bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemical clustering and visualization applied to macromolecular crystallography
Authors: Bruno Andrew , Ruby Amanda , Luft Joseph , Grant Thomas , Seetharaman Jayaraman , Hunt John , Montelione Gaetano , Snell Edward
Published: November 2015

Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and the insertion and correct placement of a sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient appears to be robust in this application and coupled with hierarchical clustering and the overlay of crystallization outcome reveals information of biological relevance. While tested with a single example the potential applications appear promising.
Optimizing buffer conditions to improve crystallizability and SAXS measurement
Authors: Boivin Stephane , Kozak Sandra , Vieira Vanessa , Rasmussen Gry , Meijers Rob
Published: November 2015

The Sample Preparation and Characterization (SPC) facility at EMBL Hamburg is situated next to the PETRA3 beamlines for protein crystallography and small angle scattering (SAXS) that are operated by EMBL. The facility is equipped with molecular biology and biophysical instrumentation to carry out purification and characterization of macromolecular samples. It serves a mixed community of local EMBL scientists, beamline visitors and scientists from the European Union research area. Most incoming samples are destined for high-throughput crystallization at the facility or characterization by SAXS. The facility offers standardized quality control reports on each incoming sample, including characterization by mass spectrometry and Thermofluor. Based on this report, local staff can suggest and perform optimization protocols that increase the stability of the sample. For instance, Thermofluor screens(1) were developed that probe the effect of buffers and additives that are commonly used in sample preparation. These systematic screens provide a high-throughput method to identify stabilizing conditions for sample purification, storage and structural characterization. This technique has been also a valuable asset providing a high-throughput method for assessing the crystallizability of proteins by screening for conditions which contribute to the protein sample homogeneity, stability and solubility. The home-made screens have been tested on more than 200 different protein constructs at SPC facility. The aim of the SPC facility is to integrate off-line biophysical techniques with synchrotron beamlines, to offer the European user community a full package for sample characterization. The facility is especially geared towards cell biologists with little experience in structure determination. Expert staff is available to help to plan, perform and interpret biophysical experiments. It is possible for users to book SPC equipment together with their synchrotron beamtime, for protein purification, circular dichroism and isothermal calorimetry. Funded access to the facility is currently provided by the European Community's Seventh Framework Programme Biostruct-X. For further information, please contact spc@embl-hamburg.de.
Focusing of hard X-ray beams in quartz crystal under the temperature gradient
Authors: Kocharyan Vahan , Khlopuzyan Sargis , Grigoryan Poghos , Baghdasaryan Edik , Amiraghyan Ruben
Published: November 2015

The research of the focusing and defocusing of the diffracted X-rays with different wave fronts in crystals under the influences of the temperature gradient and the ultrasonic vibrations is given in the works [1,2]. This work is dedicated experimentally investigation of Laue diffraction of the hard X-rays in quartz single crystals under the influence of the temperature gradient. It is shown that the reflected beams under the influence of the temperature gradient are focused. When the vector of the temperature gradient is anti parallel to the diffraction vector, in accordance to the increasing value of the temperature gradient the focus point continuously approaches the crystal. When the vector of the temperature gradient is parallel to the diffraction vector, in accordance with the increasing value of the temperature gradient the focus point continuously distances itself from the crystal, and at a certain value of the temperature gradient it becomes a plane wave. Parallel to the further increasing of the temperature gradient we see an imaginary focus, which continuously approaches the entry surface of the crystal. It is shown that by using a thicker single crystal it is possible to focus and pump a larger angular and spectral width of X-rays in the direction of diffraction.
Synthesis and crystal structure of Sr2MnGaO5-dFx, layered oxyfluorides
Authors: Katsumta Tetsuhiro , Takami Naofumi , Mori Daisuke , Inaguma Yoshiyuki
Published: November 2015

Sr2MnGaO5 brownmillerite has an interesting structure. In this compound, MnO6 octahedra and GaO4 tetrahedra are ordered along c-axis. The MnO6 octahedra are deformed due to Jahn-Teller effect with four short equatorial Mn-O distances and two long apical one. Oxygen vacancies in the GaO layer provide distorted tetrahedral coordination for the Ga cation. The oxide and/or fluoride ions are introduced into the vacancies in GaO layer. The synthesis of Sr2MnGaO4.78F1.22 using XeF2 as a fluorinating agent is reported, while the small amount SrF2 impurity is contained[1]. On the other hand, low temperature fluorination using polyvinylidenefluoride (PVDF) is powerful method for the synthesis of oxyfluoides from brownmillerite[2]. In this study, we synthesize the Sr2MnGaO5-dFx (x=0.5, 1.0, 1.5, 2.0) using PVDF and investigate the variation of crystal structure with x. Sr2MnGaO5 brownmillerites were prepared sold state reaction method. Starting materials were SrCO3, Mn2O3 and Ga2O3. The mixture was heated twice in Ar at 13000C for 72h. For the preparation of Sr2MnGaO5-dFx (x=0.5, 1.0, 1.5, 2.0), stoichiometric amounts of Sr2MnGaO5 brownmillerite and PVDF were ground and the mixture were heated in N2 at 4000C for 8h. And then, the as prepared materials were subsequently heated in O2 at 4000C for 8h. The Sr2MnGaO5-dFx were obtained without impurities. As shown in Fig., the orthorhombic distortion reduced with the increase in x. The X-ray diffraction data of Sr2MnGaO5-dF1.0 could be refined on the structure model belonging the space group Icmm. the bond valence sum of Ga3+ calculated from Ga-O bond length indicates that the fluoride ions are introduced into GaO layer preferentially. The measurements of magnetic properties for Sr2MnGaO5-dFx are in progress.
Crystallography of Vanadium-bearing Micas (Bol'shoi Karatau Range, Kazakhstan)
Authors: Bekenova Galiya , Dyussembayeva Kulyash
Published: November 2015

The mineralogical study of vanadium and vanadium-bearing micas from Cambrian carbonaceous-cherty formation of North-West of Bol'shoi Karatau range has allowed to establish four basic groups: 1. chernykhite (V2O3+V2O4 up to 23%); 2. Ba-roscoelite (V2O3 up to 18%) [1]; 3. vanadium-bearing muscovite and phengite (V2O3 up to 5%) and 4. secondary mica – V-Ba-phengite (V2O3+V2O4 up to 6-8%) [2]. Physical, optical properties as well as crystal structural parameters depend on vanadium content. The crystal structure of micas was determined by X-ray and electron diffraction techniques. The polytypes and unit cell parameter b (Å) are the main structural characteristics [3]. 2M1 polytype is spread among vanadium micas. Polytypes 1M and (1M+2M1) are only in vanadium-bearing micas – muscovite and phengite. The minimum b 9.03-9.04 Å is typical for this group. For secondary mica - V-Ba-phengite the parameter b varies from 9.6 to 9.09 Å. On the figure the secondary mica (1) is associated with mica without vanadium (2) and carbon-clay-chert (3) into polished section, where epoxy resin (4). For Ba-roscoelite b is equal 9.07-9.15 Å; for chernykhite - b 9.18 Å.
Crystal Chemistry of Some Natural Phosphates Containing Mixed Anionic Radicals
Authors: Chernyatieva Anastasia , Yakovenchuk Viktor , Britvin Sergey , Murashko Mikhail , Pekov Igor , Krivovichev Sergey
Published: November 2015

Sulfates and phosphates consisting of mixed anionic radicals (or heteropolyhedral units) constitute a large group of mineral species. In this contribution, we will summarize our recent results on some novel or poorly studied minerals, whose structures are based upon octahedral-tetrahedral structural units. During investigations of secondary pegmatite phosphates from Hagendorf (Germany), we have located a new whiteite-jahnsite-group mineral that was named whiteite-(CaMnMn) Its structure is formed by alternating anionic layers composed from MO6octahedra and PO4tetrahedra, and linked together thorugh M(2) cations and water molecules. The crystal structure of bonshtedtite, Na3Fe(PO4)(CO3), is similar to that of the other minerals of the bradleyite group. It is based upon the [Fe(PO4)(CO3)]3-layers oriented parallel to (001). Refinement of the crystal structure of girvasite at 110 K allowed to determine positions of H atoms and to reveal the hydrogen bonding scheme. The refinement confirmed that the proper chemical formula of the mineral should be written as NaCa2Mg3(PO4)4(CO3)(H2O)6, in contrast to the formula NaCa2Mg3(PO4)2[PO2(OH)2](CO3)(OH)2(H2O)4proposed in the original works. The crystal structure of cattiite, Mg3(PO4)2(H2O)22contains two symmetrically independent Mg sites, tetrahedrally coordinated by water molecules to form octahedral complexes [Mg(H2O)6]. The crystal structure of vendidaite, Al2(SO4)(OH)3Cl(H2O)6, contains one symmetrically independent Al site coordinated by three OH groups and three H2O molecules. Together with the [Al2(OH)3(H2O)6]3+chains, Cl- anions and (SO4)2-groups form pseudo-layers parallel to (010).Steklite, KAl(SO4)2, was first described as a technogenic phase in products of burning coal dumps (Chelyabinsk region, Russia). Steklite of natural origin was found in sublimates of the Yadovitaya (Poisonous) fumarole of the Second scoria cone of the Northern Breakthrough of the Great Tolbachik Fissure Eruption, Kamchatka, Russia.
Thermal expansion of monoclinic natrojarosite
Authors: Brand Helen , Scarlett Nicola , Grey Ian , Knight Kevin
Published: November 2015

Jarosites and related minerals are of great interest to a range of mineral processing and research applications. In some industrial settings jarosite formation is encouraged; for example to aid the removal of iron species from solutions in hydrometallurgical processes. In other environments such as bioleaching, jarosite formation can hinder the process by creating a kinetic barrier, in the form of a passivation layer, to the desired reaction. Jarosites are a major component of acidic soils and are present in significant amounts in acid mine drainage environments. There has been a recent resurgence in interest in jarosite minerals since their detection on Mars by the MER rover Opportunity. In this context, the presence of jarosite has been recognised as a likely indicator of the presence of water on Mars in the past. It is hoped that study of their formation mechanisms, stability and thermoelastic properties will provide insight into the environmental history of Mars as well as informing terrestrial industrial concerns. To this end we are engaged in a program to study jarosites and their formation and stability behaviour over a range of conditions. This contribution describes in situ powder diffraction experiments to determine the thermal expansion of a deuterated natrojarosite. Data were collected on the HRPD beamline at the ISIS spallation source where the natrojarosite sample was heated from 10–700K, and at the powder diffraction beamline at the Australian synchrotron where the sample was heated from 80-700K. Isothermal neutron and synchrotron datasets were refined simultaneously. Analysis of the lattice parameter variation with temperature shows that all cell edges increase smoothly to ~500 K where there is a discontinuity. This discontinuity represents the initially non-stoichiometric monoclinic jarosite converting to a stoichiometric, rhombohedral phase, shortly after which FeOHSO4 peaks become visible. Thermal expansion coefficients have been fitted from 10-470K and show that there is most variation in the monoclinic c-axis. This direction is normal to the layers of sulphate tetrahedra and iron octahedra within the jarosite structure and contains more flexible hydrogen bond linkages which more easily accommodate expansion than the more rigid polyhedra. Details of the combined neutron-synchrotron diffraction approach will also be discussed.
New Minerals from the Classic Eifel Region
Authors: Depmeier Wulf , Chukanov Nikita , Pekov Igor
Published: November 2015

In the recent four years, the authors have jointly organized and conducted several excursions into the classical volcanic field in the Eifel area, Germany. The original goal was to compare its geochemistry and mineralogy with those of the hyperalkaline intrusions of Khibiny and Lovozero on Kola peninsula, Russia. Since none of us had previous experience with the Eifel area, local amateur mineral collectors were contacted and asked for support. These collectors often have been active in their region for decades and, hence, know the various deposits and minerals by heart. Our request was met with great enthusiasm and invaluable support was given to us not only with respect to the organization of the excursions, but the collectors also shared their experience with getting access to the quarries and often offered samples from their own, very well organized and documented, collections. It soon turned out, that – a bit to our surprise - even in such a classical area as the Eifel with its long tradition of geological and mineralogical research new minerals can be found. As a result, 16 new minerals from the Eifel could be described, accepted by IMA, and the results published. Others are still under study. Some of these minerals were found in the field, others were donated by local mineral collectors. In acknowledgement of their invaluable contribution, several minerals now bear names of those or other local collectors. Several of the new minerals belong to well-known mineral groups, but a few represent quite new structures. For example, in the mineral hielscherite, the pyramidal sulfite anion substitutes for planar carbonate in thaumasite, and günterblassite is the first phyllosilicate with a triple tetrahedral layer, thus indicating somehow a structural transition into a tectosilicate.
Solid State NMR, Diffraction and Modeling of Intermetallics
Authors: Haarmann Frank
Published: November 2015

Intermetallic compounds are a fascinating class of materials with respect to structural chemistry and technological applications. The interest of basic research focuses on chemical bonding and local ordering of the atoms. Combined application of NMR spectroscopy, quantum mechanical calculations of NMR parameters based on density functional theory (DFT), and X-ray diffraction was applied to study the peculiarities of the Ga bonding situation in alkaline earth metal gallides [1,2]. The compounds were chosen as a model system to determine reliable NMR spectroscopic parameters for the investigation of intermetallic compounds possessing metallic conductivity. Very good agreement of calculated and experimental parameters was achieved. An analysis of the electric field gradient (EFG) contributions reveals its local character. It is determined by the population difference of the p-like states of the electrons of the Ga atoms. Due to the reliability of the EFG for the investigation of intermetallic compounds studies of the influence of disorder on the local bonding situation of the Ga atoms in the solid solutions of Sr1+xBaxGa2and were chosen in a next step. Super lattice structures were derived from the crystal structures of the binary parent phases to model the varying local arrangements of the atoms. DFT calculations based on these super lattice models enabled the theoretical deamination of the EFG in a good agreement with the experimental values. Thus, the EFG can also be used to study local arrangements of the atoms in disordered materials possessing metallic conductivity. The anisotropic conductivity of the powder samples can be used to align the crystallites in the magnetic field resulting in an increased experimental resolution. Line shape analysis of orientation dependent NMR experiments of M(Al1+xGax)4with M = Sr, Ba reveal local ordering of the Al atoms.
Particle statistics in powder diffraction method
Authors: Ida Takashi , Maruyama Kosuke , Togo Yuki , Funahashi Hideto , Hibino Hasashi
Published: November 2015

The statistical variation in observed powder diffraction intensity is often dominated by the limited number of crystallites that satisfy the diffraction condition. This effect has been termed with particle statistics in powder diffraction method [1]. We have reported experimental validation of the theory for particle statistics about symmetric reflection mode measurements, and proposed a new method to evaluate the crystallite size and its distribution by statistical analysis based on a generalized theoretical framework [2]. We have also demostrated improvement of structure refinement by application of the maximum likelihood estimation to statistical model explicitly taking the errors caused by the particle statistics into account [3]. As the formula suitable for the particle statistics about a continuously spinning flat specimen is still unclear, three kinds of diffraction intensity measurements, (1) in-plane (Φ)-scan, rocking angle (Ω)-scans for (2) stationary and (3) spinning flat specimens, have been conducted for standard powder samples of Si (NIST SRM640c) and lanthanum hexaboride (NIST SRM660a) at a synchrotron powder diffraction beamline BL-4B2 at the Photon Factory, KEK in Tsukuba. The statistical variance observed inΦ-scan and Ω-scan measurements for stationary specimens have shown cosecant dependence of the effective number of diffracting crystallites, just as predicted by the traditional theory. The statistical variance in Ω-scan measurements for spinning specimens has also shown a cosecant behaivior rather than the squared cosecant dependence suggested by de Wolff [1].
Determination of Crystal System from Microcrystalline Powder
Authors: Kimura Tsunehisa , Matsumoto Kenji , Kimura Fumiko
Published: November 2015

Determination of lattice constants is a crucial process in analyzing powder diffraction data, affecting the robustness of analyses in subsequent steps. A number of algorithms and software based on them to predict lattice constants from powder data have been reported. In this study, we propose a novel experimental approach to facilitate unambiguous determination of the crystal systems and resulting lattice constants from a microcrystalline powder sample. Efforts have been made for partial recovery of crystal anisotropy from a complete random orientation in powder in order to facilitate the analysis of powder data. Our approach makes use of magnetic orientation[1-3] of microcrystals occurring due to the diamagnetic anisotropy inherent to crystal. By application of a static/or rotating magnetic field, the easy/or hard magnetization axes of microcrystals undergo uniaxial alignment, giving rise to two different fiber diffraction patterns. These patterns reflect the crystal symmetry, enabling us to discriminate the crystal system. Crystals of known crystal system were pulverized and their suspensions were prepared. Each suspension was subjected to a static/or rotating magnetic field and the X-ray diffraction measurement was performed in situ to obtain two fiber diffraction patterns. It is evident that isotropic crystals only produce ring patterns for static and rotating measurement. On the other hand, biaxial crystals exhibit sharp diffraction spots in both fiber patterns. Furthermore, these fiber patterns exhibit layer lines in both patterns for the orthorhombic system, no layer lines for triclinic system, etc. In addition, overlapping of peaks in one-dimensional powder pattern can be resolved by indexing the spots in two dimensions of fiber patterns.
pH- and sodium-induced changes in a sodium/proton antiporter
Authors: Paulino Cristina , Kühlbrandt Werner
Published: November 2015

Na+/H+antiporters are essential secondary-active transporters that are found across all biological kingdoms and play a crucial role in the pH, sodium and cell volume homeostasis. MjNhaP1 is an archaeal electroneutral Na+/H+-antiporter resembling the human NHE1 exchanger. Substrate-induced conformational changes in MjNhaP1 were examined by electron crystallography of 2D crystals in a range of physiological pH and Na+conditions. In the absence of sodium, changes in pH had no major effect on the structure of MjNhaP1, whereas changes in Na+concentration caused a marked conformational change that was largely pH-independent. Crystallographically determined, apparent dissociation constants indicated ~10-fold stronger Na+binding at pH 8 than at pH 4, consistent with substrate competition for a common ion-binding site. In conjunction with a new 3D EM map of MjNhaP1 a model for transport mechanism is proposed. Conformational changes occur in the 6-helix bundle region of MjNhaP1 that is thought to harbour the ion translocation site. Na+-binding converts the antiporter from the apo- or proton-bound, outward-open state to the Na+-bound, inward-open state. Oscillation between these two states result in rapid Na+/H+antiport.
Structural basis for the recognition of Eps15 by the SGIP1 μ homology domain
Authors: Yamaguchi Atsuko , Kohda Daisuke , Shimada Atsushi
Published: November 2015

Clathrin-mediated endocytosis (CME) is a process for eukaryotic cells to internalize extracellular molecules. FCHo1 and FCHo2 are involved in the initial clathrin assembly step of CME [1, 2]. These proteins contain the lipid-binding EFC/F-BAR domain at the N-terminus [3], and the μ homology domain (μHD) at the C-terminus. The μHDs of these proteins interact with a region rich in a repeated sequence motif, Asp-Pro-Phe (DPF), of an endocytic scaffold protein, Eps15. Eps15 contains fifteen DPF motifs. SGIP1 is also involved in CME and contains the μHD highly homologous to those of FCHo1/2 at the C-terminus, which also interacts with Eps15. The μHDs of these proteins share weak amino-acid sequence homology with the μ subunits of the adaptor protein complexes, such as AP-2, which links cargo proteins and clathrin in CME. To investigate the mechanism of Eps15 recognition by the FCHo1/FCHo2/SGIP1 μHDs, we first identified the minimal Eps15 fragment retaining the ability to interact with the μHD by the interaction studies using the SGIP1 μHD. We found that two Eps15-derived 11-residue peptides each containing two DPF motifs connected by a short 2–3 residue linker interact with the SGIP1 μHD with modest affinities (Kd = 15–20 μM). In contrast, peptides containing only one DPF motif did not bind to the μHD. Thus, the SGIP1 μHD requires two DPF motifs for binding. Moreover, the structures of the SGIP1 μHD in complex with the peptides containing two DPF motifs revealed that the SGIP1 μHD extensively recognizes the two adjacent tandem DPF motifs, while not contacting the flanking residues, consistent with the interaction studies. This mode of recognition is distinct from that of the Eps15 DPF motif recognition by the AP-2 appendage domains, providing the rationale of the recruitment of Eps15 by FCHo1/2 to the nascent endocytic sites, while allowing the FCHo1/2-bound Eps15 to recruit AP-2 complex with the different parts of the Eps15 DPF repeat region for clathrin assembly.
Structural features and low-temperature adaptation of aspartate racemase
Authors: Hata Yasuo , Fujii Tomomi , Yamauchi Takae , Gogami Yoshitaka , Oikawa Tadao
Published: November 2015

Aspartate racemase (AspR) catalyzes the interconversion between L- and D-aspartates without PLP. The only crystal structure of the PLP-independent amino-acid racemase is now available from a hyperthermophilic archaeon. To elucidate structural features and low-temperature adaptation of the racemase group, we determined the crystal structures of AspR from Lactobacillus sakei NBRC 15893 (LsAspR), which works in the low-to-medium temperature range, and for comparison AspR from Thermococcus litoralis DSM 5473 (TlAspR), which has the maximum activity at 950C. LsAspR and TlAspR weree crystallized at 200C by the sitting-drop vapour-diffusion method using a precipitant solution of 25% (v/v) PEG-MME 550, 5% (v/v) 2-propanol and 0.1 M sodium acetate pH 4.8 and a precipitant solution of 24% (w/v) PEG1500, 0.2 M L-proline and 0.1 M HEPES pH 7.5, respectively. The structures of LsAspR and TlAspR were determined by molecular replacement and refined at 2.6 Å resolution (R=23.8%, Rfree = 31.6%) and 2.0 Å resolution (R=18.7%, Rfree = 25.0%), respectively. Both LsAspR and TlAspR molecules are homodimers with molecular two-fold axis. The subunit of each enzyme molecule comprises the N-terminal and C-terminal domains. The molecule is formed mainly by intersubunit interactions between the N-terminal α-helices and intersubunit hydrogen-bonds between the N-terminal β-sheets in the dimer interface. The active-site cleft exists between both the domains. The spatial arrangement of the strictly conserved cystein residues in the cleft reveals the Cys residues involved in the enzymatic catalysis. A structural comparison of LsAspR and TlAspR reveals structural factors probably involved in thermostability of AspR. The molecular volume, intersubunit interaction, and the number of ion pairs suggest that the LsAspR molecule is more loose than that of TlAspR.
Crystallographic snapshots of DesK and DesR: two component systems on the move
Authors: Trajtenberg Felipe , Albanesi Daniela , Botti Horacio , Mechaly Ariel , Larrieux Nicole , Cybulski Larisa , Nieves Marcos , Ruetalo Natalia , de Mendoza Diego , Buschiazzo Alejandro
Published: November 2015

Two-component systems (TCSs) are key players in bacterial signaling, to better understand signal-transmission with molecular detail. The TCS DesK/DesR controls fatty acid desaturation in Bacillus subtilis in response to cold shock and other membrane-altering effectors. We had previously put forward a model of signal-dependent allosteric control of the sensor kinase catalytic activity [1,2]. We have now turned our attention to the response regulator DesR. A canonical activation pathway has been widely accepted to explain phosphorylation-mediated control of response regulator function, allosterically coupling the phosphorylation site to the α4β5α5 surface. However, the structural evidence supporting the main hypotheses is still highly fragmentary. We are now reporting the crystal structure of full-length DesR, in complex with a phosphoryl-mimetic, showing the activated state [3]. Several crystal forms of the receiver domain were determined in the active and inactive configurations, revealing molecular details of the activation switch. Comparative small angle X ray scattering of full-length constructs, structure-guided point mutagenesis, as well as in vitro and in vivo functional analyses, allow us to propose an integral model of DesR activation. The phosphorylation of the receiver domain is allosterically coupled not to one, but two exposed surfaces, independently controlling its dimerization and tetramerization. Notably, a novel surface is shown to be essential for a non-canonical dimerization and activation mechanism. Direct coupling analysis highlights this interface as a shared feature of all NarL/LuxR regulators. This surface is further involved in cognate histidine kinase binding, disclosing a novel view of response regulator allosteric control. With the data we are now reporting, the DesK/DesR signaling pathway becomes, to the best of our knowledge, one of the most thoroughly studied examples of a thermosensor TCS at the molecular and biological levels.
Structure of an endotoxin modifying enzyme and virulence factor in Neisseria
Authors: Vrielink Alice , Anandan Anandhi , Piek Susannah , Moares Isabel , Kahler Charlene
Published: November 2015

Multiple drug resistance (MDR) in Gram-negative bacteria represents one of the most intractable problems facing modern medicine. Not only is antibiotic resistance incrementally increasing during clinical treatment of infections, but also the evolution and acquisition of new mechanisms of antibiotic resistance lead to the sudden loss of the capacity to treat infections. The most recent superbug, MDR-Neisseria gonorrhoeae, causes the untreatable sexually transmitted infection gonorrhoeae. Chronic gonococcal infections have a high morbidity rate and, due to the explosion in cases worldwide, the community burden is enormous. N. gonorrhoeae colonizes the mucosal surfaces of the human body and has a number of virulence mechanisms that prevent clearance by the human immune system. The most important of these mechanisms is decoration of the lipooligosaccharide lipid A headgroups with phosphoethanolamine (PEA) by the enzyme, lipid A PEA transferase (LptA). Inactivation of the LptA results in the complete loss of PEA groups from lipid A, loss of bacterial colonisation of epithelial cells (Takahashi et al., 2008), increased sensitivity to cationic antimicrobial peptides (Tzeng et al., 2005) and reduced resistance to human complement mediated killing (Lewis et al., 2013). LptA knockouts of N. gonorrhoeae also result in the complete loss of virulence in models of human and mouse infections. Based on these findings we have undertaken a structure-guided approach to develop inhibitors of LptA that will assist in controlling infection and transmission by this important human pathogen. LptA is a membrane protein that interacts with two different lipid substrates. We have determined the crystal structure of the enzyme to 2.75Å resolution. The structure provides insights into the mechanism of substrate binding and catalysis and suggests that significant conformational changes occur through its catalytic cycle.
Towards a world-wide crystal growing competition
Authors: Van Meervelt Luc
Published: November 2015

Since many years regional and national crystal growing competitions are successfully organized for pupils in countries such as Australia, Belgium, Canada, England, France and Singapore, and for sure in many schools on a more local basis. For most competitions pupils have to grow single crystals in the class room during a limited period of time (e.g. four weeks) of a limited amount of starting material provided by the organizers. Submitted single crystals are then judged by a jury based on the weight and the quality of the crystal. Typical compounds used as starting materials for such competitions are alum (aluminium potassium sulphate dodecahydrate), copper (II) sulphate pentahydrate, borax (sodium tetraborate decahydrate), ammonium iron (II) sulphate hexahydrate, potassium dihydrogen phosphate and ammonium magnesium sulphate hexahydrate. To celebrate the International Year of Crystallography a small IUCr working group of coordinators of current crystal growing competitions took the initiative to stimulate as many countries as possible to organize a regional or national crystal growing competition. To facilitate this, the IUCr offers all possible support for newcomers in the form of a time line, protocols and suggestions for judging and prize awarding. This information is available on the IYCr website www.iycr2014.org/participate/crystal-growing-competition, together with a brand new animated video 'How to grow a single crystal - with Johanna' illustrating the protocol. With the celebrations of the International Year of Crystallography in mind the lead partners IUCr and UNESCO organize also a world-wide crystal growing competition. The aim of this competition is that participants grow their own crystals (whether involved in a regional/national competition or not) and convey their experience through a short video or essay. A panel of judges will evaluate the entries using criteria such as creativity, esthetic value, description of working plan and experimental work, clarity of explanations and scientific background. For countries were no crystallographers can take the lead to initiate a competition in 2014 the network of UNESCO schools will be used, an initiative which will start in September 2014.
Implementing graphic outputs for the Material Properties Open Database (MPOD)
Authors: Fuentes-Cobas Luis , Chateigner Daniel , Pepponi Giancarlo , Muñoz-Romero Alejandro , Ramírez-Amparan Gerardo , Templeton-Olivares Ivan , Sánchez-Aroche David , Hernández-Montes Jonathan , Márquez de la Mora Núñez Andrea , López-Carrasco Marcos
Published: November 2015

The tensor nature of single- and polycrystalline materials' physical properties highlights both the diversity of possible technological applications and the difficulties of assimilation for those new to the subject. The Material Properties Open Database (MPOD) [1] is a useful tool that provides access to a wide spectrum of properties tensors for an extensive selection of materials. In the present contribution an extension of the MPOD system is reported. The introduced innovation is the output, in the form of a graphical representation, of registered second, third and fourth rank tensors. The objective, as an educational project, is to provide the crystallographic community a friendly means to help the intuitive understanding of crystalline anisotropy. The given graphical output is the so-called longitudinal surface representation [2]. The accompanying figure shows an example of the MPOD graphical output. Shown surfaces represent the compliance tensor and its inverse (Young's modulus) longitudinal surfaces for a silver single-crystal. MPOD's new version may be accessed by the original website http://www.materialproperties.org/ and also by its Mexican mirror http://mpod.cimav.edu.mx. The MPOD websites continue their development. The international MPOD group systematically adds new published data. Modeling and representing textured polycrystals' properties is on target [3].
The Krystalla Project for the dissemination of crystallography
Authors: Otálora Fermín , García-Ruiz Juan Manuel , García-Caballero Alfonso , Santana-Ibañez Martha
Published: November 2015

"The ""Krystalla Project"" comprises a series of coordinated activities designed to promote crystallography and crystallization in society in the context of International Year of Crystallography (IYCr2014). "Krystalla" is a joint venture between the Laboratory of Crystallographic Studies of the Spanish National Research Council (CSIC) and Triana Science & Technology, a company specialized in the development of crystallization technology for research and dissemination activities. "Krystalla" aims to: a) Increase awareness of the society about the importance of crystallography and its role in everyday life. b) Promote the IYCr2014 and reflect on scientific knowledge and the role of science in our society. c) Inspire young people and encourage public participation through exhibitions, lectures and demonstrations. d) Illustrate the universality of science and encourage education and research in crystallography. Through the following activities: 1) The itinerant exhibition ""Crystals: a world to discover"" which will exemplify the applications of crystallography on our daily life and the fundamentals behind it. 2) A series of workshops on ""popular crystallography"" and ""crystallography"" for kids. 3) The National Crystallization Competition in the School [1]. 4) A ""Flamenco show" entitled ""The Crystal and the Rose"" blending the art of Flamenco with crystallographic concepts like symmetry, the contrasting geometries of crystals and living forms or the emergence of order from disorder. 5) A didactic edition of the successful documentary ""The Mystery of the Giant Crystals"" including the making-off of the movie, short videos explaining the fundamentals and applications of crystallization and scientific notes for teachers. 6) The webpage "The House of Crystals" exclusively dedicated to the dissemination of crystallography and crystallization. 7) A series of didactic guides to use well known movies as crystallographic teaching and popularization materials. 8) The IYCr2014 promotional video [2]."
Crystallography at your door
Authors: Bacchi Alessia , Corriero Nicola , Guerri Annalisa , Lenco Andrea , Massera Chiara , Punzo Francesco
Published: November 2015

The idea at the basis of the project 'Crystallography at your door' is to associate crystallography with cultural, artistic, and natural beauty by creating a virtual list of `Crystallographic sites in Italy'. One of the challenges that science in general has to face is to increase awareness of the impact that research has on daily life, culture and history. In addition, crystallography is not a discipline generally known to public, and while the words chemistry, physics, biology immediately bring to people at least some memories of lessons at high schools, crystallography remains an obscure term. However the natural beauty of crystals related to their regular shape, symmetry, colours has since the dawn of humankind fascinated people; even nowadays concepts related to crystals are widely used in marketing to convey to the buyers the idea of cleanliness, purity and freshness of many products, that are not necessarily related to crystalline materials. On the wave of IYCr2014 the Italian Crystallographic Association promotes initiatives to bring people closer to crystallography [1]; one of these is aimed at stimulating people to look around for places where crystallography may be seen 'in action' in all its facets: mines, saltworks, historical places related to the work of crystallographers, museums, and most of all buildings or masterpieces of art where symmetry has been exploited to create beauty. Italy has a unique strength in the artistic and cultural heritage fields; in the last years the public awareness towards the richness of Italy in this area has been growing and has being fostered by media and public institutions. A list of 'italian crystallographic sites' has been compiled and is being continuously extended on the IYCr2014 italian website[1]; it will be advertised at tourist offices and an applet for smartphones will be implemented.
Low temperature and high pressure study of three molecular glycine co-crystals
Authors: Losev Evgeniy , Zakharov Boris , Boldyreva Elena
Published: November 2015

Only three glycine co-crystals with carboxylic acids were reported till now: those with glutaric[1a], DL-tartaric[1b] and phthalic acids[1c]. Co-crystallisation of glycine with some other carboxylic acids (oxalic, malonic, maleic) gives molecular salts. The reason why the three selected carboxylic acids form not salts, but co-crystals with glycine remains unclear. No obvious correlations with any physiochemical properties of acidic co-formers such as solubility, acidity, dissolution rate, geometry of molecule, etc. could be suggested. Intermolecular interactions in these crystals are of great interest and can be probed, in particular, by varying temperature and pressure in a wide range. The effect of pressure and temperature on a co-crystal of glycine with glutaric acid was investigated in our research group under low temperatures[2] and high pressure[3] and a first order phase transition giving the same new polymorph was observed (at 220 K and 1.75 GPa, respectively). No variable-temperature or variable-pressure studies of co-crystals of glycine with DL-tartaric and phthalic acids were reported. The aim of the present study was to compare the behavior of three glycinium co-crystals at low temperature and high pressure. The changes in the unit cell volumes and parameters, as well as in the geometry of the hydrogen bonds were analysed. The orientation of principal axes of strain ellipsoid with respect to the main structural motifs and relative linear strain values along these axes were calculated. The conformations and the local environment of glycine molecules, as well as the hydrogen-bonded motifs were compared for three co-crystals. The work was supported by the Russian Foundation for Basic Research (RFBR) (Grants No. 14-03-31866 mol_a, 13-03-92704 IND_a), Russian Ministry of Science and Education and Russian Academy of Sciences.
Structures and Properties of Diastereomeric Multi-component Crystals
Authors: Bock Dominique , Lehmann Christian
Published: November 2015

Multi-component crystals composed of two different chiral molecules have the potential to form diastereomers. In the present study a selection of chiral amides and acids was employed to form multi-component crystals. Since growing these multi-component crystals from solution failed, solvent assisted grinding was used. The resulting diastereomeric pairs, which are present as polycrystalline powders showed distinctly different powder diffraction patterns. In order to elucidate the crystal structures direct space global optimization structure solution methods were successfully used in several cases. A potential application of these diastereomeric multi-component crystals is the determination of the absolute configuration of one of the two components based on the known absolute configuration of the other.[1] In addition, Raman spectroscopy and DSC were employed to determine thermodynamic properties. In subsequent grinding experiments racemic conglomerates and racemates formed the starting material. These experiments demonstrated in several cases a relationship between melting point differences and preferential formation of only one diastereomer.
Uncovering Charge Transfer Interactions of Energetic Molecules
Authors: Hill Tania , Levendis Demetrius , Lemmerer Andreas
Published: November 2015

Energetic materials are systems that store a large amount of chemical energy, which can be converted into mechanical energy though molecular decomposition, e.g. explosives, propellants and fuels. Co-crystallization of energetic materials with desirable co-crystal formers provides a novel way of tailoring existing energetic materials without structural manipulation. Examples include trinitrotoluene (TNT) with electron rich aromatics along with other energetic materials (CL-20, DADP) [1-3]. In order to take advantage of this methodology it is necessary to develop an understanding of the synthons involved in non-covalent interactions. The interpretation of non-covalent interactions has been highlighted in many recent publications, notably the publications by Gilli et al. which classifies short contacts as interactions, where the distance between atoms is less than the sum of their van der Waals radii. Depending on the type of interactions, the complexes can be divided into different categories, the most well known and studied are: H-bond theory and charge transfer (CT). In this study, a systematic series of crystal structures of organic CT complexes were determined to allow for the identification of structural packing trends, variations in aromaticity, decomposition temperatures and enthalpies along with non-covalent interactions, focusing mainly on the π···π interactions. The complexes investigated were of the electron donor acceptor type, with polycyclic hydrocarbons acting as the donor (D) molecules, whilst 1,3,5-trinitrobenzene was selected as the energetic acceptor (A) molecule, due to its similarity with TNT. The CT complexes were observed to exhibit strong colours in the yellow to red regions of visible light with the co-crystals forming alternating DA stacks.
Mechanism of dehydration in a non-porous variable hydrate
Authors: Fabian Laszlo
Published: November 2015

Paroxetine hydrochloride form II (PHCl-II) is a variable hydrate with a peculiar behaviour [1]. It changes its water content in response to changes in relative humidity with remarkable speed and in a completely reversible fashion. This is commonly observed for channel hydrates, but no continuous channels exist in the PHCl-II structure [2]. Powder diffraction results showed that loss of water produces an isostructural anhydrate, suggesting a simple, non-destructive mechanism of dehydration. The aim of the present contribution is to explain this unusual behaviour at a molecular level by using molecular dynamics simulations. Models of both the hydrated and anhydrous state could be created from the experimental hydrate structure by simple energy minimisation, which is in accordance with the experimentally observed smooth transition. A partially dehydrated supercell model was used to study the mechanism which allows water molecules to cross the steric barrier between adjacent solvent cavities. Since such transitions are rare on the simulation timescale (µs to ms), a steered molecular dynamics approach was applied. The results show that the passage of water molecules is facilitated by conformational changes, in which a ring system acts as a gate between cavities. When passing through the 'gate', water molecules are relayed between two chloride ions: as one Cl...HOH hydrogen bond is broken, another HOH...Cl one is formed. The progress of water molecules along the gated channel is not continuous, they spend a significant amount of time in each cavity between consecutive passages.