bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of the polymorphism effects in the dissolution of Carvedilol tablets
Authors: Viana Olimpia Maria , Alves Ramon , Jacon Jennifer , Doriguetto Antonio Carlos , Araújo Magali , Bonfilio Rudy
Published: November 2015

Polymorphism in solids is a common phenomenon in drugs, which occurs when an active pharmaceutical ingredient shows up in two or more crystalline forms. The polymorphism may influence the physical and chemical properties of pharmaceutical solids, particularly, solubility and dissolution rates which are very important properties because changes in these parameters may affect the absorption and consequently the bioavailability of drugs (especially those that have a low solubility). Carvedilol is an alpha and beta blocking agent that is used for the treatment of various cardiovascular disorders such as angina pectoris, congestive heart failure and hypertension. This work aims to prepare and characterize the forms II and III of Carvedilol drug and compare them in terms of solubility and dissolution rates. Carvedilol raw material was used as source of form II and Form III, and the last is a hemihydrate of Carvedilol that was obtained by a recrystallization process in ethanol/water 1:1 v/v. Both of the crystalline forms have been identified in this study by Powder X-Ray Diffraction experiments and attenuated total reflectance Fourier transform infrared spectroscopy studies demonstrated that the spectra of forms II and III of Carvedilol have no significant differences. The Thermal Analysis curves, as expected, allowed us to discriminate between the two forms due to a hydratation of Form III. In the solubility study, it was found that the polymorphic Form II is more soluble than Form III in certain conditions (pH 1.0 to 7.2). Dissolution studies have shown that polymorphism may influence the quality of Carvedilol tablets, since form III showed a higher drug release after 20 minutes of dissolution testing. Our results suggest that the identification of polymorphic phases should be a mandatory test for Carvedilol in an official compendium. Acknowledgments: We thank FAPEMIG, FINEP, CAPES and CNPq for their financial support.
A new polymorphic form of Otilonium Bromide
Authors: Vega Daniel , Baggio Ricardo
Published: November 2015

"Otilonium bromide (C29H43 N2 O4+.Br-) is a quaternary ammonium derivative which has been proven a potent spasmolytic drug with a good tolerability profile, used in the treatment of irritable bowel syndrome. We present herein the structural analysis of an unreported polymorphic form (I), comparing with the only one known so far and already reported [1] polymorphic form of the compound (II). The data set for I was obtained from a twinned specimen. The poor quality of the data thus available did not pose any problem in the structure resolution, but it did instead in refinement: the alkyloxy chains and ethyl branches in the quaternary ammonium groups needed some continuity restraints in their anisotropic displacement factors. In form II this effect appeared enhanced, ending up in unusually large anisotropic displacement parameters for most atoms in the chain. The main points of molecular disagreement reside in the torsion angles where the alkyloxy chains and quaternary ammonium groups leave the planar mainframe. The only notorious intermolecular contacts in both structures appear to be a number of rather weak C–H···Br ones involving the quaternary ammonium groups somehow ""wrapping"" the bromide counterion. There are a few C–H···O contacts interlinking molecules to each other. The phase transformation occurs at 124(2)°C and can be followed by DSC and XRPD. A detailed analysis shows some features in common, viz., in both structures packing stability is mainly due to the ionic interaction between the N+ and the Br-, with the latter ion being evenly surrounded by a number of ammonium groups in a way that they define regular 2D arrays "sandwiching" the neutral part of the molecules, which thus act as spacers. These similarities allow giving a plausibility argument about the way in which the transition may take place."
Difference of shear and impact treatment for mechanochemical co-cristallization.
Authors: Tumanov Ivan , Achkasov Andrey , Myz Svetlana , Boldyreva Elena , Boldyrev Vladimir
Published: November 2015

Currently one of the most popular methods to obtain various molecular co-crystals is mechanochemical synthesis, i.e. mechanical treatment of a mixture of powder reactants. Traditional approach for mechanical treatment is milling in a ball mill or grinding in a mortar. However, using these methods causes a number of problems related to investigation of the reaction's mechanism. For instance, ball mill produces impact treatment and shear treatment simultaneously and it is almost impossible to separate these two types of mechanical treatment. So, if detailed analysis of reaction is required, alternative methods of mechanical treatment are necessary. This study describes how mechanochemical co-crystallization of piroxicam and succinic acid has been investigated by using special model devices constructed for separated impact and shear mechanical treatment. Such devices allowed us to perform controlled impact or shear mechanical treatment, what was necessary for detailed investigation of mechanochemical processes for molecular crystals, based on the X-ray powder diffraction analysis. We could change and control energy and frequency of mechanical pulses in the impact model device and average velocity and pressure in the shear model device. For some other systems applying controlled impact treatment allowed us to detect the intermediate products of the mechanochemical synthesis of molecular complexes [1-2]. As for `piroxicam – succinic acid" system, a comparison of impact and shear mechanical treatment had lead to opposite results for mechanochemical reactions – shear treatment appeared to disintegrate co-crystal obtained by impact mechanical treatment. Acknowledgements This work was supported by grants from RFBR (No. 11-03-00684, 12-03-31663, 13-03-00795, 13-03-92704) and Ministry of Education and Science Agreement (No. 14.B37.21.1093).
Evaluation of Polymorphism Influence in the Finasteride
Authors: da Silva Lucélia , Montanari Cristina , Ângelo Marilene , Cazedey Edith Cristina , Bonfilio Rudy , Araújo Magali
Published: November 2015

Finasteride is a specific competitive inhibitor of steroid type-II 5α-reductase, an intracellular enzyme that converts testosterone to dihydrotestosterone (DHT) and is widely used for the treatment of benign prostatic hyperplasia (BPH), prostate cancer , and androgenetic alopecia. Polymorphs are known to give rise to significant differences in the physicochemical properties of the compound as melting point, density, morphology, solubility and colour. Thus, proper monitoring of solid-state forms, both qualitative and quantitative, is crucial in order to ensure high-quality products. The crystal structures of finasteride appear in the Cambridge Crystal Structure Database (CSD) under the codes WOLXOK01 and WOLXOK02 for Form I and WOLXOK03 for Form II. In this context, the aim of this work was study the behavior of the chemical structure and physicochemical properties of polymorphic forms, and to evaluate the possible influence in the dissolution profile and stability of capsules. A stability study was carried out at 500C for 3 months. The Form II of finasteride was obtained by heating Form I to 2350C for 30 minutes. The techniques X-ray diffraction, infrared spectroscopy and thermal analysis were applied to characterize the Forms. The solubility of finasteride polymorphs was determined by equilibrium solubility method. For the dissolution test, water was used as dissolution medium and the basket apparatus at 100 rpm. The samples were analyzed by HPLC at 210 nm. Differences in X-ray diffraction and infrared spectra of the two polymorphs were observed. The DSC curves showed Form I melting peak at 2570C and solid-solid transformation to Form II at about 2300C. In the solubility study was observed higher Form II solubility than Form I in most evaluated pHs. The interaction of the Forms I and II with capsule excipients may have been different since the dissolution profile of the capsules showed higher release to the Form I. In the stability study, the finasteride content was stable for two Forms, however, the dissolution profile of Form II showed greater decline than the Form I. In conclusion, the results show that the dissolution profiles polymorphism may influence the quality of finasteride capsules, being necessary there be a polymorphic quality control for this dosage Form. Acknowledgments: PNPD CAPES and FAPEMIG
X-ray powder diffraction: A powerful tool for industrial protein production
Authors: Frankær Christian , Thymark Majbritt , Ståhl Kenny , Moroz Olga , Wilson Keith , Harris Pernille
Published: November 2015

X-ray powder diffraction (XRPD) offers a method of characterizing a crystalline protein suspension [1], and data can be collected within 30 minutes, which is appealing for industrial applications. In industry, enzymes are produced and handled in high concentrations, which can in turn cause problems for the processes due to protein precipitation in the production pipeline. XRPD is useful for identification of the crystal forms present, by fitting calculated patterns of known single crystal forms to the observed XRPD pattern. For this purpose we have developed a streamlined program for calculation of diffraction patterns from pdb-files taking into account bulk-solvent, peak asymmetry and background [2]. XRPD was applied to a suspension from a large-scale industrial production of the widely used Bacillus lentus subtilisin. A dominant crystal form was identified by XRPD, but two other different crystal forms were found by a complementary single crystal micro-diffraction analysis of the larger single crystals present in the sample [3]. The study serves as a reminder that when a crystal is picked out from a batch crystallization for single crystal analysis, it might not be representative of the bulk microcrystalline material in the sample. To estimate the fraction of the different crystal forms in production samples with significant polymorphism, a further XRPD study was performed on binary mixtures of different lysozyme and subtilisin crystal forms. Quantitative XRPD generally requires careful sample preparation, and working with protein slurries leads to further challenges in terms of varying crystal density. After careful optimisation of suspension medium, the relative composition of crystal forms can be determined within 10%. This work demonstrates the value of in-house XRPD as an analysis tool in industrial enzyme production, and its potential to help troubleshooting the production process and to provide information for further refining the manufacturing of enzymes.
Redox orbitals in LixMn2O4(0 < x < 2) studied by X-ray Compton scattering
Authors: Suzuki Kosuke , Minegishi Katsuhiko , Hamano Kenta , Sakurai Hiroshi , Barbiellini Bernardo , Bansil Arun , Orikasa Yuki , Uchimoto Yoshiharu , Itou Masayoshi , Sakurai Yoshiharu , Kaprzyk Stanishaw , Wang Yung Jui , Yamamoto Kentarou
Published: November 2015

LixMn2O4 is attracting much interest as a positive electrode material for Li-ion rechargeable batteries. Redox orbitals of LixMn2O4 under the charge or discharge process are not fully understood yet. Some band calculations have pointed out that intercalated Li 2s electrons occupy Mn sites or down-spin Mn 3d bands [1,2]. On the other hand molecular orbital calculation has reported the Li 2s electrons occupy O sites [3]. To clarify the redox orbital is important to understand the electrochemical reaction in the electrodes. In this study we have investigated the redox orbitals in LixMn2O4 by X-ray Compton scattering. Compton profiles were measured at BL08W of SPring-8, Japan. The energy of incident X-rays were 115keV and the scattering angle was 165 degrees. Energy spectra of Compton scattered X-rays were measured using a two-dimensional position sensitive detector. The measurements were performed under room temperature and vacuum conditions. Samples are polycrystalline of LixMn2O4 (x=0.5, 1.1, 1.2, 1.8 and 2.0). In order to clarify the redox orbitals of LixMn2O4, we obtained difference Compton profiles which represent the incremental electronic states on Li intercalation. Comparing the results with KKR-CPA and DFT calculations, we found that the O 2p bands play an important role for the redox process in LixMn2O4 with 0<x<2.
Material Design Inputs from Charge Density Analysis in Organic Semiconductors
Authors: Hathwar Venkatesha , Jørgensen Mads , Sist Mattia , Overgaard Jacob , Iversen Bo , Wang Xiaoping , Hoffmann Christina , Briseno Alejandro
Published: November 2015

In recent years, semiconducting organic materials have attracted a considerable amount of interest to develop all-organic or hybrid organic-inorganic electronic devices such as organic light-emitting diodes (OLEDs), organic field-effect transistors (OFETs), or photovoltaic cells. Rubrene (5,6,11,12-tetraphenyltetracene, RUB) is one of the most explored compound in this area as it has nearly 100% fluorescence quantum efficiency in solution. Additionally, the OFET fabricated by vacuum-deposited using orthorhombic rubrene single crystals show p-type characteristics with high mobility up to 20cm2/Vs (Podzorov et al., 2004). The large charge-carrier mobilities measured have been attributed to the packing motif (Fig a) which provides enough spatial overlap of the π-conjugated tetracene backbone. In the same time, RUB undergoes an oxidation in the presence of light to form rubrene endoperoxide (RUB-OX) (Fumagalli et al., 2011). RUB-OX molecules show electronic and structural properties strikingly different from those of RUB, mainly due to the disruption in the conjugate stacking of tetracene moieties. The significant semiconducting property of RUB is not clear yet. In this context, high resolution single crystal X-ray data of RUB (Fig b) and RUB-OX have been collected at 100K. Owing to the presence of weak aromatic stacking and quadrupolar interactions, the neutron single crystal data is also collected at 100K. The C-H bond distances and scaled anisotropic displacement parameters (ADP) of hydrogens from the neutron experiment are used in the multipolar refinements of electron density. The chemical bonding features (Fig c), the topology of electron density and strength of weak interaction are calculated by the Atoms in Molecules (AIM) theory (Bader, 1990). It is further supported by the source function description and mapping of non-covalent interactions based on the electron density. The detailed comparison of two organic semiconductors, RUB and RUB-OX will be discussed.
Data quality as a driver for ever more subtle charge density analyses
Authors: Pinkerton A , Zhurov Vladimir , Zhurova Elizabeth
Published: November 2015

The constant progress in both X-ray source and detector technology has clearly led not only to faster data collection, but also to improvements in data quality. As we move towards the unattainable "holy grail" of error free diffraction data, it is possible to address ever more subtle questions concerning the electron density distribution and associated properties. Current applications to the study of weak interactions, core polarization, heavy element compounds, anharmonic atomic displacements, and anisotropic motion of hydrogen atoms will be presented. The reliability of these studies will be discussed based on evaluations of data quality and refinement statistics.
Empirical Magnetic Structure Solution of Frustrated Spin Systems
Authors: Paddison Joe , Stewart Ross , Gutmann Matthias , Keen David , Petrenko Oleg , Goodwin Andrew
Published: November 2015

Frustrated spin systems can exhibit a macroscopic degeneracy of magnetic ground states which suppresses periodic magnetic order [1]. The importance of understanding these correlations lies primarily in determining the origin of exotic phenomena that emerge from frustrated spin systems, e.g. the evolution of high-temperature superconductivity from spin liquids and the ability of spin ices to support emergent magnetic charges [2]. The magnetic structures of ordered magnets can usually be determined by crystallographic analysis of the magnetic Bragg scattering observed in neutron diffraction experiments. However, the suppression of periodic magnetic order in frustrated magnets means that only magnetic diffuse scattering is observed. This has led to a consensus that single-crystal data are needed for a detailed understanding of spin correlations in frustrated systems. In my presentation, I will explore how the powder magnetic diffuse scattering pattern I(Q) can be converted robustly into a magnetic-structure model. Our approach is to consider simulated I(Q) data for a number of test cases. These data are then fitted using the reverse Monte Carlo (RMC) method. Finally, the quality of the models obtained is assessed by calculating the 3D scattering function I(Q). I will show that the extent of information loss during spherical averaging of I(Q) is surprisingly minimal, and that the full I(Q) is recoverable from powder diffraction data for each frustrated system that we explore [3]. I will go on to discuss real examples where we have used the RMC approach to obtain insight into frustrated materials. First, I will examine the interplay between geometrical frustration and low dimensionality in the paramagnetic phase of the spin-chain compound Ca3Co2O6. Finally, I will show how the RMC method can be extended for the analysis of large single-crystal diffuse scattering datasets, using as an example the canonical antiferromagnet MnO.
Computational Materials design by Evolutionary Structure Prediction
Authors: Zhu Qiang , Oganov Artem , Qian Guangrui
Published: November 2015

Crystal structure prediction (CSP) has been viewed as a major challenge in condensed matter science for a long time. Until recently, we developed a USPEX method based on evolutionary algorithms, and it proved to be a powerful tool enabling accurate and reliable prediction of structures from the beginning. How does it work - and why? In this lecture, I will summarize the principles, recent developments, and some applications of the USPEX code. 1) Optimizing chemical compositional space for compounds and co-crystals. A scheme is proposed to allow the automatic search for all the stable compounds with variation of chemical compositions. This function can be applied to study binary/ternary systems composed of both atomic/molecular blocks (Na-Cl, Mg-O, CaCl2-H2O, etc) [1]. 2) Predicting structures containing complex inorganic/organic molecular motifs. We designed a constrained evolutionary algorithm [2]. The key feature of this new approach is that each motif is treated as a building block which significantly reduces the search space. This method has been applied to a wide range of systems including inorganic complex, small molecular crystals, pharmaceuticals and even polymers crystals. 3) Predicting low dimensional system is different from predicting the bulk crystals. Surface brings another independent thermodynamic parameter, chemical potential. Since the stability of surface configuration depends on the chemical potential, the established phase diagram for multi-component system is quite different from that of bulk crystals [3].
Mechanism of Polymorphic Transformations in the Chemical Elements
Authors: Boulfelfel Salah Eddine , Selli Daniele , Leoni Stefano
Published: November 2015

The prediction of a crystal structure at given composition and thermodynamic coupling parameters is a major challenge. Powerful methods have boosted progress in this field, recently, and have promoted this are of research into a multidisciplinary one. The capacity of anticipating the outcome of a synthetic effort, or the search for novel materials with distinct, improved properties greatly benefit from numerical methods able to efficiently scan for novel structural motifs. Several techniques based on evolutionary algorithms, metadynamics, random structure prediction, or transition path sampling are contributing important advances in the understanding of polymorphic transformation, and are enriching the catalogue of crystalline matter by surprising novel packings [1]. One of the central aspects to fully unfold the impact of crystal structure prediction is the elucidation of transformation mechanisms, which are productive towards a particular structural motif under experiment-relavant conditions. In the recent dispute on the structural identity of the product of graphite cold compression, the true product was confirmed to be Oganov's M-Carbon by applying transition path sampling [2]. While many carbon polymorphs can exist in principle, kinetic control will typically select a particular mechanism of formation of a distinct carbon. This proves that, while the enumeration of crystal structures is invaluable in discovering novel material with improved properties, and in exploring novel compositions, it is important to associate a mechanism with the formation of a particular structure, for a realistic crystal structure prediction, one that can be turned into a real material. The talk will have a review character, and will touch upon recent results in the filed of the polymorphism of the elements and binary semiconductors [3].
X-ray Absorption Spectroscopic studies of Single Crystal SrFeO3-δ
Authors: Hsieh Shang Hsien , Limaye Mukta Vinayak , Singh Shashi Bhushan , Shao Yu Cheng , Wang Yu Fu , Yao Chang Hung , Du Chao Hung , Wang Hsiao Tsu , Chiou Jau Wern , Tsai Huang Ming , Pao Chih Wen , Lee Jyh Fu , Pong Way Faung
Published: November 2015

We have prepared a high quality single crystal of SrFeO3-δ (δ ~ 0.14) by the floating-zone method to study the electronic and atomic structures using temperature-dependent x-ray absorption near-edge structure (XANES), x-ray linear dichroism (XLD), and extended x-ray absorption fine structure (EXAFS) at the O K-edge, Fe L3,2- and K-edge. Resistivity measurements indicate that the SrFeO2.86 shows an anisotropic behavior, and thermal hysteresis behavior between 70 K and 40 K. The temperature dependent Fe K-edge EXAFS studies shows that the Fe-O bond length changes in ab-plane below transition temperature. The XLD results illustrate that as temperature is reduced from room temperature to below the transition temperature, the preferential occupancy of Fe majority-spin eg orbitals changes from the 3d3z2-r2 to 3dx2-y2, but restore to 3dx2-y2 after thermal hysteresis. Experimental findings suggest that the charge transfer during thermal hysteresis is induced by lattice distortions of the FeO6 octahedra in SrFeO2.86.
XAS at the Canadian Macromolecular Crystallography Facility
Authors: Cotelesage Julien , Grochulski Pawel , Fodje Michel , Gorin James , Janzen Kathryn , Labiuk Shaun , George Graham , Pickering Ingrid
Published: November 2015

Recent additions to the Canadian Macromolecular Crystallography Facility have expanded the capabilities of its bending magnet beamline. It is now possible to perform x-ray absorption spectroscopy (XAS) on crystals. A wide range of biologically relevant metals can be further studied, supplementing diffraction data. XAS can be used to determine if metalloproteins are photoreducing during diffraction data collection. The geometries of metal complexes can also be inferred with near-edge and EXAFS data, often more accurately than crystallography. CMCF-BM can be employed to do the abovementioned techniques on powder and solution samples that contain a metal of interest. One XAS-based technique that shows promise is single crystal plane polarized EXAFS. This technique combines crystallographic data with the findings from XAS to yield a high resolution three dimensional atomic model. More recently a number of the procedural steps required for the acquisition of XAS-based data have been automated in the MxDC software suite. These changes to data collection make it easier for users new to these disciplines to run the XAS-based experiments. By having the necessary equipment to do XAS at a protein crystallography facility, researchers who may not have had the opportunity delve into the field of XAS now can do so with minimal risk in terms of materials, funds and time.
Volume I: X-ray Absorption Spectroscopy, International Tables
Authors: Chantler Christopher
Published: November 2015

Research in core physics and atomic and condensed matter science are increasingly relevant for diverse fields and are finding application in chemistry, engineering and biological sciences, linking to experimental research at synchrotrons, reactors and specialized facilities. A plethora of different approaches are popular in the literature and the Volume will hope to capture their greatest achievements and value by representation of all the leading groups from Europe, America, Asia, Australia plus elsewhere! Specifically, common elements and novel elements of XAFS, XANES, EXAFS, RIXS and diverse and related techniques will be represented, together with historical perspectives and latest developments. Over recent synchrotron experiments and publications methods have developed for measuring the absorption coefficient far from the edge and in the XAFS (X-ray absorption fine structure) region in neutral atoms, simple compounds and organometallics reaching accuracies of below 0.02%. This is 50–500 times more accurate than earlier methods, and 50–250 times more accurate than claimed uncertainties in theoretical computations for these systems. The data and methodology are useful for a wide range of applications, including major synchrotron and laboratory techniques relating to fine structure, near- edge analysis and standard crystallography. A comment on some key features of the new Volume in its infancy are presented, and contributions, support and suggestions will be warmly welcomed by all Editors.
Redox modulation of Low-Volume (100 µL) Solutions for XAFS measurements
Authors: Best Stephen , Islam M. Tauhid , Chantler Christopher , Bourke Jay
Published: November 2015

A key to the understanding of transition metal catalysis is a detailed knowledge of the changes in coordination environment that accompany a change in redox state. The capacity of a given metal complex to support the high rates of electron transfer needed for effective catalysis is strongly dependent on the magnitude of structural reorganization coupled to the redox step. The ability of the ligand to control the dynamics of electron transfer is beautifully illustrated by copper redox proteins such as plastocyanin.[1] The polypeptide-imposed constraints on the environment at the coordination site of the metal minimize the structural change attendant on interconversion between the CuI and CuII redox states of the metal, facilitating fast electron transfer. Further, unravelling the molecular details of enzyme catalysis often hinges on knowledge of the structural changes attendant on oxidation or reduction. XAFS can provide the key structural information for reactive or unstable redox states of biological and abiological molecules. Our research has mostly centred on the use of a combination of spectroscopic and computational techniques to reveal the chemistry associated with dihydrogen activation in diiron compounds related to [FeFe]-hydrogenases [2], where a combination of XAFS, IR spectroscopy and theory can provide reliable structural information. Sampling of such species can provide a comparable challenge to spectral analysis – an issue made more difficult in cases where the quantity of sample is limited. We have developed low-volume electrosynthesis cells suitable for the study of electrogenerated species where the total volume of solution required for XAS data collection is of order 100 µL [3]. The design and operation of cells designed to allow freeze quenching and tow-temperature spectral collection or RT on-line measurement will be described.
X-ray Natural Circular Dichroism
Authors: Rogalev Andrei , Bosak Alexei , Wilhelm Fabrice , Goulon Jose
Published: November 2015

Natural Circular Dichroism was only recently discovered in the x-ray range[1]. This effect stems from the interference terms which mix multipole transition moments of opposite parity: the Electric Dipole-Electric Quadrupole (E1.E2) and the Electric Dipole-Magnetic Dipole (E1.M1) exist only in structures with broken space inversion symmetry. The scalar E1.M1 term known to be responsible for Circular Dichroism at optical wavelengths is usually considered to be vanishingly small for core level spectroscopies. The E1.E2 interference term, on the contrary, can be large in the X-ray region, but it is a parity odd second rank tensor and therefore observable only in 13 non-centrosymmetric crystal classes. X-ray Natural Circular Dichroism has now been detected in the XANES region for several uniaxial and biaxial crystals. It can give access to the absolute configuration of chiral absorbing centers. On the other hand, Chiral-EXAFS, i.e. the analog of Magnetic-EXAFS for Natural Circular Dichroism has also been measured recently using a uniaxial optically active crystal of paratellurite (TeO2). Chiral-EXAFS originates from symmetry allowed multiple scattering paths. In this presentation, we wish to report on recent advances in X-ray natural circular dichroism and its applications. Determination of absolute configuration is illustrated with measurements of both E1.E2 and E1.M1 terms in chiral alpha-Ni(H2O)6·SO4 single crystals. Manifestation of X-ray optical acitivity in magnetoelectric crystals will be illustrated with various dichroisms measured at the Fe K-edge in multiferroic GaFeO3 crystal. Finally, we will review briefly the perspectives open by our experiments.
Conservation of cofactor pockets in proteins
Authors: Yennawar Neela , Fecko Julia , Chapla Rani
Published: November 2015

Enzymes, organic cofactors and metal ions are crucial for many biochemical reactions for catalysis. Nearly half of all enzyme reactions are catalyzed by cofactors. So far a systematic assessment of the enzyme residues interacting with organic enzyme cofactors in biocatalysts has not been performed. Here, we analyze the environment, physicochemical nature and pockets of thirty organic cofactors. The cofactor pocket and residues lining it share a remarkable degree of structural convergence despite the rest of the protein having different three-dimensional folds and different enzymatic functions. There is a common network of electrostatic and hydrophobic interactions stabilizing the cofactors. Functional groups of cofactors have complementary charge interactions with polar residues in the active site. Rings are positioned in snug nonpolar pockets either completely or partially. Distance matrices have been derived for each of the cofactor pockets based on the protein residues interacting with functional groups. These distance matrices and the representative pocket sizes of cofactor can be used as a fingerprint to identify a cofactor pocket. Examples of proteins from the PDB classified as with unknown function have been screened for the derived cofactor pocket criteria.
S9 is Essential to Ribosomal Function and LUCA is a Micrococcineae
Authors: Duax William , Huck Connor , Sass Nick , Chen Sam
Published: November 2015

A minimum universal fingerprint has been designed that captures and aligns over 10,116 bacterial, 939 eukaryotic, and 221 archaeal members of the family of ribosomal proteins that are labeled as S9 in most bacteria and archaea and S9 or S16 in eukaryota. All of the aligned S9/16 ribosomal proteins have five residues whose identities are 100% conserved and 58 residues whose identities are conserved at 70% or greater. Full length accurate alignment of all S9s was achieved by locating Gly(G), Ala(A), Arg(R) and Pro(P) residues that are highly conserved and by accurate location of sites of insertion and deletion. Gly residues in regions of the Ramachandran plot where other amino acids are rarely tolerated appear to be immutable. Crystal structures of bacterial, plant, fungal, and mammalian ribosomes support the conclusion that all S9/16 RibPros retain a common fold. All S9/16s end in a fully conserved Arg residue that extends deep into the ribosome forming hydrogen bonds to nucleotide residues of rRNA and the anticodon sequence of tRNAs. The significance of this remarkable conservation of amino acid identity, its interaction with tRNA and critical role in ribosome function has previously escaped detection. Hydrogen bonds link the terminal Arg of S9/16 with the tRNA in crystallographically determined structures in which the tRNA is in the polymerase (P) and exit(E) sites. Two ribosomal proteins of the large subunit (L28 and L35) form hydrogen bonds to neucleotides of the acceptor stem. A histidine of L35 that contacts the acceptor stem is conserved in 8000 L35s. Examination of the DNA encoding the S9s of all 730 species of actinobacteria reveals that the majority of them use only codons ending in G or C, have antisense open reading frames, rarely contain cystiene , and have GTG (Val) as their start code. Thus far examination of DNA encoding other ribosomal proteins of the small subunit (S2,S4,S7,S11,S19) finds a similar pattern only in S4s of Micrococcineae( a class of actinobacteria). These data indicate a critical role for S9/16 in ribosomal function throughout evolution and indicate that the last universal common ancestor is a Micrococcineae.
Prediction of horseshoe configuration in neural receptors: Dscam isoforms
Authors: Thiruvenkatam Vijay , Chen Qiang , Wang Jia-huai
Published: November 2015

Dscam (Down Syndrome Cell Adhesion Molecule), a member of immunoglobulin superfamily (IgSF), is a receptor for netrin-1 [1,2], a classical axon guidance cue. The interaction between netrin-1 and Dscam plays an important role in the development of the nervous system. Here, we present the crystal structure of the N-terminal four Ig-like domains of Dscam. The molecule folds into a horseshoe-like configuration. A comparison of this Dscam horseshoe with the previously described horseshoe structures of other cell-surface receptors has revealed fascinating conserved structural features and important sequence markers for these IgSF proteins. This discovery can help us predict the horseshoe configuration N-terminal arrangements in a number of other structurally unknown neural receptors. The N-terminal horseshoe has been shown to be engaged in homophilic and heterophilic interactions between two cell-surface receptors.
Visualization of lipid bilayer in the crystals by solvent contrast modulation
Authors: Norimatsu Yoshiyuki , Tsueda Junko , Hirata Ayami , Iwasawa Shiho , Toyoshima Chikashi
Published: November 2015

A new method of X-ray solvent contrast modulation was developed to visualize lipid bilayers in crystals of membrane proteins at a high enough resolution to resolve individual phospholipids molecules (~3.5 Å ). Visualization of lipid bilayer has been escaping from conventional crystallographic methods due to its extreme flexibility, and our knowledge on the behavior of lipid bilayer is still very much limited. Here we applied the new method of X-ray solvent contrast modulation to crystals of Ca2+-ATPase in 4 different physiological states. As phospholipids have to be added to make crystals of Ca2+-ATPase, it is expected that lipid bilayers are present in the crystals. Moreover, transmembrane helices of Ca2+-ATPase rearrange drastically during the reaction cycle and some of them show substantial movements perpendicular to the bilayer plane. Thus these crystals provide a rare opportunity to directly visualize phospholipids interacting with a membrane protein in different conformations. Complete diffraction data covering from 200 to 3.2 Å resolution were collected at BL41XU, Spring-8, using an R-Axis V imaging plate detector for crystals soaked in solvent of different electron density. A new concept "solvent exchange probability", which should be 1 in the bulk solvent, 0 inside the protein and an intermediate at interface, was introduced and used as a restraint for real space phase improvement. The electron density maps thus obtained clearly show that: (i) Phospholipid molecules surrounding the protein are fixed apparently by Arg/Lys-phosphate salt bridges or Trp-carbonyl hydrogen bonds and follow the movements of transmembrane helices. Movements of as large as 12 Å are allowed. (ii) If the movement of a transmembrane helix exceeds this limit, associated phospholipids change the partners for fixation or change the orientation of the entire protein molecule.
Substrate discrimination by size-exclusion in the intramembrane protease RseP
Authors: Hizukuri Yohei , Oda Takashi , Tabata Sanae , Tamura-Kawakami Keiko , Oi Rika , Sato Mamoru , Takagi Junichi , Akiyama Yoshinori , Nogi Terukazu
Published: November 2015

Regulated intramembrane proteolysis (RIP), wherein a target membrane protein is specifically cleaved within the transmembrane region, is now accepted as a form of cellular signaling. As a result of proteolysis, a soluble portion of the target membrane protein is liberated to act as a signaling molecule. RIP is catalyzed by intramembrane-cleaving proteases, which are now classified into site-2 protease, rhomboid and γ-secretase/SPP families based on the mechanism of catalysis. E. coli possesses a site-2 protease homolog RseP, which is implicated in the extracytoplasmic stress response. RseP cleaves a membrane-spanning anti-σE protein RseA to release σE from the membrane, where truncation of the C-terminal periplasmic part of RseA by a membrane-anchored protease DegS triggers the action of RseP. Hence, there must be some mechanism by which RseP senses the DegS-cleavage of RseA. RseP possesses two tandemly-arranged PDZ domains (PDZ tandem) in the periplasmic region, which have been suggested to be involved in the regulation of cleavage. Although PDZ domains generally recognize the C-terminal sequence of a ligand, most of the previous works suggested that the RseP PDZ domains are involved in the suppression of the intramembrane cleavage of RseA. In this study, we determined the 3D structure of the PDZ tandem by X-ray crystallography and SAXS and showed that the two PDZ domains are arranged in an overall "clam-like" configuration to constitute a "pocket-like" structure. Sequence analysis suggested that the PDZ tandem would lie just above the active center sequestrated within the membrane. Furthermore, chemical modification demonstrated that the interior of the pocket is inaccessible to a bulky reagent in the full-length RseP. Taken together, we have made a proposal that RseP accommodates the truncated RseA into the active center by a steric size-exclusion mechanism through the PDZ tandem, rather than by recognition of a specific sequence/motif of RseA.
A lateral gate for autotransporter and outer membrane protein assembly
Authors: Gruss Fabian , Zaehringer Franziska , Jakob Roman , Burmann Björn , Hiller Sebastian , Maier Timm
Published: November 2015

β-barrel proteins are key functional components of the outer membranes of gram-negative bacteria, mitochondria and plastids. They mediate transport across the membrane, act as receptors and are involved in bacterial pathogenicity. Despite their crucial roles, assembly and membrane insertion of β-barrel outer membrane proteins, which are mediated by β-barrel membrane proteins of the OMP85 family, have remained elusive. The crystal structure of the Escherichia coli OMP85 protein TamA [1], which is involved in autotransporter biogenesis, now provides a novel perspective on β-barrel membrane protein assembly. The protein was crystallized in lipidic phase and microseeding was employed to obtain high-quality 2.3 Å diffraction data. TamA comprises a 16-stranded transmembrane β-barrel and three N-terminal POTRA domains. The barrel is closed at the extracellular face by a conserved lid loop tightly interacting with a conserved lock region on the inner barrel wall. The C-terminal β-strand of the barrel forms an unusual inward kink, which creates a gate for substrate access to the lipid bilayer and weakens lateral inter-strand connection. These structural features immediately suggest a mechanism of autotransporter insertion based on barrel expansion and lateral release. Based on structural conservation of all core elements [2], this mechanism might well be relevant for the entire OMP85 family.
Crystal structures of Bax and Bak Reveal Molecular Events Initiating Apoptosis
Authors: Czabotar Peter , Brouwer Jason , Westphal Dana , Thompson Geoff , Colman Peter
Published: November 2015

A key event in apoptosis is the conversion of Bax or Bak from inert monomers into cytotoxic mitochondrial membrane perforating oligomers. Certain BH3-only relatives can initiate this step through direct interactions, yet the means by which conformational changes are invoked, the nature of the conformational changes themselves, the mechanism by which they insert into membranes and the process by which they perforate these barriers has largely remained a mystery. Our recent structural studies provided the first insights into this process for Bax [1]. We found that BH3 domains activate Bax by binding to a hydrophobic groove on its surface. Crystal structures of these complexes revealed an unexpected conformational change involving dissociation of a previously unrecognized "core" domain from a "latch' domain. A further structure of the freed Bax "core" domains revealed that these form dimers that possess a surface of aromatic residues which we hypothesis engage the outer leaflet of the mitochondrial membrane and induce curvature. We have now extended our studies to include structures of Bax bound to alternative BH3-only proteins providing new insights into key interactions occurring at this interface. Additionally, we have solved structures of activated Bak and of the freed Bak "core" domain dimers. These results further our understanding of the molecular mechanisms by which these highly dynamic proteins engage the mitochondrial membrane and thus control the life/death switch in cells.
Crystallographic studies of voltage-gated sodium and calcium channels
Authors: Payandeh Jian
Published: November 2015

Voltage-gated ion channels (VGICs) mediate electrical signaling within the nervous system and regulate a wide range of physiological processes. Voltage-gated sodium (Nav) channels are responsible for initiating action potentials and their rapid activation, sodium selectivity, and drug sensitivity are unique among VGICs. Nav channels are the molecular targets of drugs used in local anaesthesia and in the treatment of genetic and sporadic Nav channelopathies including inherited epilepsy, migraine, periodic paralysis, cardiac arrhythmia, and chronic pain syndromes. Recent crystal structures of a Nav channel from the bacterium Arcobacter butzleri (NavAb) have revealed surprising insights into the structural basis for voltage-dependent activation, sodium selectivity, drug block, and slow inactivation (1,2). The available structures of NavAb will be described alongside complementary functional and molecular dynamic studies. Distinct from Nav channels, the closely related voltage-gated calcium (Cav) channels initiate processes such as synaptic transmission, muscle contraction, and hormone secretion in response to membrane depolarization. Cav channels catalyze the rapid and highly selective influx of calcium ions into cells despite a 70-fold higher extracellular concentration of sodium. By grafting a Cav channel selectivity filter onto NavAb, crystallographic and functional analyses of the resulting CavAb channel will be described that have revealed a multi-ion selectivity filter which establishes a structural framework for understanding the mechanisms of ion selectivity and conductance in vertebrate Cav channels (3).
Structure Refinement at Low-resolution: Strategies and Validation
Authors: Schröder Gunnar , Levitt Michael , Brunger Axel
Published: November 2015

In the refinement of macromolecular structures at low resolution (worse than 3.5 A) over-fitting becomes a serious problem since the number of degrees of freedom (i.a. atomic coordinates) is often much larger than the number of experimental observables (number of unique reflections). Applying additional restraints help to reduce the effective number of degrees of freedom but will necessarily limit the conformational freedom of the structure during the refinement. These restraints could therefore prevent finding the optimum solution, which means the choice of restraints is important. Strategies will be presented to choose such restraints. For example the Deformable Elastic Network (DEN) approach adapts restraints automatically, on the one hand to allow for relevant conformational changes to occur and on the other hand to keep those degrees of freedom well restrained for which no experimental data are available [1]. Some recent examples [2] of low-resolution structures will be presented including the refinement of the chaperonin TRiC in a closed (3.8 A) and open (5.5 A) conformation [3]. This example also shows that new validation tools might be important at low resolution in a addition to traditional cross-validation. For example exhaustive sampling of alternative models can provide additional information on the reliability and statistical significance of the optimum structure solution.
Validation of carbohydrate structures: not just nomenclature
Authors: Agirre Jon , Cowtan Kevin
Published: November 2015

Despite the key implications carbohydrates have in a multitude of pathological processes, a large number of the sugar-containing structures deposited into the Protein Data Bank (PDB) show nomenclature errors [1] that persist even after the remediation of the PDB archive [2]. Here we present the results from a systematic study of the conformation and ring distortion of cyclic carbohydrate models for which structure factors have been deposited into the PDB. These models have also been scored using a real-space correlation coefficient calculated between model and experimental electron density. The results have enabled us to produce a database of well-refined carbohydrate structures for use in the framework of an automated sugar-detecting software, to be announced shortly.
Protein-Ligand Analysis and Validation
Authors: Emsley Paul
Published: November 2015

A number of tools related to handling of ligands have been added to Coot in recent years - these include 2D depictions, ligand binding pocket layout and a ligand scoring system. Coot also incorporates a number interface to other tools (CCP4's Refmac, Molprobity's probe and reduce and the CCDC's Mogul) to generate score for protein ligand complexes. This scoring system has been applied to models (with data) from the PDB. The details of the ligand scoring, and its application to one's own complex structure will be discussed.
New wwPDB validation pipelines for X-ray, NMR and 3DEM structures
Authors: Gore Swanand , Hendrickx Pieter , Sanz-Garcia Eduardo , Velankar Sameer , Kleywegt Gerard
Published: November 2015

The Protein Data Bank (PDB) is the single global archive of 3D biomacromolecular structure data. The archive is managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org) organisation through its partners, the Research Collaboratory for Structural Bioinformatics (RCSB PDB), the Protein Data Bank Japan (PDBj), the Protein Data Bank in Europe and the Biological Magnetic Resonance Bank (BMRB). Analogously, the Electron Microscopy Data Bank (EMDB) is managed by the EMDataBank (emdatabank.org) organisation. A few years ago, realising the needs and opportunities to assess the quality of biomacromolecular structures deposited in the PDB, the wwPDB and EMDataBank partners established Validation Task Forces (VTFs) to advice them on up-to-date and community-agreed methods and standards to validate X-ray, NMR and 3DEM structures and data. All three VTFs have now published their recommendations (1, 2, 3) and these are getting implemented as validation-software pipelines . The pipelines are integrated in the new joint wwPDB deposition and annotation system (http://deposit.wwpdb.org/deposition/). In addition, stand-alone servers are provided to allow practising structural biologists to validate models prior to publication and deposition (http://wwpdb.org/validation-servers.html). The validation pipelines and the output they produce (human-readable PDF reports and machine-readable XML files) will be described.