bluuebunny/crossref_metadata_2025 huggingface dataset:
New intermetallic La117Ru57Sn112.
Authors: Gribanova Vera , Gribanov Alexander , Murashova Elena , Kalmykov Konstantin
Published: November 2015

The new ternary compound with giant unit cell La117Ru57Sn112 has been yielded by interaction between pure components lanthanum, ruthenium and tin and investigated by X-ray diffraction and scanning electron microscopy (SEM) in combination with energy dispersive X-ray spectroscopy (EDX) means. Previously, intermetallics with cobalt of similar composition and structure were found in the ternary systems and Dy-Co-Sn and Pr-Co-Sn – Dy117Co57Sn112 and Pr117Co57Sn112 respectively [1, 2]. The intermetallic La117Ru57Sn112 crystallizes in a cubic Dy117Co57Sn112 type structure with space group Fm-3m (No. 225) and lattice parameter a = 31.529(5). A single-crystal suitable for the X-ray measurements was isolated from the of the equiatomic alloy La33.3Ru33.3Sn33.4. The structure was solved by means of direct methods and refined using the SHELXS-97 and SHELXL-97 programs (R1 = 0.033 for 1042 Fo > 4σ(Fo) and 0.061 for all collected data). The additional sample of the La40.2Ru19.9Sn39.9 composition was prepared and investigated X-ray by powder diffraction technique (CuKα1 radiation, 5 < 2Θ < 900). The collected intensities data were refined by the Rietveld method using the La117Ru57Sn112 single crystal model and FullProf program. Based on a minimum of differences between the observed and calculated theoretically intensities one can judge the good convergence results.
The Protein Geometry Database: exploring protein conformational features
Authors: Tronrud Dale , Karplus P.
Published: November 2015

Have you ever seen a feature in your structure and asked, "I wonder how novel this is?" For instance a residue with a certain phi/psi angle, or an Asp residue followed by three further residues that make a tight turn centered on the side chain, or a peptide unit deviating 25° from planarity? If so, the Protein Geometry Database (PGD) is something you'll want to know about. The PGD web service (pgd.science.oregonstate.edu, Berkholz 2009a) manages access to a database containing the geometric details of 1.9 million amino acids. Working with the PGD involves two easy steps - using a search form to find a set of peptides matching your interests, and analyzing the geometric details of the set. The search form allows you to find examples of peptide fragments that have any specified combination of backbone conformations and sequence. Filtering can also be performed based on side chain conformations, or bond angles. You can also specify the quality of models included in the search. Once a set of peptides has been identified, their geometric properties can be analyzed on the web site. You can look at the averages and standard deviations for any bond length, bond angle, or conformational angle, or you can explore relationships between properties by displaying highly customizable plots. An option to export the search results allows you to perform any further analyses you might devise. We will show how the PGD has been used to develop a Conformation Dependent Library of main chain bond angle targets for crystallographic refinement (Berkholz 2009b), as well as to advance our understanding of peptide non-planarity, and of conformational preferences for pairs of residues and of cis-peptides. We will also describe how simple searches for outliers in bond lengths and angles are a powerful validation tool that can both uncovering errors in PDB models and can lead to the discovery of very interesting and real deviations from what is normally considered ideal geometry.
A knowledgebase of macromolecular non-covalent interactions including precision
Authors: Helliwell John , Gurusaran Manickam , Sekar Kanagaraj
Published: November 2015

We have established a user knowledge base centred in Bangalore, but obviously accessible from anywhere in the world, for displaying ion pair distances for any protein deposited in the Protein Data Bank. We have published a description, its theoretical basis and examples of its use in IUCrJ [1]. The special characteristic is that the precisions on these distances is also displayed. These are based on the Diffraction Precision Index (DPI) approach [2] adapted to the pair of atoms involved in the non-covalent interaction and their specific B factors. Thus the display of the true precision can readily be seen by the user. We described other situations [1] where this approach could be used namely where restraints of a protein model refinement are not used such as metal ligand sites in proteins and protonation state determinations i.e. where a bond distance restraint is explicitly removed. We will report firstly on the ion pairs knowledgebase, as recently published, but with more examples from the user point of view. This will include a discussion of the range of precisions of the protein structures in the PDB as exemplified by using the DPI. Secondly, progress towards a knowledgebase, again including precision, for metal ligand interactions in the structures of metalloproteins and nucleic acids will be described.
Rule and Root-based Metadata-Ecosystem for Structural Bioinformatics & Facebook
Authors: Bhat Talapady
Published: November 2015

Despite the widespread efforts to develop flexible formats such as PDB, mmCIF, CIF., to store and exchange data, the lack of best practice metadata pose major challenges. Readily adoptable methods with demonstrated usability across multiple solutions to create on-demand metadata are critical for the effective archive and exchange of data in a user-centric fashion. It is important that there exists a metadata-ecosystem where metadata of all structural and biological research evolve synchronously. Previously we described (Chem-BLAST, http://xpdb.nist.gov/chemblast/pdb.pl) a new `root' based concept used in language development (Latin & Sanskrit) to simplify the selection or creation of terms for metadata for millions of chemical structures from the PDB and the PubChem. Subsequently we extended it to text-based data on Cell-image-data (BMC, doi:10.1186/1471-2105-12-487). Here we describe further extension of this concept by creating roots and rules to define an ecosystem for composing new or modifying existing metadata for demonstrated inter-operability. A major focus of the rules is to ensure that the metadata terms are self-explaining (intuitive), highly-reused to describe many experiments and also that they are usable in a federated environment to construct new use-cases. We illustrate the use of this concept to compose semantic terminology for a wide range of disciplines ranging from material science to biology. Examples of the use of such metadata to create demonstrated solutions to describe data on cell-image data will also be presented. I will present ideas and examples to foster discussion on metadata architecture a) that is independent of formats and b) that is better suited for a federated environment c) that could be used readily to build components such as resource description framework (RDF) and Web services for Semantic web.
Crystal structures of bacterial flavin reductase GraD and its complex with NADH
Authors: Yamauchi Takae , Fujii Tomomi , Yoshida Masahiro , Oikawa Tadao , Hata Yasuo
Published: November 2015

Rhizobium sp. strain MTP-10005 uses the aromatic compound γ-resorcylate as a sole source of carbon and energy for growth. Resorcinol hydroxylase, which converts resorcinol to hydroxyquinol, plays an important role in the aerobic microbial catabolism of γ-resorcylate. Resorcinol hydroxylase from Rhizobium sp. strain MTP-10005 is a two-component enzyme consisting of the reductase and the monooxygenase components. The reductase component (GraD) is an oxidoreductase containing a flavin molecule as a cofactor. GraD catalyzes the NADH-dependent reduction of free FAD according to a ping-pong bisubstrate-biproduct mechanism. The reduced FAD is then used by the monooxygenase component GraA to hydroxylate resorcinol to hydroxyquinol. We have determined the three-dimensional structures of recombinant GraD with a bound FAD and in complex with NAD. GraD was crystallized at 293 K by the sitting-drop vapour-diffusion method using a precipitant solution containing 13 - 14% (w/v) PEG 2000, 6 - 9% (v/v) 2-propanol, 100 mM sodium citrate pH 5.6, 100 mM DTT and 200 μM FAD. The approximate dimensions of the obtained crystals were 0.1 × 0.1 × 0.15 mm3. The crystal diffracted to 1.8Å and belongs to space group P41212 with unit-cell parameters of a = b = 77.8 Å and c = 124.2 Å. The crystal structure has been determined by the molecular replacement and refined at 1.8 Å resolution. GraD exists as a homodimer, and each monomer contains an FAD. The probable binding site for NADH is covered with the N-terminal sub-domain in chain A, whereas the site is completely exposed to bulk solvent in chain B. The NAD-complex crystals were prepared by soaking the GraD crystals in the reservoir solution supplemented with NADH. The crystal diffracted to 1.8 Å, and the crystal structure was determined at 1.8 Å resolution. The Fo-Fc maps for the crystal soaked with NADH showed the electron densities corresponding to the nicotinamide ring and the adenyl moiety in chain B.
Tubulin tyrosine ligase - structural and functional studies
Authors: Szyk Agnieszka , Deaconescu Alexandra , Piszczek Grzegorz , Roll-Mecak Antonina
Published: November 2015

Microtubules are polymers essential for cell morphogenesis, cell division and intracellular transport. This polymer's basic building block is the α/β tubulin heterodimer, which associates head-to-tail and laterally to form the microtubule. Tubulin is subject to diverse, abundant and evolutionarily conserved post-translational modifications that mark subpopulations of microtubules. The highest density and variety of post-translational modifications are found in neurons or cilia. Not surprisingly, tubulin modification enzymes have been linked to human diseases including cancers and neurodegenerative disorders. We will present our recent work using a combination of X-ray crystallography, small angle X-ray scattering and functional assays to investigate the mechanism of tubulin tyrosine ligase (TTL). TTL catalyzes the ATP-dependent post-translational addition of a tyrosine to the C-terminal end of detyrosinated α-tubulin. The detyrosination/tyrosination cycle regulates recruitment of motors and proteins that track with the growing end of the microtubule. TTL function is essential for neuronal development and reduction in TTL levels is strongly associated with aggressive tumors resistant to chemotherapy. Our first X-ray crystal structure of TTL, defines the structural fold of the TTL-like family of tubulin-modifying enzymes. We show that TTL recognizes tubulin via a dual strategy: it engages the tubulin tail through low-affinity, high-specificity interactions through a conserved positively charged surface, and co-opts what is otherwise a homo-oligomerization interface in structurally related enzymes to form a tight hetero-oligomeric complex with tubulin. TTL forms an elongated complex with the tubulin dimer and prevents incorporation of the dimer into microtubules by capping the tubulin polymerization interface. Interestingly, TTL and stathmin, a ubiquitously expressed tubulin sequestering protein, compete for tubulin binding in vitro and stathmin inhibits tubulin tyrosination. These results suggest that TTL and stathmin have either a partially overlapping footprint on the tubulin dimer or that stathmin induces a tubulin conformation incompatible with stable TTL binding.
Structural studies on dehydroshikimate dehydratase
Authors: Peek James , Christendat Dinesh
Published: November 2015

The soil bacterium, Pseudomonas putida, is capable of using the alicyclic compound quinate as a sole carbon source. During this process, quinate is converted to 3-dehydroshikimate, which subsequently undergoes a dehydration to form protocatechuate. The latter transformation is performed by the enzyme dehydroshikimate dehydratase (DSD). We have recombinantly produced DSD from P. putida and are currently performing x-ray crystallographic studies on the enzyme to gain structural insight into its catalytic mechanism and mode of substrate recognition. Initial crystals of DSD diffracted to 2.7 Ä resolution, but exhibited strong twinning. A redesigned construct has recently yielded crystals that diffract to similar resolution, but with a significantly reduced tendency toward twinning. Interestingly, sequence analysis of P. putida DSD reveals that the protein is in fact a fusion of two distinct domains: an N-terminal sugar phosphate isomerase-like domain associated with DSD activity, and a C-terminal hydroxyphenylpyruvate dioxygenase (HPPD)-like domain with unknown functional significance. Structural characterization of the protein may provide novel insight into the functional relevance of the unusual HPPD-like domain.
Design and structure determination of thermally stable adenylate kinase variants
Authors: Moon Sojin , Jung Du-kyo , Phillips George , Bae Euiyoung
Published: November 2015

Thermally stable proteins are desirable for research and industrial purposes, but redesigning proteins for higher thermal stability can be challenging. A number of different techniques have been used to improve the thermal stability of proteins even though the extent of stability enhancement remains unpredictable and is often not significant. Here, we systematically tested the effects of multiple stabilization techniques on a single protein, thereby providing an integrated approach to protein thermal stabilization. Using mesophilic adenylate kinase as a model, we identified stabilizing mutations based on various stabilization techniques, and generated a series of adenylate kinase variants by introducing mutations both individually and collectively. The redesigned proteins displayed a range of increased thermal stabilities, the most stable of which was comparable to a naturally-evolved thermophilic homologue with more than a 25 degree increase in its thermal denaturation midpoint. We also solved crystal structures of three representative variants including the most stable variant, to confirm the structural basis for their increased stabilities. These results provide a unique opportunity for systematically analyzing the effectiveness and additivity of various stabilization mechanisms, and they represent a useful approach for improving protein stability by simultaneously optimizing global non-covalent interactions and local structural entropy.
Crystal structures of human dihydroxyacetone kinase
Authors: Kwok Jane , Kotaka Masayo
Published: November 2015

Dihydroxyacetone (Dha), also known as glycerone, is a metabolically active carbohydrate. Dha kinase (DAK) is highly conserved enzyme that utilizes mainly Dha as substrate. In bacteria, DAK converts dihydroxyacetone to dihydroxyacetone phosphate in the glycerol fermentation pathway. In higher eukaryotes, DAK can accomplish two enzymatic activities, namely, ATP-dependent dihydroxyacetone phosphorylation and FMN cyclization. The biological significance of cFMN is still not identified. Possible speculations of the functions are as signaling molecule, minor redox flavocoenzyme or intermediate of a degradative pathway for FAD. In order to understand the mechanisms of the FMN cyclizing reaction, we here present the crystal structures of hDAK soaked with FAD and its apo state. The crystals are diffracted up to 2.0 Å in space group C2 with a dimer in each asymmetric unit. hDAK contains 2 domains: L domain and K domain, joined together by a linker region. In the FAD and Mn2+ soaked DAK structure, AMP is seen on K domain. The second cyclization product, cFMN, however is diffused during soaking and cannot be seen in the density map. Mammalian DAK is also shown to be a negative regulator of MDA5. MDA5 is a cytoplasmic protein that has important role in viral RNA detection and initiate innate immune response. Specifically, MDA5 undergoes conformational change upon viral RNA binding and allows its N terminal CARD domain to expose and bind to the CARD domain of the downstream signaling protein IPS-1. IPS-1 is essential for the activation of proinflammatory cytokines and type 1 interferon. Pulldown assays indicated that MDA5 CARD domain is responsible for the interaction of IPS-1 CARD as well as hDAK. The competition and the exact mechanisms are still unknown. We shall apply biophysical techniques such as ITC and SPR to quantify the binding parameters. Last but not least, to crystallize the complex in order to provide a clear molecular detail of the interaction between MDA5 and its binding partners.
Structural studies of Plasmodium falciparum GTP:AMP phosphotransferase
Authors: Ko Reamonn , Kotaka Masayo
Published: November 2015

Malaria is a global health concern accounting for approximately 219 million cases and an estimated 660 000 deaths in 2010[1]. The most fatal strain of malarial parasite, Plasmodium falciparum is found to contain 3 adenylate kinases (PfAK1, PfAK2 and PfGAK). Adenylate kinases are important enzymes that essentially catalyze and regulate energy metabolism processes. PfAK1 and PfAK2 catalyze the reversible MG2+ reaction ATP + AMP -> 2ADP whereas, the PfGAK catalyzes the Mg2+ dependent reaction GTP+AMP -> ADP+GDP. PfGAK was successfully cloned and expressed in Escherichia Coli. Furthermore, using 2-step chromatography the enzyme was purified and screened for crystallization conditions. PfGAK crystallized into brown hexagonal crystals and diffracted at a 2.9 Å resolution. The apo-structure have been solved and now we are working on determining the structure for PfGAK when bound to its substrate analog GP5A.
Structural snapshots of GALC: The Krabbe Disease enzyme
Authors: Hill Chris , Graham Stephen , Spratley Samantha , Read Randy , Deane Janet
Published: November 2015

Glycosphingolipids are ubiquitous components of mammalian cell membranes, and defects in their catabolism by lysosomal enzymes cause a diverse array of diseases. Deficiencies in the enzyme β-galactocerebrosidase (GALC) cause Krabbe disease, a devastating genetic disorder characterized by widespread demyelination and rapid, fatal neurodegeneration[1]. Many disease-causing mutations throughout the GALC gene have been identified; rather than rendering the enzyme catalytically incompetent, many of these are predicted to destabilise the protein, compromising lysosomal delivery by causing retention in the endoplasmic reticulum. In these cases, pharmacological chaperone therapy (PCT) may be an appropriate treatment strategy, whereby the specific binding of a small molecule may stabilise folding of the mutant protein sufficiently to correct trafficking defects. Here we present a series of high resolution crystal structures that illustrate key steps in the catalytic cycle of GALC, including enzyme-substrate, enzyme-intermediate and enzyme-product complexes[2]. These structures reveal active site conformational changes accompanying the catalytic steps and provide key mechanistic insights. Building on this, we identify two candidate molecules that stabilise GALC by specific binding to the active site. The nature of several disease-causing missense mutations is also explored using secretion and activity assays, and we show that mutations can be classified into two groups based on defects in catalysis or trafficking. Overall, this study provides an atomic framework for the rational design of GALC pharmacological chaperones, and helps to identify which mutations may be suitable for PCT, bringing the prospect of a drug-based therapy one step closer.
NRPS condensation domain–substrate studies using X-ray crystallography
Authors: Bloudoff Kristjan , Schmeing Thomas
Published: November 2015

Nonribosomal peptide synthetases (NRPSs) are a family of large multimodular enzymes that synthesize structurally and functionally diverse peptides including siderophores, toxins, agriculturally-important compounds and pharmaceutically-important compounds. The condensation (C) domain is responsible for peptide bond formation, the central chemical step in nonribosomal peptide synthesis. Here we present the crystal structure of the first condensation domain of the calcium-dependent antibiotic (CDA) synthetase (CDA-C1) from Streptomyces coelicolor soaked with a small molecule compound representing the acceptor substrate. To increase the likelihood of complex formation, we designed the compound to contain a free thiol group in order to form a covalent bond between the substrate and a cysteine residue of the CDA-C1. The tethering of the substrate to the active site mimics delivery of substrate to the active site by the NRPS PCP domain, and the disulfide bond it forms with the protein will ensure a high local concentration of substrate. Initial maps, calculated from diffraction datasets collected at the home source, indicated density corresponding to the presence of substrate at the active site. This result, along with activity assay data, will help implicate residues important to enzyme catalysis and substrate specificity. In all, these studies will help characterize C domain function in NRPSs and potentiate the use of NRPSs in bioengineering experiments to produce novel or improved therapeutics.
Remodeling of the AAA+ ATPase p97 by the UBX Adaptor Protein ASPL
Authors: Heinemann Udo , Roske Yvette , Arumughan Anup , Wanker Erich
Published: November 2015

The hexameric mammalian AAA+ ATPase p97, also known as VCP (valosin-containing protein; CDC48 in yeast), is a very abundant cytosolic protein and serves a wide variety of cellular functions. p97 is a central component in endoplasmic reticulum-associated degradation (ERAD) of proteins where it delivers ubiquitinated ERAD substrates to the proteasome. In addition, cellular roles of p97 in organelle membrane fusion, mitosis, DNA repair and suppression of apoptosis have been described. These different functions are linked to the binding of adaptor proteins to p97. Many of these adaptors contain ubiquitin regulatory X (UBX) domains. ASPL (alveolar soft part sarcoma locus, also known as TUG) was recenty identified as a p97 adaptor protein. As shown by crystal structure analysis, ASPL uses a substantially extended UBX domain for binding to the N domain of p97 where a lariat-like, mostly α-helical extension wraps around one subunit of p97. By this binding ASPL triggers the dissociation of functional p97 hexamers and the formation of p97:ASPL heterotetramers with 2:2 stoichiometry, leading to inactivation of the AAA+ ATPase. The p97-ASPL interaction in the heterotetramer is very tight, but p97 hexamer dissociation and heterotetramer formation may be suppressed by single-site mutations at p97-ASPL interfaces. p97 hexamer dissociation and p97-ASPL heterotetramer formation are linked to reduced ATPase activity of p97, cellular accumulation of ERAD substrates and apoptosis induction. To the best of our knowledge, this is the first time that the structural basis for adaptor protein-induced inactivation by hexamer dissociation of p97 and, indeed, any AAA+ ATPase has been demonstrated. This observation has far reaching implications for AAA+ ATPase-regulated processes.
Analysis of macromolecular flexibility in solution by combining SAXS with MX
Authors: Tria Giancarlo , Kachala Mikhail , Svergun Dmitri
Published: November 2015

Proteins containing significant disordered regions are difficult for crystallization. Consequently, individual structured domains or subunits are often crystallized to determine their high resolution structures. These structures, not containing the disordered parts, are available from the protein databases. Small-Angle X-ray Scattering (SAXS) in solution is a complementary structural technique offering the possibility to characterize full length proteins including inter-domain disordered regions. Modern approaches for the analysis of the SAXS data from flexible systems utilize the representation of the system as ensembles of co-existing structures (e.g. Ensemble Optimization Method (EOM), Bernado et al. 2007). Here, the high resolution models of the domains are employed as rigid bodies together with the flexible parts represented by chains of dummy residues in order to construct models covering the configurational space of the full length proteins. Until now, the use of the ensemble approach was mostly limited to relatively simple cases like single chain proteins. We present improvements for the SAXS modeling including the possibilities to characterize flexible particles for complicated scenarios, in particular, for the cases when disorder comes in combination with point group symmetry. A new strategy for missing sections generation allows a rapid and accurate construction of the full length protein. Further, two metrics, Rflex and Rrat, are introduced for a quantitative assessment of the EOM results. Rflex is used as a measure of flexibility – based on the concept of entropy (information communication) – whereas Rrat is employed as a control parameter to detect potential artifacts. These developments implemented in the new version EOM 2.0 further promote the hybrid approach synergistically employing SAXS and MX in the analysis of complicated flexible systems. The capacity of the enhanced method will be illustrated by practical examples.
Combining SAXS with Rosetta for Identification of Native-like Protein Complexes
Authors: Sønderby Pernille , Peters Günther , Bukrinski Jens , Harris Pernille
Published: November 2015

It is well-known that recombinant human serum albumin (rHSA) has the ability to stabilize proteins in solution preventing protein adsorption, aggregation and oxidation. For this reason, rHSA is used as an excipient in the formulation of protein pharmaceuticals. To shed light on the molecular interactions, we have studied a variety of protein drugs that are known to bind to rHSA and thereby being stabilized. We observe that the interactions depend on protein concentrations and differ significantly between protein drugs. One approach to study these systems on a molecular level is the combination of small angle X-ray scattering (SAXS) and in-silico modelling. SAXS can be used to identify the overall shape of proteins and protein complexes and ab initio models can be derived from the scattering profile using programs such as Dammif [1]. These programs allow us to assess the overall conformation of the macromolecular structures, but cannot provide detailed information on the molecular level regarding protein-protein interfaces of the complexes. Here, the Rosetta modelling suite, a multipurpose software suite, can be utilized to perform protein-protein docking and to study the complexes. The challenge in using the Rosetta docking tool [2] is the difficulties in efficiently identifying the native-like structure. For better identification we apply SAXS constrains during the docking procedure. Although the method has been applied previously [3], no benchmarking has been published regarding the relative success of using SAXS constrains. We therefore have conducted an elaborate benchmarking, where we have used SAXS constrains for determination of complexes of non-identical components using the Rosetta docking protocol. A pool of complex structures has been chosen to evaluate the difference between conventional docking and docking performed using SAXS constrains. This allows us to optimize the parameters in the protocol and pave the way to study unknown complex structures.
Structural studies on leukotriene A4 hydrolases reveal their catalytic mechanism
Authors: Hasan Mahmudul , Rinaldo-Matthis Agnes , Thunnissen Marjolein
Published: November 2015

Vertebrate leukotriene A4 hydrolases are zinc metalloenzymes with an epoxide hydrolase and aminopeptidase activity belonging to the M1 family of aminopeptidases. Bestatin, an amino peptidase inhibitor, can inhibit both the activities. The human enzyme produces LTB4, a powerful mediator of inflammation and is implicated in a wide variety of rheumatoid diseases. The yeast homolog scLTA4H contains only a rudimentary epoxide hydrolase activity. Both the structure of the human enzyme and recently the structure of scLTA4H and have been solved to investigate the molecular architecture of the active site both with and without inhibitor Bestatin. The structure of scLTA4H shows large domain movements creating an open active site. In the human enzyme the LTA4 binding side is a narrow hydrophobic channel. Upon inhibitor a domain shifts occurs and the final binding pocket is formed. The fact that scLTA4H displays this induced fit is an interesting observation. Many members of the M1 family seem to display a certain degree of induced fit, a feature, which however, has never been observed for humLTA4H. Our recent solution SAXS studies show that humLTA4H does not make any conformational changes upon inhibitor binding which is consistent with our previous speculation that it functions by a lock and key mechanism rather than induced fit and is better suited to supply the protective and precise environment for hydrolysis of LTA4 into LTB4. On the other hand Xenopus LTA4H shows conformational change in the higher/wide angular region ( >1 nm-1) and decrease in Porod volume of approximately 20 nm3 but no change in Rg or Dmax was observed. It is also observed that like in crystal structure Xenopus LTA4H forms dimer in solution. Similarly scLTA4H forms dimer in solution, which is unlike the crystal structure, and also make conformational changes upon inhibitor binding. Taken together, Xenopus and scLTA4H makes more compact form, with decrease in flexibility, to perform it's catalytic action.
X-ray diffraction analysis of homodimeric yeast hexokinases
Authors: Kuettner Bartholomeus , Kettner Karina , Kriegel Thomas , Sträter Norbert
Published: November 2015

Yeast hexokinases are described in textbooks as classical open/close-switch monomeric enzymes. The hexokinase isoenzymes ScHxk1 and ScHxk2 of the budding yeast Saccharomyces cerevisiae share 77 % sequence identity. They exist in either an open or closed conformation, however, the published states were not of the same isoform. Crystal structures of the hexokinase KlHxk1 of the milk yeast Kluyvermyces lactis demonstrated open/close states of the same yeast hexokinase isoenzyme for the first time. KlHxk1 has 70 or 73 % sequence identity with ScHxk1 or 2, respectively. ScHxk2 and KlHxk1 contain an N-terminal binding stretch for the transcriptional repressor Mig1 which is the structural link to their function in glucose repression. They also exhibit monomer-dimer equilibria depending on protein concentration and phosphorylation of an N-terminal serine residue (S15). Experimental evidence for an expected ring-shaped homodimer of ScHxk2 was still missing to explain the phosphorylation-dependent oligomerization as demonstrated for KlHxk1 (figure). Structural data of other yeast glucose kinases were also limited in order to support a similar phenomenon. Therefore, we comparatively explored the oligomeric structure of ScHxk2 and K. lactis glucokinase 1 (KlGlk1) by means of X-ray diffraction in solution and in the crystalline state. The crystal structure of ScHxk2 was solved at high resolution (<1.5Å), and small-angle X-ray data of ScHxk2 were collected. Data analysis indicated that all three glucose-phosphorylating enzymes share a similar oligomeric architecture.
In-situ nanoscale imaging of charge transfer of BiNiO3 under high pressure
Authors: Yang Wenge , Liu Yijin , Wang Junyue , Mao Wendy , Mao Ho-kwang
Published: November 2015

Over last decades, both synchrotron radiation techniques and high pressure research have made great progress. Advanced synchrotron capabilities with high spatial resolution, high flux, and high energy resolution provides us many new avenues to conduct advanced high pressure researches. In this talk, we will focus on the new developments of the nanoscale imaging techniques on the pressure induced phase separation in three dimensions. BiNiO3 under goes a charge transfer induced phase transition under high pressure or temperature, which shows excellent colossal negative thermal expansion effect [1]. Co-exist of both high density and low density phases over a wide range pressure or temperature plays the key roles on the negative thermal expansion behavior. We utilized a newly developed X-ray absorption near edge spectroscopy tomography method, and successfully resolved the mixture of high/low pressure phases as a function of pressure at tens of nanometer resolution. By choosing incident x-ray energy near Ni absorption edge, the pressure induced valence transition can be mapped at tens of nanometer scale in 3d, which provides crucial information on the HP-LP phase boundary [2]. As temperature driven grain growth upon heating, we can draw fundamental information on the pressure-induced phase growth mechanism.
Recent Micro X-ray Focusing Optics and High-Pressure Applications at SPring-8
Authors: Ohishi Yasuo , Hirao Naohisa , Matsuoka Takahiro , Shimizu Katsuya , Hirose Kei
Published: November 2015

We have developed unique x-ray focusing optics by using compound x-ray refractive lens (CRL) designated for the high-pressure XRD beamline BL10XU [1] of SPring-8. The CRL is a set of planar cross-lenses with a quasi-parabolic profile for focusing in two directions, and are fabricated from the SU-8 polymer by deep x-ray lithography at the IMT in Germany [2]. The focusing optics consisted by two sets of CRL and a pinhole in tandem. The set of the upstream CRL and the pinhole as a virtual source are used for generation of homogeneously divergent beam. The downstream CRL, which is placed between a pinhole and a focal point (sample position), is utilized for focusing the x-ray towards the micron size. The focused beam size is defined by the relationship between a pinhole diameter and the ratio of source-lens versus lens-focal point distances. We have succeeded in focusing the x-ray beam down to 2.4 microns in vertical and 2.1 microns in horizontal, as we had designed, under the following conditions: 30 keV x-ray, 10 micron pinhole in diameter and 11:1 ratio of source-lens:lens-sample distances. The beam flux, which was converted to flux density as about 1015 cps/mm2, was enough strong to obtain XRD profiles in sub-second exposure, even at the sample condition under few hundred GPa. Using this system, we have obtained clearly districted XRD profiles from sub-structures of microns size in DAC, such as electrodes for electrical resistance measurement, micro-anvils settled in the sample chamber, and so on. Micro-beam technique will bring us new applications for high-pressure experiments, and become more important in order to enhance precise analysis, such as grains/elements distribution, partial melting, solution and/or chemical reactions in a sample chamber of DAC, as well as in order to collect high-quality XRD under above 500 GPa. Furtehrmore, the sub-micron beam focusing is now achievable and will be a key-technique for a probe of a scanning XRD microscope.
In situ Investigations from Spinels under high pressure and high Temperatures
Authors: Wehber Michael , Schilling Frank , Lathe Christian , Mueller Hans
Published: November 2015

Spinels seem to be important constituents of the deep interior of the Earth while transition with spinel or pseudospinel structure strongly influence the dynamic of the mantle. On the other hand, spinels are widely used as artificial material. The spinels Magnetite, Franklinite, and Gahnite are investigated at the Hamburger Synchrotron Laboratory (HASYLAB) at Hamburg. The experiments were carried out using the high pressure multi anvil devices MAX80 (F2.1 Beamline) and MAX200x (W2 Beamline). The MAX80 is a single state apparatus located at a bending magnet, MAX200x is a double state system located at a wiggler. Energy-dispersive X-ray diffraction in combination with Rietveld refinement [1, 2] was used to determine the pressure and temperature induced volume change. Isothermal experiments were performed up to 15 GPa at ambient temperature. The temperature and pressure dependent volume change were derived from compression experiments using MAX80 apparatus up to 5 GPa at temperatures of 298, 500, 700, 900 and 1100 K. Bulk moduli at ambient temperatures using a Birch-Murnaghan equation of state result in KT=184(7) GPa with K'=4.5(2) for Magnetite, KT =178(6) with K'=4.6(4) for Franklinite, and KT =204(9) with K'=4.9(6) for Gahnite.
Instrumentation development for crystallography at high-pressure
Authors: Kamenev Konstantin , Jacobsen Matthew , Ridley Christopher , Wang Xiao , Bull Craig , Kirichek Oleg , Attfield J. Paul
Published: November 2015

Historically high-pressure (HP) research has been an area that is heavily dependent on the availability of the experimental equipment. Many of the discoveries in HP science followed promptly from breakthroughs in instrumentation development, which provided researchers with higher pressure limits or larger sample volumes. A limited availability of commercial pressure cells and the need to remain at the cutting edge of the research make it likely that anyone working in this field will at some point engage in designing new or in modifying existing HP equipment. This presentation aims to introduce an engineering approach to developing pressure cells and to present such generic tools as computer aided design (CAD) and finite element analysis (FEA). The use of engineering methods in the design of HP equipment will be illustrated using recently developed pressure cells. This includes some new devices for neutron scattering such as gas-driven sapphire anvil pressure cell for changing pressure at cryogenic temperatures in neutron diffraction experiments [1]. Another example is a gas loader for the P-E press which can be used to load gases into the sample space at elevated pressures for subsequent studies of gases and gas mixtures as well as for use of gases as pressure-transmitting media to pressures of over 18 GPa [2]. The examples of use of FEA for miniaturization of the pressure cells and their components will include miniature pressure cells for X-ray diffraction with cryo-flow refrigerators shown in the Figure below [3].
Study La0.5Sr1.5MnO4with Multi-Beam X-ray Diffraction
Authors: Liu Wen-Chung , Chiu Yi-Hua , Liao Po-Yu , Cheng Chih-Hao , Tsai Yi-Wei , Chu Chia-Hung , Chang Shih-Lin
Published: November 2015

We have used resonant multi-beam diffraction with the primary reflections G=(h/2 h/2 0) and G=(h/4 h/4 0) (h is an odd number) to investigate the charge ordering and Jahn-Teller distortion, respectively, in La0.5Sr1.5MnO4 low temperature phase. While the Renninger scans with G=(h/2 h/2 0) shows several Aulfhellung-type four-beam diffraction, most of the multi-beam diffraction with G=(h/4 h/4 0) has an Umweganregung-type nature. A detailed study of multi-beam diffraction anomalous fine structure (M-DAFS) of (0 0 0)/(3/2 3/2 0)/(1 -1 0)/(5/2 1/2 0) OUT diffraction is carried out. Its triplet invariant phase approach 1800when the x-ray energy is tuned away from manganese K-edge, and approach 900when the x-ray energy is tuned on manganese K-edge. In other words, its multi-beam diffraction profile shows strong asymmetry when (3/2 3/2 0) diffraction intensity is dominated by Jahn-Teller distortion, and becomes more symmetric when charge ordering dominated. This characteristic can be successfully simulated by tensor form dynamical x-ray diffraction theory accompanied with FDMNES software [1] calculations.
Modeling of the optical properties of molecular crystals
Authors: Seidler Tomasz , Gryl Marlena , Champagne Benoît , Stadnicka Katarzyna
Published: November 2015

In this contribution we present our current findings in the calculations of the linear and second-order nonlinear electric susceptibility tensor components of organic crystals. The methodology used for this purpose is based on a combination of the electrostatic interaction scheme developed by Hurst and Munn (Hurst & Munn, 1986) with electronic structure calculations for the isolated molecules. Our modification of the method consists in i) running periodic boundary condition (PBC) calculations for an adequate chromophore geometry (either experimental or optimized) to obtain atomic charges and in ii) performing the calculations of the molecular properties within a non-uniform embedding field generated by point charges located spherically around the reference molecule. Using this approach good accuracy is achieved on the electric susceptibility tensor components in comparison with the uniform dipole electric field (Seidler et al., 2013). We extend here the application of this method to other molecular crystals as well as we present the first attempt to predict the chi(1) and chi(2) components of two-component organic crystals (Gryl et al., 2014).
DFT and Plasmon-Coupling Models for Optical and Electronic Scattering Properties
Authors: Bourke Jay , Chantler Christopher
Published: November 2015

We present calculations and applications of optical energy loss data for use in studies of inelastic electron scattering in condensed matter systems. A new model of plasmon coupling and excitation broadening is implemented along with high-precision density functional theory to evaluate fundamental material properties critical to many areas of spectroscopic analysis. Recent developments in x-ray and electron spectroscopies have demonstrated critical dependence on low-energy electron scattering and optical loss properties, and significant discrepancies between theoretical and experimental scattering values [1]. Resolution of these discrepancies is required to validate experimental studies of material structures, and is particularly relevant to the characterization of small molecules and organometallic systems for which electron scattering data is often sparse or highly uncertain [2]. We have devised a new theoretical approach linking the optical dielectric function and energy loss spectrum of a material with its electron scattering properties and characteristic plasmon excitations. For the first time we present a model inclusive of plasmon coupling, allowing us to move beyond the longstanding statistical approximation and explicitly demonstrate the effects of band structure on the detailed behavior of bulk electron excitations in a solid or small molecule. This is a novel generalization of the optical response of the material, which we obtain using density functional theory [3]. We find that our developments improve agreement with experimental electron scattering results in the low-energy region (<~100 eV) where plasmon excitations are dominant; a region that is particularly crucial for structural investigations using x-ray absorption fine structure and electron diffraction. This work is further relevant to several commissions of the IUCr including the commissions on XAFS, International Tables, and Electron Crystallography.
Optical properties of chiral photomechanical salicylideneaniline crystal
Authors: Takanabe Akifumi , Tanaka Masahito , Koshima Hideko , Shiro Motoo , Asahi Toru
Published: November 2015

Mechanical motion caused by UV/VIS radiation onto bulk materials is called a photomechanical effect. In other words, the photomechanical effect is a type of energy conversion systems. Recently, a mechanical bending of photochromic diarylethene crystals was reported, and the molecular-scale motion was found to produce the macroscale bending of the crystals (Kobatake et al., 2007). Subsequently, several photomechanical crystals have been reported to provide promising opportunities for artificial molecular machinery. The mechanism of the conversion of light energy to mechanical energy, however, has not quantitatively been understood. In photomechanical effect, microscale structural change and stress should be involved with optical properties of anisotropy and chirality; linear birefringence (LB), linear dichroism (LD), circular dichroism (CD) and optical rotatory power (ORP). CD and ORP in a chiral anisotropic crystal are extremely difficult to be measured owing exclusively to the contribution of strong linear anisotropy. The High Accuracy Universal Polarimeter generalized by our group (G-HAUP) enables us to measure LB, LD, CD, and ORP simultaneously and quantitatively (Tanaka et al., 2012). The purpose of our study is to investigate the relationship between microscale structural change or stress induced by UV/VIS radiation and the four optical properties. We synthesized chiral N-3,5-di-tert-butylsalicylidene-1-phenylethylamine photochromic crystal, as shown in Scheme 1, because the mechanism of photomechanical effect in this crystal has been revealed qualitatively by analyzing single-crystal structure under UV/VIS radiation (Koshima et al., 2013). The LB, LD, CD, and ORP spectra in the direction perpendicular to (001) were successfully measured under VIS radiation. Furthermore, LD spectrum was found to change by UV radiation in 30mW/cm2. These results could contribute to an elucidation of the mechanism of photomechanical effect quantitatively.
Charge Density and Optical Properties of Multicomponent Crystals Containing APIs
Authors: Gryl Marlena , Seidler Tomasz , Stadnicka Katarzyna
Published: November 2015

Technological progress forces improved material performance therefore controlling synthesis of new crystal phases requires moving from the trial-and-error method to comprehensive solutions. Active Pharmaceutical Ingredients (API) are of particular interest in crystal engineering [1]. Molecular flexibility reflected in many polymorphic forms and appropriate spatial distribution of hydrogen bond donors and acceptors make many known drugs useful for designing optically active materials [2]. The effective correlation between properties and structural features of a given material is possible through quantitative crystal engineering combined with in silico crystal engineering. Quantitative crystal engineering utilizes modern charge density analysis and properties calculations, whereas in silico crystal engineering assesses synthon formation capability probing weak interactions existing within the crystal phases. Optical properties of a crystal strongly depend upon spatial distribution of molecules in the crystal structure, as well as on the electronic properties of molecular building blocks (dipole moments, polarizabilities, hyperpolarizabilities)[3]. Recently we have investigated materials based on pharmaceutically active ingredients: barbiturates, antiarrhythmic drugs, alkaloids, combined with organic molecules and/or transition metal salts. Partial results of our research have already been published [2]. Factors that contribute to molecular recognition in the selected polar/chiral crystal phases (derived through charge densityand Hirshfeld Surfaces Analysis) have been determined. The predicted values of refractive indices were confirmed experimentally using the immersion oil method. Second Harmonic Generation efficiency was assessed using a modified Kurtz-Perry technique [2].