bluuebunny/crossref_metadata_2025 huggingface dataset:
Conductive hybrid crystals comprising oxide clusters and surfactants
Authors: Ito Takeru , Mikurube Keisuke , Taira Minako , Naruke Haruo
Published: November 2015

Conductive hybrid layered crystals were successfully constructed by employing polyoxometalate anionic clusters and cationic surfactants. Such ionic crystals are a rare series of materials, and both polyoxometalate and surfactant components can be flexibly selected to construct functional inorganic-organic hybrids [1-3]. Their layered structures contribute to the emergence of conductive property. The conductivity was estimated by alternating current (AC) impedance spectroscopy. Decatungstate (W10) and tetramolybdate (Mo4) anions formed stable single crystals together with hexadecylpyridinium (C16py), and the crystal structures were revealed by X-ray diffraction analyses. The crystals exhibited the alternate stacking of W10 or Mo4 layers and surfactant layers. The obtained conductivity values were in the range of 10–6 to 10–5 S cm–1 order over 423 K. On the other hand, decavanadate (V10) anion formed layered crystals with alkyltrimethylammonium (Cn, n = 10 – 16). The hybrid crystals contained diprotonated V10 anions, and exhibited proton conductivity at intermediate temperatures (> 373 K) without humidification. The conductivities for C14-V10 and C16-V10 were ca. 1 x 10–4 S cm–1 over 393 K under argon atmosphere. Anhydrous proton conduction is crucial property for fuel-cell technology, and V10-surfactant crystals are possible candidates for proton-conducting electrolyte of fuel cells. The polyoxometalate-surfactant hybrid crystals having appropriate combination would pave a way to another class of hybrid conductors.
Rhodium dimers as structural hubs for multichromophore assemblies
Authors: Chartrand Daniel , Hanan Garry
Published: November 2015

Our main building blocks for forming supra-molecular assemblies of chromophoric units are the rhodium amidinate dimers. They offer an excellent structural backbone for rigid polynuclear assemblies with their paddle wheel motif and strongly bonded ligands. We already showed that with a well designed amidinate ligand with a pyridyl group up to four metallic centers can be attached to the dimer.[1,2] Two main approaches were used to extend these assemblies: the first is through Suzuki coupling reactions which allows for an extended ligand and a control on the number of pyridyl present on the dimer; The second is through bisisocyanide ligands which are used to bridge the dimers though their axial site, thus forming 1D coordination polymer in the solid state. These different assemblies will be presented with their solid state structure, photophysical and electrochemical properties.
The Transition-Metal Citrate Cubane as a Synthon for a Large Family of SMM's
Authors: Forcen-Vazquez Elena , Campo Javier , Falvello Larry , Palacio Fernando , Tomás Milagros
Published: November 2015

The transition-metal citrate cubane is a symmetrical, anionic molecular fragment that possesses twelve partially negatively charged oxygen atoms around its periphery. The cobalt variants have proved to be single molecule magnets (SMM), as demonstrated in studies by Murrie and by others.[1] All of the negatively charged points on the surface of the fragment are potential linkage positions for metal atoms, and extended products of from zero- to three dimensions have been synthesized and characterized.[2] In this presentation we describe products with five different combinations of linkage points for cobalt or manganese. A one-dimensional Co-containing cubane polymer has been found to undergo reversible cross-linking in the crystal to produce a two-dimensional polymer. A second Co-containg product, a discrete molecular solid with SMM behavior, undergoes reversible reaction in the crystal to produce an unsymmetrical product, also with SMM behavior -- a switchable SMM pair. A third product, a symmetrical two-dimensional Co-containing polymer, is an SMM with two blocking processes. A one-dimensional polymer of manganese citrate cubanes has been demonstrated to conduct protons via the Grotthuss mechanism.[3] All of these products have different patterns of peripheral metal-atom linkage to the twelve surface-resident oxygen atoms of the cubane fragment. A systematic naming scheme for the citrate cubane topology is used to provide simple descriptions of the diverse linkage geometries found to date.
Structural study of new cytotoxic heteroleptic Copper (II) complexes
Authors: Alvarez Natalia , Iglesias Sebastián , Viñas Diana , Torre María , Kremer Eduardo , Ellena Javier , Costa-Filho Antonio , Kramer Gabriela , Facchin Gianella
Published: November 2015

The widespread success of Cisplatin in the treatment of several neoplasias has arisen the interest in coordination compounds as drugs for the treatment of cancer. In the search for new compounds with antitumor activity, copper coordination complexes are being studied by our group. This work presents the synthesis and structural characterization of four new copper complexes with general stoichiometry [Cu(L-dipeptide)(phen)]·nH2O and their cytotoxicity against tumor cell lines. Single crystal X-ray diffraction experiments show that the copper ion is situated in a distorted squared pyramidal environment. The phen ligand is perpendicular to the plane defined by the coordinated dipeptide, therefore exposed and potentially available for interaction with biological molecules, e.g. DNA. The availability of the phen ligand and the physico-chemical properties of the complexes are modulated by the dipeptide. Complementary techniques (elemental analysis, infrared and UV-vis spectroscopies) were used to further characterize the complexes in solid state and aqueous solution, confirming that the coordination is maintained in solution. Lipophilicity and DNA binding constants were also measured, being able to discriminate between the behavior of even the complexes containing the ala-phe and phe-ala dipeptide. All the complexes induce cell death in the cell lines of human cervical adenocarcinoma, human metastatic breast adenocarcinoma and human lung epithelial carcinoma. Among the six complexes studied, [Cu(ala-phe)(phen)] presents the lowest half maximal inhibitory concentration (IC50) values. In an attempt to increase the activity, studies are presently being carried out using 2,9-dimethyl-10-phenanthroline. X-ray diffraction studies on the latter show slight deviations in the coordination geometries and different results are expected in their biological activities. Acknoledgements: CSIC, CAPES-UdelaR, PEDECIBA.
The Road to Functional Lanthanide-Phosphonate Metal-Organic Frameworks
Authors: Almeida Paz Filipe
Published: November 2015

The endless possible combination of metal centers and organic ligands renders the field of Metal-Organic Frameworks (MOFs) an extremely rich playground for the design of new functional materials. The symbiotic co-existence of organic and inorganic components in these compounds embody the final products with unusual properties, which may, for example, ally photoluminescence with catalysis and even thermal robustness for more advanced technological applications. Our research group has focused on the development of functional MOFs based on rare-earth cations and polyphosphonate organic ligands, many of which designed and prepared in our laboratories. This poster summarizes the synthesis, structural elucidation and photophysical and catalytic properties of the novel one- (1D) and three-dimensional (3D) materials prepared using the tripodal (benzene-1,3,5-triyltris(methylene))triphosphonic acid (H6bmt) and the bipodal 1,4-phenylenebis(methylene)diphosphonic acid (H4pmd) organic ligands: [Ln(H4bmt)(H5bmt)(H2O)2]·3H2O (system 1: 1D), [Ln2(H3bmt)2(H2O)2]·H2O (system 2: 3D), and [Ln(Hpmd)(H2O)] (system 3: 3D) (please note: Ln stands for a rare-earth cation) [1-3]. System 1 is an outstanding heterogeneous catalyst in the methanolysis of styrene oxide at nearly room temperature, even outperforming the well-known nano-sized HKUST-1 MOF material. System 2 exhibits unusual photoluminescent properties: the Tb-containing material has an absolute emission quantum yield of ca. 46%; for the Eu-containing compound this value is easily increased from ca. 15% to 54% by removing, under vacuum, all water molecules in the material, this being only possible due to its typical zeolitic behaviour. System 3 can be prepared in large quantitites as either micro- or nano-sized crystals, with the latter exhibiting a remarkable high heterogeneous catalytic activity. Fundação para a Ciência e a Tecnologia (FCT, Portugal; EXPL/CTM-NAN/0013/2013 - FCOMP-01-0124-FEDER-041282), Bruker AXS (Karlsruhe, Germany), the European Union, QREN, FEDER, COMPETE and Laboratório Associado CICECO (PEst-C/CTM/LA0011/2013) are gratefully acknowledged for funding the research and the dissemination of the results. The presenting author also wishes to thank all the collaborators involved in the referenced publications.
Pillared 2-D MOFs Based on a Lower-Rim Acid-Appended Calix[4]arene.
Authors: Elsegood Mark , Horsburgh Lynne , Redshaw Carl , Rowe Oliver , Teat Simon
Published: November 2015

Calixarenes have been the focus of intense research study of both their organic and metal-coordinated chemistry over the past twenty or so years. Calixarenes generally have intrinsic cavities in their cone or partial cone structures, often filled with coordinated or non-coordinated solvent of crystallization, or filled with substituents from neighboring calixarene molecules. Much of this research has generated molecular, or zero-dimensional compounds, rather than oligomeric or polymeric materials. The shape and size of the calixarene molecules and complexes has led to their use in separation science, catalysis, imaging, etc. Over the same time period, studies on metal-organic frameworks (MOFs) have also been prominent, driven mainly by the ambition to store gases like hydrogen or trap CO2. Metal ions form nodes and bond to organic spacers which generate a rigid or flexible poly-dimensional framework with pores. This research contribution marries the two fields and incorporates calixarene molecules, with their inherent pores, into MOFs. Solvothermal reactions of the lower-rim functionalized diacid calix[4]arene 25,27-bis(methoxycarboxylic acid)-26,28-dihydroxy-4-tert-butylcalix[4]arene (LH2) with Zn(NO3)2·6H2O and the dipyridyl ligands 4,4′-bipyridyl (4,4′-bipy), 1,2-di(4-pyridyl)ethylene (DPE) or 4,4′-azopyridyl (4,4′-azopy) afforded a series of 2-D structures of the formulae {[Zn(4,4′-bipy)(L)]·2¼DEF}n (1, Fig. 1.), {[Zn2(L)(DPE)]·DEF}n (2) and {[Zn(OH2)2(L)(4,4′-azopy)]·DEF}n (3) (DEF = diethylformamide)1. Figure 1. {[Zn(4,4′-bipy)(L)]·2¼DEF}n (1)
Recent Progress in the Synthesis and Characterization of Diarylethene-based MOFs
Authors: Benedict Jason , Walton Ian , Patel Dan , Cox Jordan
Published: November 2015

Metal-organic Frameworks (MOFs) remain an extremely active area of research given the wide variety of potential applications and the enormous diversity of structures that can be created from their constituent building blocks. While MOFs are typically employed as passive materials, next-generation materials will exhibit structural and/or electronic changes in response to applied external stimuli including light, charge, and pH. Herein we present recent results in which advanced photochromic diarylethenes are combined with MOFs through covalent and non-covalent methods to create photo-responsive permanently porous crystalline materials. This presentation will describe the design, synthesis, and characterization of next-generation photo-switchable diarylethene based ligands which are subsequently used to photo-responsive MOFs. These UBMOF crystals are, by design, isostructural with previously reported non-photoresponsive frameworks which enables a systematic comparison of their physical and chemical properties. While the photoswitching of the isolated ligand in solution is fully reversible, the cycloreversion reaction is suppressed in the UBMOF single crystalline phase. Spectroscopic evidence for thermally induced cycloreversion will be presented, as well as a detailed analysis addressing the limits of X-ray diffraction techniques applied to these systems.
Neutron crystallographic analysis of human α-thrombin using iBIX at J-PARC
Authors: Yamada Taro , Kusaka Katsuhiro , Hosoya Takaaki , Ohhara Takashi , Tomoyori Katsuaki , Tanaka Ichiro , Niimura Nobuo , Katagiri Masaki
Published: November 2015

α-Thrombin is a serine protease, which plays the central role in the coagulation system. Investigating the protonation states of the enzyme is useful to reveal the reaction mechanism and to design anticoagulant drugs. We have studied the protonation states of the α-Thrombin-bivalirudin complex using neutron diffraction method. The complex is regarded as the enzyme-product complex, because the hydrolyzed bivalirudin fragments keep staying in the binding sites in the crystal. Previously we had performed a neutron crystallographic analysis of α-Thrombin-bivalirudin complex at pD 5.0 (space group P21212) at 2.8 Å resolution.[1] To observe the protonation states of the active site more clearly, we carried out time-of-flight neutron diffraction experiments for a different crystal form of this complex (space group C2 at pD 7.9) using IBARAKI biological crystal diffractometer, iBIX, installed in J-PARC. Using improved 30 neutron detectors with high-efficiency, we have succeeded in collecting the reflections at around 2.0 Å resolution. XN-joint refinements were performed using PHENIX program. The neutron scattering length OMIT map showed a density on the hydroxyl group of serine 195, which could be a deuterium. Since the density was not observed for P21212 crystal at pD 5.0 and the position was too far from an acceptor atom to form a stiff hydrogen bond, currently we are confirming the result. In this presentation, details of the neutron crystallographic analysis and the comparison between the structures, especially, the protonation states of amino acid residues in the active site of the complex at pD 5.0 and pD 7.9 will be given.
Neutron Structure of Phycocyanobilin:oxidoreductase Complexed with Biliverdin
Authors: Unno Masaki , Ishikawa-Sudo Kumiko , Kusaka Katsuhiro , Tamada Taro , Hagiwara Yoshinori , Sugishima Masakazu , Wada Kei , Yamada Taro , Ishihara Makiko , Fukuyama Keiichi
Published: November 2015

Phytobilins are linear tetrapyrrole compounds used as chromophore for light harvesting and photoreceptor proteins in higher plants, algae, and cyanobacteria. Phytobilins are synthesized from biliverdin IX(alpha) (BV). Phycocianobilin:oxidoreductase (PcyA) is an enzyme to produce phycocyanobilin (PCB) used as chromophore for light harvesting and photoreceptor proteins. PcyA is unique because it catalyzes the reduction of BV by two sequential steps; the first step is the reduction of the vinyl of the BV D-ring to produce 18(1)-18(2)-dihydrobiliverdin (18EtBV), and the second step is the reduction of the A-ring. In these reduction steps, four hydrogen atoms are delivered to BV. The earlier studies showed that the carboxyl group of Asp105 showed dual conformations. This has been attributed to the difference of its protonation states. The catalytically essential His88 was suggested to be protonated (i. e. His88 is a proton donor) to donate the proton to BV. BVH+ (N-protonated) state, in which four pyrrole N atoms of BV were fully protonated, was proposed to be partially formed when BV was bound to PcyA. Further, another tautomeric BVH+ state in which three of four pyrrole N atoms of BV were protonated and the lactam (C=O) group of BV D-ring was protonated as lactim (C-OH; O-protonated) was proposed. Additionally, newly identified water molecule near BV has been suggested to be a proton donor. To elucidate the H atom positions of these molecules, we determined the neutron crystal structure of the PcyA-BV complex at 1.95 Å resolution. Crystal with approximately 2.2 X 1.8 X 0.8 mm3 size, which was soaked into the deuterium-exchanged crystallization solution, was used in the diffraction experiment. The neutron diffraction intensity data was collected using IBARAKI Biological Crystal Diffractometer (iBIX) in J-PARC. In this conference, we report the protonation states of catalytically important residues and BV as well as orientations of water molecules in the PcyA-BV complex.
Radical doping and high-pressure freezing in an advanced neutron crystallography
Authors: Morita Naomichi , Tanaka Ichiro , Chatake Toshiyuki , Asaki Satoru , Iwata Takahiro , Kusaka Katsuhiro , Niimura Nobuo
Published: November 2015

The isotope effect in conventional neutron protein crystallography (NPC) can be eliminated by the proton polarization technique (ppt) as an advanced NPC. Furthermore, the ppt can improve detection sensitivity of hydrogen (relative neutron scattering length of polarized proton) by approximately eight times in comparison with conventional NPC. Several technical difficulties, however, should be overcome in order to perform the ppt. In this poster, two developing fundamental studies to realize ppt will be presented; 1) radical doping into protein crystals that facilitates sample electron polarization, which was analyzed by X-ray crystallography, liquid-chromatography/mass-spectrometry (LC/MS) and electron spin resonance (ESR) measurement, 2) high-pressure flash freezing performed especially using a new machine of HPC-201 (ADC Inc.), which has the advantage of making bulk water amorphous without destroying the single large crystal, may easily realize the low temperature environment of crystal at around 1K. The former results were that radical molecules distributed non-specifically around proteins, and that they were included in protein crystal to some extent [1]. These are a favorable tendency for better proton polarization.
Joint neutron/Xray cryocrystallography: developments for cryocooling experiments
Authors: Romoli Filippo , Mossou Estelle , Cuypers Maxime , Carpentier Philippe , Van der Linden Peter , Mason Sax , De Sanctis Daniele , Mc Sweeney Sean , Forsyth Trevor
Published: November 2015

Cryo-cooling of protein crystals is not often used in neutron crystallography. However cryo-temperatures are used to block the reaction processes at specific intermediate stages, and this has been widely used in X-ray studies (1); (2). In order to develop this area for joint neutron/X-ray applications, trypsin was chosen as a suitable system for which its interaction with the substrate succinyl-Ala-Ala-Pro-Arg-p-nitro-aniline could be studied (3). Here the neutron developments were carried out in parallel with complementary X-ray techniques, and also using in crystallo UV-visible and Raman spectroscopy. Various strategies for doing this have been tested. The installation of an N2-gas-cryostream system on the D19 single crystal diffractometer at the Institut Laue Langevin (ILL) and the development of a new carboloop mounting system, has opened new avenues to perform cryo-cooling experiments using a neutron source. Preliminary data collection carried out at the ILL and at the European Synchrotron Radiation Facility (ESRF), have confirmed the feasibility of the approach. A full description of the experimental procedures and results will be presented. As part of this a new carboloop mounting system has been developed that is suitable for both X-ray and neutron data collection. These mounts resolve the problems of activation and hydrogen incoherent scattering in neutron experiments We describe the use of these and their advantages over conventional X-ray mounting systems - including compatibility with standard magnetic goniometer heads and resistance to cryogenic temperatures.
Observation of a metal-hydride in [NiFe] hydrogenase
Authors: Ogata Hideaki , Nishikawa Koji , Lubitz Wolfgang
Published: November 2015

Hydrogenases catalyze the reversible hydrogen oxidation process by cleaving dihydrogen heterolytically.(1) For this reaction, the enzyme uses the transition metals Ni and Fe, which are abundant in Nature. Standard [NiFe] hydrogenaes are mainly composed of two subunits (total ~90 kDa) The [NiFe] active site is located in the center of the molecule. The active site of [NiFe] hydrogenase is composed of the dinuclear Ni-Fe center, where the Fe ion is coordinated by non-protein ligands (1CO and 2CN¯ ). Two thiolates of cysteine residues are bridging both metals. Furthermore, the Ni is coordinated to the two thiolates of cysteine residues in a terminal fashion. A third bridging ligand is found between the Ni and Fe atom, depending on the redox state.(1) In the inactive form, a third bridging ligand (OH¯¯¯ ) is found between Ni and Fe. Once the enzyme is activated, the bridging position is supposed to be vacant or bridged by a hydride. A previous X-ray crystallographic study at 1.4 Å resolution revealed that the bridging ligand (OH) is removed upon H2 reduction.(2) Electron paramagnetic resonance (EPR) spectroscopy showed that a hydride is located in the bridge between Ni and Fe, which is lost upon illumination at cryogenic temperature.(3) Here we present a crystallographic analysis of the fully reduced (Ni-R) state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F at 0.89 Å resolution. The ultra-high resolution analysis revealed the presence of the hydride bridge at the NiFe active site in the catalytically active state. Furthermore the CO and CN ligands could be identified and a protonated thiolate sulfur ligand of the Ni is postulated based on the electron density.
A crystallographic study of the Toho-1 β-lactamase acylation mechanism
Authors: Coates Leighton
Published: November 2015

β-lactam antibiotics have been used effectively over several decades against many types of highly virulent bacteria. The predominant cause of resistance to these antibiotics in Gram-negative bacterial pathogens is the production of serine β-lactamase enzymes. A key aspect of the class A serine β-lactamase mechanism that remains unresolved and controversial is the identity of the residue acting as the catalytic base during the acylation reaction. Multiple mechanisms have been proposed for the formation of the acyl-enzyme intermediate that are predicated on understanding the protonation states and hydrogen-bonding interactions among the important residues involved in substrate binding and catalysis of these enzymes. For resolving a controversy of this nature surrounding the catalytic mechanism, neutron crystallography is a powerful complement to X-ray crystallography that can explicitly determine the location of deuterium atoms in proteins, thereby directly revealing the hydrogen-bonding interactions of important amino acid residues. Neutron crystallography was used to unambiguously reveal the ground-state active site protonation states and the resulting hydrogen-bonding network in two ligand-free Toho-1 β-lactamase mutants which provided remarkably clear pictures of the active site region prior to substrate binding and subsequent acylation [1,2] and an acylation transition-state analog, benzothiophene-2-boronic acid (BZB), which was also isotopically enriched with 11B. The neutron structure revealed the locations of all deuterium atoms in the active site region and clearly indicated that Glu166 is protonated in the BZB transition-state analog complex. As a result, the complete hydrogen-bonding pathway throughout the active site region could then deduced for this protein-ligand complex that mimics the acylation tetrahedral intermediate [3].
New Methods for the Visualization of Incommensurately Modulated Structures
Authors: Hanson Robert
Published: November 2015

While the theory of incommensurate structure and composite crystallography is well established, methods for the visualization of modulated and composite crystal structures are few.[1] At the same time, databases featuring such structures have arisen [2], and there is a growing need for web-based tools that allow users to interactively explore such structures. This presentation is by the principal developer of Jmol, an international open-source collaborative molecular visualization project. It will focus on recent developments that have been made in this area. Jmol provides a flexible and crystallographically rich suite of functionality, including depiction of specific symmetry operations and selective sets of unit cells, selection of specific modes of modulation, use of color to show long-range low-frequency modulation components, and the depiction of relative modulation phasing through animation. From an archival perspective, Jmol development has been an opportunity to test the basic ontology of the IUCr msCIF standard [3], and a number of issues relating to this standard will be discussed, particularly in relation to multidimensional modulation. From an general educational perspective, Jmol for the first time allows easy access to a wide variety of examples of incommensurately and commensurately modulated structures and composite structures. Being accessible on virtually all platforms and within all major browsers, Jmol offers a novel mechanism for the wide-spread dissemination of understanding of this important class of crystal structure.
Structural study of the pressure adaptation of proteins from deep-sea bacteria
Authors: Watanabe Nobuhisa , Nagae Takayuki , Yamada Hiroyuki , Shimoaka Naoto
Published: November 2015

In recent years, significant development in the high-pressure macromolecular crystallography (HPMX) using a diamond anvil cell (DAC) has been performed especially by Prof. R. Fourme's group in combination with shorter wavelength X-ray of synchrotron radiation [1]. We are also trying to establish HPMX experimental environment at the Photon Factory, Japan [2]. HPMX is a unique method that provides high-resolution structural informations under pressure including hydration waters at a molecular surface and an internal cavity. One of the important applications is studying functional sub-states of biological macromolecules, and we are attempting to elucidate a mechanism of pressure tolerance of proteins from several organisms living in deep seas such as the Mariana Trench. For example, 3-isopropylmalate dehydrogenase (IPMDH) from the deep-sea bacterium Shewanella benthica DB21MT-2 is much more tolerant to the pressure stress than its counterpart from the land bacterium S. oneidensis MR-1 (So-IPMDH), even though these two enzymes share about 85% amino-acid identity. Crystal structures of So-IPMDH have been determined at about 2 Å resolution under pressures ranging from 0.1 to 650 MPa. Waters penetrating into the internal cavity at the dimer interface and squeezing into a molecular surface cleft opposite the active site are observed at above 410 MPa and 580 MPa, respectively [3]. The bottom of the cleft of So-IPMDH is characterized by the presence of Ser266 at the bottom, which is able to form a hydrogen bond to the squeezed water molecule. On the other hand, IPMDHs from deep-sea bacterium favors an alanine at the same position (Ala266). As expected, no water penetration is observed there at the same pressure range for the S266A mutated So-IPMDH, and the mutation develops tolerance to the pressure. In addition, some results of the high-pressure structure analysis of other proteins, and pressure-induced phase transitions in some protein crystals will also be mentioned.
Pressure and high-pressure macromolecular crystallography at the ESRF
Authors: Van Der Linden Peter , Royant Antoine , Mc Sweeney Sean , Mueller-Dieckmann Christoph , Carpentier Philippe
Published: November 2015

Almost all diffraction experiments in structural biology are done at cryogenic temperature to mitigate radiation damage with cryoprotected crystals to avoid solvent crystallization and its harmful consequences: formation of ice rings, loss of diffraction and exaggeration of mosaicities. Crystallographers often protect crystals with glycerol rather than with genuine conditions whose search is time consuming. Moreover, cryo-protection has detrimental consequences: Soaking somewhat destabilizes crystals, mosaicity expend upon cooling, cryo-agents may interact with macromolecules and in extreme cases, cryo-conditions are destructive. High pressure (HP) cooling is an alternative method which consists of flash-cooling cryoprotectant-free samples under 200 MPa of Helium [1]. The solvent is directly turned into high density amorphous (HDA) ice avoiding water crystallization and preserving/improving the sample quality owing to the absence of cryo-agents and to HAD-ice properties. We have developed a HP-cooling system and its associated methodology paying attention to user-friendliness and throughput aspects through a new pluggable Spine compatible base-pin and to its handling-toolkit [2]. The machine allows vitrifying solution with 5% glycerol for cooling diluted bio-objects, but importantly, it is very effective for cryoprotectant-free crystals since the sole mother liquor components act as anti-freeze agents. Its capability was demonstrated with test crystals and resulting structures appear isomorphous to those deposited in the PDB since the structural changes are limited to flexible loops. Nevertheless, pressure is a key thermodynamic variable which produces structural modifications associated with different conformational protein substates or reaction coordinates [3], and we provide examples of HP structures which address biological questions. On the basis of the HP-cooling technique, we have designed a novel of pressure cell for gases of biological interest. The method takes advantage of thermodynamic properties which allow liquefying pressurized gases; crystals are soaked in the gas phase prior to be flash-frozen in the liquid phase without pressure relaxation. This technique has been applied to noble gas derivatives and oxygen sensitive macromolecules.
Novel Insights into the Mechanistic Routes of Lyotropic Phase Transitions
Authors: Ces Oscar , Seddon John , Law Robert , Brooks Nicholas , Templer Richard
Published: November 2015

When mixed with water, biological amphiphiles such as phospholipids can self-assemble to form a variety of lyotropic liquid crystalline structures including 1-D flat lamellar bilayers, 2-D hexagonal phases and 3-D bicontinuous cubic structures1. The role of the lamellar phase in nature is well understood – flat bilayers maintain the fundamental integrity of all living cells. However, non-lamellar phases also play a vital role in vivo. Extended cubic phases have been directly observed in cells and in addition, the repeating pores which form the continuously accessible structure of these bicontinuous phases are very closely structurally related to membrane pores formed during membrane fusion and fission. The equilibrium phase behaviour of pure phospholipids in water and simple model membrane mixtures has been widely studied but their out of equilibrium behaviour remains poorly understood. We have addressed this knowledge gap through pioneering work looking at the kinetics of phase transitions in phospholipid/water systems and phospholipid/protein/water mixtures using the pressure jump relaxation technique in conjunction with high speed, time resolved small angle X-ray diffraction. This presentation will provide an overview of how our bottom-up approach using model membrane systems has enabled us to establish the mechanistic routes and intermediates in a number of phase transition schemes including bicontinuous cubic to lamellar, hexagonal to lamellar and inter-cubic phase transitions.
From Atoms to Layers: Gold Cluster Growth Kinetics during Sputter Deposition
Authors: Schwartzkopf Matthias , Koerstgens Volker , Metwalli Ezzeldin , Benecke Gunthard , Schlage Kai , Rothkirch André , Roehlsberger Ralf , Mueller-Buschbaum Peter , Gehrke Rainer , Roth Stephan
Published: November 2015

The adjustment of the size-dependent catalytic and optoelectronic properties of gold cluster assemblies is a very significant topic in modern applied nanotechnology [1]. For an efficient and controlled production of active nanostructured cluster surfaces, sputter deposition plays an important role [2]. In order to characterize the self-organization during nanocluster film formation, it is mandatory to understand how growth kinetics influences the cluster film morphology during sputter deposition. The first real-time investigations of gold nanocluster growth kinetics into a gold layer are enabled by combining sputter deposition and surface sensitive X-ray scattering (GISAXS). High frame-rate 2D X-ray detectors in combination with the high photon flux of micro beam spot size, available at the PETRA III beamline P03, enables a non-invasive in situ and real-time investigation of gold growth during sputter deposition. With an acquisition throughput of 67 frames per second, we were able to identify 4 different stages of growth including their thresholds with sub-monolayer resolution and concomitant phase transitions. Each stage can be characterized by a predominant surface process and its intrinsic kinetic: nucleation, diffusion, adsorption and grain growth. Moreover we introduced a flexible geometrical model to extract morphological real space parameters, such as cluster size, correlation distance, layer porosity and surface coverage, directly from the reciprocal space scattering data. The model allowed simulating, visualizing and interpreting gold cluster growth kinetics in terms of nanoscopic processes. Furthermore, we were able to deduce wetting angle on the nanoscale and onset of long-range connectivity during the deposition process [3]. This approach is a prerequisite for future investigations of the influence of different process parameters on thin metal film morphology, which is essential for optimization of manufacturing parameters, saving energy and resources.
In situ PXRD studies of heterogeneous catalysts and pre-catalysts
Authors: Billing David
Published: November 2015

During the course of the last couple of years, my collaborators and I have studied a number of catalytic systems using a lab based PXRD facility at our disposal. Of particular interest to us has been the supported catalysts used in Fischer Tropsch catalysis as well as those used in the synthesis of multiwalled carbon nano tubes. These studies have all proven invaluable to the understanding of the often complex phase evolution that is an intricate and inherent part of the heterogeneous processes of interest to us. Selected results will be presented to illustrate the usefulness and value of these studies. For example below is the intensity profile of the diffraction patterns collected during the heat-treatment of the pre-catalyst: A – anatase, R – rutile, S – silicon, H – hematite and P – pseudobrookite
Tracking Cation Migration in Catalysts by Modulated Enhanced Powder Diffraction
Authors: Dooryhee Eric , Yakovenko Andrey , Hanson Jonathan , Ghose Sanjit , Rodriguez Jose , Senanayake Sanjaya
Published: November 2015

Mixtures of Cu-Fe oxides are used for numerous industrial catalytic processes including the Water-gas shift reaction (WGS: CO + H2O -> CO2 + H2). In this work we measure the structural changes of CuFe2O4 under redox (oxidizing and reducing) and WGS reaction conditions. A key component associated with the catalytic properties of this material is the reversible transfer of Cu in and out of the spinel structure during the reaction. The WGS reaction is the most active when Cu is metallic and on the surface of the spinel which has become Fe3O4. The reversible nature of the Cu migration preserves the activity of the catalyst and protects the Cu species from deactivation. We investigate the cation migration process from the octahedral site inside the spinel to the surface as Cu metal, using modulation measurements that perturb the dynamic structural properties of the spinel structure in a time resolved manner. The experiments termed MED [1] involve the switching of co-reactants (i.e. CO -> O2 -> CO -> O2) so that the residence time of specific adsorbates can be controlled, thus we can probe directly the role of the reactant and the redox sensitivity in the migration of the Cu cation. We demonstrate how distinguishable this technique is from previous steady-state measurements. The powder patterns are averaged over several cycles of gas (CO/H2/O2) variations. Phase-sensitive detection is applied to demodulate the data, picking up structural changes which occur in phase with reactant in-flow variations. Oscillations of the diffracted signal can be observed at the stimulation frequency ω, but also at the harmonic 2ω. Therefore the Fourier analysis of the components provides selective access to partial diffraction contributions otherwise merged into one average diffraction signal. This work is supported by the BNL LDRD program and experiments were performed at the APS and at the NSLS.
Human U2AF65 Recognizing the Major Polypyrimidine Splice Site Signal
Authors: Agrawal Anant , Kielkopf Clara
Published: November 2015

Disease-causing mutations often occur in the polypyrimidine (Py) tract splice site signals of human gene transcripts. The essential U2AF65 protein recognizes Py tracts near 3´ splice sites and initiates assembly of the splicing "machine", a megadalton complex comprised of approximately 100 proteins and five small nuclear RNAs. Our prior structures of a shortened U2AF65 variant reveal the basis for nucleotide interactions at subset of binding sites. How intact U2AF65 recognizes the Py tract splice site signal remains unknown to date. We determined a 2.0 Å resolution structure of intact U2AF65 recognizing an optimal, all-uridine Py tract. The new structure and complementary biochemical experiments reveal integral roles for main-chain atoms of the interdomain linker and residues surrounding two core RNA recognition motifs (RRM1 and RRM2) in recognition of the Py tract. The new U2AF65 structural information sheds light on the splicing defects caused by Py tract mutations in human genetic diseases. We test the U2AF65 structural relationship for a representative Py mutation that causes X-linked retinitis pigmentosa.
First structure of a cGMP-dependent protein kinase
Authors: Hui Raymond
Published: November 2015

PKA and PKG are two of the eponymous members of the AGC family of protein kinases as well as two of the earliest protein kinases discovered. Due largely to contributions from structural biology, the mechanism of cooperative and allosteric regulation of PKA is well understood. On the other hand, no structure of PKG from any organism has been available until recently. We present the first ever structure of PKG from the malaria parasite Plasmodium falciparum. The structure features PKG in its auto-inhibited form - a pentagonal arrangement of 4 cGMP-binding sites and the catalytic kinase domain. By comparing of this structure with PKA structures, we propose a novel mechanism of cooperativity and allostery by which Plasmodium PKG is regulated.
Increasing the probability of successful crystallization by using symmetric tag
Authors: Yao Min , Komoda Keisuke , Sakurai Naofumi , Yu Jian , Fujiwara Takaaki , Tanaka Yoshikazu , Tanaka Isao
Published: November 2015

Recent progress in the techniques of bio-macromolecular crystallography makes crystal structure analysis more powerful and useful for life science. The structure analysis of huge super-molecular (eukaryotic Ribosome, Vault etc.) and membrane proteins related to diseases were successful. Moreover, the structure/fragment drug design using crystal structure analysis method is also becoming reliable. However, crystallization still remains as a major bottleneck for determining bio-macromolecular structures, although many methods have been developed such as crystallization kits, crystallization robot, crystallizing in gel, space, and magnetic field, laser excitation, using antibody, modification of protein surface, and so forth. The current situation of crystallization is still dependent on the accidental method searching for a crystallization reagent and the growth environment since the methodology for obtaining a quality crystal for structure analysis is not established yet. Therefore, further development of more advanced crystallization methods is required to increase the probability of successful crystallization. In principal, probability of successful crystallization could be increased by polymerized molecules with 2 or 3-fold rotation symmetry [1]. We have solved more than 100 structures, and found some fragments which is isolated from core structure, and seem to contribute to form high quality crystal by forming a polymer with 2 or 3-fold axial symmetry. Thus, we developed a novel method by fussing target protein with crystallization tags named 2/3RS-tag. These 2/3RS-tags polymerize target proteins with 2 or 3-fold axial symmetry, and consequently accelerate formation of crystal. We will report and discuss this new method in this presentation.
JCSG – Adapting Structural Genomics to Eukaryotic Complexes
Authors: Elsliger Marc-André , Deacon Ashley , Godzik Adam , Lesley Scott , Hodgson Keith , Wooley John , Wüthrich Kurth , Wilson Ian
Published: November 2015

For over a decade, the Joint Center for Structural Genomics (JCSG.org) has been at the forefront of developing tools and methodologies that enable the application of high-throughput structural biology (HTBSB) approaches to a broad range of challenging biological and biomedical problems. In PSI:Biology (2010-2015) to meet the challenges and embrace the opportunities that arise from our Partnerships projects, we have leveraged our gene-to-structure pipeline to explore challenging projects focused on structural characterization of interaction networks involved in stem cell regulation, T-cell activation and nuclear receptor signaling. These highly collaborative efforts have enabled development of systematic and integrative approaches for identifying and investigating networks of key multi-domain eukaryotic proteins and higher order assemblies of multi-component eukaryotic protein/protein and protein/nucleic acid complexes. In parallel, our biomedical theme project has focused on investigating host/microbe interactions of the microbial communities that inhabit specific niches and environments of the human body, e.g. the human gut microbiome. These efforts to date have been centered on secreted proteins from commensal bacteria in the human gut. The symbiotic relationship and influence on human development, physiology, immunity, and nutrition represent an exciting new frontier for HTBSB where we can investigate how these microorganisms contribute to human health as well as to disease. The JCSG also strives to promote widespread use of PSI resources, materials, methodologies and data to the general scientific community, via Community Nominated Target (CNT) projects and development and use of new technologies and methodologies. We also continue to contribute to the original PSI mission of structural coverage of the expanding protein universe. Supported by NIH U54-GM094586.
Crystal Structure Analysis of Magnetically Oriented D-Arabinitol Microcrystal
Authors: Yamane Shuhei , Matsumoto Kenji , Kimura Fumiko , Kimura Tsunehisa
Published: November 2015

We have proposed magnetically oriented microcrystal array (MOMA) technique as a new technique of crystal structure analysis. With this technique, single crystal X-ray diffraction analysis is made possible from a microcrystalline powder. Biaxial crystals, having three different values of magnetic susceptibility (χ1>χ2>χ3), are aligned three dimensionally under a frequency-modulated elliptical magnetic field. Biaxial microcrystal suspended in an ultraviolet (UV) light-curable monomer matrix is aligned three dimensionally under the magnetic field, followed by consolidation of the alignment by the photopolymerization the matrix. Biaxial crystal group has three crystal systems: orthorhombic, monoclinic and triclinic systems. The analysis of crystals belonging to the triclinic system is important because ca. 23 % of organic crystals are triclinic. We have so far succeeded in determining crystal structures of orthorhombic and monoclinic systems by using the MOMA technique[1, 2, 3] but crystals of triclinic system have not been examined yet. Therefore, in this report, we attempt to determine the crystal structure of D-arabinitol, belonging to the triclinic system, by using the MOMA technique. 10 wt% D-arabinitol / XVL14 (UV light-curable monomer) suspension was subjected to 8-T magnetic field (the speed of rotation changed between 10 rpm and 40 rpm at every 900) and was consolidated by irradiation of UV light. The prepared MOMA was subjected to the X-ray diffraction measurement. The obtained diffraction spots were well resolved and the average of half widths was about 3.90. These results indicate that the D-arabinitol microcrystals were aligned three dimensionally in the MOMA and the high quality of alignment was achieved. These results indicate that the obtained diffraction patterns are equivalent to those obtained from corresponding single crystal.
Fighting Counterfeit Drugs Using Micro-X-Ray Diffraction
Authors: Musumeci Daniele , Hu Chunhua , Ward Michael
Published: November 2015

A new protocol using micro-X-ray diffraction is developed to certify the authenticity of drug tablets, and therefore to prevent, deter, or detect counterfeit medicinal products. The method uses X-ray to map hidden patterns printed under the tablet coating and on packages. The patterns such as barcodes and logos are made of compounds approvoved by the Food and Drug Administration. The method is nondestructive, automated and user-friendly. The protocol relies on verification of phase, composition, and pattern readout in a single measurement, which reduces the risk of circumvention.
Synthesis of MOFs from Zn,Cd,Ni-4-carboxyphenylboronic acid with DMF solvent
Authors: Dimowa Louiza , Nikolova Rositsa , Dyulgerov Ventsi , Kostov-Kytin Vladislav , Shivachev Boris
Published: November 2015

Synthesis and characterization of porous metal organic frameworks (MOFs) has prompted considerable interest because of the possibility to design the pore size and physical/chemical properties by suitable selection of the organic linkers (ligands). In this work, we have chosen a classical solvothermal synthesis strategy involving 4-carboxyphenylboronic acid, a molecule that is analogic to the terephthalic acid, Zn- Cd- Ni-OAc metal salts and DMF as solvent. It is known that during solvothermal synthesis DMF decomposes to dimethylamine which is easily incorporated in MOF's [1], [2]. The obtained MOFs are characterized by single-crystal X-ray diffraction, X-ray powder diffraction, TG analyses, IR spectroscopy and BET analyses. Preliminary X-ray single crystal diffraction results showed that a new type of structure may be produced in function of the temperature. The Cd- structure crystalizes in the hexagonal Space group P6222, with respective parameters of a = 14.4113(12), c = 13.0416(7) Å (Fig. 1). The cadmium ion is tetra coordinated by the oxygens of the B(OH)2 and COO- moieties. The 4-carboxyphenylboronic acid is disorder and attempts to lower the symmetry to model the disorder resulted in unstable refinement. In the studied systems in addition to the reported new compound isotypical structures to MOF-5 containing 4-carboxyphenylboronic acid instead of 1,4-benzenedicarboxylate were also obtained.