acyl coenzyme A carboxylase interactome. Ultimately, it is our goal to solve this and related structures of ACCase holo complexes by high-resolution crystallography as well. The abstract is dedicated to Louis Delbaere with whom I shared time during my PhD at the University of Basel, Switzerland.
Structure-Function Studies of A. thaliana heterotrimeric G-protein subunits
Authors: Quarantini Sandra , Kose Hazal , Kaplan-Turkoz Burcu , Akturk Anil , Sayers Zehra
Published: November 2015

Heterotrimeric G-proteins, consisting of alpha, beta, and gamma subunits, participate in major signaling pathways in eurkaryotes and mammals, including those in the nervous and sensory systems. G proteins are activated upon stimulation of G-protein coupled receptors and function as molecular switches through nucleotide cycling by the alpha subunit and by their interactions with intracellular effectors. The mechanism of activation and deactivation of the mammalian heterotrimer is well understood through extensive structural and functional studies, and is being used as a basis for predictions for mechanisms involving the plant heterotrimer. Recent evidence, however, indicates significant differences in the two systems [1]. We undertook a structural investigation of the A. thaliana complex in order to gain insights for G-protein activation and the molecular interactions in the G-protein related signaling pathways in plants. The alpha subunit GPA1 was cloned and expressed in P. pastoris and purified with high yield and homogeneity in functional form. Similarly the beta and gamma subunits (AGB1 and AGG2) were cloned and expressed in E. Coli. AGB1 expression resulted in production of unfolded protein whereas AGG2 could be obtained on its own with high yield and purity. Biochemical analyses and biophysical studies using SAXS, CD, DLS, UV-vis spectroscopy reveal structural parameters of GPA1 for comparison with its mammalian counterparts and indicate the propensity of GPA1 to form oligomers in solution. After purification form E. coli AGG2, can be stabilized in dimeric form and has a flexible and extended structure. Structure of the dimer is sensitive to the concentration of salt and reducing agent in the solution.
Paip1 and Paip2: conformational modulators of PABP
Authors: Safaee Nozhat , Gehring Kalle
Published: November 2015

Translation is regulated in cells. Key among the different stages of translation, translation initiation is controlled by regulatory interactions of eIFs and also translation regulatory proteins interacting with eIFs and PABP. PABP-interacting protein (Paip) 1 and 2 have been identified as regulatory proteins affecting the rate of translation initiation through their interactions with PABP. These interactions are mediated by the PABP interacting Motifs (PAM) 1 and 2 of Paips. Paip1 enhances the rate of translation while Paip2 suppresses it. To further understand their mechanisms of actions, here, we have studied the interactions of PABP RRMs with the PAM1 regions of Paip1 and 2. Compared to Paip1, affinity measurements using ITC show that Paip2 binds to PABP with higher affinity. While Paip2 dissociates poly(A) from PABP RRMs, Paip1 can not compete with poly(A) binding to PABP. Our binding studies show that Paip1 increases eIF4G-binding to PABP RRM1-2, supporting its stimulatory role in translation. Upon binding, Paip1 and Paip2 affect the conformation of the PABP RRMs differently. Compared to RRMs–Paip1, the complex of RRMs–Paip2 has a compact conformation. Our data suggest that Paip1 and Paip2 regulate PABP function through modulating its conformation, stimulating its incorporation in the pre-initiation complex, or sequestering it from translational machinery.
Macromolecule solution studies with high brilliance, low background SAXS camera
Authors: Panine Pierre , Desvergne-Bleneau Sandra , Bossan Frédéric , Hoghoj Peter , Mahé Ronan , Lantz Blandine , Rodrigues Sergio
Published: November 2015

Small angle x-ray scattering technique is a powerful method to study the 3D envelope of proteins or the arrangement of individual domains in protein complexes through minimized sample preparation. SAXS is thus becoming a mainstream technique to study macromolecules in solutions in an interdisciplinary approach combined with NMR and Electron Microscopy. This is symbolized by a fast growing number of structures published, and initiatives on SAS structures publication guidelines[1]. Progress in instrumentation also led to emergence of high quality laboratory bio SAXS equipments. We will present the impact of relevant equipment features on structure characterization through data measurements examples on various protein samples. Using a high flux with controlled beam properties (size and divergence) at detector plane is important to achieve sufficient signal to noise at larger wave vectors (Q) range together with the capability to measure large protein complexes (related to minimum wave vector detectable, Qmin). We will be discussing figure of merits for evaluating data quality at high Q range and presenting the impact of incident flux and various detection schemes on such criteria. Data measurements on large protein complexes will be shown highligthing the impact of instrument Qmin. Low backgroung scattering generation inside SAXS camera and low noise detection are other critical requirements for faithful and accurate sample to buffer data subtraction. A new generation of scatterless collimation with variable resolution, and improved sample environments open the door to unprecedented ratios of primary beam intensity to background and to measurements on weakly scattering samples. Impact on data quality will be emphasized. Data processing and struture modeling of various proteins of different sizes acquired with laboratory SAXS camera using low maintenance high brighness source will be presented and compared to synchrotron data.
Small-angle X-ray scattering of BAMLET protein-oleic acid complexes at pH 12
Authors: Rath Emma , Duff Anthony , Knott Robert , Church W.
Published: November 2015

BAMLET and HAMLET represent a new class of compound having unrealised potential for treating a broad spectrum of cancers and some multi-drug resistant bacterial infections (Brinkmann et al. 2013; Marks et al. 2013). These compounds are composed of protein (14 to 84 kDa) and oleic acid (282 Da), the latter being the main active component. Hypothesised molten-globularity makes structural determination by NMR and X-ray crystallography very challenging. We carried out small angle X-ray scattering (SAXS) on BAMLET at pH 12 (Rath et al. 2014), the pH at which the complex can be prepared. SAXS showed that the protein component was an ensemble of extended, irregular, partially-unfolded conformations that varies with the amount of oleic acid incorporated into the complex. Increases in oleic acid concentration (from 1 to 20 molecules of oleate per protein molecule) correlate with increasing radius of gyration (from 21 to 29 Ang) without an increase in maximum particle dimension, indicating decreasing protein density. Three-dimensional models were generated that satisfy the probability distribution function that was derived by indirect Fourier transform of the SAXS data (Figure A). Models for the highest oleic acid content BAMLET (Figure B) indicate a partially unfolded conformation with the majority of the protein mass distributed around the periphery of the complex. Our results suggest that oleic acid inhibits the folding or collapse of the protein component of BAMLET to the globular form. SAXS was not able to identify the structure of the oleic acid component due to the very weak X-ray scattering contrast. However, the results support a model in which BAMLET retains oleic acid by non-specific association in the core of the partially unfolded protein. This represents a new type of lipid-binding protein structure. The structure of BAMLET will guide efforts to incorporate BAMLET into a delivery vehicle with the aim of realising the significant clinical potential of BAMLET.
Low resolution models of membrane proteins in detergent micelles and nanodiscs
Authors: Preu Julia , Safarian Schara , Jähme Michael , Michel Hartmut
Published: November 2015

Membrane transport systems play a crucial role in the regulation of essential cellular functions. Understanding the structural-functional relationship for this class of proteins is of due importance on the background of a detailed view of cellular functions and their regulation. Functionality of membrane proteins is often depending on the lipid environment, also reflected by specifically bound lipid molecules found in membrane protein crystal structures. Therefore, it is favorable to do functional and structural characterization in a lipid-based platform. Nanodiscs, consisting of two copies of an amphipathic scaffold protein wrapped around a lipid bilayer patch, are such a synthetic membrane model system. They represent a more native environment compared to bicelles, liposomes and detergent micelles. Reconstitution of membrane proteins in nanodiscs is bringing them back into their native local environment. A prerequisite for studies of membrane proteins in nanodiscs is a detailed understanding of the reconstitution process and the corresponding driving forces. For an initial structural characterization small angle x-ray scattering (SAXS) is applied, yielding parameters like particle dimensions and low resolution models. For selected membrane transport proteins the structural features of detergent solubilized and nanodisc reconstituted targets are compared. These analyses yield valuable information on the oligomeric state and structural rearrangements upon reconstitution of membrane proteins into lipid surroundings as well as insights into the mechanism of nanodisc assembly.
Structural characterization of transient interactions in DNA mismatch repair
Authors: Pillon Monica , Babu Vignesh , Sutton Mark , Guarne Alba
Published: November 2015

DNA mismatch repair (MMR) is a conserved pathway that safeguards genome integrity by correcting replication errors. The initiation of MMR is orchestrated by two proteins –MutS and MutL. MutS detects replication errors and recruits MutL, a key regulator in coordinating downstream MMR events. The processivity clamp, typically known to tether the replicative polymerase to DNA during DNA synthesis, also has a role in several steps in MMR. We have previously shown that MutL transiently interacts with the clamp and that this complex is important for MMR in vivo. The role of the clamp in eukaryotes and most bacteria is believed to license MutL endonuclease activity. In bacterial organisms where MutL does not have endonuclease activity, such as in Escherichia coli, the clamp also interacts with MutL and this interaction is also important for MMR activity. However, the transient nature of this complex prevents its functional and structural characterization. Here, we develop a method to stabilize the E. coli MutL-clamp complex by engineering a disulfide bond at the known protein complex interface and characterize its structure using small angle X-ray scattering (SAXS). MutL binds the clamp through a consensus motif found in its dimerization domain. Using this domain (MutL-CTD) we monitor complex formation with the clamp. We observe two complexes using SAXS. In one complex the MutL-CTD occupies a single hydrophobic cleft of the clamp, while the other occupies both hydrophobic clefts simultaneously. To identify the physiological complex, we used the full length MutL protein to impose further constraints. Analysis of complex formation suggests that full length MutL binds a single cleft on the clamp. Altogether, our data reveals how MutL interacts with the clamp in the early steps of MMR and this approach could be implemented to structurally characterize other transient complexes, an aspect of structural biology that is largely unexplored.
Fast SAXS data at home--Your personal SAXS beamline
Authors: Del Campo Mark , Criswell Angela , Sasaki Katsunari
Published: November 2015

Small angle X-ray scattering (SAXS) is a useful technique for extracting structural information from biological samples in solution. Our SAXS instrument, the BioSAXS-1000, combines Kratky collimation with confocal optics to achieve maximum X-ray flux on the sample without beam shape corrections. Recently, we offered three new upgrades to the BioSAXS-1000: (1) 2.3 times more flux with the OptiSAXS optic, (2) automatic sample loading, and (3) automatic data analysis. Here, we evaluate the quality of SAXS data collected in short exposure times on the BioSAXS-1000 with these 3 upgrades by using X-rays supplied by an FR-X rotating anode X-ray generator. We measured a concentration series for each of several protein standards (lysozyme, HSA, etc.). Our results show that 1-minute exposures were sufficient to determine the basic structural parameters: radius of gyration, extrapolated intensity at zero angle, and molecular weight. The upgraded BioSAXS-1000 provides a beamline experience in the home laboratory.
X-ray scattering methods for accurate analyses of flexible complexes
Authors: Rambo Robert , Hura Greg , Hammel Michal , Tainer John
Published: November 2015

A grand challenge for structural biology is to efficiently inform macromolecular functions that involve flexible or unstructured regions and require multiple conformational states including membrane proteins and protein-nucleic acid complexes. Small angle X-ray scattering (SAXS) can probe at resolutions sufficient to distinguish conformational states, characterize flexible macromolecules, and screen in high-throughput under most solution conditions. However, methods for analyzing SAXS data and models have restricted progress. We are therefore developing SAXS methods that provide high-throughput, quantitative and superposition-independent evaluation of solution-state conformations and quantitatively define flexibility and disorder. The SIBYLS beamline provides hardware and software to integrate SAXS and crystal structure results. Our SAXS methods aim to improve crystallization and interpretation of crystal structures and NMR structure quality. We have invented a statistically robust method for assessing model-data agreements (chi-square free) akin to cross-validation. We also developed a metric and method for rapid quantitative and comprehensive assessment of molecular similarity suitable to examine functionally important conformational changes. To extend SAXS analysis to low concentrations and complex mixtures, we are developing SAXS with gold nano-crystal labels to enable examination of protein-induced DNA distortions along pathways key to the DNA repair, replication, transcription, and packaging. Collective results suggest SAXS can provide accurate shapes, assembly states, and comprehensive conformations of flexible complexes in solution that inform biology in fundamental ways.
Plasticity and cooperativity of cytokine-receptor assemblies at the cell surface
Authors: Felix Jan , Moharana Kedar , Demunck Steven , Pannecoucke Erwin , Elegheert Jonathan , Verstraete Kenneth , Shkumatov Alexander , Svergun Dmitri , Gutsche Irina , Savvides Savvas
Published: November 2015

Hybrid approaches in structural biology have had a tremendous impact on our ability to tackle complex biological problems including large and flexible protein-protein assemblies. We have been employing creative combinations of X-ray crystallography, Small-angle X-ray Scattering (SAXS) and electron microscopy in conjunction with molecular interaction studies and cellular interrogation of the systems under study to elucidate the structural and mechanistic principles underlying diverse cytokine-receptor assemblies. Our studies have revealed the unexpected structural diversity of such assemblies, and have established that structural plasticity and molecular cooperativity both at the level of the cytokines and the receptors play critical roles in the assembly of signaling complexes. My presentation will provide a coherent overview of how we have tackled cytokine-receptor signalling complexes in a hypothesis-driven manner with the help of hybrid approaches in structural biology.
Automated structural modeling in biological small-angle X-ray scattering
Authors: Svergun Dmitry
Published: November 2015

Small-angle X-ray scattering (SAXS) experiences a renaissance in the studies of macromolecular solutions allowing one to study the structure of native particles and complexes and to rapidly analyze structural changes in response to variations in external conditions. New high brilliance sources and novel data analysis methods significantly enhanced resolution and reliability of structural models provided by the technique (Graewert & Svergun, 2013). Automation of the experiment, data processing and interpretation make solution SAXS a streamline tool for large scale structural studies in molecular biology. The recent developments will be presented including robotic sample changers, pipelines for data processing, computation of structural parameters and ab initio models, classification of the folding states of macromolecules. A prototype of an expert systems allowing for automated generation and assessment of structural models will be considered. A synergistic use of SAXS with the high resolution methods like crystallography and NMR, but also with complementary biophysical and biochemical techniques will be discussed. The problems of validation of SAXS-generated models, and the use of data quality assessment tools for the deposition of the models and experimental data will be discussed. Further perspectives of the hybrid applications of SAXS with other techniques in structural biology will be outlined.
Single crystal diffraction at high energy and high pressure on I15 at DLS
Authors: Casati Nicola , Kleppe Annette , Nestola Fabrizio , Wilhelm Heribert
Published: November 2015

The Extreme Condition beamline (I15) at the Diamond Light Source is a dedicated beamline for powder as well as single crystal diffraction on samples at extreme conditions in pressure or temperature. Single crystal data on either pressurized samples in a diamond anvil cell (DAC) or at ambient conditions are routinely done on a diffractometer scanning φ and ω using X-rays with energies in the range from 20 keV to 80 keV. Depending on the sample beam sizes varying from 20 μm to several 100 μm can be used. Data are recorded with an Atlas CCD (Agilent Technologies) and then treated with the Crysalis software package. In this contribution we highlight the very high accuracy of single-crystals data obtainable at I15 on two examples of single crystals in a DAC (E = 40 keV) and a sample at ambient conditions (E = 60 keV). A single crystal of the binary transition metal compound FeGe (B20 structure, space group P213, Z=4) was studied up to 11 GPa to determine the evolution of the inter-atomic distances (both atoms occupy the 4a Wyckoff positions). More than 200 unique data could be used to refine 7 parameters with an average R1 on all data of ~7%. Very high quality data have also been obtained for single crystals from the field of chemical crystallography, for which not only connectivity but also small bonding features can be detected. For example in l,6;8,13 biscarbonyl[14]annulene the progressive loss of aromatic character could be monitored and, in a special setup, the data allowed for the refinement of an unconstrained multipolar model. The use of 60 keV photons was crucial for an experiment on natural diamonds containing a variety of inclusions. At these energies the absorption of the diamond can be neglected. The aim of the study was to obtain information on possible recurrent crystallographic relationships between the inclusions and the diamond host on a significant number of extremely rare natural diamonds containing minerals.
Lattice dynamics and macroscopic properties in complex metallic alloys
Authors: Lory Pierre-François , de Boissieu Marc , Gille Peter , Johnson Mark , Mihalkovic Marek , Schober Helmut
Published: November 2015

Complex metallic alloys are long-range ordered materials, characterized by large unit cells, comprising several tens to thousands of atoms [1]. These complex alloys often consist of characteristic, cluster building blocks, which in many cases show icosahedral symmetry. Numerous complex phases are known, that can be described in a rather simple way as the periodic or quasi-periodic packing of such atomic clusters. The lattice dynamics of CMAs has been the subject of both theoretical and experimental investigations in view of their interesting macroscopic properties such as low thermal conductivity. In aperiodic crystals in the higher wave-vector regime, theory predicts that the lattice modes are critical: they are neither extended as in simple crystals nor localized as in disordered systems [2]. Experimentally phonons have been studied in different CMAs systems like clathrates, approximant-crystals and quasicrystals. For all of them, acoustic modes are well-defined for wave-vectors close to Brillouin zone centres, but then broaden rapidly as the result of coupling with other excitations [3]. We will present a combined experimental and atomistic simulation study of the lattice dynamics of the complex metallic alloy Al13Co4 phase [4], which is a periodic approximant of the decagonal phase. Particular attention will be paid to the differences between the periodic and `quasiperiodic' directions. Inelastic neutron scattering measurements carried out on a large, single grain on a triple-axis spectrometer will be compared to simulations, focussing on the dispersion relations and the intensity distribution of the S(Q,ω) scattering function, which is a very sensitive test of the model [3]. Simulations are performed with DFT methods and empirical, oscillating, pair potentials [5]. In addition, thermal conductivity calculations, based on the Green-Kubo method, will be compared with measurements, which show a weak anisotropy [6-7]. In this way, the structure-dynamics-properties relation for CMAs is thoroughly explored.
Neutron diffraction at high pressure, low temperature under light irradiation
Authors: Parisiades Paraskevas , Payre Claude , Gonzales Jean-Paul , Laborier Jean-Luc , Bidet Jean-Paul , Lelièvre-Berna Eddy , Allibon John , Lemée-Cailleau Marie-Hélène
Published: November 2015

The exploration of multi-dimensional phase diagrams is a topical subject. However, the simultaneous variation of several control parameters such as temperature, pressure and light irradiation requires a suitably optimized sample environment, particularly when the aim of the experiment is to obtain structural information. We report on a new such sample environment, developed in the context of neutron diffraction measurements, in which the sample can be submitted to pressures up to 7 kbar, temperatures down to 1.7 K and light irradiation in the 660 to 852nm wavelength range, simultaneously. The Ti-Zr alloy pressure cell combines a high mechanical resistance over a wide temperature range with an acceptable neutron background level. The pressure medium is helium gas, ensuring the best possible hydrostatic conditions over a very broad temperature range. The low-temperature environment is obtained from an ILL-type `orange cryostat'. After focusing into an optical fiber, laser light is transmitted to the sample through a sapphire optical window implemented in the pressure cell. The laser flux density at the sample position is of ~30mW/cm2. The geometry of the set-up is optimized to offer a wide optical access (+/- 500vertical, +/-1650horizontal), particularly well suited for Laue neutron diffraction techniques. First results obtained on the pressure-photo-induced spin crossover of a model coordination complex will be presented.
Non-crystalline samples under high-pressure conditions
Authors: Li Liangliang , Li Renfeng , Liu Lisa Luhongwang , Liu Arthur Haozhe , Chupas Peter , Chapman Karena , Yu Tony
Published: November 2015

Taking advantage of synchrotron x-ray diffraction, PDF and tomographic techniques, the P-V curve of non-crystalline samples were studied under high-pressure conditions. Two element and several metallic glass cases were performed. The procedure of crystallization of amorphous Se upon compression at room temperature, which was studied in diamond anvil cell combined synchrotron x-ray PDF and 3D imaging techniques; the melting and solidification procedure of Ga in large volume press at room and high temperature; and complicated crystallization, re-rystalization, melting behavior of Ce-based metallic glass, will be presented to show the capability of revealing structure and dynamics behaviors in P-V-T-t domains using these advanced techniques.
Structure, magnetic and magnetoelectric properties of Ca(Co,Mn)Ge2O6pyroxenes
Authors: Ding Lei , Colin Claire , Darie Céline , Bordet Pierre
Published: November 2015

Compounds belonging to the Pyroxene family are well known as rock-forming minerals, and have thus drawn substantial interest by mineralogists. In this family of general chemical formula AM(Si, Ge)2O6, A is usually an alkali metal monovalent cation or a divalent alkaline earth cation, and B may be a trivalent or divalent transition metal cation. Among pyroxene compounds, the monoclinic clinopyroxenes are characterized by isolated one-dimensional chains of MO6 octahedra linked by edge-sharing. Due to this specific arrangement, clinopyroxene compounds where M is a magnetic transition metal cation have attracted considerable attention in recent years. Investigations revealed that these compounds present a rich diversity of intriguing low-dimensional magnetic properties. The existence and possible interplay of low dimensionality and magnetic frustration results in multiferroic and/or magneto- electric (ME) properties. We have undertaken the study of the CaCo1-xMnxGe2O6 (0<x<1) solid solution to investigate the effect of the Co/Mn substitution on the magnetic and ME properties by means of neutron diffraction, magnetic and magneto-electric measurements. In CaCoGe2O6, strong FM interactions within the M chains dominate the AFM coupling between the chains. In contrary, the magnetic structure of CaMnGe2O6 is made of AFM chains coupled ferromagnetically. These two commensurate magnetic structures adopt two different magnetic point group that allows for linear (for Mn) and bilinear (for Co) magnetoelectric effect. For the Co/Mn solid solution, a competition exists between FM and AFM coupling within and between the chains. This results in the apparition of a spin glass state above the long range magnetic transition and for certain composition in a magnetic structure described by two propagation vectors. We will present detailed investigation of the relationship between structure, magnetic structure and ME properties for this rich series of ME compounds.
Electric polarization from spiral order below 200K in multiferroic YBaCuFeO5
Authors: Morin Mickael , Scheptyakov Denis , Keller Lukas , Rodríguez-Carvajal Juan , Scaramucci Andrea , Spaldin Nicola , Kenzelmann Michel , Pomjakushina Ekaterina , Conder Kazimierz , Medarde Marisa
Published: November 2015

Ferroelectric materials have been known for almost one century [1]. While their potential for applications was rapidly recognized, the possibility of combining ferroelectricity with magnetic order -preferably with ferromagnetism- has resulted in an enormous deal of interest during the last decade. Several new materials combining both types of order have been recently reported, although their promising multifunctionalities have been obscured by two facts: on one side, most of them are antiferromagnetic; on the other, their transition temperatures, typically below 40K, are too low for most practical applications. The oxygen-defficient double perovskite YBaFeCuO5 constitutes a remarkable exception. Spontaneous electric polarization has been recently reported to exist below an unusually high temperature of TC ≍ 200K [2] coinciding with the occurrence of a commensurate - to - incommensurate reorientation of the Fe3+ and Cu2+ magnetic moments [3,4]. From a more fundamental point of view the observation of incommensurable magnetic order in a tetragonal material at such high temperatures is rather surprising. In particular, the nature of the relevant competing magnetic interactions and its possible link to low dimensionality or geometrical frustration is not understood at present. Although the existence of the spin reorientation in this material is known since 1995 [3] the low temperature magnetic structure has not yet been solved. Using neutron powder diffraction we have recently been able to propose a spiral model which satisfactorily describes the measured magnetic intensities below TC. Further, investigation of the crystal structure showed the existence of small anomalies in the lattice parameters and some interatomic distances at TC. The relevance of these findings for the magnetoelectric coupling, the direction of the polarization, the modification of the different exchange paths in the structure and the stabilization of the incommensurate magnetic order below TC is discussed.
Magnetic structure of the chiral triangular magnet MnSb2O6
Authors: Sato Taku , Nambu Yusuke , Hong Tao , Matsuda Masaaki , Cao Huibo , Kinoshita Masataka , Seki Shinichiro , Ishiwata Shintaro , Tokura Yoshinori
Published: November 2015

Incommensurate helical (or cycloidal) magnetic structure may have left- and right-wound states (helicity), which are in principle equally populated in a magnet with inversion symmetry. In addition, for a Heisenberg triangular antiferromagnet, clockwise and counter-clockwise rotations of the 120 degree spin structure provide another intriguing degree of freedom. Hence, a triangular magnet that has incommensurate helical ordering along the stacking direction will show intriguing interplay of the helicity (of the helical structure) and chirality (in the triangular plane). Such phenomenon is, however, rarely studied in the past since only one example, the Ba3NbFe3Si2O14 langathite, has been known to date [1]. In this work, we study MnSb2O6, which consists of distorted triangular lattice stacking along the c-axis [2,3]. MnSb2O6 belongs to the space group P321, and hence lacks inversion symmetry. Due to this fact, unique selection of the helicity and chirality may be expected. However, the earlier studies were carried out using unpolarized neutron diffraction with mostly the powder sample, and thus helicity and chirality selection cannot be concluded. Here, we have performed single-crystal diffraction experiment using polarized neutrons in addition to the unpolarized ones, and have succeeded in determination of the magnetic structure of MnSb2O6. The resulting magnetic structure is nearly cycloidal with the magnetic modulation vector q = (0, 0, 0.182) (see figure below). The spin rotation plane is, however, inclined from the ac-plane toward the b-axis for approximately 30 degrees. Polarization analysis indicates that both the helicity of the (nearly-) cycloidal structure and chirality of the in-plane 120 degree structure are uniquely selected. The 30 degree inclination from the ac-plane is a key finding of this work, allowing new kind of multiferroicity in this material.
Ferroelectricity and magnetic orderings in Delafossite family compounds
Authors: Terada Noriki
Published: November 2015

Since discovery of the ferroelectric polarization induced by magnetic field in CuFeO2, delafossite family compounds have attracted much attention, because some theoretical formula, which had been presented, could not explain the ferroelectric polarization of CuFeO2. We have been investigating correlation among their magnetic orderings, lattice symmetry and ferroelectric polarization in AFeO2 (A=Cu, Ag, Na) systems. In CuFeO2, the ferroelectric polarization is induced by chemical substitutions for Fe sites in CuFe1-xBxO2 (B=Al, Ga, Rh, Mn) as well as magnetic field. The magnetic structure in the ferroelectric phase is proper screw type with magnetic point group 21' determined by the neutron diffraction experiments.[1] The ferroelectric polarization parallel to the propagation vector in CuFeO2 can be explained by both extended inverse-Dzyaloshinsky-Moriya(DM) effect and d-p hybridization mechanism. We have also demonstrated that the spin-orbit interaction in Fe ions, coupling spin and orbital orders, plays a crucial role to the ferroelectricity in both of which break the crystal symmetry, by observing incommensurate 2q orbital modulation in the ferroelectric phase of CuFe1-xGaO2 by soft X-ray resonant diffraction.[2] When nonmagnetic Cu ions on A-site are substituted by Ag or Na ions, the magnetic orderings are completely modified from CuFeO2. In AgFeO2, cycloid type magnetic structure with m1' point group is stabilized, which is concomitant with ferroelectric polarization, as the lowest temperature phase in zero-field.[3] Also in alpha-NaFeO2, the other type of cycloidal ordering (m1') appears mainly in magnetic field. In these systems, taking account of extended inverse DM effect, ferroelectric polarization direction is along general direction in the ac plane and does not follow the well-known inverse DM formula. In this presentation, I will discuss the relationship between the magnetic ordering and ferroelectricity in these delafossite family compounds.
6D electron microscopy: combining real-space and reciprocal-space tomography
Authors: Eggeman Alexander , Krakow Robert , Midgley Paul
Published: November 2015

STEM and TEM-based tomography has been used widely to study the 3D morphology of a wide range of materials. Similarly reciprocal space tomography in which a tilt-series of diffraction patterns are acquired offers a powerful method for the analysis of the atomic structure of crystalline materials. The natural progression is to combine these techniques into a complete three dimensional morphology and crystallography data set, allowing both features to be studied simultaneously. Using a tilt series of scanning precession electron diffraction measurements from a commercially available Ni-base superalloy as an example, the complete reciprocal lattice orientation for a number of components embedded within the matrix could be determined. It was straightforward to identify reciprocal lattice vectors that allowed dark-field images representing each phase to be produced post-acquisition. In turn these were combined using geometric tomography methods to yield a 3-D tomogram of the superalloy. Imaging these phases using conventional ADF STEM tomography would potentially be challenging given the compositional similarity between the different phases. From the combined dataset the spatial distribution of the component phases could be easily recovered but more importantly the orientational relationships between these different components could be unambiguously determined. In this way the thermo-mechanical history of the sample could be inferred from the arrangement of coherent and semi-coherent interfaces and a previously unreported crystallographic registry between metal carbide (MC) and the matrix f.c.c. phases could been identified. The possibilities for development and applications of this technique will be discussed further.
Electron diffraction tomography for structure analysis of nanomaterials
Authors: Gorelik Tatiana
Published: November 2015

For decades electron crystallography had not been considered as a reliable method of structure analysis, being more a curious scattering experiment. The introduction of electron diffraction tomography brought to light a novel structure analysis technique able to resolve structures of nanocrystalline samples, not assessable by other methods. Electron diffraction tomography is based on the systematically sampling of the reciprocal space by means of electron diffraction. Being in principle very close to single crystal X-ray diffraction experiment, electron diffraction has nevertheless specialities, which make it in a first row an attractive alternative technique, on the other side a demanding experiment and not straight-forward data analysis. The power of electron diffraction tomography method has been clearly demonstrated within the last years – a number of crystalline structures of various material types has been solved. The achievements and potentials of electron diffraction tomography method will be presented, supported by numerous structure analysis examples.