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Sample records for complex crystal structures

  1. Topological complexity of crystal structures: quantitative approach.

    Science.gov (United States)

    Krivovichev, Sergey

    2012-05-01

    The topological complexity of a crystal structure can be quantitatively evaluated using complexity measures of its quotient graph, which is defined as a projection of a periodic network of atoms and bonds onto a finite graph. The Shannon information-based measures of complexity such as topological information content, I(G), and information content of the vertex-degree distribution of a quotient graph, I(vd), are shown to be efficient for comparison of the topological complexity of polymorphs and chemically related structures. The I(G) measure is sensitive to the symmetry of the structure, whereas the I(vd) measure better describes the complexity of the bonding network. © 2012 International Union of Crystallography

  2. Zinc (II) complexes of carboxamide derivatives: Crystal structures ...

    Indian Academy of Sciences (India)

    The two complexes were characterized by physicochemical and spectroscopic tools, and by X-ray crystal structures of both ligands and the complex 1. In complex 1, zinc(II) is chelated by three ligands with a distorted octahedral geometry. The DNA-binding properties of zinc complexes 1 and 2 have been investigated by ...

  3. Simulating complex crystal structures using the phase-field crystal model

    Science.gov (United States)

    Alster, Eli; Montiel, David; Thornton, Katsuyo; Voorhees, Peter W.

    2017-11-01

    We introduce a phase-field crystal model that creates an array of complex three- and two-dimensional crystal structures via a numerically tractable three-point correlation function. The three-point correlation function is designed in order to energetically favor the principal interplanar angles of a target crystal structure. This is achieved via an analysis performed by examining the crystal's structure factor. This approach successfully yields energetically stable simple cubic, diamond cubic, simple hexagonal, graphene layers, and CaF2 crystals. To illustrate the ability of the method to yield a particularly complex and technologically important crystal structure, we show how this three-point correlation function method can be used to generate perovskite crystals.

  4. Synthesis and crystal structure of trinuclear potassium(I) complex ...

    African Journals Online (AJOL)

    A furazan-based trinuclear potassium(I) complex derived from the oxy-bridged bis(gem-dinitro)furazan (OBNF) and triaminoguanidinium (TGA) units was synthesized and characterized by elemental analyses, nuclear magnetic resonance (NMR) and infrared (IR) spectroscopy. The single crystal X-ray structure of the ...

  5. Oxoglaucine-lanthanide complexes: synthesis, crystal structure and cytotoxicity.

    Science.gov (United States)

    Liu, Yan-Cheng; Chen, Zhen-Feng; Shi, Yan-Fang; Huang, Ke-Bin; Geng, Bo; Liang, Hong

    2014-01-01

    To evaluate the in vitro cytotoxicity of oxoglaucine (OG) complexes: [Sm(OG)2(NO3)3]•H2O (1), [Eu(OG)2(NO3)3]•1.5CH3OH (2) and [Er(OG)2(NO3)3]•H2O (3) through comparison to oxoglaucine and lanthanide salts. The reactions of OG with corresponding lanthanide salts gave rise to complexes 1-3. The crystal structures of complexes 1-3 were determined by single-crystal X-ray diffraction analysis. The in vitro cytotoxicity of oxoglaucine and complexes 1-3 against five human cancer cell lines were evaluated by the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl tetrazolium Bromide (MTT) method. Complexes 1-3 have similar mononuclear structures. The 50% inhibitory concentration (IC50) of complex 1 against SGC7901 cells was 32.1 μM; that of complex 2 against MCF-7 cells was 3.2 μM; those of complex 3 on HeLa and MCF-7 cells were 8.3 and 1.4 μM, respectively. The three OG-lanthanide complexes exhibited significantly enhanced cytotoxicity vs. OG and corresponding lanthanide salts.

  6. Synthesis, crystal structure and applications of palladium thiosalicylate complexes

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    S.B. Moosun

    2017-05-01

    Full Text Available Three palladium thiosalicylate complexes [Pd(tb(bipy]·3H2O (1, [Pd2(tb2(bipy2]·(dtdb2 (2 and [Pd2(tb2(phen2]·dtdb·H2O (3 (bipy = bipyridine; phen = phenanthroline were prepared from the reaction of PdCl2(CH3CN2 with dithiosalicylic acid (dtdb which underwent cleavage to form thiobenzoate anion (tb in DMF/MeOH. Square planar geometries of the complexes with a N2SO coordination type were proposed on the basis of single crystal X-ray structural study. The presence of trapped and uncoordinated dtdb was observed in complexes 2 and 3. Complexes 1–3 were evaluated as catalysts for Heck coupling reactions of methyl acrylate with iodobenzene, and showed moderate activities at a very low catalyst loading. Complex 1 was found to inhibit the growth of bacteria and scavenge free radicals efficiently.

  7. Synthesis and crystal structure of a polymeric zinc(II) complex ...

    African Journals Online (AJOL)

    A new polymeric zinc(II) complex, [ZnL2(PDA)]n, has been prepared by the reaction of zinc sulfate, 4-nitrophenylacetic acid, and propane-1,3-diamine (PDA) in water. Structure of the complex has been characterized by single-crystal X-ray diffraction. The complex crystallizes as orthorhombic space group Pnma, with unit cell ...

  8. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; Campbell, Elizabeth A.

    2017-07-13

    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

  9. Synthesis, characterization and crystal structures of oxovanadium(V complexes derived from similar aroylhydrazone ligands

    Directory of Open Access Journals (Sweden)

    X-Z Zhang

    2015-10-01

    Full Text Available Reaction of [VO(acac2] (acac = acetylacetonate with N’-(5-chloro-2-hydroxybenzylidene-3-methoxybenzohydrazide (H2L1 and N’-(2-hydroxy-4-methoxybenzylidene-4-nitrobenzohydrazide (H2L2 in methanol affords methanol-coordinated mononuclear oxovanadium(V complexes, [VOL1(OMe(MeOH] (1 and [VOL2(OMe(MeOH] (2, respectively. The complexes were characterized by elemental analysis, FT-IR, 1H NMR and 13C NMR spectra. Crystal and molecular structures of the complexes were determined by single crystal X-ray diffraction method. Single crystal X-ray structural studies indicate that the hydrazone ligands coordinate to the VO core through enolate oxygen, phenolate oxygen and azomethine nitrogen. The V atoms in the complexes are in octahedral coordination. Thermal stabilities of the complexes have also been studied. DOI: http://dx.doi.org/10.4314/bcse.v29i3.10

  10. Three-Dimentional Structures of Autophosphorylation Complexes in Crystals of Protein Kinases

    KAUST Repository

    Dumbrack, Roland

    2016-01-26

    Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Several autophosphorylation complexes have been identified in crystals of protein kinases, with a known serine, threonine, or tyrosine autophosphorylation site of one kinase monomer sitting in the active site of another monomer of the same protein in the crystal. We utilized a structural bioinformatics method to identify all such autophosphorylation complexes in X-ray crystallographic structures in the Protein Data Bank (PDB) by generating all unique kinase/kinase interfaces within and between asymmetric units of each crystal and measuring the distance between the hydroxyl oxygen of potential autophosphorylation sites and the oxygen atoms of the active site aspartic acid residue side chain. We have identified 15 unique autophosphorylation complexes in the PDB, of which 5 complexes have not previously been described in the relevant publications on the crystal structures (N-terminal juxtamembrane regions of CSF1R and EPHA2, activation loop tyrosines of LCK and IGF1R, and a serine in a nuclear localization signal region of CLK2. Mutation of residues in the autophosphorylation complex interface of LCK either severely impaired autophosphorylation or increased it. Taking the autophosphorylation complexes as a whole and comparing them with peptide-substrate/kinase complexes, we observe a number of important features among them. The novel and previously observed autophosphorylation sites are conserved in many kinases, indicating that by homology we can extend the relevance of these complexes to many other clinically relevant drug targets.

  11. Two organoantimony (V) coordination complexes modulated by isomers of trifluoromethylbenzoate ligands: Syntheses, crystal structure, photodegradation properties

    Science.gov (United States)

    Zhang, Xiao-Yin; Cui, Lian-sheng; Zhang, Xia; Jin, Fan; Fan, Yu-Hua

    2017-04-01

    Two organoantimony (V) coordination complexes, namely Ph3Sb(2-tmbc) (1) and Ph3Sb(3-tmbc) (2) (2-tmbc = 2-(trifluoromethyl)benzoic carboxyl, 3-tmbc = 3-(trifluoromethyl)benzoic carboxyl) have been synthesized and characterized by IR spectra, elemental analysis, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. Single-crystal X-ray diffraction analysis reveals that complexes 1 and 2 show different architectures by the intermolecular hydrogen bonds (Csbnd H⋯F), complex 1 displays an 1D straight chain structure, while complex 2 shows an 1D zigzag chain structure. The photodegradation properties of complexes 1 and 2 has been investigated in organic dyes (RhB, MV, MB) the results indicated that the two complexes are good candidates for the photocatalytic degradation of three dyes. The tentative photocatalytic degradations mechanism is discussed.

  12. Quantum Mechanics Calculations, Basicity and Crystal Structure: The Route to Transition Metal Complexes of Azahelicenes

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    Isabella Natali Sora

    2012-01-01

    Full Text Available Quantum mechanics density functional calculations provided gas-phase electron distributions and proton affinities for several mono- and diaza[5]helicenes; computational results, together with experimental data concerning crystal structures and propensity to methylation of the nitrogen atom(s, provide a basis for designing azahelicene complexes with transition metal ions.

  13. CRYSTAL-STRUCTURE OF AN ELECTRON-TRANSFER COMPLEX BETWEEN METHYLAMINE DEHYDROGENASE AND AMICYANIN

    NARCIS (Netherlands)

    CHEN, LY; DURLEY, R; POLIKS, BJ; HAMADA, K; CHEN, ZW; MATHEWS, FS; DAVIDSON, VL; SATOW, Y; HUIZINGA, E; VELLIEUX, FMD; HOL, WGJ

    1992-01-01

    The crystal structure of the complex between the quinoprotein methylamine dehydrogenase (MADH) and the type I blue copper protein amicyanin, both from Paracoccus denitrificans, has been determined at 2.5-angstrom resolution using molecular replacement. The search model was MADH from Thiobacillus

  14. Crystal Structures of Inhibitir Complexes of Human T-Cell Leukemia Virus (HTLV-1) Protease

    Energy Technology Data Exchange (ETDEWEB)

    Satoh, Tadashi; Li, Mi; Nguyen, Jeffrey-Tri; Kiso, Yoshiaki; Gustchina, Alla; Wlodawer, Alexander (NCI); (Kyoto)

    2010-09-17

    Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailed study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.

  15. Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease

    Energy Technology Data Exchange (ETDEWEB)

    Satoh, Tadashi; Li, Mi; Nguyen, Jeffrey-Tri; Kiso, Yoshiaki; Gustchina, Alla; Wlodawer, Alexander (NCI); (Kyoto)

    2010-09-28

    Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailed study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.

  16. Nickel (II and Iron (II Complexes with Azole Derivatives: Synthesis, Crystal Structures and Antifungal Activities

    Directory of Open Access Journals (Sweden)

    Emmanuel N. Nfor

    2013-01-01

    Full Text Available Two new complexes of nickel (II with 4-amino-3, 5-bis(pyridyl-1, 2, 4-triazole (abpt and iron (II with 2-(3-phenyl-1H-pyrazole-5-yl pyridine (phpzpy have been synthesized and characterized by elemental analysis and IR spectroscopy. The crystal structures of the complexes have been determined by single crystal X-ray diffraction techniques. In the nickel and iron complexes, the ligands are coordinated through nitrogen atoms in bidentate manner. The ligands and their respective complexes have been tested for their antifungal activity against Aspergillus niger, Aspergillus flavus, and Candida albicans. From the study, the complexes showed enhanced activities against the tested organisms compared to the ligands.

  17. Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.

    Directory of Open Access Journals (Sweden)

    Peng Gong

    Full Text Available RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymerases are also a target for antiviral drug development. However, both drug discovery efforts and our understanding of fidelity determinants have been hampered by a lack of detailed structural information about functional polymerase-RNA complexes and the structural changes that take place during the elongation cycle. Many of the molecular details associated with nucleotide selection and catalysis were revealed in our recent structure of the poliovirus polymerase-RNA complex solved by first purifying and then crystallizing stalled elongation complexes. In the work presented here we extend that basic methodology to determine nine new structures of poliovirus, coxsackievirus, and rhinovirus elongation complexes at 2.2-2.9 Å resolution. The structures highlight conserved features of picornaviral polymerases and the interactions they make with the template and product RNA strands, including a tight grip on eight basepairs of the nascent duplex, a fully pre-positioned templating nucleotide, and a conserved binding pocket for the +2 position template strand base. At the active site we see a pre-bound magnesium ion and there is conservation of a non-standard backbone conformation of the template strand in an interaction that may aid in triggering RNA translocation via contact with the conserved polymerase motif B. Moreover, by engineering plasticity into RNA-RNA contacts, we obtain crystal forms that are capable of multiple rounds of in-crystal catalysis and RNA translocation. Together, the data demonstrate that engineering flexible RNA contacts to promote crystal lattice formation is a versatile platform that can be used to solve the structures of viral RdRP elongation complexes and their catalytic cycle

  18. Synthesis, characterization, crystal structure and electrochemical studies of ionic iron(III) dipicolinato complex

    Science.gov (United States)

    Ghasemi, Fatemeh; Ghasemi, Khaled; Rezvani, Ali Reza; Rosli, Mohd Mustaqim; Razak, Ibrahim Abdul

    2017-09-01

    The new complex (NH4)[Fe(dipic)2] (1) (dipicH2 = 2,6-pyridinedicarboxylic acid), was synthesized and characterized by elemental analysis, FTIR and UV-Vis spectroscopy and single crystal X-ray method. The crystal system is tetragonal with space group I41/a. The FeIII ion and the N atom of the ammonium cation are located on a crystallographic fourfold rotoinversion axis (4 bar). The Nsbnd H⋯O and Csbnd H⋯O intermolecular hydrogen bonding and π⋯π stacking interactions play an important role in the formation of a 3-dimensional anion-cation network and stabilization of the crystal structure. The redox behavior of the complex was also investigated by cyclic voltammetry.

  19. Crystal structures and nitrosation reactions of triazido complexes of chromium(III)

    DEFF Research Database (Denmark)

    Døssing, Anders Rørbæk; Kadziola, Anders

    2008-01-01

      The two triazido chromium(III) complexes [Cr(tame)(N3)3]×H2O (1) and [Cr(tacn)(N3)3] (2) (tame  = 1,1,1-tris(aminomethyl)ethane and tacn = 1,4,7-triazacyclononane) have been prepared and characterized by single-crystal X-ray crystallography at 122 K. The crystal structure of 1 is monoclinic, sp...... in the cell. The reactions between NOBF4  and 1 or 2 in acetonitrile give [Cr(tame)(NCCH3)3](BF4)3, and [Cr(tacn)(NCCH3)3](BF4)3, respectively....

  20. Crystal Structure of Oxidative Stress Sensor Keap1 in Complex with Selective Autophagy Substrate p62

    Science.gov (United States)

    Kurokawa, Hirofumi

    Keap1, an adaptor protein of cullin-RING ubiquitin ligase complex, represses cytoprotective transcription factor Nrf2 in an oxidative stress-dependent manner. The accumulation of selective autophagy substrate p62 also activates Nrf2 target genes, but the detailed mechanism has not been elucidated. Crystal structure of Keap1-p62 complex revealed the structural basis for the Nrf2 activation in which Keap1 is inactivated by p62. The accumulation of p62 is observed in hepatocellular carcinoma. The activation of Nrf2 target genes, including detoxifying enzymes and efflux transporters, by p62 may protect the cancer cells from anti-cancer drugs.

  1. Crystal structure of zwitterionic 4-(ammoniomethylbenzoate: a simple molecule giving rise to a complex supramolecular structure

    Directory of Open Access Journals (Sweden)

    Ana María Atria

    2014-11-01

    Full Text Available The asymmetric unit of the title compound, C8H9NO2·H2O consists of an isolated 4-(ammoniomethylbenzoate zwitterion derived from 4-aminomethylbenzoic acid through the migration of the acidic proton, together with a water molecule of crystallization that is disordered over three sites with occupancy ratios (0.50:0.35:0.15. In the crystal structure, N—H...O hydrogen bonds together with π–π stacking of the benzene rings [centroid–centroid distance = 3.8602 (18 Å] result in a strongly linked, compact three-dimensional structure.

  2. Synthesis and crystal structure of thiosemicarbazide complexes of nickel(II) and copper(II)

    Science.gov (United States)

    Sadikov, G. G.; Antsyshkina, A. S.; Koksharova, T. V.; Sergienko, V. S.; Kurando, S. V.; Gritsenko, I. S.

    2012-07-01

    Thiosemicarbazide complexes of nickel(II) [Ni( TSC)2](H Sal)2 ( I) and copper(II) [Cu( TSC)2](H Sal)2 ( Ia) ( TSC is thiosemicarbazide and H Sal is a salycilate anion), as well as complexes [Ni( TSC)2](SO4) · 2H2O ( II) and [Ni( TSC)3]Cl2 · H2O ( III), are synthesized and characterized by IR spectroscopy and X-ray diffraction. Monoclinic crystals I and Ia are isostructural; space group P21/ n, Z = 2. Crystals II are monoclinic, space group P21/ m, Z = 2. Crystals III are orthorhombic, space group Pbca, Z = 8. In I and Ia, two planar salycilate anions sandwich a planar centrosymmetric [Ni( TSC)2]2+ cation to form a supermolecule. The cation and anions are additionally bound by hydrogen bonds. Other hydrogen bonds connect supermolecules into planar layers. In structure II, centrosymmetric [Ni( TSC)2]2+ cations are connected by π-stacking interactions into supramolecular ensembles of a specific type. The ensembles, water molecules, and (SO4)2- anions are bound in the crystal via hydrogen bonds. In the [Ni( TSC)3]2+ cation of structure III, ligands coordinate the Ni atom by the bidentate chelate pattern with the formation of five-membered metallocycles. These metallocycles have an envelope conformation unlike those in I and II, which are planar. In III (unlike in analogous complexes), a meridional isomer of the coordination octahedron of the Ni atom is formed. Together with Cl1- and Cl2- anions, cations form supermolecules, which are packed into planar layers with a square-cellular structure. The layers are linked by hydrogen bonds formed by crystallization water molecules that are located between the layers.

  3. Flexible and Asymmetric Ligand in Constructing Coordinated Complexes: Synthesis, Crystal Structures and Fluorescent Characterization

    Directory of Open Access Journals (Sweden)

    Jianhua Lin

    2010-12-01

    Full Text Available Flexible and asymmetric ligand L [L = 1-((pyridin-3-ylmethyl-1H-benzotriazole], is used as a basic backbone to construct complicated metal-organic frameworks. Two new polymers, namely, [Ag2(L2(NO32]n (1 and [Ag(L(ClO4]n (2, were synthesized and characterized by X-ray structure analysis and fluorescent spectroscopy. The complex 1 gives an “S” type double helical conformation, whereas complex 2 exhibits a 1D zigzag configuration. Different anions affect the silver coordination geometry and crystal packing topology.

  4. A new Co(II) complex of diniconazole: synthesis, crystal structure and antifungal activity.

    Science.gov (United States)

    Xi, Teng; Li, Jie; Yan, Biao; Yang, Mingyan; Song, Jirong; Ma, Haixia

    2015-10-01

    A new Co(II) complex of diniconazole, namely diaqua[(E)-(RS)-1-(2,4-dichlorophenyl)-4,4-dimethyl-2-(1H-1,2,4-triazol-1-yl-κN(4))pent-1-en-3-ol]cobalt(II) dinitrate dihydrate, [Co(C15H17Cl2N3O)3(H2O)2](NO3)2·2H2O, was synthesized and characterized by elemental analysis, IR spectroscopy and single-crystal X-ray diffraction. Crystal structural analysis shows that the centrosymmetric Co(II) cation is coordinated by four diniconazole ligands and two water molecules, forming a six-coordinated octahedral structure. There are also two free nitrate counter-anions and two additional solvent water molecules in the structure. Intermolecular O-H...O hydrogen bonds link the complex cations into a one-dimensional chain. In addition, the antifungal activity of the complex against Botryosphaeria ribis, Gibberella nicotiancola, Botryosphaeria berengriana and Alternariasolani was studied. The results indicate that the complex shows a higher antifungal activity for Botryosphaeria ribis and Botryosphaeria berengriana than diniconazole, but a lower antifungal activity for Gibberella nicotiancola and Alternariasolani.

  5. Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II

    Directory of Open Access Journals (Sweden)

    Weissenhorn Winfried

    2004-12-01

    Full Text Available Abstract Background Down-regulation of plasma membrane receptors via the endocytic pathway involves their monoubiquitylation, transport to endosomal membranes and eventual sorting into multi vesicular bodies (MVB destined for lysosomal degradation. Successive assemblies of Endosomal Sorting Complexes Required for Transport (ESCRT-I, -II and III largely mediate sorting of plasma membrane receptors at endosomal membranes, the formation of multivesicular bodies and their release into the endosomal lumen. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. Results Here we report the crystal structure of Vps25 at 3.1 Å resolution. Vps25 crystallizes in a dimeric form and each monomer is composed of two winged helix domains arranged in tandem. Structural comparisons detect no conformational changes between unliganded Vps25 and Vps25 within the ESCRT-II complex composed of two Vps25 copies and one copy each of Vps22 and Vps36 12. Conclusions Our structural analyses present a framework for studying Vps25 interactions with ESCRT-I and ESCRT-III partners. Winged helix domain containing proteins have been implicated in nucleic acid binding and it remains to be determined whether Vps25 has a similar activity which might play a role in the proposed transcriptional control exerted by Vps25 and/or the whole ESCRT-II complex.

  6. Crystal structure of phosphoethanolamine methyltransferase from Plasmodium falciparum in complex with amodiaquine

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Soon Goo; Alpert, Tara D.; Jez, Joseph M. (WU)

    2012-07-17

    Phosphoethanolamine N-methyltransferase (PMT) is essential for phospholipid biogenesis in the malarial parasite Plasmodium falciparum. PfPMT catalyzes the triple methylation of phosphoethanolamine to produce phosphocholine, which is then used for phosphatidylcholine synthesis. Here we describe the 2.0 {angstrom} resolution X-ray crystal structure of PfPMT in complex with amodiaquine. To better characterize inhibition of PfPMT by amodiaquine, we determined the IC{sub 50} values of a series of aminoquinolines using a direct radiochemical assay. Both structural and functional analyses provide a possible approach for the development of new small molecule inhibitors of PfPMT.

  7. Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex.

    Science.gov (United States)

    Jeong, Hanbin; Park, Jumi; Lee, Changwook

    2016-12-01

    The endoplasmic reticulum-mitochondria encounter structure (ERMES) is a protein complex that plays a tethering role in physically connecting ER and mitochondria membranes. The ERMES complex is composed of Mdm12, Mmm1, and Mdm34, which have a SMP domain in common, and Mdm10. Here, we report the crystal structure of S. cerevisiae Mdm12. The Mdm12 forms a dimeric SMP structure through domain swapping of the β1-strand comprising residues 1-7. Biochemical experiments reveal a phospholipid-binding site located along a hydrophobic channel of the Mdm12 structure and that Mdm12 might have a binding preference for glycerophospholipids harboring a positively charged head group. Strikingly, both full-length Mdm12 and Mdm12 truncated to exclude the disordered region (residues 74-114) display the same organization in the asymmetric unit, although they crystallize as a tetramer and hexamer, respectively. Taken together, these studies provide a novel understanding of the overall organization of SMP domains in the ERMES complex, indicating that Mdm12 interacts with Mdm34 through head-to-head contact, and with Mmm1 through tail-to-tail contact of SMP domains. © 2016 The Authors.

  8. Theoretical Studies on the Electronic Structures and Properties of Complex Ceramic Crystals and Novel Materials

    Energy Technology Data Exchange (ETDEWEB)

    Ching, Wai-Yim

    2012-01-14

    This project is a continuation of a long program supported by the Office of Basic Energy Science in the Office of Science of DOE for many years. The final three-year continuation started on November 1, 2005 with additional 1 year extension to October 30, 2009. The project was then granted a two-year No Cost Extension which officially ended on October 30, 2011. This report covers the activities within this six year period with emphasis on the work completed within the last 3 years. A total of 44 papers with acknowledgement to this grant were published or submitted. The overall objectives of this project are as follows. These objectives have been evolved over the six year period: (1) To use the state-of-the-art computational methods to investigate the electronic structures of complex ceramics and other novel crystals. (2) To further investigate the defects, surfaces/interfaces and microstructures in complex materials using large scale modeling. (3) To extend the study on ceramic materials to more complex bioceramic crystals. (4) To initiate the study on soft condensed matters including water and biomolecules. (5) To focus on the spectroscopic studies of different materials especially on the ELNES and XANES spectral calculations and their applications related to experimental techniques. (6) To develop and refine computational methods to be effectively executed on DOE supercomputers. (7) To evaluate mechanical properties of different crystals and those containing defects and relate them to the fundamental electronic structures. (8) To promote and publicize the first-principles OLCAO method developed by the PI (under DOE support for many years) for applications to large complex material systems. (9) To train a new generation of graduate students and postdoctoral fellows in modern computational materials science and condensed matter physics. (10) To establish effective international and domestic collaborations with both experimentalists and theorists in materials

  9. Crystal structure of human heme oxygenase-1 in a complex with biliverdin.

    Science.gov (United States)

    Lad, Latesh; Friedman, Jonathan; Li, Huying; Bhaskar, B; Ortiz de Montellano, Paul R; Poulos, Thomas L

    2004-04-06

    Heme oxygenase oxidatively cleaves heme to biliverdin, leading to the release of iron and CO through a process in which the heme participates both as a cofactor and as a substrate. Here we report the crystal structure of the product, iron-free biliverdin, in a complex with human HO-1 at 2.19 A. Structural comparisons of the human biliverdin-HO-1 structure with its heme complex and the recently published rat HO-1 structure in a complex with the biliverdin-iron chelate [Sugishima, M., Sakamoto, H., Higashimoto, Y., Noguchi, M., and Fukuyama, K. (2003) J. Biol. Chem. 278, 32352-32358] show two major differences. First, in the absence of an Fe-His bond and solvent structure in the active site, the distal and proximal helices relax and adopt an "open" conformation which most likely encourages biliverdin release. Second, iron-free biliverdin occupies a different position and orientation relative to heme and the biliverdin-iron complex. Biliverdin adopts a more linear conformation and moves from the heme site to an internal cavity. These structural results provide insight into the rate-limiting step in HO-1 catalysis, which is product, biliverdin, release.

  10. Crystal structure of λ exonuclease in complex with DNA and Ca(2+).

    Science.gov (United States)

    Zhang, Jinjin; Pan, Xinlei; Bell, Charles E

    2014-12-02

    Bacteriophage λ exonuclease (λexo) is a ring-shaped homotrimer that resects double-stranded DNA ends in the 5'-3' direction to generate a long 3'-overhang that is a substrate for recombination. λexo is a member of the type II restriction endonuclease-like superfamily of proteins that use a Mg(2+)-dependent mechanism for nucleotide cleavage. A previous structure of λexo in complex with DNA and Mg(2+) was determined using a nuclease defective K131A variant to trap a stable complex. This structure revealed the detailed coordination of the two active site Mg(2+) ions but did not show the interactions involving the side chain of the conserved active site Lys-131 residue. Here, we have determined the crystal structure of wild-type (WT) λexo in complex with the same DNA substrate, but in the presence of Ca(2+) instead of Mg(2+). Surprisingly, there is only one Ca(2+) bound in the active site, near the position of Mg(A) in the structure with Mg(2+). The scissile phosphate is displaced by 2.2 Å relative to its position in the structure with Mg(2+), and the network of interactions involving the attacking water molecule is broken. Thus, the structure does not represent a catalytic configuration. However, the crystal structure does show clear electron density for the side chain of Lys-131, which is held in place by interactions with Gln-157 and Glu-129. By combining the K131A-Mg(2+) and WT-Ca(2+) structures, we constructed a composite model to show the likely interactions of Lys-131 during catalysis. The implications with regard to the catalytic mechanism are discussed.

  11. Crystal Structure of the Herpesvirus Nuclear Egress Complex Provides Insights into Inner Nuclear Membrane Remodeling

    Directory of Open Access Journals (Sweden)

    Tzviya Zeev-Ben-Mordehai

    2015-12-01

    Full Text Available Although nucleo-cytoplasmic transport is typically mediated through nuclear pore complexes, herpesvirus capsids exit the nucleus via a unique vesicular pathway. Together, the conserved herpesvirus proteins pUL31 and pUL34 form the heterodimeric nuclear egress complex (NEC, which, in turn, mediates the formation of tight-fitting membrane vesicles around capsids at the inner nuclear membrane. Here, we present the crystal structure of the pseudorabies virus NEC. The structure revealed that a zinc finger motif in pUL31 and an extensive interaction network between the two proteins stabilize the complex. Comprehensive mutational analyses, characterized both in situ and in vitro, indicated that the interaction network is not redundant but rather complementary. Fitting of the NEC crystal structure into the recently determined cryoEM-derived hexagonal lattice, formed in situ by pUL31 and pUL34, provided details on the molecular basis of NEC coat formation and inner nuclear membrane remodeling.

  12. Crystal Structure of an L-Carnitine Complex with Pyrogallol[4]arene

    Science.gov (United States)

    Fujisawa, I.; Takeuchi, D.; Kitamura, Y.; Okamoto, R.; Aoki, K.

    2012-03-01

    L-Carnitine is essential for the transport of long-chain fatty acids from cytosol into mitochondria for generating metabolic energy. The survey of crystal structures of carnitine-containing proteins in the Protein Data Bank reveals that carnitine can take several conformations with the quarternary trimethylammonium terminal being always bound to aromatic residues through cation-π interactions in acyltransferases or carnitine-binding proteins. In order to demonstrate the importance of cation-π interaction as a carnitine recognition mechanism in the artificial receptor-ligand system that mimics the carnitine-binding sites, we have determined the crystal structure of a complex formed between L-carnitine and pyrogallol[4]arene (pyrogallol cyclic tetramer: PCT) as a carnitine receptor, 2PCT·2(L-carnitine)·4EtOH. There form two crystallographically independent monomeric [PCT·L-carnitine] substructures, which further form an obliquely arranged capsule-like dimeric [PCT·L-carnitine]2 structure through a pair of O-H (PCT)···O (L-carnitine) hydrogen bonds. This is the first report of PCT complex with chiral molecules. In each of the two monomeric [PCT·L-carnitine] substructures, the L-carnitine molecule takes the elongated form with an intramolecular hydrogen bond between the hydroxyl group and the carboxylate oxygen, and the cationic trimethylammonium moiety is incorporated into the cavity of the bowl-shaped PCT molecule through cation-π interactions. These features are similar to those at the D-carnitine-binding site in the crystal structure of the glycine betaine/carnitine/choline-binding protein complex.

  13. The Adaptability of the Active Site of Trypanosomal Triosephosphate Isomerase as Observed in the Crystal Structures of Three Different Complexes

    NARCIS (Netherlands)

    Noble, Martin E.M.; Wierenga, Rik K.; Lambeir, Anne-Marie; Opperdoes, Fred R.; Thunnissen, Andy-Mark W.H.; Kalk, Kornelis; Groendijk, Hillie; Hol, Wilhelmus

    1991-01-01

    Crystals of triosephosphate isomerase from Trypanosoma brucei brucei have been used in binding studies with three competitive inhibitors of the enzyme's activity. Highly refined structures have been deduced for the complexes between trypanosomal triosephosphate isomerase and a substrate analogue

  14. Crystal Structure of the Human NKX2.5 Homeodomain in Complex with DNA Target

    Energy Technology Data Exchange (ETDEWEB)

    Pradhan, Lagnajeet; Genis, Caroli; Scone, Peyton; Weinberg, Ellen O.; Kasahara, Hideko; Nam, Hyun-Joo (BU-M); (Florida); (Texas)

    2012-10-16

    NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 {angstrom} resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.

  15. Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli.

    Science.gov (United States)

    Su, Chih-Chia; Long, Feng; Zimmermann, Michael T; Rajashankar, Kanagalaghatta R; Jernigan, Robert L; Yu, Edward W

    2011-02-24

    Gram-negative bacteria, such as Escherichia coli, expel toxic chemicals through tripartite efflux pumps that span both the inner and outer membrane. The three parts are an inner membrane, substrate-binding transporter; a membrane fusion protein; and an outer-membrane-anchored channel. The fusion protein connects the transporter to the channel within the periplasmic space. A crystallographic model of this tripartite efflux complex has been unavailable because co-crystallization of the various components of the system has proven to be extremely difficult. We previously described the crystal structures of both the inner membrane transporter CusA and the membrane fusion protein CusB of the CusCBA efflux system of E. coli. Here we report the co-crystal structure of the CusBA efflux complex, showing that the transporter (or pump) CusA, which is present as a trimer, interacts with six CusB protomers and that the periplasmic domain of CusA is involved in these interactions. The six CusB molecules seem to form a continuous channel. The affinity of the CusA and CusB interaction was found to be in the micromolar range. Finally, we have predicted a three-dimensional structure for the trimeric CusC outer membrane channel and developed a model of the tripartite efflux assemblage. This CusC(3)-CusB(6)-CusA(3) model shows a 750-kilodalton efflux complex that spans the entire bacterial cell envelope and exports Cu I and Ag I ions.

  16. SYNTHESIS AND CRYSTAL STRUCTURE OF A Ni(II COMPLEX WITH 1,5-NAPHTHALENEDISULFONATE

    Directory of Open Access Journals (Sweden)

    WANG LI-HUA

    2014-11-01

    Full Text Available A new Ni(II complex, [Ni(H2O6]•(L (L=1,5-naphthalenedisulfonate has been obtained by the reaction of Ni(OAc2•4H2O with sodium 1,5-naphthalenedisulfonate in the CH3CH2OH/H2O (V:V=1:1 solution. The complex was characterized by elemental analysis, IR and X-ray single crystal diffraction analysis. The results showed that the local geometry around central Ni(II ion can be described as distorted octahedral environment which connected by six coordinated water molecules. The complex molecules formed one dimensional chained structure by hydrogen bonds and π-π stacking.

  17. Crystal structure of the β2 adrenergic receptor-Gs protein complex

    DEFF Research Database (Denmark)

    Rasmussen, Søren Gøgsig Faarup; DeVree, Brian T; Zou, Yaozhong

    2011-01-01

    G protein-coupled receptors (GPCRs) are responsible for the majority of cellular responses to hormones and neurotransmitters as well as the senses of sight, olfaction and taste. The paradigm of GPCR signalling is the activation of a heterotrimeric GTP binding protein (G protein) by an agonist......-occupied receptor. The β(2) adrenergic receptor (β(2)AR) activation of Gs, the stimulatory G protein for adenylyl cyclase, has long been a model system for GPCR signalling. Here we present the crystal structure of the active state ternary complex composed of agonist-occupied monomeric β(2)AR and nucleotide-free Gs...... by a GPCR....

  18. Crystal Structures of Murine Carnitine Acetyltransferase in Ternary Complexes with Its Substrates

    Energy Technology Data Exchange (ETDEWEB)

    Hsiao,Y.; Jogl, G.; Tong, L.

    2006-01-01

    Carnitine acyltransferases catalyze the reversible exchange of acyl groups between coenzyme A (CoA) and carnitine. They have important roles in many cellular processes, especially the oxidation of long-chain fatty acids in the mitochondria for energy production, and are attractive targets for drug discovery against diabetes and obesity. To help define in molecular detail the catalytic mechanism of these enzymes, we report here the high resolution crystal structure of wild-type murine carnitine acetyltransferase (CrAT) in a ternary complex with its substrates acetyl-CoA and carnitine, and the structure of the S554A/M564G double mutant in a ternary complex with the substrates CoA and hexanoylcarnitine. Detailed analyses suggest that these structures may be good mimics for the Michaelis complexes for the forward and reverse reactions of the enzyme, representing the first time that such complexes of CrAT have been studied in molecular detail. The structural information provides significant new insights into the catalytic mechanism of CrAT and possibly carnitine acyltransferases in general.

  19. Crystal structures of the kinase domain of the sulfate-activating complex in Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Ömer Poyraz

    Full Text Available In Mycobacterium tuberculosis the sulfate activating complex provides a key branching point in sulfate assimilation. The complex consists of two polypeptide chains, CysD and CysN. CysD is an ATP sulfurylase that, with the energy provided by the GTPase activity of CysN, forms adenosine-5'-phosphosulfate (APS which can then enter the reductive branch of sulfate assimilation leading to the biosynthesis of cysteine. The CysN polypeptide chain also contains an APS kinase domain (CysC that phosphorylates APS leading to 3'-phosphoadenosine-5'-phosphosulfate, the sulfate donor in the synthesis of sulfolipids. We have determined the crystal structures of CysC from M. tuberculosis as a binary complex with ADP, and as ternary complexes with ADP and APS and the ATP mimic AMP-PNP and APS, respectively, to resolutions of 1.5 Å, 2.1 Å and 1.7 Å, respectively. CysC shows the typical APS kinase fold, and the structures provide comprehensive views of the catalytic machinery, conserved in this enzyme family. Comparison to the structure of the human homolog show highly conserved APS and ATP binding sites, questioning the feasibility of the design of specific inhibitors of mycobacterial CysC. Residue Cys556 is part of the flexible lid region that closes off the active site upon substrate binding. Mutational analysis revealed this residue as one of the determinants controlling lid closure and hence binding of the nucleotide substrate.

  20. Syntheses, crystal structures, and properties of four complexes based on polycarboxylate and imidazole ligands

    Science.gov (United States)

    Qiao, Rui; Chen, Shui-Sheng; Sheng, Liang-Quan; Yang, Song; Li, Wei-Dong

    2015-08-01

    Four metal-organic coordination polymers [Zn(HL)(H2O)]·4H2O (1), [Zn(HL)(L1)]·4H2O (2), [Cu(HL)(H2O)]·3H2O (3) and [Cu(HL)(L1)]·5H2O (4) were synthesized by reactions of the corresponding metal(II) salts with semirigid polycarboxylate ligand (5-((4-carboxypiperidin-1-yl)methyl)isophthalic acid hydrochloride, H3L·HCl) or auxiliary ligand (1,4-di(1H-imidazol-4-yl)benzene, L1). The structures of the compounds were characterized by elemental analysis, FT-IR spectroscopy and single-crystal X-ray diffraction. The use of auxiliary ligand L1 has great influence on the structures of two pairs of complexes 1, 2 and 3, 4. Complex 1 is a uninodal 3-connected rare 2-fold interpenetrating ZnSc net with a Point (Schlafli) symbol of (103) while 2 is a one-dimensional (1D) ladder structure. Compound 3 features a two-dimensional (2D) honeycomb network with typical 63-hcb topology, while 4 is 2D network with (4, 4) sql topology based on binuclear CuII subunits. The non-covalent bonding interactions such as hydrogen bonds, π···π stacking and C-H···π exist in complexes 1-4, which contributes to stabilize crystal structure and extend the low-dimensional entities into high-dimensional frameworks. And the photoluminescent property of 1 and 2 and gas sorption property of 4 have been investigated.

  1. Spectral characterization, crystal structures and biological activities of iminodiacetate ternary complexes

    Science.gov (United States)

    Shahid, M.; Anjuli; Tasneem, Sana; Mantasha, I.; Ahamad, M. Naqi; Sama, Farasha; Fatma, Kehkeshan; Siddiqi, Zafar A.

    2017-10-01

    The ternary complexes with stoichiometry [M(imda)(bipy)]·6H2O (M = Cu) and [M(imda)(bipy)(H2O)]·4H2O (M = Ni, Co and Mn) where H2imda = iminodiacetic acid and bipy = 2,2‧-bipyridine, are prepared and characterized to exploit as novel antimicrobial agents and SOD mimics. The chemical structures were elucidated by IR, FAB-Mass, 1H, 13C NMR, EPR and spectral techniques. Single crystal X-ray and spectral studies of the complexes (1) and (2) have confirmed a square pyramidal geometry around Cu(II) ion while a saturated six coordinate (distorted octahedral) geometry around the Ni(II), Co(II) and Mn(II) ions due to the additional coordination from water. A supramolecular network is formed by extensive H-bonding in complex (1). The supramolecular assembly in complex (1) is additionally consolidated via the existence of unusual cyclic hexameric water clusters. The antimicrobial activities for the present complexes have been examined against Escherichia coli (K-12), Bacillus subtilis (MTC-121), Staphylococcus aureus (IOASA-22), Salmonella typhymurium (MTCC-98), Candida albicans, Aspergillus fumigatus and Penicillium marneffei. The superoxide dismutase (SOD) activity of the Cu(II) complex (1) is also assessed employing nitrobluetetrazolium (NBT) assay.

  2. Crystal Structures of EF-G-Ribosome Complexes Trapped in Intermediate States of Translocation

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jie; Lancaster, Laura; Donohue, John Paul; Noller, Harry F. [UCSC

    2013-11-12

    Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA–EF-G complexes trapped with β,γ-imidoguanosine 5'-triphosphate (GDPNP) or fusidic acid reveal conformational changes occurring during intermediate states of translocation, including large-scale rotation of the 30S subunit head and body. In all complexes, the tRNA acceptor ends occupy the 50S subunit E site, while their anticodon stem loops move with the head of the 30S subunit to positions between the P and E sites, forming chimeric intermediate states. Two universally conserved bases of 16S ribosomal RNA that intercalate between bases of the mRNA may act as “pawls” of a translocational ratchet. These findings provide new insights into the molecular mechanism of ribosomal translocation.

  3. Crystal structure and functional interpretation of the erythrocyte spectrin tetramerization domain complex

    Energy Technology Data Exchange (ETDEWEB)

    Ipsaro, Jonathan J.; Harper, Sandra L.; Messick, Troy E.; Marmorstein, Ronen; Mondragón, Alfonso; Speicher, David W. (Wistar); (NWU)

    2010-09-07

    As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrin fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.

  4. Crystal Structure and Functional Interpretation of the Erythrocyte spectrin Tetramerization Domain Complex

    Energy Technology Data Exchange (ETDEWEB)

    J Ipsaro; S Harper; T Messick; R Marmorstein; A Mondragon; D Speicher

    2011-12-31

    As the principal component of the membrane skeleton, spectrin confers integrity and flexibility to red cell membranes. Although this network involves many interactions, the most common hemolytic anemia mutations that disrupt erythrocyte morphology affect the spectrin tetramerization domains. Although much is known clinically about the resulting conditions (hereditary elliptocytosis and pyropoikilocytosis), the detailed structural basis for spectrin tetramerization and its disruption by hereditary anemia mutations remains elusive. Thus, to provide further insights into spectrin assembly and tetramer site mutations, a crystal structure of the spectrin tetramerization domain complex has been determined. Architecturally, this complex shows striking resemblance to multirepeat spectrin fragments, with the interacting tetramer site region forming a central, composite repeat. This structure identifies conformational changes in {alpha}-spectrin that occur upon binding to {beta}-spectrin, and it reports the first structure of the {beta}-spectrin tetramerization domain. Analysis of the interaction surfaces indicates an extensive interface dominated by hydrophobic contacts and supplemented by electrostatic complementarity. Analysis of evolutionarily conserved residues suggests additional surfaces that may form important interactions. Finally, mapping of hereditary anemia-related mutations onto the structure demonstrate that most, but not all, local hereditary anemia mutations map to the interacting domains. The potential molecular effects of these mutations are described.

  5. Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives

    Science.gov (United States)

    Masuno, Hiroyuki; Ikura, Teikichi; Morizono, Daisuke; Orita, Isamu; Yamada, Sachiko; Shimizu, Masato; Ito, Nobutoshi

    2013-01-01

    The secondary bile acid lithocholic acid (LCA) and its derivatives act as selective modulators of the vitamin D receptor (VDR), although their structures fundamentally differ from that of the natural hormone 1α,25-dihydroxyvitamin D3 [1,25(OH)2D3)]. Here, we have determined the crystal structures of the ligand-binding domain of rat VDR (VDR-LBD) in ternary complexes with a synthetic partial peptide of the coactivator MED1 (mediator of RNA polymerase II transcription subunit 1) and four ligands, LCA, 3-keto LCA, LCA acetate, and LCA propionate, with the goal of elucidating their agonistic mechanism. LCA and its derivatives bind to the same ligand-binding pocket (LBP) of VDR-LBD that 1,25(OH)2D3 binds to, but in the opposite orientation; their A-ring is positioned at the top of the LBP, whereas their acyclic tail is located at the bottom of the LBP. However, most of the hydrophobic and hydrophilic interactions observed in the complex with 1,25(OH)2D3 are reproduced in the complexes with LCA and its derivatives. Additional interactions between VDR-LBD and the C-3 substituents of the A-ring are also observed in the complexes with LCA and its derivatives. These may result in the observed difference in the potency among the LCA-type ligands. PMID:23723390

  6. Crystal structure of an engineered subtilisin inhibitor complexed with bovine trypsin.

    Science.gov (United States)

    Takeuchi, Y; Nonaka, T; Nakamura, K T; Kojima, S; Miura, K; Mitsui, Y

    1992-05-15

    Proteinase specificity of a proteinaceous inhibitor of subtilisin (SSI; Streptomyces subtilisin inhibitor) can be altered so as to strongly inhibit trypsin simply by replacing P1 methionine with lysine (with or without concomitant change of the P4 residue) through site-directed mutagenesis. Now the crystal structure of one such engineered SSI (P1 methionine converted to lysine and P4 methionine converted to glycine) complexed with bovine trypsin has been solved at 2.6 A resolution and refined to a crystallographic R factor of 0.173. Comparing this structure with the previously established structure of the native SSI complexed with subtilisin BPN', it was found that (i) P1 lysine of the mutant SSI is accommodated in the S1 pocket of trypsin as usual, and (ii) upon complex formation, considerable conformation change occurs to the reactive site loop of the mutant SSI. Thus, in this case, flexibility of the reactive site loop seems important for successfully changing the proteinase specificity through mere replacement of the P1 residue.

  7. Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex.

    Science.gov (United States)

    Cardote, Teresa A F; Gadd, Morgan S; Ciulli, Alessio

    2017-06-06

    Cullin RING E3 ubiquitin ligases (CRLs) function in the ubiquitin proteasome system to catalyze the transfer of ubiquitin from E2 conjugating enzymes to specific substrate proteins. CRLs are large dynamic complexes and attractive drug targets for the development of small-molecule inhibitors and chemical inducers of protein degradation. The atomic details of whole CRL assembly and interactions that dictate subunit specificity remain elusive. Here we present the crystal structure of a pentameric CRL2VHL complex, composed of Cul2, Rbx1, Elongin B, Elongin C, and pVHL. The structure traps a closed state of full-length Cul2 and a new pose of Rbx1 in a trajectory from closed to open conformation. We characterize hotspots and binding thermodynamics at the interface between Cul2 and pVHL-EloBC and identify mutations that contribute toward a selectivity switch for Cul2 versus Cul5 recognition. Our findings provide structural and biophysical insights into the whole Cul2 complex that could aid future drug targeting. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  8. Crystal structures of Mycobacterium tuberculosis GlgE and complexes with non-covalent inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Lindenberger, Jared J.; Veleti, Sri Kumar; Wilson, Brittney N.; Sucheck, Steven J.; Ronning, Donald R. (Toledo)

    2015-08-06

    GlgE is a bacterial maltosyltransferase that catalyzes the elongation of a cytosolic, branched α-glucan. In Mycobacterium tuberculosis (M. tb), inactivation of GlgE (Mtb GlgE) results in the rapid death of the organism due to a toxic accumulation of the maltosyl donor, maltose-1-phosphate (M1P), suggesting that GlgE is an intriguing target for inhibitor design. In this study, the crystal structures of the Mtb GlgE in a binary complex with maltose and a ternary complex with maltose and a maltosyl-acceptor molecule, maltohexaose, were solved to 3.3 Å and 4.0 Å, respectively. The maltohexaose structure reveals a dominant site for α-glucan binding. To obtain more detailed interactions between first generation, non-covalent inhibitors and GlgE, a variant Streptomyces coelicolor GlgEI (Sco GlgEI-V279S) was made to better emulate the Mtb GlgE M1P binding site. The structure of Sco GlgEI-V279S complexed with α-maltose-C-phosphonate (MCP), a non-hydrolyzable substrate analogue, was solved to 1.9 Å resolution, and the structure of Sco GlgEI-V279S complexed with 2,5-dideoxy-3-O-α-D-glucopyranosyl-2,5-imino-D-mannitol (DDGIM), an oxocarbenium mimic, was solved to 2.5 Å resolution. These structures detail important interactions that contribute to the inhibitory activity of these compounds, and provide information on future designs that may be exploited to improve upon these first generation GlgE inhibitors.

  9. Syntheses, crystal structures, and properties of four complexes based on polycarboxylate and imidazole ligands

    Energy Technology Data Exchange (ETDEWEB)

    Qiao, Rui [School of Chemistry and Chemical Engineering, Fuyang University, Fuyang 236041 (China); Chen, Shui-Sheng, E-mail: chenss@fync.edu.cn [School of Chemistry and Chemical Engineering, Fuyang University, Fuyang 236041 (China); Coordination Chemistry Institute, State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093 (China); Sheng, Liang-Quan; Yang, Song; Li, Wei-Dong [School of Chemistry and Chemical Engineering, Fuyang University, Fuyang 236041 (China)

    2015-08-15

    Four metal–organic coordination polymers [Zn(HL)(H{sub 2}O)]·4H{sub 2}O (1), [Zn(HL)(L{sub 1})]·4H{sub 2}O (2), [Cu(HL)(H{sub 2}O)]·3H{sub 2}O (3) and [Cu(HL)(L{sub 1})]·5H{sub 2}O (4) were synthesized by reactions of the corresponding metal(II) salts with semirigid polycarboxylate ligand (5-((4-carboxypiperidin-1-yl)methyl)isophthalic acid hydrochloride, H{sub 3}L·HCl) or auxiliary ligand (1,4-di(1H-imidazol-4-yl)benzene, L{sub 1}). The structures of the compounds were characterized by elemental analysis, FT-IR spectroscopy and single-crystal X-ray diffraction. The use of auxiliary ligand L{sub 1} has great influence on the structures of two pairs of complexes 1, 2 and 3, 4. Complex 1 is a uninodal 3-connected rare 2-fold interpenetrating ZnSc net with a Point (Schlafli) symbol of (10{sup 3}) while 2 is a one-dimensional (1D) ladder structure. Compound 3 features a two-dimensional (2D) honeycomb network with typical 6{sup 3}-hcb topology, while 4 is 2D network with (4, 4) sql topology based on binuclear Cu{sup II} subunits. The non-covalent bonding interactions such as hydrogen bonds, π···π stacking and C–H···π exist in complexes 1–4, which contributes to stabilize crystal structure and extend the low-dimensional entities into high-dimensional frameworks. And the photoluminescent property of 1 and 2 and gas sorption property of 4 have been investigated. - Graphical abstract: Four new coordination polymers have been obtained and their photoluminescent and gas sorption properties have also been investigated. - Highlights: • Two pairs of Zn{sup II}/ Cu{sup II} compounds have been synthesized. • Auxiliary ligand-controlled assembly of the complexes is reported. • The luminescent properties of complexes 1–2 were investigated. • The gas sorption property of 4 has been investigated.

  10. Crystal structure of the β2 adrenergic receptor-Gs protein complex

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, Søren G.F.; DeVree, Brian T; Zou, Yaozhong; Kruse, Andrew C; Chung, Ka Young; Kobilka, Tong Sun; Thian, Foon Sun; Chae, Pil Seok; Pardon, Els; Calinski, Diane; Mathiesen, Jesper M; Shah, Syed T.A.; Lyons, Joseph A; Caffrey, Martin; Gellman, Samuel H; Steyaert, Jan; Skiniotis, Georgios; Weis, William I; Sunahara, Roger K; Kobilka, Brian K [Brussels; (Trinity); (Michigan); (Stanford-MED); (Michigan-Med); (UW)

    2011-12-07

    G protein-coupled receptors (GPCRs) are responsible for the majority of cellular responses to hormones and neurotransmitters as well as the senses of sight, olfaction and taste. The paradigm of GPCR signalling is the activation of a heterotrimeric GTP binding protein (G protein) by an agonist-occupied receptor. The β2 adrenergic receptor (β2AR) activation of Gs, the stimulatory G protein for adenylyl cyclase, has long been a model system for GPCR signalling. Here we present the crystal structure of the active state ternary complex composed of agonist-occupied monomeric β2AR and nucleotide-free Gs heterotrimer. The principal interactions between the β2AR and Gs involve the amino- and carboxy-terminal α-helices of Gs, with conformational changes propagating to the nucleotide-binding pocket. The largest conformational changes in the β2AR include a 14Å outward movement at the cytoplasmic end of transmembrane segment 6 (TM6) and an α-helical extension of the cytoplasmic end of TM5. The most surprising observation is a major displacement of the α-helical domain of Gαs relative to the Ras-like GTPase domain. This crystal structure represents the first high-resolution view of transmembrane signalling by a GPCR.

  11. Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Guiqing; Sun, Dawei; Rajashankar, Kanagalaghatta R.; Qian, Zhaohui; Holmes, Kathryn V.; Li, Fang (Cornell); (UMM-MED); (Colorado)

    2011-09-28

    Coronaviruses have evolved diverse mechanisms to recognize different receptors for their cross-species transmission and host-range expansion. Mouse hepatitis coronavirus (MHV) uses the N-terminal domain (NTD) of its spike protein as its receptor-binding domain. Here we present the crystal structure of MHV NTD complexed with its receptor murine carcinoembryonic antigen-related cell adhesion molecule 1a (mCEACAM1a). Unexpectedly, MHV NTD contains a core structure that has the same {beta}-sandwich fold as human galectins (S-lectins) and additional structural motifs that bind to the N-terminal Ig-like domain of mCEACAM1a. Despite its galectin fold, MHV NTD does not bind sugars, but instead binds mCEACAM1a through exclusive protein-protein interactions. Critical contacts at the interface have been confirmed by mutagenesis, providing a structural basis for viral and host specificities of coronavirus/CEACAM1 interactions. Sugar-binding assays reveal that galectin-like NTDs of some coronaviruses such as human coronavirus OC43 and bovine coronavirus bind sugars. Structural analysis and mutagenesis localize the sugar-binding site in coronavirus NTDs to be above the {beta}-sandwich core. We propose that coronavirus NTDs originated from a host galectin and retained sugar-binding functions in some contemporary coronaviruses, but evolved new structural features in MHV for mCEACAM1a binding.

  12. [Synthesis, Crystal Structure and Fluorescence Properties of Two Tb(III) Complexes].

    Science.gov (United States)

    Fan, Ting-ting; Song, Shuang; Zhang, Yi-hua; Huo, Rui; Li, Xia; Ding, Xing-yi; Liu, Yang; Zhao, Xu; Yan, Chun-hui

    2015-07-01

    Two coordination polymers with formula of [Tb(3-SBA) (IP)OH(H2O)] · H2O(1) and [Tb(dpdc)1.5 (IP) (H2O)]n (2) (3-SBA==3-sulfobenzoate, dpdc=2,2'-diphenyldicarboxylate and IP=1H-imidazo[4,5-f][1,10]-phenanthroline) have been synthesised under hydrothermal condition and characterizated by X-ray single crystal diffraction. The complex 1 possesses a 1D chain structure constructed from Tb(III) ions by 3-SBA ligands and OH groups. Complex 2 shows a 1D chain structure constructed from Tb(III) ions by dpdc ligands. The two complexes display the characteristic (5)D4-->7Fj (J=6-3) transitions at 492, 544,584 and 619 nm of Tb(III) ion, respectively. No emission from the ligand could be observed, which indicates that the ligands absorb and transfer energy efficiently to central Tb( M) ion. The emission decay curves reveal a monoexponential behaviour yielding the lifetime values of 0.287 ms for 1 and 0.439 ms for 2. The quantum yields of luminescence are 9.28% for 1 and 7.07% for 2.

  13. Crystal structure and magnetic behaviour of a five-coordinate iron(III) complex of pyridoxal-4-methylthiosemicarbazone

    NARCIS (Netherlands)

    Tido, Eddy W. Yernell; Vertelman, Esther J. M.; Meetsma, Auke; van Koningsbruggen, Petra J.; Yemeli Tido, Eddy W.

    2007-01-01

    The crystal structure and magnetic properties of a penta-coordinate iron(III) complex of pyridoxal-4-methylthiosemicarbazone, [Fe(H(2)mthpy)Cl-2](CH3C6H4SO3), are reported. The synthesised ligand and the metal complex were characterised by spectroscopic methods (H-1 NMR, IR, and mass spectroscopy),

  14. Crystal structure of the PIM2 kinase in complex with an organoruthenium inhibitor.

    Directory of Open Access Journals (Sweden)

    Alex N Bullock

    2009-10-01

    Full Text Available The serine/threonine kinase PIM2 is highly expressed in human leukemia and lymphomas and has been shown to positively regulate survival and proliferation of tumor cells. Its diverse ATP site makes PIM2 a promising target for the development of anticancer agents. To date our knowledge of catalytic domain structures of the PIM kinase family is limited to PIM1 which has been extensively studied and which shares about 50% sequence identity with PIM2.Here we determined the crystal structure of PIM2 in complex with an organoruthenium complex (inhibition in sub-nanomolar level. Due to its extraordinary shape complementarity this stable organometallic compound is a highly potent inhibitor of PIM kinases.The structure of PIM2 revealed several differences to PIM1 which may be explored further to generate isoform selective inhibitors. It has also demonstrated how an organometallic inhibitor can be adapted to the binding site of protein kinases to generate highly potent inhibitors.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

  15. Crystal structures of Pseudomonas syringae pv. tomato DC3000 quinone oxidoreductase and its complex with NADPH

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Xiaowei [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 (China); Graduate University of the Chinese Academy of Sciences, Beijing 100049 (China); Zhang, Hongmei; Gao, Yu; Li, Mei [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 (China); Chang, Wenrui, E-mail: wrchang@sun5.ibp.ac.cn [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 (China)

    2009-12-18

    Zeta-crystallin-like quinone oxidoreductase is NAD(P)H-dependent and catalyzes one-electron reduction of certain quinones to generate semiquinone. Here we present the crystal structures of zeta-crystallin-like quinone oxidoreductase from Pseudomonas syringae pv. tomato DC3000 (PtoQOR) and its complexes with NADPH determined at 2.4 and 2.01 A resolutions, respectively. PtoQOR forms as a homologous dimer, each monomer containing two domains. In the structure of the PtoQOR-NADPH complex, NADPH locates in the groove between the two domains. NADPH binding causes obvious conformational changes in the structure of PtoQOR. The putative substrate-binding site of PtoQOR is wider than that of Escherichia coli and Thermus thermophilus HB8. Activity assays show that PtoQOR has weak 1,4-benzoquinone catalytic activity, and very strong reduction activity towards large substrates such as 9,10-phenanthrenequinone. We propose a model to explain the conformational changes which take place during reduction reactions catalyzed by PtoQOR.

  16. Crystal structure and stability of gyrase–fluoroquinolone cleaved complexes from Mycobacterium tuberculosis

    Science.gov (United States)

    Williamson, Benjamin H.; Kerns, Robert J.; Berger, James M.

    2016-01-01

    Mycobacterium tuberculosis (Mtb) infects one-third of the world’s population and in 2013 accounted for 1.5 million deaths. Fluoroquinolone antibacterials, which target DNA gyrase, are critical agents used to halt the progression from multidrug-resistant tuberculosis to extensively resistant disease; however, fluoroquinolone resistance is emerging and new ways to bypass resistance are required. To better explain known differences in fluoroquinolone action, the crystal structures of the WT Mtb DNA gyrase cleavage core and a fluoroquinolone-sensitized mutant were determined in complex with DNA and five fluoroquinolones. The structures, ranging from 2.4- to 2.6-Å resolution, show that the intrinsically low susceptibility of Mtb to fluoroquinolones correlates with a reduction in contacts to the water shell of an associated magnesium ion, which bridges fluoroquinolone–gyrase interactions. Surprisingly, the structural data revealed few differences in fluoroquinolone–enzyme contacts from drugs that have very different activities against Mtb. By contrast, a stability assay using purified components showed a clear relationship between ternary complex reversibility and inhibitory activities reported with cultured cells. Collectively, our data indicate that the stability of fluoroquinolone/DNA interactions is a major determinant of fluoroquinolone activity and that moieties that have been appended to the C7 position of different quinolone scaffolds do not take advantage of specific contacts that might be made with the enzyme. These concepts point to new approaches for developing quinolone-class compounds that have increased potency against Mtb and the ability to overcome resistance. PMID:26792525

  17. Crystal structure and stability of gyrase-fluoroquinolone cleaved complexes from Mycobacterium tuberculosis.

    Science.gov (United States)

    Blower, Tim R; Williamson, Benjamin H; Kerns, Robert J; Berger, James M

    2016-02-16

    Mycobacterium tuberculosis (Mtb) infects one-third of the world's population and in 2013 accounted for 1.5 million deaths. Fluoroquinolone antibacterials, which target DNA gyrase, are critical agents used to halt the progression from multidrug-resistant tuberculosis to extensively resistant disease; however, fluoroquinolone resistance is emerging and new ways to bypass resistance are required. To better explain known differences in fluoroquinolone action, the crystal structures of the WT Mtb DNA gyrase cleavage core and a fluoroquinolone-sensitized mutant were determined in complex with DNA and five fluoroquinolones. The structures, ranging from 2.4- to 2.6-Å resolution, show that the intrinsically low susceptibility of Mtb to fluoroquinolones correlates with a reduction in contacts to the water shell of an associated magnesium ion, which bridges fluoroquinolone-gyrase interactions. Surprisingly, the structural data revealed few differences in fluoroquinolone-enzyme contacts from drugs that have very different activities against Mtb. By contrast, a stability assay using purified components showed a clear relationship between ternary complex reversibility and inhibitory activities reported with cultured cells. Collectively, our data indicate that the stability of fluoroquinolone/DNA interactions is a major determinant of fluoroquinolone activity and that moieties that have been appended to the C7 position of different quinolone scaffolds do not take advantage of specific contacts that might be made with the enzyme. These concepts point to new approaches for developing quinolone-class compounds that have increased potency against Mtb and the ability to overcome resistance.

  18. Crystal structure of 2-nitropropane dioxygenase complexed with FMN and substrate. Identification of the catalytic base.

    Science.gov (United States)

    Ha, Jun Yong; Min, Ji Young; Lee, Su Kyung; Kim, Hyoun Sook; Kim, Do Jin; Kim, Kyoung Hoon; Lee, Hyung Ho; Kim, Hye Kyung; Yoon, Hye-Jin; Suh, Se Won

    2006-07-07

    Nitroalkane compounds are widely used in chemical industry and are also produced by microorganisms and plants. Some nitroalkanes have been demonstrated to be carcinogenic, and enzymatic oxidation of nitroalkanes is of considerable interest. 2-Nitropropane dioxygenases from Neurospora crassa and Williopsis mrakii (Hansenula mrakii), members of one family of the nitroalkane-oxidizing enzymes, contain FMN and FAD, respectively. The enzymatic oxidation of nitroalkanes by 2-nitropropane dioxygenase operates by an oxidase-style catalytic mechanism, which was recently shown to involve the formation of an anionic flavin semiquinone. This represents a unique case in which an anionic flavin semiquinone has been experimentally observed in the catalytic pathway for oxidation catalyzed by a flavin-dependent enzyme. Here we report the first crystal structure of 2-nitropropane dioxygenase from Pseudomonas aeruginosa in two forms: a binary complex with FMN and a ternary complex with both FMN and 2-nitropropane. The structure identifies His(152) as the proposed catalytic base, thus providing a structural framework for a better understanding of the catalytic mechanism.

  19. Synthesis, characterization, and crystal structure of mercury(II) complex containing new phosphine oxide salt

    Science.gov (United States)

    Samiee, Sepideh; Kooti, Nadieh; Gable, Robert W.

    2017-02-01

    The reaction of new phosphonium-phosphine oxide salt [P(O)Ph2(CH2)2PPh2CH2C(O)C6H4NO2]Br (1) with mercury(II) iodide in a methanolic solution yielded [P(O)Ph2(CH2)2PPh2CH2C(O)C6H4NO2]2[Hg2I5Br](2). These two compounds were fully characterized by elemental analysis, IR, 1H, 31P, and 13C NMR spectra. Crystal and molecular structure of 2 has been determined by means of X-ray diffraction. In mercury compound, the phosphine oxide salt is found as a counter ion letting the mercury(II) ion to bound halides to all four coordination sites and to give dimermercurate(II) ions as the structure-constructing species. The neighboring [P(O)Ph2(CH2)2PPh2CH2C(O)C6H4NO2]2+cations are joined together by intramolecular Csbnd H⋯O hydrogen bonds to give a 1-D chain structure along the crystallographic b-axis. The [Hg2I5Br]2-anions act as cross-linkers between neighbouring strands extending the supramolecular structure into 2D layers in (110) planes as well as balances the charge of the complex. The significant effects of Csbnd H⋯X (Xdbnd O, Br and I) and π⋯π aromatic interactions play a major role in the crystal packing of compound 2.

  20. Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies

    Energy Technology Data Exchange (ETDEWEB)

    AhYoung, Andrew P.; Lu, Brian; Cascio, Duilio; Egea, Pascal F.

    2017-06-01

    Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum – Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited for structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data.

  1. Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies.

    Science.gov (United States)

    AhYoung, Andrew P; Lu, Brian; Cascio, Duilio; Egea, Pascal F

    2017-06-17

    Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum - Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited for structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. The crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with adenosine

    Energy Technology Data Exchange (ETDEWEB)

    Giuseppe, P.O.; Meza, A.N.; Martins, N.H.; Santos, C.R.; Murakami, M.T. [Laboratorio Nacional de Luz Sincrotron (LNLS), Campinas, SP (Brazil)

    2012-07-01

    Full text: Purine nucleoside phosphorylases (PNPs) play a key role in the purine-salvage pathway in both prokaryotes and eukaryotes. Its ribosyltransferase activity is of great biotechnological interest due to potential application in the synthesis of nucleoside analogues used in the treatment of antiviral infections and in anticancer chemotherapy. Trimeric PNPs are found mainly in vertebrates and are specific for 6-oxo-purines whereas hexameric PNPs are prevalent in prokaryotes and exhibit a broad range of substrates including 6-oxo and 6-amino purines. BsPNP233, the hexameric PNP from B. subtilis, is able to catalyze the bioconversion of ribavirin, an anti-viral drug, and is relatively thermostable, being a good target for industrial use. Here we report the crystal structures of BsPNP233 in the apo form and in complex with adenosine solved at 2.65 and 1.91 resolution, respectively. The apo and ligand-bound BsPNP233 subunits superposed with an overall r.m.s. deviation of 0.31 for all C{alpha} atoms, which suggests that no major conformational changes occur upon substrate binding. Based on the crystal structure of BsPNP233 in complex with adenosine we have defined the active site residues implicated in binding the ribose (H4{sup *}, R43{sup *}, M64, R87, E178, M179, E180) and the nitrogenous base (S90, C91, G92, S202, V177, F159). These residues are highly conserved among the bacterial hexameric PNPs, suggesting they share the same mode of interaction with the substrates. This work will probably contribute to a better understanding of the molecular basis for the broad substrate specificity of hexameric PNPs and to projects aiming the rational design of PNPs for industrial purposes. (author)

  3. Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA*

    Science.gov (United States)

    Burmeister, Wim P.; Tarbouriech, Nicolas; Fender, Pascal; Contesto-Richefeu, Céline; Peyrefitte, Christophe N.; Iseni, Frédéric

    2015-01-01

    Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase catalytic subunit E9 associated with its heterodimeric co-factor A20·D4 required for processive genome synthesis. Although A20 has no known enzymatic activity, D4 is an active uracil-DNA glycosylase (UNG). The presence of a repair enzyme as a component of the viral replication machinery suggests that, for poxviruses, DNA synthesis and base excision repair is coupled. We present the 2.7 Å crystal structure of the complex formed by D4 and the first 50 amino acids of A20 (D4·A201–50) bound to a 10-mer DNA duplex containing an abasic site resulting from the cleavage of a uracil base. Comparison of the viral complex with its human counterpart revealed major divergences in the contacts between protein and DNA and in the enzyme orientation on the DNA. However, the conformation of the dsDNA within both structures is very similar, suggesting a dominant role of the DNA conformation for UNG function. In contrast to human UNG, D4 appears rigid, and we do not observe a conformational change upon DNA binding. We also studied the interaction of D4·A201–50 with different DNA oligomers by surface plasmon resonance. D4 binds weakly to nonspecific DNA and to uracil-containing substrates but binds abasic sites with a Kd of DNA complex structure of a family I UNG gives new insight into the role of D4 as a co-factor of vaccinia virus DNA polymerase and allows a better understanding of the structural determinants required for UNG action. PMID:26045555

  4. Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA.

    Science.gov (United States)

    Burmeister, Wim P; Tarbouriech, Nicolas; Fender, Pascal; Contesto-Richefeu, Céline; Peyrefitte, Christophe N; Iseni, Frédéric

    2015-07-17

    Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase catalytic subunit E9 associated with its heterodimeric co-factor A20·D4 required for processive genome synthesis. Although A20 has no known enzymatic activity, D4 is an active uracil-DNA glycosylase (UNG). The presence of a repair enzyme as a component of the viral replication machinery suggests that, for poxviruses, DNA synthesis and base excision repair is coupled. We present the 2.7 Å crystal structure of the complex formed by D4 and the first 50 amino acids of A20 (D4·A201-50) bound to a 10-mer DNA duplex containing an abasic site resulting from the cleavage of a uracil base. Comparison of the viral complex with its human counterpart revealed major divergences in the contacts between protein and DNA and in the enzyme orientation on the DNA. However, the conformation of the dsDNA within both structures is very similar, suggesting a dominant role of the DNA conformation for UNG function. In contrast to human UNG, D4 appears rigid, and we do not observe a conformational change upon DNA binding. We also studied the interaction of D4·A201-50 with different DNA oligomers by surface plasmon resonance. D4 binds weakly to nonspecific DNA and to uracil-containing substrates but binds abasic sites with a Kd of DNA complex structure of a family I UNG gives new insight into the role of D4 as a co-factor of vaccinia virus DNA polymerase and allows a better understanding of the structural determinants required for UNG action. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Kailang; Li, Weikai; Peng, Guiqing; Li, Fang; (Harvard-Med); (UMM-MED)

    2010-03-04

    NL63 coronavirus (NL63-CoV), a prevalent human respiratory virus, is the only group I coronavirus known to use angiotensin-converting enzyme 2 (ACE2) as its receptor. Incidentally, ACE2 is also used by group II SARS coronavirus (SARS-CoV). We investigated how different groups of coronaviruses recognize the same receptor, whereas homologous group I coronaviruses recognize different receptors. We determined the crystal structure of NL63-CoV spike protein receptor-binding domain (RBD) complexed with human ACE2. NL63-CoV RBD has a novel {beta}-sandwich core structure consisting of 2 layers of {beta}-sheets, presenting 3 discontinuous receptor-binding motifs (RBMs) to bind ACE2. NL63-CoV and SARS-CoV have no structural homology in RBD cores or RBMs; yet the 2 viruses recognize common ACE2 regions, largely because of a 'virus-binding hotspot' on ACE2. Among group I coronaviruses, RBD cores are conserved but RBMs are variable, explaining how these viruses recognize different receptors. These results provide a structural basis for understanding viral evolution and virus-receptor interactions.

  6. Synthesis, structural characterization, crystal structure and theoretical study of a Pd(II)-salen complex with propylene linkage

    Science.gov (United States)

    Azam, Mohammad; Al-Resayes, Saud I.; Soliman, Saied M.; Kruszynska, Agata Trzesowska; Kruszynski, Rafal

    2017-06-01

    A Pd(II)-salen complex derived from salen ligand is reported. The reported complex is investigated by microanalyses (C, H, N), ESI-MS spectrometry, FT-IR, 1H and 13C NMR and UV/Vis spectroscopic studies. In addition, crystal structure measurement study has also been carried out in order to confirm the structure of Pd(II)-salen complex. In order to explore the insights into the structural bonding of the studied complex, computational measurements has been carried out. Combined topology and NBO studies were made to explore the nature of Pdsbnd O and Pdsbnd N bonding in the complex. The natural charges showed that the transfers of the negative charge from the ligand to palladium atom is at 1.4157-1.4312 e. Atom in a molecule (AIM) analysis showed the electron density (ρ(r) > 0.1) and its Laplacian (∇2 ρ(r) > 0). These topological parameters showed that covalent bonding interactions are dominant in Pdsbnd N and Pdsbnd O bonds. However, Pdsbnd N bonds have more covalent characters than Pdsbnd O bonds, which is further confirmed by the ratio of local electron potential energy density to the local electron kinetic energy density (|V(r)|/G(r)) found to be higher for Pdsbnd N bonds (1.1683-1.1993) as compared to Pdsbnd O bonds (1.0689-1.0926). AIM and NBO reveal that shorter Pdsbnd N and Pdsbnd O bonds have higher interaction energies (Eint) and hence higher bond covalence.

  7. Synthesis, spectral, crystal structure, thermal behavior, antimicrobial and DNA cleavage potential of two octahedral cadmium complexes: A supramolecular structure

    Science.gov (United States)

    Montazerozohori, M.; Musavi, S. A.; Masoudiasl, A.; Naghiha, A.; Dusek, M.; Kucerakova, M.

    2015-02-01

    Two new cadmium(II) complexes with the formula of CdL2(NCS)2 and CdL2(N3)2 (in which L is 2,2-dimethyl-N,N‧-bis-(3-phenyl-allylidene)-propane-1,3-diamine) have been synthesized and characterized by elemental analysis, molar conductivity measurements, FT/IR, UV-Visible, 1H and 13C NMR spectra and X-ray studies. The crystal structure analysis of CdL2(NCS)2 indicated that it crystallizes in orthorhombic system with space group of Pbca. Two Schiff base ligands are bonded to cadmium(II) ion as N2-donor chelate. Coordination geometry around the cadmium ion was found to be partially distorted octahedron. The Cd-Nimine bond distances are found in the range of 2.363(2)-2.427(2) Å while the Cd-Nisothiocyanate bond distances are 2.287(2) Å and 2.310(2) Å. The existence of C-H⋯π and C-H⋯S interactions in the CdL2(NCS)2 crystal leads to a supramolecular structure in its network. Then cadmium complexes were screened in vitro for their antibacterial and antifungal activities against two Gram-negative and two Gram-positive bacteria and also against Candida albicans as a fungus. Moreover, the compounds were subjected for DNA-cleavage potential by gel electrophoresis method. Finally thermo-gravimetric analysis of the complexes was applied for thermal behavior studies and then some thermo-kinetics activation parameters were evaluated.

  8. Crystal structure of an EAL domain in complex with reaction product 5'-pGpG.

    Directory of Open Access Journals (Sweden)

    Julien Robert-Paganin

    Full Text Available FimX is a large multidomain protein containing an EAL domain and involved in twitching motility in Pseudomonas aeruginosa. We present here two crystallographic structures of the EAL domain of FimX (residues 438-686: one of the apo form and the other of a complex with 5'-pGpG, the reaction product of the hydrolysis of c-di-GMP. In both crystal forms, the EAL domains form a dimer delimiting a large cavity encompassing the catalytic pockets. The ligand is trapped in this cavity by its sugar phosphate moiety. We confirmed by NMR that the guanine bases are not involved in the interaction in solution. We solved here the first structure of an EAL domain bound to the reaction product 5'-pGpG. Though isolated FimX EAL domain has a very low catalytic activity, which would not be significant compared to other catalytic EAL domains, the structure with the product of the reaction can provides some hints in the mechanism of hydrolysis of the c-di-GMP by EAL domains.

  9. Crystal Structure of the Conserved Herpes Virus Fusion Regulator Complex gH–gL

    Energy Technology Data Exchange (ETDEWEB)

    Chowdary, T.; Cairns, T; Atanasiu, D; Cohen, G; Eisenberg, R; Heldwein, E

    2010-01-01

    Herpesviruses, which cause many incurable diseases, infect cells by fusing viral and cellular membranes. Whereas most other enveloped viruses use a single viral catalyst called a fusogen, herpesviruses, inexplicably, require two conserved fusion-machinery components, gB and the heterodimer gH-gL, plus other nonconserved components. gB is a class III viral fusogen, but unlike other members of its class, it does not function alone. We determined the crystal structure of the gH ectodomain bound to gL from herpes simplex virus 2. gH-gL is an unusually tight complex with a unique architecture that, unexpectedly, does not resemble any known viral fusogen. Instead, we propose that gH-gL activates gB for fusion, possibly through direct binding. Formation of a gB-gH-gL complex is critical for fusion and is inhibited by a neutralizing antibody, making the gB-gH-gL interface a promising antiviral target.

  10. Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Zhiqiang; Su, Lijing; Pei, Jimin; Grishin, Nick V.; Zhang, Hong (UTSMC)

    2017-08-01

    In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 interacts with coregulator(s) is not well understood. Here we report the crystal structures of the mouse CLOCK transactivating domain Exon19 in complex with CIPC, a potent circadian repressor that functions independently of CRY and PER. The Exon19:CIPC complex adopts a three-helical coiled-coil bundle conformation containing two Exon19 helices and one CIPC. Unique to Exon19:CIPC, three highly conserved polar residues, Asn341 of CIPC and Gln544 of the two Exon19 helices, are located at the mid-section of the coiled-coil bundle interior and form hydrogen bonds with each other. Combining results from protein database search, sequence analysis, and mutagenesis studies, we discovered for the first time that CLOCK Exon19:CIPC interaction is a conserved transcription regulatory mechanism among mammals, fish, flies, and other invertebrates.

  11. Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor.

    Science.gov (United States)

    Hou, Zhiqiang; Su, Lijing; Pei, Jimin; Grishin, Nick V; Zhang, Hong

    2017-08-01

    In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 interacts with coregulator(s) is not well understood. Here we report the crystal structures of the mouse CLOCK transactivating domain Exon19 in complex with CIPC, a potent circadian repressor that functions independently of CRY and PER. The Exon19:CIPC complex adopts a three-helical coiled-coil bundle conformation containing two Exon19 helices and one CIPC. Unique to Exon19:CIPC, three highly conserved polar residues, Asn341 of CIPC and Gln544 of the two Exon19 helices, are located at the mid-section of the coiled-coil bundle interior and form hydrogen bonds with each other. Combining results from protein database search, sequence analysis, and mutagenesis studies, we discovered for the first time that CLOCK Exon19:CIPC interaction is a conserved transcription regulatory mechanism among mammals, fish, flies, and other invertebrates. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Crystal structure of the conserved herpesvirus fusion regulator complex gH—gL

    Energy Technology Data Exchange (ETDEWEB)

    Chowdary, Tirumala K.; Cairns, Tina M.; Atanasiu, Doina; Cohen, Gary H.; Eisenberg, Roselyn J.; Heldwein, Ekaterina E. [UPENN; (Tufts-MED)

    2015-02-09

    Herpesviruses, which cause many incurable diseases, infect cells by fusing viral and cellular membranes. Whereas most other enveloped viruses use a single viral catalyst called a fusogen, herpesviruses, inexplicably, require two conserved fusion-machinery components, gB and the heterodimer gH–gL, plus other nonconserved components. gB is a class III viral fusogen, but unlike other members of its class, it does not function alone. We determined the crystal structure of the gH ectodomain bound to gL from herpes simplex virus 2. gH–gL is an unusually tight complex with a unique architecture that, unexpectedly, does not resemble any known viral fusogen. Instead, we propose that gH–gL activates gB for fusion, possibly through direct binding. Formation of a gB–gH–gL complex is critical for fusion and is inhibited by a neutralizing antibody, making the gB–gH–gL interface a promising antiviral target.

  13. Crystal structure of the conserved herpes virus fusion regulator complex gH-gL

    Energy Technology Data Exchange (ETDEWEB)

    Chowdary, Tirumala K; Cairns, Tina M; Atanasiu, Doina; Cohen, Gary H; Eisenberg, Roselyn J; Heldwein, Ekaterina E [UPENN; (Tufts-MED)

    2010-09-13

    Herpesviruses, which cause many incurable diseases, infect cells by fusing viral and cellular membranes. Whereas most other enveloped viruses use a single viral catalyst called a fusogen, herpesviruses, inexplicably, require two conserved fusion-machinery components, gB and the heterodimer gH-gL, plus other nonconserved components. gB is a class III viral fusogen, but unlike other members of its class, it does not function alone. We determined the crystal structure of the gH ectodomain bound to gL from herpes simplex virus 2. gH-gL is an unusually tight complex with a unique architecture that, unexpectedly, does not resemble any known viral fusogen. Instead, we propose that gH-gL activates gB for fusion, possibly through direct binding. Formation of a gB-gH-gL complex is critical for fusion and is inhibited by a neutralizing antibody, making the gB-gH-gL interface a promising antiviral target.

  14. Crystal structure of reovirus attachment protein σ1 in complex with sialylated oligosaccharides.

    Directory of Open Access Journals (Sweden)

    Dirk M Reiter

    2011-08-01

    Full Text Available Many viruses attach to target cells by binding to cell-surface glycans. To gain a better understanding of strategies used by viruses to engage carbohydrate receptors, we determined the crystal structures of reovirus attachment protein σ1 in complex with α-2,3-sialyllactose, α-2,6-sialyllactose, and α-2,8-di-siallylactose. All three oligosaccharides terminate in sialic acid, which serves as a receptor for the reovirus serotype studied here. The overall structure of σ1 resembles an elongated, filamentous trimer. It contains a globular head featuring a compact β-barrel, and a fibrous extension formed by seven repeating units of a triple β-spiral that is interrupted near its midpoint by a short α-helical coiled coil. The carbohydrate-binding site is located between β-spiral repeats two and three, distal from the head. In all three complexes, the terminal sialic acid forms almost all of the contacts with σ1 in an identical manner, while the remaining components of the oligosaccharides make little or no contacts. We used this structural information to guide mutagenesis studies to identify residues in σ1 that functionally engage sialic acid by assessing hemagglutination capacity and growth in murine erythroleukemia cells, which require sialic acid binding for productive infection. Our studies using σ1 mutant viruses reveal that residues 198, 202, 203, 204, and 205 are required for functional binding to sialic acid by reovirus. These findings provide insight into mechanisms of reovirus attachment to cell-surface glycans and contribute to an understanding of carbohydrate binding by viruses. They also establish a filamentous, trimeric carbohydrate-binding module that could potentially be used to endow other trimeric proteins with carbohydrate-binding properties.

  15. Crystal Structure of the Bcl-XL-Beclin 1 Peptide Complex

    Energy Technology Data Exchange (ETDEWEB)

    Oberstein,A.; Jeffrey, P.; Shi, Y.

    2007-01-01

    Bcl-2 family proteins are key regulators of apoptosis and have recently been shown to modulate autophagy. The tumor suppressor Beclin 1 has been proposed to coordinate both apoptosis and autophagy through direct interaction with anti-apoptotic family members Bcl-2 and/or Bcl-X{sub L}. However, the molecular basis for this interaction remains enigmatic. Here we report that Beclin 1 contains a conserved BH3 domain, which is both necessary and sufficient for its interaction with Bcl-X{sub L}. We also report the crystal structure of a Beclin BH3 peptide in complex with Bcl-X{sub L} at 2.5{angstrom} resolution. Reminiscent of previously determined Bcl-X{sub L}-BH3 structures, the amphipathic BH3 helix of Beclin 1 bound to a conserved hydrophobic groove of Bcl-X{sub L}. These results define Beclin 1 as a novel BH3-only protein, implying that Beclin 1 may have a direct role in initiating apoptotic signaling. We propose that this putative apoptotic function may be linked to the ability of Beclin 1 to suppress tumor formation in mammals.

  16. Crystal structure and substrate specificity of D-galactose-6-phosphate isomerase complexed with substrates.

    Science.gov (United States)

    Jung, Woo-Suk; Singh, Raushan Kumar; Lee, Jung-Kul; Pan, Cheol-Ho

    2013-01-01

    D-Galactose-6-phosphate isomerase from Lactobacillus rhamnosus (LacAB; EC 5.3.1.26), which is encoded by the tagatose-6-phosphate pathway gene cluster (lacABCD), catalyzes the isomerization of D-galactose-6-phosphate to D-tagatose-6-phosphate during lactose catabolism and is used to produce rare sugars as low-calorie natural sweeteners. The crystal structures of LacAB and its complex with D-tagatose-6-phosphate revealed that LacAB is a homotetramer of LacA and LacB subunits, with a structure similar to that of ribose-5-phosphate isomerase (Rpi). Structurally, LacAB belongs to the RpiB/LacAB superfamily, having a Rossmann-like αβα sandwich fold as has been identified in pentose phosphate isomerase and hexose phosphate isomerase. In contrast to other family members, the LacB subunit also has a unique α7 helix in its C-terminus. One active site is distinctly located at the interface between LacA and LacB, whereas two active sites are present in RpiB. In the structure of the product complex, the phosphate group of D-tagatose-6-phosphate is bound to three arginine residues, including Arg-39, producing a different substrate orientation than that in RpiB, where the substrate binds at Asp-43. Due to the proximity of the Arg-134 residue and backbone Cα of the α6 helix in LacA to the last Asp-172 residue of LacB with a hydrogen bond, a six-carbon sugar-phosphate can bind in the larger pocket of LacAB, compared with RpiB. His-96 in the active site is important for ring opening and substrate orientation, and Cys-65 is essential for the isomerization activity of the enzyme. Two rare sugar substrates, D-psicose and D-ribulose, show optimal binding in the LacAB-substrate complex. These findings were supported by the results of LacA activity assays.

  17. Crystal structure and substrate specificity of D-galactose-6-phosphate isomerase complexed with substrates.

    Directory of Open Access Journals (Sweden)

    Woo-Suk Jung

    Full Text Available D-Galactose-6-phosphate isomerase from Lactobacillus rhamnosus (LacAB; EC 5.3.1.26, which is encoded by the tagatose-6-phosphate pathway gene cluster (lacABCD, catalyzes the isomerization of D-galactose-6-phosphate to D-tagatose-6-phosphate during lactose catabolism and is used to produce rare sugars as low-calorie natural sweeteners. The crystal structures of LacAB and its complex with D-tagatose-6-phosphate revealed that LacAB is a homotetramer of LacA and LacB subunits, with a structure similar to that of ribose-5-phosphate isomerase (Rpi. Structurally, LacAB belongs to the RpiB/LacAB superfamily, having a Rossmann-like αβα sandwich fold as has been identified in pentose phosphate isomerase and hexose phosphate isomerase. In contrast to other family members, the LacB subunit also has a unique α7 helix in its C-terminus. One active site is distinctly located at the interface between LacA and LacB, whereas two active sites are present in RpiB. In the structure of the product complex, the phosphate group of D-tagatose-6-phosphate is bound to three arginine residues, including Arg-39, producing a different substrate orientation than that in RpiB, where the substrate binds at Asp-43. Due to the proximity of the Arg-134 residue and backbone Cα of the α6 helix in LacA to the last Asp-172 residue of LacB with a hydrogen bond, a six-carbon sugar-phosphate can bind in the larger pocket of LacAB, compared with RpiB. His-96 in the active site is important for ring opening and substrate orientation, and Cys-65 is essential for the isomerization activity of the enzyme. Two rare sugar substrates, D-psicose and D-ribulose, show optimal binding in the LacAB-substrate complex. These findings were supported by the results of LacA activity assays.

  18. Crystal structure, Hirshfeld surfaces and DNA cleavage investigation of two copper(II) complexes containing polypyridine and salicylide ligands.

    Science.gov (United States)

    Luo, Yang-Hui; Sun, Bai-Wang

    2014-05-21

    Two copper complexes 1 [Cu2(phen)2(salicylaldehyde)2(ClO4)2] and 2 [Cu2 (2,2'-dipyridyl)2(salicylaldehyde)2(ClO4)2] have been synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. These two complexes were display binuclear structure with Cu(II) ions in distorted octahedral environment but antipodal orientation of the binuclear units between them. Molecular Hirshfeld surfaces revealed that the crystal structures of 1 and 2 were supported mainly by H-H, C-H⋯π, π⋯π (C-C), and C-H⋯O intermolecular interactions. DNA cleavage experiments of complexes 1 and 2 revealed that these complexes can intercalation with DNA. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Synthesis, Characterization, and Crystal Structure of a Triazine Anion Pentafluoroosmium(VI Complex

    Directory of Open Access Journals (Sweden)

    Monther A. Khanfar

    2018-01-01

    Full Text Available The synthesis and characterization of a novel triazine anion pentafluoroosmium(VI complex are presented. The single crystal determination of the title compound (hereafter denoted 1 was carried out at −140 °C. Compound 1, C3F4N3OsF5, crystallizes in the monoclinic space group, P21/n, with unit cell dimensions: a = 8.6809(17 Å, b = 7.6848(15 Å, c = 12.415(3 Å, β = 102.633(4°, V = 808.2(3 Å3, and Z = 4. Synthesis, characterization, X-ray diffraction study along with the crystal supramolecular analysis of the title complex were carried out. The complex contains the anionic triazine unit C3N3F4− acting as a mono dentate ligand to osmium(VI with five fluoro ligands in a slightly distorted octahedral geometry around osmium(VI ion (osmium is denoted as Os. The C3N3F4−, triazine anion ring deviates from planarity, only with the C1 being tetrahedral. The crystal lattice of the title compound displays significant intermolecular X···X interactions, namly F···F, F···N and F···C. All types of X···X bonding consolidate to form a three-dimensional network.

  20. Synthesis and crystal structure of an iron(II) dimeric complex

    OpenAIRE

    Roy, Partha; Dhara, Koushik; Chakraborty, Jishnunil; Nethaji, Munirathinam; Banerjee, Pradyot

    2007-01-01

    An iron(II) complex, $[Fe_2(salen)_2]$ has been prepared by the reaction of $[Fe^{III}(salen)Cl]$ with copper(II) malonate dihydrate [salen = N,N'-ethylenebis(salicylideneiminato) dianion] in N,N-dimethylformamide-water mixture. The complex has been characterized by FT-IR spectroscopy, UV-vis spectra, thermogravimetric analysis, cyclic voltammetry and X-ray crystallography. The iron(II) complex 1 crystallizes in the monoclinic, space group C2/c, a = 26.664(5) \\AA, b = 6.9943(11) \\AA, c = 14.7...

  1. Syntheses, crystal structures and characterization of divalent transition metal sulfonate complexes with o-phenanthroline

    Science.gov (United States)

    Yang, Jin; Ma, Jian-Fang; Wu, Dong-Mei; Guo, Li-Ping; Liu, Jing-Fu

    2003-09-01

    Three new complexes, namely [Cu(phen)(L)(H 2O) 2]L·H 2O 1, [M(phen) 2(H 2O) 2]2L·6H 2O [M=Co( 2), Ni( 3)], where, HL=4-methylbenzenesulfonic acid and phen= o-phenanthroline, have been synthesized. The crystal structures were determined by X-ray diffraction method and refined by full-matrix least-squares methods to R=0.0535 and wR=0.1492 using 3567 reflections with I>2 σ( I) for 1; R=0.0388 and wR=0.1223 using 3844 reflections with I>2 σ( I) for 2; and R=0.0401 and wR=0.1222 using 3425 reflections with I>2 σ( I) for 3. 1 Consists of cationic species [Cu(phen)(L)(H 2O) 2] +, in which Cu(II) ion is five-coordinated by two nitrogen atoms of o-phenanthroline, two water molecules and one sulfonate oxygen atom. The cations and the non-coordinating sulfonate anions are linked by hydrogen bonds to form infinite chains. Complexes 2 and 3 are isostructral compounds. Each of them consists of cationic species [M(phen) 2(H 2O) 2] 2+, in which metal ion is six-coordinated by four nitrogen atoms from two o-phenanthroline molecules and two water oxygen atoms. The sulfonate ions do not coordinate to metal ion. The cations, non-coordinating sulfonate ions and lattice water molecules are linked by hydrogen bonds to form infinite zigzag chains. CV, FT-IR, UV-Vis and TGA were also used to characterize these compounds.

  2. Tubular duplex alpha-cyclodextrin triply bridged with disulfide bonds: synthesis, crystal structure and inclusion complexes

    Czech Academy of Sciences Publication Activity Database

    Krejčí, Lucie; Buděšínský, Miloš; Císařová, I.; Kraus, Tomáš

    -, č. 24 (2009), s. 3557-3559 ISSN 1359-7345 R&D Projects: GA AV ČR IAA400550810; GA ČR GA203/06/1550; GA MŠk OC 172 Institutional research plan: CEZ:AV0Z40550506 Keywords : cyclodextrin es * synthesis * crystal structure Subject RIV: CC - Organic Chemistry Impact factor: 5.504, year: 2009

  3. Crystal and Molecular Structure of Bis(2,2-diphenyl-N-(di-n-propylcarbamothioyl acetamidocopper(II Complex

    Directory of Open Access Journals (Sweden)

    Hakan Arslan

    2011-01-01

    Full Text Available Bis(2,2-diphenyl-N-(di-n-propylcarbamothioyl acetamidocopper(II complex has been synthesized and characterized by elemental analysis and FT-IR spectroscopy. The crystal and molecular structure of the title compound has been determined from single crystal X-ray diffraction data. It crystallizes in the triclinic space group P-1, with a = 13.046(2 Å, b = 13.135(2 Å, c = 13.179(2 Å, α= 67.083(4°, β= 67.968(4°, γ = 84.756(4° and Dcalc =1.330 g/cm3 for Z = 2. The crystal structure confirms that the complex is a mononuclear copper(II complex and the 2,2-diphenyl-N-(di-n-propyl-carbamothioylacetamide ligand is a bidentate chelating ligand, coordinating to the copper atom through the thiocarbonyl and carbonyl groups. This coordination has a slightly distorted square-planar geometry (O1-Cu1-O2: 86.48(11°, O1-Cu1-S1: 93.85(9°, O2-Cu1-S2: 94.20(9° and S1-Cu1-S2: 91.21(4°. The title molecule shows a cis-arrangement and C–O, C–S and C–N bond lengths of the complex suggest considerable electronic delocalization in the chelate rings.

  4. Synthesis, structural characterization and crystal structure of some dimethyltin complexes containing substituted 1,10-phenanthroline

    Science.gov (United States)

    Momeni, Badri Z.; Haghshenas, Fahimeh; Hadi, Saba

    2017-08-01

    The reaction of dimethyltin dichloride with four substituted 1, 10- phenanthroline has been studied. The reactions of dimethyltin dichloride with 5-methyl-1,10-phenanthroline (Mephen); 5,6-dimethyl-1,10-phenanthroline (Me2phen); 5-nitro-1,10-phenanthroline (NO2phen); 5-chloro-1,10-phenanthroline (Clphen) resulted in the formation of the hexa-coordinated complexes of [SnMe2Cl2(NN)] {Mephen (1), Me2phen (2), NO2phen (3), Clphen (4)}. The resulting products have been fully characterized by elemental analysis, multinuclear (1H, 13C, 119Sn) NMR, DEPT-135, HHCOSY and HSQC NMR spectroscopy. The solid state X-ray determination of complexes [SnMe2Cl2(Mephen)] (1) and [SnMe2Cl2(Me2phen)] (2) revealed that the complexes 1 and 2 contain the hexa-coordinated tin(IV) atom in an octahedral geometry with the trans-[SnMe2] configuration. The Snsbnd N bond distances in 1-2 are 2.47-2.48 Å which are almost among the largest values.

  5. Liquid crystal infiltration of complex dielectrics

    Energy Technology Data Exchange (ETDEWEB)

    Gottardo, Stefano; Wiersma, Diederik S.; Vos, W.L

    2003-10-01

    Liquid crystal infiltration is becoming an important tool to control the optical properties of complex dielectric systems like photonic crystals and disordered dielectrics. We discuss the technical aspects of liquid crystal infiltration in meso-porous structures, give some details of the sample preparation process, and discuss possibilities for tuning the optical properties of both ordered and disordered systems.

  6. A stable aquo-complex of lithiated di-tert-butylfluorosilanol. Synthesis and crystal structure

    OpenAIRE

    Schütte, Steffen; Pieper, Ursula; Klingebiel, Uwe; Stalke, Dietmar

    1993-01-01

    It was possible by crystallizing the lithiated derivative of di-tert-butylfluorosilanol to isolate a stable aquo-complex of this tetrameric compound as the first hydrolysis product. An X-ray diffraction study has revealed the existence of ([R2Si(F)OLi]3·[R2Si(OH)OLi] ·THF·H2O (R = CMe3; THF = tetrahydrofuran). The mechanism of hydrolysis from [R2Si(F)OLi]4 to this aquo-complex is discussed. peerReviewed

  7. Syntheses, Crystal Structures and Thermal Behaviors of Two Supramolecular Salamo-Type Cobalt(II and Zinc(II Complexes

    Directory of Open Access Journals (Sweden)

    Gang Li

    2017-07-01

    Full Text Available This paper reports the syntheses of two new complexes, [Co(L1(H2O2] (1 and [{Zn(L2(μ-OAcZn(n-PrOH}2] (2, from asymmetric halogen-substituted Salamo-type ligands H2L1 and H3L2, respectively. Investigation of the crystal structure of complex 1 reveals that the complex includes one Co(II ion, one (L12− unit and two coordinated water molecules. Complex 1 shows slightly distorted octahedral coordination geometry, forming an infinite 2D supramolecular structure by intermolecular hydrogen bond and π–π stacking interactions. Complex 2 contains four Zn(IIions, two completely deprotonated (L23− moieties, two coordinated μ-OAc− ions and n-propanol molecules. The Zn(II ions in complex 2 display slightly distorted trigonal bipyramidal or square pyramidal geometries.

  8. cis-Dioxomolybdenum(VI) complexes of a new ONN chelating thiosemicarbazidato ligand; Synthesis, characterization, crystal, molecular structures and antioxidant activities

    Science.gov (United States)

    İlhan Ceylan, Berat; Deniz, Nahide Gulsah; Kahraman, Sibel; Ulkuseven, Bahri

    2015-04-01

    5-Chloro-4-methyl-2-hydroxybenzophenone S-propyl-4-phenyl-thiosemicarbazone (H2L) and its cis-dioxomolybdenum(VI) complexes, in the general formula [MoO2(L)R-OH)] (R: methyl, 1; ethyl, 2; n-propyl, 3; n-butyl, 4; n-pentyl, 5), were synthesized and characterized by micro analysis, electronic, infrared and 1H and 13C NMR spectra. The crystal structures of complexes, 1 and 3, have been solved by direct methods (SIR92) and refined to the residual indexes R1 = 0.098 and R1 = 0.052 respectively. Complexes 1 and 3 are crystallized in the triclinic space group P-1 with Z = 2. The crystal study of complex 1 showed the first example of intermolecular hydrogen bond for this type of molybdenum-thiosemicarbazone complexes. The hydrogen bond is between the hydroxyl proton of attached alcohol and an oxo oxygen (in MoO22+ unit) of another complex molecule, and its bond distance (1.767(1) Å) is shorter than from the σ-coordination bonds in complex 1. Antioxidant activities of the compounds were determined by using 1,1-diphenyl-2-picrylhydrazyl (DPPH) method. Ligand showed 23.61% DPPH radical scavenging activity at 250 mg/L concentration. Cupric Reducing Antioxidant Capacity (CUPRAC) was also evaluated and trolox-equivalent antioxidant capacity (TEAC) values were found for ligand, 1 and 3 as 0.51, 0.33 and 0.30 respectively.

  9. Synthesis, Crystal Structure, and Characterization of Ternary Copper(II Complex Derived from N-(salicylidene-L-valine

    Directory of Open Access Journals (Sweden)

    Sundaramurthy Santha Lakshmi

    2016-01-01

    Full Text Available Ternary Schiff base copper(II complex [CuL(tmpda] (where H2L is N-(salicylidene-L-valine; tmpda is N,N,N′,N′-tetramethyl-1,3-propanediamine has been characterized by UV-Vis., FTIR, and single crystal XRD. The crystal structure displays a distorted square pyramidal geometry in which Schiff base is bonded to the Cu(II ion via phenolate oxygen, imine nitrogen, and an oxygen atom of the carboxylate group through the basal plane and the chelating diamine, N,N,N′,N′-tetramethyl-1,3-propanediamine, displays an axial and equatorial mode of binding via NN-donor atoms.

  10. ST1710?DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators

    OpenAIRE

    Kumarevel, Thirumananseri; Tanaka, Tomoyuki; Umehara, Takashi; Yokoyama, Shigeyuki

    2009-01-01

    ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global health problem. Here, we present the crystal structure of ST1710 from Sulfolobus tokodaii strain 7 complexed with salicylate, a well-known inhibitor of MarR proteins and the ST1710 complex with its promoter DNA, refined to 1.8 and 2.10 ? resolutions, respectively. The ST1710?DNA complex shares the...

  11. Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target

    Energy Technology Data Exchange (ETDEWEB)

    Mulepati, Sabin [Johns Hopkins Univ., Baltimore, MD (United States); Heroux, Annie; Bailey, Scott [Johns Hopkins Univ., Baltimore, MD (United States)

    2014-09-19

    In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.

  12. Ethambutol analysis by copper complexation in pharmaceutical formulations: spectrophotometry and crystal structure

    OpenAIRE

    Faria,Adriana F.; Marcellos,Luiza F; Vasconcelos,Juliana P; Marcus V. N. de Souza; S. Júnior,Antônio L; Carmo,Weberton R. do; Diniz, Renata; Oliveira,Marcone A. L. de

    2011-01-01

    An alternative method for ethambutol (ETB) determination by UV spectrophotometry in pharmaceutical formulations using ETB complexation with Cu(II) was optimized employing a 3² full experimental design having Cu(II) and aqueous acetic acid/sodium acetate buffer at pH 4.6 as variables. The predominant complex stoichiometry in aqueous buffer solution at this pH and formation constant were obtained by using Job's method and Scatchard diagram, respectively. The complex crystalline structure of mon...

  13. Synthesis, characterization and crystal structure of a 2-(diethylaminomethylindole ligated dimethylaluminium complex

    Directory of Open Access Journals (Sweden)

    Logan E. Shephard

    2015-10-01

    Full Text Available The title compound, [Al(CH32(C13H17N2] (systematic name; {2-[(diethylaminomethyl]indol-1-yl-κ2N,N′}dimethylaluminium, was prepared by methane elimination from the reaction of 2-(diethylaminomethylindole and trimethylaluminium. The complex crystallizes readily from a concentrated toluene solution in high yield. The asymmetric unit contains two crystallographically independent molecules. Each molecule has a four-coordinate aluminium atom that has pseudo-tetrahedral geometry. C—H...π interactions link the independent molecules into chains extending along the b-axis direction.

  14. Mononuclear mercury(II) complexes containing bipyridine derivatives and thiocyanate ligands: Synthesis, characterization, crystal structure determination, and luminescent properties

    Science.gov (United States)

    Amani, Vahid; Alizadeh, Robabeh; Alavije, Hanieh Soleimani; Heydari, Samira Fadaei; Abafat, Marzieh

    2017-08-01

    A series of mercury(II) complexes, [Hg(Nsbnd N)(SCN)2] (Nsbnd N is 4,4‧-dimethyl-2,2‧-bipyridine in 1, 5,5‧-dimethyl-2,2‧-bipyridine in 2, 6,6‧-dimethyl-2,2‧-bipyridine in 3 and 6-methyl-2,2‧-bipyridine in 4), were prepared from the reactions of Hg(SCN)2 with mentioned ligands in methanol. Suitable crystals of these complexes were obtained for X-ray diffraction measurement by methanol diffusion into a DMSO solution. The four complexes were thoroughly characterized by spectral methods (IR, UV-Vis, 13C{1H}NMR, 1H NMR and luminescence), elemental analysis (CHNS) and single crystal X-ray diffraction. The X-ray structural analysis indicated that in the structures of these complexes, the mercury(II) cation is four-coordinated in a distorted tetrahedral configuration by two S atoms from two thiocyanate anions and two N atoms from one chelating 2,2‧-bipyridine derivative ligand. Also, in these complexes intermolecular interactions, for example Csbnd H⋯N hydrogen bonds (in 1-4), Csbnd H⋯S hydrogen bonds (in 1, 2 and 4), π … π interactions (in 2-4), Hg⋯N interactions (in 2) and S⋯S interactions (in 4), are effective in the stabilization of the crystal structures and the formation of the 3D supramolecular complexes. Furthermore, the luminescence spectra of the title complexes show that the intensity of their emission bands are stronger than the emission bands for the free bipyridine derivative ligands.

  15. Synthesis, spectral and luminescence study, crystal structure determination and DFT calculation of binuclear palladium(II) complexes

    Science.gov (United States)

    Seyfi, S.; Alizadeh, R.; Darvish Ganji, M.; Amani, V.

    2018-02-01

    Binuclear palladium(II) complexes with metal-metal (d8-d8) bonding interaction were synthesized by reactions of the 1-methyl-1H-1,2,3,4-tetrazole-5-thiol (Hmtzt) or a mixture of Hmtzt and 1,3-propanediamine (1,3-pda) ligands. Complex [Pd2(μ-mtzt)4]·2CH3CN (1) was synthesized by the reaction of Pd(OAc)2 with Hmtzt dissolved in acetonitrile and complex [Pd2(μ-mtzt)2(mtzt)2(1,3-pda)] (2) was synthesized by reaction of a mixture of Hmtzt and 1,3-propanediamine (dissolved in methanol) with PdCl2 (dissolved in acetonitrile) and were identified through elemental analysis, IR, UV-Vis, 1H NMR, luminescence spectroscopy as well as single-crystal X-ray diffraction method. A single-crystal of complex 1 shows that two Pd(II) centers are linked together by four bridging tetrazole ligands providing a paddle wheel-like arrangement. Also a crystal structure of complex 2 shows that this complex possesses a symmetric structure in which one Pd atom is tetra-coordinated by four sulfur atoms to forms PdS4 and other Pd atom is tetra-coordinated by four nitrogen to forms PdN4 coordination sphere. Density functional theory (DFT) was performed in this study for the Hmtzt ligand and binuclear palladium(II) complexes (1) and (2). The DFT calculation shows PdII-PdII bond lengths of 2.831 and 3.086 Å in complex 1 and 2, respectively which are close to the observed bond lengths of 2.802(11) and 3.0911(17) Å from single-crystal X-ray structure. The optimized geometry of the complexes is shown good agreement by X-ray data. Structural properties and molecular descriptors including bond lengths, bond angles, chemical hardness, dipole moment, HOMO-LUMO energy levels, electron transfer were analyzed. The IR spectroscopy was performed using VEDA4 software and UV-Vis spectra were analyzed using time-dependent density functional theory (TD-DFT) method. The theoretical and experimental data were also compared with each other.

  16. Crystal growth of semiorganic complex- samarium chloride coordinated thiourea-L-tartaric acid and its studies on structure and optical characteristics

    Science.gov (United States)

    Slathia, Goldy; Singh, Harjinder; Ramya, E.; Rao, D. Narayana; Bamzai, K. K.

    2017-05-01

    The semi-organic complex of samarium chloride coordinated thiourea-L-tartaric acid (SCTLT) has been grown as a single crystal by slow evaporation technique at room temperature. For structural studies, the grown crystal was subjected to single crystal X-ray diffraction and Fourier transform infra-red (FTIR) spectroscopy. Low cut off wavelength and transparent characteristics were explored by UV-VIS optical characterization. Third-order nonlinear optical properties of grown crystal were investigated by Z-scan technique.

  17. Detailed Investigation of the Structural, Thermal, and Electronic Properties of Gold Isocyanide Complexes with Mechano-Triggered Single-Crystal-to-Single-Crystal Phase Transitions.

    Science.gov (United States)

    Seki, Tomohiro; Sakurada, Kenta; Muromoto, Mai; Seki, Shu; Ito, Hajime

    2016-02-01

    Mechano-induced phase transitions in organic crystalline materials, which can alter their properties, have received much attention. However, most mechano-responsive molecular crystals exhibit crystal-to-amorphous phase transitions, and the intermolecular interaction patterns in the daughter phase are difficult to characterize. We have investigated phenyl(phenylisocyanide)gold(I) (1) and phenyl(3,5-dimethylphenylisocyanide)gold(I) (2) complexes, which exhibit a mechano-triggered single-crystal-to-single-crystal phase transition. Previous reports of complexes 1 and 2 have focused on the relationships between the crystalline structures and photoluminescence properties; in this work we have focused on other aspects. The face index measurements of complexes 1 and 2 before and after the mechano-induced phase transitions have indicated that they undergo non-epitaxial phase transitions without a rigorous orientational relationship between the mother and daughter phases. Differential scanning calorimetry analyses revealed the phase transition of complex 1 to be enthalpically driven by the formation of new aurophilic interactions. In contrast, the phase transition of complex 2 was found to be entropically driven, with the closure of an empty void in the mother phase. Scanning electron microscopy observation showed that the degree of the charging effect of both complexes 1 and 2 was changed by the phase transitions, which suggests that the formation of the aurophilic interactions affords more effective conductive pathways. Moreover, flash-photolysis time-resolved microwave conductivity measurements revealed that complex 1 increased in conductivity after the phase change, whereas the conductivity of complex 2 decreased. These contrasting results were explained by the different patterns in the aurophilic interactions. Finally, an intriguing disappearing polymorphism of complex 2 has been reported, in which a polymorph form could not be obtained again after some period of time

  18. Complexes of uranyl nitrate with 2,6-pyridinedicarboxamides: synthesis, crystal structure, and DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Alyapyshev, Mikhail; Babain, Vasiliy [ITMO University, 49, Kronverksky pr., 197101, St. Petersburg (Russian Federation); ThreeArc Mining Ltd., 5, Stary Tolmachevskiy per., 115184, Moscow (Russian Federation); Tkachenko, Lyudmila; Lumpov, Alexander [Khlopin Radium Institute, 28, 2nd Murinskiy pr., 194021, St. Petersburg (Russian Federation); Gurzhiy, Vladislav; Zolotarev, Andrey; Dar' in, Dmitriy [St. Petersburg State University, 7-9, Universitetskaya nab., 199034, St. Petersburg (Russian Federation); Ustynyuk, Yuriy; Gloriozov, Igor [M.V. Lomonosov Moscow State University, 119991, Moscow (Russian Federation); Paulenova, Alena [Department of Nuclear Engineering, Oregon State University, Corvallis, OR (United States)

    2017-05-04

    Two complexes of uranyl nitrate with N,N,N',N'-tetrabutyl-2,6-pyridinedicarboxamide (TBuDPA) and N,N'-diethyl-N,N'-diphenyl-2,6-pyridinedicarboxamide (EtPhDPA) were synthesized and studied. The complex of tetraalkyl-2,6-pyridinedicarboxamide with metal nitrate was synthesized for the first time. XRD analysis revealed the different type of complexation: a 1:1 metal:ligand complex for EtPhDPA and complex with polymeric structure for TBuDPA. The quantum chemical calculations (DFT) confirm that both ligands form the most stable complexes that match the minimal values pre-organization energy of the ligands. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. Synthesis, characterization, and crystal structures of diruthenium complexes containing bridging salicylato ligands

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Mingxuan; Yau, Chun Huan; Hu, Yuxin; Tan, Yong Leng Kelvin [Hwa Chong Institution (Singapore); Li, Yingzhou; Ganguly, Rakesh; Leong, Weng Kee [Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University (Singapore)

    2017-08-03

    The thermal reaction of Ru{sub 3}(CO){sub 12} (1) with salicylic acid, in the presence of triphenylphosphine, pyridine, or dimethylsulfoxide, afforded the dinuclear complexes Ru{sub 2}(CO){sub 4}(μ-O{sub 2}CC{sub 6}H{sub 4}OH){sub 2}L{sub 2} (2) [L = PPh{sub 3} (2a). C{sub 5}H{sub 5}N (2b); (CH{sub 3}){sub 2}SO (2c)]. Complex 2b was further reacted with the aromatic dimmines 2,2'-dipyridine or 1,10-phenanthroline to give the cationic diruthenium complexes [Ru{sub 2}(CO){sub 2}(μ-CO){sub 2}(μ-O{sub 2}CC{sub 6}H{sub 4}OH)(N intersection N){sub 2}]{sup +} (3) [(N intersection N) = 2,2'-dipyridine (3a); 1,10-phenanthroline (3b)], which were isolated as their tetraphenylborate salts. All five novel complexes were characterized spectroscopically and analytically. For 2a-2b and 3a-3b, single-crystal X-ray diffraction studies were also carried out. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  20. SYNTHESIS, CHARACTERIZATION AND CRYSTAL STRUCTURE ...

    African Journals Online (AJOL)

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    The Mo atom in the complex is in octahedral coordination. Thermal stability of the complex has also been studied. KEY WORDS: Molybdenum complex, Hydrazone ligand, Crystal structure, X-ray diffraction, Thermal property. INTRODUCTION. Coordination chemistry of molybdenum(VI) has attracted considerable attention ...

  1. Screw dislocations in complex, low symmetry oxides: core structures, energetics, and impact on crystal growth.

    Science.gov (United States)

    Shahsavari, Rouzbeh; Chen, Lu

    2015-02-04

    Determining the atomic structure and the influence of defects on properties of low symmetry oxides have long been an engineering pursuit. Here, we focus on five thermodynamically reversible monoclinic and orthorhombic polymorphs of dicalcium silicates (Ca2SiO3)-a key cement constituent-as a model system and use atomistic simulations to unravel the interplay between the screw dislocation core energies, nonplanar core structures, and Peierls stresses along different crystallographic planes. Among different polymorphs, we found that the α polymorphs (α-C2S) has the largest Peierls stress, corresponding to the most brittle polymorph, which make it attractive for grinding processes. Interestingly, our analyses indicate that this polymorphs has the lowest dislocation core energy, making it ideal for reactivity and crystal growth. Generally, we identified the following order in terms of grinding efficiency based on screw dislocation analysis, α-C2S > αH-C2S > αL-C2S > β-C2S > γ-C2S, and the following order in term of reactivity, α -C2S > αL-C2S > γ-C2S > αH-C2S > β-C2S. This information, combined with other deformation-based mechanisms, such as twinning and edge dislocation, can provide crucial insights and guiding hypotheses for experimentalists to tune the cement grinding mechanisms and reactivity processes for an overall optimum solution with regard to both energy consumption and performance. Our findings significantly broaden the spectrum of strategies for leveraging both crystallographic directions and crystal symmetry to concurrently modulate mechanics and crystal growth processes within an identical chemical composition.

  2. Crystal structures of human group-VIIA phospholipase A2 inhibited by organophosphorus nerve agents exhibit non-aged complexes

    Energy Technology Data Exchange (ETDEWEB)

    Samanta, Uttamkumar; Kirby, Stephen D.; Srinivasan, Prabhavathi; Cerasoli, Douglas M.; Bahnson, Brian J.; (Delaware); (USAMRIID)

    2009-09-02

    The enzyme group-VIIA phospholipase A2 (gVIIA-PLA2) is bound to lipoproteins in human blood and hydrolyzes the ester bond at the sn-2 position of phospholipid substrates with a short sn-2 chain. The enzyme belongs to a serine hydrolase superfamily of enzymes, which react with organophosphorus (OP) nerve agents. OPs ultimately exert their toxicity by inhibiting human acetycholinesterase at nerve synapses, but may additionally have detrimental effects through inhibition of other serine hydrolases. We have solved the crystal structures of gVIIA-PLA2 following inhibition with the OPs diisopropylfluorophosphate, sarin, soman and tabun. The sarin and soman complexes displayed a racemic mix of P{sub R} and P{sub S} stereoisomers at the P-chiral center. The tabun complex displayed only the P{sub R} stereoisomer in the crystal. In all cases, the crystal structures contained intact OP adducts that had not aged. Aging refers to a secondary process OP complexes can go through, which dealkylates the nerve agent adduct and results in a form that is highly resistant to either spontaneous or oxime-mediated reactivation. Non-aged OP complexes of the enzyme were corroborated by trypsin digest and matrix-assisted laser desorption ionization mass spectrometry of OP-enzyme complexes. The lack of stereoselectivity of sarin reaction was confirmed by gas chromatography/mass spectrometry using a chiral column to separate and quantitate the unbound stereoisomers of sarin following incubation with enzyme. The structural details and characterization of nascent reactivity of several toxic nerve agents is discussed with a long-term goal of developing gVIIA-PLA2 as a catalytic bioscavenger of OP nerve agents.

  3. The crystal structure of BamB suggests interactions with BamA and its role within the BAM complex.

    Science.gov (United States)

    Noinaj, Nicholas; Fairman, James W; Buchanan, Susan K

    2011-03-25

    Escherichia coli BamB is the largest of four lipoproteins in the β-barrel assembly machinery (BAM) complex. It interacts with the periplasmic domain of BamA, an integral outer membrane protein (OMP) essential for OMP biogenesis. Although BamB is not essential, it serves an important function in the BAM complex, significantly increasing the folding efficiency of some OMPs in vivo and in vitro. To learn more about the BAM complex, we solved structures of BamB in three different crystal forms. BamB crystallized in space groups P2(1)3, I222, and P2(1)2(1)2(1), with one molecule per asymmetric unit in each case. Crystals from the space group I222 diffracted to 1. 65-Å resolution. BamB forms an eight-bladed β-propeller with a central pore and is shaped like a doughnut. A DALI search revealed that BamB shares structural homology to several eukaryotic proteins containing WD40 repeat domains, which commonly have β-propeller folds and often serve as scaffolding proteins within larger multi-protein complexes that carry out signal transduction, cell division, and chemotaxis. Using mutagenesis data from previous studies, we docked BamB onto a BamA structural model and assessed known and possible interactions between these two proteins. Our data suggest that BamB serves as a scaffolding protein within the BAM complex by optimally orienting the flexible periplasmic domain of BamA for interaction with other BAM components and chaperones. This may facilitate integration of newly synthesized OMPs into the outer membrane. Published by Elsevier Ltd.

  4. Synthesis, crystal structure and thermodynamic properties of a new praseodymium Schiff-base complex

    Energy Technology Data Exchange (ETDEWEB)

    Li, Chuan-Hua, E-mail: lichuanhua0526@126.com [School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan (China); Hunan Provincial Key Laboratory of Xiangnan Rare-Precious Metals Compounds and Applications, Department of Chemistry and Life Science, Xiangnan University, Chenzhou 423000, Hunan (China); Song, Xiang-Zhi, E-mail: xzsong@csu.edu.cn [School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan (China); Jiang, Jian-Hong [Hunan Provincial Key Laboratory of Xiangnan Rare-Precious Metals Compounds and Applications, Department of Chemistry and Life Science, Xiangnan University, Chenzhou 423000, Hunan (China); Gu, Hui-Wen [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan (China); Tao, Li-Ming; Yang, Ping; Li, Xu; Xiao, Sheng-Xiong; Yao, Fei-Hong; Liu, Wen-Qi; Xie, Jin-Qi; Peng, Meng-Na; Pan, Lan; Wu, Xi-Bin; Jiang, Chao; Wang, Song; Xu, Man-Fen [Hunan Provincial Key Laboratory of Xiangnan Rare-Precious Metals Compounds and Applications, Department of Chemistry and Life Science, Xiangnan University, Chenzhou 423000, Hunan (China); Li, Qiang-Guo, E-mail: liqiangguo@163.com [Hunan Provincial Key Laboratory of Xiangnan Rare-Precious Metals Compounds and Applications, Department of Chemistry and Life Science, Xiangnan University, Chenzhou 423000, Hunan (China)

    2014-04-01

    Highlights: • A new mononuclear Schiff base praseodymium complex was synthesized. • Based on Hess's law, thermochemical cycles of two reactions were designed. • The dissolution enthalpies were measured by a solution–reaction calorimeter. • The standard molar enthalpy of formation of the complex was calculated. - Abstract: The title complex [Pr(H{sub 2}vanen)(NO{sub 3}){sub 2}(H{sub 2}O){sub 2}·NO{sub 3}] was synthesized reacting of Valen Schiff-base ligand [H{sub 2}vanen = N,N′-ethylene-bis(3-methoxysalicylideneimine)] and Pr(NO{sub 3}){sub 3}·6H{sub 2}O in ethanol at 60 °C. The complex was crystallized in the monoclinic crystal system with space group P21/c. The coordination polyhedron of Pr(III) ion was consisted of two bidentate nitrate ions, two molecules of water and one ligand which coordinated through oxygen atoms of the two phenolic and methoxy groups. After designing two reasonable thermochemical cycles according to Hess's law, the calorimetric experiments were conducted using isoperibol solution–reaction calorimeter at a constant temperature of 298.15 K. The standard molar enthalpy changes of two reactions were determined to be Δ{sub r}H{sub m}{sup θ}(1a)=−(51.94±1.26) kJ mol{sup −1} and Δ{sub r}H{sub m}{sup θ}(1b)=−(8.62±1.34) kJ mol{sup −1}. Then the standard molar enthalpies of formation of the ligand and the title complex were calculated to be Δ{sub f}H{sub m}{sup θ} [H{sub 2}vanen(s), 298.15 K] = −(517.75 ± 2.36) kJ mol{sup −1} and Δ{sub f}H{sub m}{sup θ} [Pr(H{sub 2}vanen)(NO{sub 3}){sub 2}(H{sub 2}O){sub 2}·NO{sub 3} (s), 298.15 K] = −(2454.8 ± 2.7) kJ mol{sup −1}, respectively. The rationality of two thermochemical cycles was verified by UV spectra and refractive indexes.

  5. Lanthanide complexes with 2,3-dimethoxybenzoic acid and terpyridine. Crystal structures, thermal properties, and antibacterial activities

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Pan-Pan; Wu, Xiao-Hui; Zhang, Jian-Jun [Testing and Analysis Center, Hebei Normal University, Shijiazhuang (China); College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang (China); Ren, Ning [College of Chemical Engineering and Material, Handane College (China); Wang, Shu-Ping [College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang (China)

    2017-08-03

    The lanthanide coordination complexes Er(2,3-DMOBA){sub 3}(terpy)(H{sub 2}O) (1) and [Nd(2,3-DMOBA){sub 3}(terpy)(H{sub 2}O)]{sub 2} (2) (2,3-DMOBA = 2,3-dimethoxybenzoate; terpy = 2,2':6',2{sup ''}-terpyridine) were synthesized and characterized by IR spectroscopy, powder X-ray diffraction (XRD), single-crystal X-ray diffraction, and thermogravimetric analysis. Complex 1 crystallizes in the triclinic system, space group P1, and the mononuclear subunits form a 1D chain structure along the a axis by hydrogen bonds. Complex 2 crystallizes in the monoclinic system, space group P2{sub 1}/c, and the dinuclear subunits are further linked via the offset face-to-face π..π weak stacking interactions to form a supramolecular 2D layered structure. Thermal analysis showed that the complexes have three decomposition steps. The first step is the loss of coordination water molecules. The neutral terpy ligands and partial 2,3-DMOBA ligands are lost in the second step. The remaining 2,3-DMOBA ligands are lost in the third step. The 3D stacked plots for the FT-IR spectra of the evolved gases are recorded and the gaseous products are identified by the typical IR spectra obtained at different temperatures from the 3D stacked plots. Meanwhile, the results of the antibacterial action tests show that 1 and 2 have better antibacterial activities to Candida albicans than to Escherichia coli or Staphylococcus aureus. In addition, complex 2 has better antibacterial action to Candida albicans than complex 1. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. The first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D-NaI complex

    Energy Technology Data Exchange (ETDEWEB)

    Olczak, A.; Glówka, M.L.; Szczesio, M.; Bojarska, J.; Wawrzak, Z.; Duax, W.L. (Poland); (NWU); (HWMRI)

    2010-11-15

    The crystal structure of the nonstoichiometric complex of gramicidin D with NaI has been studied using synchrotron radiation at 100 K. The limiting resolution was 1.25 {angstrom} and the R factor was 16% for 19,883 observed reflections. The general architecture of the antiparallel two-stranded gramicidin dimers in the studied crystal was a right-handed antiparallel double-stranded form that closely resembles the structures of other right-handed species published to date. However, there were several surprising observations. In addition to the significantly different composition of linear gramicidins identified in the crystal structure, including the absence of the gramicidin C form, only two cationic sites were found in each of the two independent dimers (channels), which were partially occupied by sodium, compared with the seven sites found in the RbCl complex of gramicidin. The sum of the partial occupancies of Na{sup +} was only 1.26 per two dimers and was confirmed by the similar content of iodine ions (1.21 ions distributed over seven sites), which was easily visible from their anomalous signal. Another surprising observation was the significant asymmetry of the distributions and occupancies of cations in the gramicidin dimers, which was in contrast to those observed in the high-resolution structures of the complexes of heavier alkali metals with gramicidin D, especially that of rubidium.

  7. Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group.

    Science.gov (United States)

    Kondo, Jiro; François, Boris; Russell, Rupert J M; Murray, James B; Westhof, Eric

    2006-08-01

    Amikacin is the 4,6-linked aminoglycoside modified at position N1 of the 2-deoxystreptamine ring (ring II) by the L-haba group. In the present study, the crystal structure of a complex between oligonucleotide containing the bacterial ribosomal A site and amikacin has been solved at 2.7 A resolution. Amikacin specifically binds to the A site in practically the same way as its parent compound kanamycin. In addition, the L-haba group interacts with the upper side of the A site through two direct contacts, O2*...H-N4(C1496) and N4*-H...O6(G1497). The present crystal structure shows how the introduction of the L-haba group on ring II of aminoglycoside is an effective mutation for obtaining a higher affinity to the bacterial A site.

  8. Targeted crystal growth of rare Earth intermetallics with synergistic magnetic and electrical properties: structural complexity to simplicity.

    Science.gov (United States)

    Schmitt, Devin C; Drake, Brenton L; McCandless, Gregory T; Chan, Julia Y

    2015-03-17

    The single-crystal growth of extended solids is an active area of solid-state chemistry driven by the discovery of new physical phenomena. Although many solid-state compounds have been discovered over the last several decades, single-crystal growth of these materials in particular enables the determination of physical properties with respect to crystallographic orientation and the determination of properties without possible secondary inclusions. The synthesis and discovery of new classes of materials is necessary to drive the science forward, in particular materials properties such as superconductivity, magnetism, thermoelectrics, and magnetocalorics. Our research is focused on structural characterization and determination of physical properties of intermetallics, culminating in an understanding of the structure-property relationships of single-crystalline phases. We have prepared and studied compounds with layered motifs, three-dimensional magnetic compounds exhibiting anisotropic magnetic and transport behavior, and complex crystal structures leading to intrinsically low lattice thermal conductivity. In this Account, we present the structural characteristics and properties that are important for understanding the magnetic properties of rare earth transition metal intermetallics grown with group 13 and 14 metals. We present phases adopting the HoCoGa5 structure type and the homologous series. We also discuss the insertion of transition metals into the cuboctahedra of the AuCu3 structure type, leading to the synthetic strategy of selecting binaries to relate to ternary intermetallics adopting the Y4PdGa12 structure type. We provide examples of compounds adopting the ThMn12, NaZn13, SmZn11, CeCr2Al20, Ho6Mo4Al43, CeRu2Al10, and CeRu4Al16-x structure types grown with main-group-rich self-flux methods. We also discuss the phase stability of three related crystal structures containing atoms in similar chemical environments: ThMn12, CaCr2Al10, and YbFe2Al10. In

  9. Synthesis, crystal structures, luminescent and magnetic properties of homodinuclear lanthanide complexes with a flexible tripodal carboxylate ligand.

    Science.gov (United States)

    Zhang, Ai-Jiang; Wang, Ya-Wen; Dou, Wei; Dong, Ming; Zhang, Yan-Ling; Tang, Yu; Liu, Wei-Sheng; Peng, Yu

    2011-03-28

    Six new homodinuclear lanthanide(III) complexes with a flexible tripodal carboxylate ligand (H(3)L), of formulae [Ln(2)L(2)(DMF)(4)]·4DMF (Ln = La (1), Nd (2), Eu (3), Gd (4), Tb (5), Dy (6), DMF = N, N-Dimethylformamide) have been synthesized. Among them, 1, 2, 3, 4, 6 were characterized by single-crystal X-ray diffraction, which crystallized in the monoclinic space group P2(1)/n with a = 13.309(2) Å, b = 27.404(4) Å, c = 16.686(3) Å, β = 105.115(2) and V = 5875.2(17) Å(3) for 1, a = 13.3016(5) Å, b = 27.1952(12) Å, c = 16.6339(7) Å, β = 105.030(2) and V = 5811.3(4) Å(3) for 2, a = 13.2797(10) Å, b = 27.072(2) Å, c = 16.6564(13) Å, β = 104.9390(10) and V = 5785.7(8) Å(3) for 3, a = 13.2855(3) Å, b = 27.0074(6) Å, c = 16.6357(3) Å, β = 104.9790(10) and V = 5766.2(2) Å(3) for 4, a = 13.2837(5) Å, b = 26.9105(10) Å, c = 16.6066(6) Å, β = 104.917(2) and V = 5736.3(4) Å(3) for 6. The crystal structures reveal that these complexes are isostructural, and molecules are connected from 0D to 3D supramolecular structures by hydrogen bonds. All of them were characterized by elemental analysis, IR spectroscopy, XRD and TGA. Unusually, non-luminescent Tb(III) complex was obtained. The photophysical property of the Eu(III) complex and the magnetic property of Gd(III) complex are investigated and discussed in detail.

  10. Crystal structure of a TAPBPR–MHC I complex reveals the mechanism of peptide editing in antigen presentation

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Jiansheng; Natarajan, Kannan; Boyd, Lisa F.; Morozov, Giora I.; Mage, Michael G.; Margulies, David H. (NIH); (Hebrew)

    2017-10-12

    Central to CD8+ T cell–mediated immunity is the recognition of peptide–major histocompatibility complex class I (p–MHC I) proteins displayed by antigen-presenting cells. Chaperone-mediated loading of high-affinity peptides onto MHC I is a key step in the MHC I antigen presentation pathway. However, the structure of MHC I with a chaperone that facilitates peptide loading has not been determined. We report the crystal structure of MHC I in complex with the peptide editor TAPBPR (TAP-binding protein–related), a tapasin homolog. TAPBPR remodels the peptide-binding groove of MHC I, resulting in the release of low-affinity peptide. Changes include groove relaxation, modifications of key binding pockets, and domain adjustments. This structure captures a peptide-receptive state of MHC I and provides insights into the mechanism of peptide editing by TAPBPR and, by analogy, tapasin.

  11. Synthesis, Crystal Structure, Spectroscopic Properties and Potential Biological Activities of Salicylate‒Neocuproine Ternary Copper(II Complexes

    Directory of Open Access Journals (Sweden)

    Lenka Kucková

    2015-01-01

    Full Text Available Mixed ligand copper(II complexes containing derivatives of salicylic acid and heterocyclic ligands with nitrogen donor atoms have been the subject of various studies and reviews. In this paper, synthesis and characterization of the ternary copper(II complexes of neocuproine (2,9-dimethyl-1,10-phenanthroline, Neo and salicylate ligands (Sal are reported. In addition, the crystal structures of ([Cu(H2O(5-Cl-Sal(Neo] (1, [Cu(μ-Sal(Neo]2 (2, Cu2(μ-5-Cl-Sal(5-Cl-HSal2(Neo2]·EtOH (3 were determined. In order to compare structural and biological properties of the prepared complexes, spectroscopic and biological studies were performed. Results of X-ray diffraction show that prepared complexes form three types of crystal structures in a given system: monomeric, dimeric and dinuclear complex. The preliminary study on the DNA cleavage activity has shown that the complexes under study behave as the chemical nucleases in the presence of added hydrogen peroxide with slight differences in the activity (1 > 2 > 3. The complexes 1 and 2 exhibited nuclease activity itself indicating the interaction of complexes with the DNA. It has been proposed that the enhanced destructive effect of the complexes 1 and 2 on the DNA is a result of two possible mechanisms of action: (i the conversion of closed circular DNA (form I to the nicked DNA (form II caused by the copper complex itself and (ii damage of DNA by Reactive Oxygen Species (ROS—products of the interaction of copper with hydrogen peroxide by means of Fenton reaction (hydroxyl radicals. Thus the biological activity of the prepared Cu(II complexes containing derivatives of salicylic acid and phenanthroline molecules is substantiated by two independent mechanisms. While derivatives of salicylic acids in the coordination sphere of copper complexes are responsible for radical-scavenging activity (predominantly towards superoxide radical anion, the presence of chelating ligand 2,9-dimethyl-1,10-phenanthroline

  12. Crystal structure, physical, and photophysical properties of a ruthenium(II) bipyridine diazafluorenone complex

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Y.; Jackman, D.C.; Rillema, D.P. [Univ. of North Carolina, Charlotte, NC (United States)] [and others

    1995-09-01

    The complex [Ru(bpy){sub 2}(dafo)](PF{sub 6}){sub 2}, where bpy is 2,2{prime}-bipyridine and dafo is diazafluorenone crystallizes in the space group P2{sub 1}/n with a = 9.5059(3){angstrom}, b = 14.002(2){angstrom} and c = 25.783(8){angstrom}. The coordination geometry of the Ru atom is that of a distorted octahedron with a RuN{sub 6} core. The two Ru-N bond distances to the dafo ligand are 2.13(1) and 2.15(1) {angstrom}; the four Ru-N bond distances to the bipyridine ligands are 2.03(1), 2.05(1), 2.06(1), and 2.07(1) {angstrom}. The three shortest Ru-N distances are trans to the three longest Ru-N distances. The complex is oxidized and reduced reversibly at 1.41 and -0.65 V vs. SSCE, respectively. It displays absorptions at 438 nm (1.6 x 10{sup 4}), 285 nm (6.2 x 10{sup 4}), and 240 nm (4.1 x 10{sup 4}) and a broad emission centered at 626 nm in water at room temperature. The emission lifetime is 420 ns and the emission quantum yield is 5.3 x 10{sup -4}.

  13. Crystal structure of peroxiredoxin from Aeropyrum pernix K1 complexed with its substrate, hydrogen peroxide.

    Science.gov (United States)

    Nakamura, Tsutomu; Kado, Yuji; Yamaguchi, Takafumi; Matsumura, Hiroyoshi; Ishikawa, Kazuhiko; Inoue, Tsuyoshi

    2010-01-01

    Peroxiredoxin (Prx) reduces hydrogen peroxide and alkyl peroxides to water and corresponding alcohols, respectively. The reaction is dependent on a peroxidatic cysteine, whose sulphur atom nucleophilically attacks one of the oxygen atoms of the peroxide substrate. In spite of the many structural studies that have been carried out on this reaction, the tertiary structure of the hydrogen peroxide-bound form of Prx has not been elucidated. In this paper, we report the crystal structure of Prx from Aeropyrum pernix K1 in the peroxide-bound form. The conformation of the polypeptide chain is the same as that in the reduced apo-form. The hydrogen peroxide molecule is in close contact with the peroxidatic Cys50 and the neighbouring Thr47 and Arg126 side chain atoms, as well as with the main chain nitrogen atoms of Val49 and Cys50. Bound peroxide was also observed in the mutant C50S, in which the peroxidatic cysteine was replaced by serine. Therefore, the sulphur atom of the peroxidatic cysteine is not essential for peroxide binding, although it enhances the binding affinity. Hydrogen peroxide binds to the protein so that it fills the active site pocket. This study provides insight into the early stage of the Prx reaction.

  14. Crystal Structure of the Cohesin Gatekeeper Pds5 and in Complex with Kleisin Scc1

    Directory of Open Access Journals (Sweden)

    Byung-Gil Lee

    2016-03-01

    Full Text Available Sister chromatid cohesion is mediated by cohesin, whose Smc1, Smc3, and kleisin (Scc1 subunits form a ring structure that entraps sister DNAs. The ring is opened either by separase, which cleaves Scc1 during anaphase, or by a releasing activity involving Wapl, Scc3, and Pds5, which bind to Scc1 and open its interface with Smc3. We present crystal structures of Pds5 from the yeast L. thermotolerans in the presence and absence of the conserved Scc1 region that interacts with Pds5. Scc1 binds along the spine of the Pds5 HEAT repeat fold and is wedged between the spine and C-terminal hook of Pds5. We have isolated mutants that confirm the observed binding mode of Scc1 and verified their effect on cohesin by immunoprecipitation and calibrated ChIP-seq. The Pds5 structure also reveals architectural similarities to Scc3, the other large HEAT repeat protein of cohesin and, most likely, Scc2.

  15. Crystal structure of the G3BP2 NTF2-like domain in complex with a canonical FGDF motif peptide

    DEFF Research Database (Denmark)

    Kristensen, Ole

    2015-01-01

    The crystal structure of the NTF2-like domain of the human Ras GTPase SH3 Binding Protein (G3BP), isoform 2, was determined at a resolution of 2.75 Å in complex with a peptide containing a FGDF sequence motif. The overall structure of the protein is highly similar to the homodimeric N-terminal do......The crystal structure of the NTF2-like domain of the human Ras GTPase SH3 Binding Protein (G3BP), isoform 2, was determined at a resolution of 2.75 Å in complex with a peptide containing a FGDF sequence motif. The overall structure of the protein is highly similar to the homodimeric N......-terminal domains of the G3BP1 and Rasputin proteins. Recently, a subset of G3BP interacting proteins was recognized to share a common sequence motif, FGDF. The most studied binding partners, USP10 and viral nsP3, interfere with essential G3BP functions related to assembly of cellular stress granules. Reported...

  16. Crystal structure of the mineralocorticoid receptor DNA binding domain in complex with DNA.

    Science.gov (United States)

    Hudson, William H; Youn, Christine; Ortlund, Eric A

    2014-01-01

    The steroid hormone receptors regulate important physiological functions such as reproduction, metabolism, immunity, and electrolyte balance. Mutations within steroid receptors result in endocrine disorders and can often drive cancer formation and progression. Despite the conserved three-dimensional structure shared among members of the steroid receptor family and their overlapping DNA binding preference, activation of individual steroid receptors drive unique effects on gene expression. Here, we present the first structure of the human mineralocorticoid receptor DNA binding domain, in complex with a canonical DNA response element. The overall structure is similar to the glucocorticoid receptor DNA binding domain, but small changes in the mode of DNA binding and lever arm conformation may begin to explain the differential effects on gene regulation by the mineralocorticoid and glucocorticoid receptors. In addition, we explore the structural effects of mineralocorticoid receptor DNA binding domain mutations found in type I pseudohypoaldosteronism and multiple types of cancer.

  17. Luminescent lanthanide complexes with 4-acetamidobenzoate: Synthesis, supramolecular assembly via hydrogen bonds, crystal structures and photoluminescence

    Science.gov (United States)

    Yin, Xia; Fan, Jun; Wang, Zhi Hong; Zheng, Sheng Run; Tan, Jing Bo; Zhang, Wei Guang

    2011-07-01

    Four new luminescent complexes, namely, [Eu(aba) 2(NO 3)(C 2H 5OH) 2] ( 1), [Eu(aba) 3(H 2O) 2]·0.5 (4, 4'-bpy)·2H 2O ( 2), [Eu 2(aba) 4(2, 2'-bpy) 2(NO 3) 2]·4H 2O ( 3) and [Tb 2(aba) 4(phen) 2(NO 3) 2]·2C 2H 5OH ( 4) were obtained by treating Ln(NO 3) 3·6H 2O and 4-acetamidobenzoic acid (Haba) with different coligands (4, 4'-bpy=4, 4'-bipyridine, 2, 2'-bpy=2, 2'-bipyridine, and phen=1, 10-phenanthroline). They exhibit 1D chains ( 1- 2) and dimeric structures ( 3- 4), respectively. This structural variation is mainly attributed to the change of coligands and various coordination modes of aba molecules. Moreover, the coordination units are further connected via hydrogen bonds to form 2D even 3D supramolecular networks. These complexes show characteristic emissions in the visible region at room temperature. In addition, thermal behaviors of four complexes have been investigated under air atmosphere. The relationship between the structures and physical properties has been discussed.

  18. Crystal structure, spectroscopic characterization and antibacterial activities of a silver complex with sulfameter

    Science.gov (United States)

    Nakahata, Douglas H.; Lustri, Wilton R.; Cuin, Alexandre; Corbi, Pedro P.

    2016-12-01

    A silver complex with the sulfonamide sulfameter, also known as sulfamethoxydiazine (SMTR), was prepared and characterized. Chemical analyses were consistent with the [Ag(C11H11N4O3S)] composition (AgSMTR), while conductivity measurements in DMSO indicated a non-electrolyte behavior of the complex in this solvent. High-resolution ESI(+)-QTOF mass spectrometric experiments revealed the presence of the [Ag(C11H11N4O3S)+H]+ and [Ag2(C11H11N4O3S)2+H]+ species in solution. Infrared and NMR spectroscopies indicated coordination of the ligand to the metal by the nitrogen atoms of the sulfonamide group and of the pyrimidine ring. The structure of AgSMTR was solved by powder X-ray diffraction technique using the Rietveld method. The solved structure confirms the formation of a dimer, where each silver ion is coordinated by one of the nitrogen atoms of the pyrimidine ring, the nitrogen of the sulfonamide group and by an oxygen atom from the sulfonyl group. An argentophilic interaction of 2.901(1) Å is present in this dimeric structure. The AgSMTR complex was assayed over Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas aeruginosa and Escherichia coli) bacterial strains, and it was found that the compound is 8 times more active over the Gram-negative bacteria in DMSO solution, with MIC values in the micromolar range.

  19. Synthesis, Crystal Structure, Stacking Effect and Antibacterial Studies of a Novel Quaternary Copper (II) Complex with Quinolone

    OpenAIRE

    Longguan Zhu; Xuchun Fu; Guoping Wang; Guangguo Wu

    2003-01-01

    The structural properties of a new copper (II) complex [Cu2(cip)2(bpy)2(pip)]·6H2O (bpy=2,2’-bipyridyl, cip=1-cyclopropyl-6-4-oxo-1,4-dihydroquinoline-3-carboxylic acid, pip= piperazinyl anion), obtained during the synthesis of the copper complex with ciprofloxacin (cpf), has been investigated. The complex crystallizes in the triclinic system, space group P-1. The cell dimensions are: a=6.874(2) Å, b= 10.761(3) Å, c= 17.969(5) Å, α =80.071(6)°, β= 85.253(6)°, γ...

  20. Preparation and Single-Crystal X-Ray Structures of Four Related Mixed-Ligand 4-Methylpyridine Indium Halide Complexes

    Science.gov (United States)

    Hepp, Aloysius F.; Clark, Eric B.; Schupp, John D.; Williams, Jennifer N.; Duraj, Stan A.; Fanwick, Philip E.

    2013-01-01

    We describe the structures of four related indium complexes obtained during synthesis of solid-state materials precursors. Indium adducts of halides and 4-methylpyridine, InX3(pic)3 (X = Cl, Br; pic = 4-methylpyridine) consist of octahedral molecules with meridional (mer) geometry. Crystals of mer-InCl3(pic)3 (1) are triclinic, space group P1(bar) (No. 2), with a = 9.3240(3), b = 13.9580(6), c = 16.7268 (7) A, alpha = 84.323(2), beta = 80.938(2), gamma = 78.274(3)Z = 4, R = 0.035 for 8820 unique reflections. Crystals of mer-InBr3(pic)3 (2) are monoclinic, space group P21/n (No. 14), with a = 15.010(2), b = 19.938(2), c = 16.593(3), beta = 116.44(1)Z = 8, R = 0.053 for 4174 unique reflections. The synthesis and structures of related compounds with phenylsulfide (chloride) (3) and a dimeric complex with bridging hydroxide (bromide) (4) coordination is also described. Crystals of trans-In(SC6H5)Cl2(pic)3 (3) are monoclinic, space group P21/n (No. 14), with a = 9.5265(2), b = 17.8729(6), c = 13.8296(4), beta = 99.7640(15)Z = 4, R = 0.048 for 5511 unique reflections. Crystals of [In(mu-OH)Br2(pic)22 (4) are tetragonal, space group = I41cd (No. 110) with a = 19.8560(4), b = 19.8560(4), c = 25.9528(6), Z = 8, R = 0.039 for 5982 unique reflections.

  1. Crystal structure and ligand affinity of avidin in the complex with 4‧-hydroxyazobenzene-2-carboxylic acid

    Science.gov (United States)

    Strzelczyk, Paweł; Bujacz, Grzegorz

    2016-04-01

    Avidin is a protein found in egg white that binds numerous organic compounds with high affinity, especially biotin and its derivatives. Due to its extraordinary affinity for its ligands, avidin is extensively used in biotechnology. X-ray crystallography and fluorescence-based biophysical techniques were used to show that avidin binds the dye 4‧-hydroxyazobenzene-2-carboxylic acid (HABA) with a lower affinity than biotin. The apparent dissociation constant determined for the avidin complex with HABA by microscale thermophoresis (MST) is 4.12 μM. The crystal structure of avidin-HABA complex was determined at a resolution of 2.2 Å (PDB entry 5chk). The crystals belong to a hexagonal system, in the space group P6422. In that structure, the hydrazone tautomer of HABA is bound at the bottom part of the central calyx near the polar residues. We show interactions of the dye with avidin and compare them with the previously reported avidin-biotin complex.

  2. Six-coordinate oxo-vanadium(V) dimer complex with methoxy bridging: synthesis, crystal structure, biological activity and molecular docking

    Czech Academy of Sciences Publication Activity Database

    Heidari, F.; Fatemi, S.J.A.; Yousef Ebrahimipour, S.; Ebrahimnejad, H.; Castro, J.; Dušek, Michal; Eigner, Václav

    2017-01-01

    Roč. 76, Feb (2017), s. 1-4 ISSN 1387-7003 R&D Projects: GA ČR(CZ) GA14-03276S EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510; European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : oxo-vanadium(V) * Schiff base complex * antimicrobial activity * X-ray crystal structure Subject RIV: CA - Inorganic Chemistry Impact factor: 1.640, year: 2016

  3. Synthesis, X-ray crystal structures, electrochemistry and theoretical investigation of a tetradentate nickel and copper Schiff base complexes

    Science.gov (United States)

    Rahmouni, Samra; Djedouani, Amel; Anak, Barkahem; Tabti, Salima; Bendaas, Abderrahmen; Bencharif, Mustapha; François, Michel; Fleutot, Solenne; Rabilloud, Franck

    2017-11-01

    New tetradentate mononuclear nickel(II) [NiL] and pentadentate binuclear copper(II) [Cu2L2H2O], H2O Schiff base complexes have been synthesized. The crystal structures of [NiL] and [Cu2L2H2O], H2O have been determined by X-ray diffraction method showing distorted square-planar geometry for [NiL] and distorted tetragonal pyramid geometry for [Cu2L2H2O], H2O. In both complexes, the dehydroacetic acid functional group engages in a deprotonated manner and coordination occurs through the nitrogen atoms of the imine function and the phenolic oxygen. Density Functional Theory calculations are carried out for the determination of the optimized structures. The fundamental vibrational wave numbers are calculated and a good agreement between observed and calculated wave numbers is achieved.

  4. Crystal structure of patatin-17 in complex with aged and non-aged organophosphorus compounds.

    Directory of Open Access Journals (Sweden)

    Sanjeeva J Wijeyesakere

    Full Text Available Patatin is a non-specific plant lipase and the eponymous member of a broad class of serine hydrolases termed the patatin-like phospholipase domain containing proteins (PNPLAs. Certain PNPLA family members can be inhibited by organophosphorus (OP compounds. Currently, no structural data are available on the modes of interaction between the PNPLAs and OP compounds or their native substrates. To this end, we present the crystal structure of patatin-17 (pat17 in its native state as well as following inhibition with methyl arachidonyl fluorophosphonate (MAFP and inhibition/aging with diisopropylphosphorofluoridate (DFP. The native pat17 structure revealed the existence of two portals (portal1 and portal2 that lead to its active-site chamber. The DFP-inhibited enzyme underwent the aging process with the negatively charged phosphoryl oxygen, resulting from the loss of an isopropyl group, being within hydrogen-binding distance to the oxyanion hole. The MAFP-inhibited pat17 structure showed that MAFP did not age following its interaction with the nucleophilic serine residue (Ser77 of pat17 since its O-methyl group was intact. The MAFP moiety is oriented with its phosphoryl oxygen in close proximity to the oxyanion hole of pat17 and its O-methyl group located farther away from the oxyanion hole of pat17 relative to the DFP-bound state. The orientation of the alkoxy oxygens within the two OP compounds suggests a role for the oxyanion hole in stabilizing the emerging negative charge on the oxygen during the aging reaction. The arachidonic acid side chain of MAFP could be contained within portals 1 or 2. Comparisons of pat17 in the native, inhibited, and aged states showed no significant global conformational changes with respect to their Cα backbones, consistent with observations from other α/β hydrolases such as group VIIA phospholipase A2.

  5. Synthesis, crystal structure and reactivity of copper(II) complexes of tetradentate N2S2 donor ligands

    Science.gov (United States)

    Sarkar, Sandipan; Paul, Hena; Drew, Michael G. B.; Zangrando, Ennio; Chattopadhyay, Pabitra

    2009-09-01

    Two new hexa-coordinated mononuclear copper(II) complexes of two ligands L 1 and L 2 containing NSSN donor sets formulated as [Cu(L)(H 2O) 2](NO 3) 2 [ 1a, L = 1,2-bis(2-pyridylmethylthio)ethane (L 1), 1b L = 1,3-bis(2-pyridyl-methylthio)propane (L 2)] were synthesized and characterized by physico-chemical and spectroscopic methods. In 1a the single crystal X-ray crystallography analysis showed a distorted octahedral geometry about copper(II) ion. The crystal packing evidences pairs of complexes arranged about a center of symmetry and connected through a H-bond occurring between aquo ligands and nitrate anions. On reaction with chloride and pseudohalides (N 3- and SCN -), in acetonitrile at ambient temperature, complexes 1 changed to monocationic penta-coordinated mononuclear copper(II) species formulated as [Cu(L)(Cl)]NO 3 ( 2), [Cu(L)(N 3)]NO 3 ( 3), and [Cu(L)(SCN)]NO 3 ( 4). These copper(II) complexes have been isolated in pure form from the reaction mixtures and characterized by physico-chemical and spectroscopic tools. The solid-state structure of 2a, established by X-ray crystallography, shows a trigonal bipyramidal geometry about the metal ion with a trigonality index ( τ) of 0.561.

  6. Template Syntheses, Crystal Structures and Supramolecular Assembly of Hexaaza Macrocyclic Copper(II) Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Taehyung; Kim, Ju Chang [Pukyong National Univ., Busan (Korea, Republic of); Lough, Alan J. [Univ. of Toronto, Toronto (Canada)

    2013-06-15

    Two new hexaaza macrocyclic copper(II) complexes were prepared by a template method and structurally characterized. In the solid state, they were self-assembled by intermolecular interactions to form the corresponding supramolecules 1 and 2, respectively. In the structure of 1, the copper(II) macrocycles are bridged by a tp ligand to form a macrocyclic copper(II) dimer. The dimer extends its structure by intermolecular forces such as hydrogen bonds and C-H···π interactions, resulting in the formation of a double stranded 1D supramolecule. In 2, the basic structure is a monomeric copper(II) macrocycle with deprotonated imidazole pendants. An undulated 1D hydrogen bonded array is achieved through hydrogen bonds between imidazole pendants and secondary amines, where the imidazole pendants act as a hydrogen bond acceptor. The 1D hydrogen bonded supramolecular chain is supported by C-H···π interactions between the methyl groups of acetonitrile ligands and imidazole pendants of the copper(II) macrocycles. In both complexes, the introduction of imidazoles to the macrocycle as a pendant plays an important role for the formation of supramolecules, where they act as intermolecular hydrogen bond donors and/or acceptors, C-H···π and π-π interactions.

  7. Crystal structure of the potassium-importing KdpFABC membrane complex

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Ching-Shin; Pedersen, Bjørn Panyella; Stokes, David L.

    2017-06-21

    Cellular potassium import systems play a fundamental role in osmoregulation, pH homeostasis and membrane potential in all domains of life. In bacteria, the kdp operon encodes a four-subunit potassium pump that maintains intracellular homeostasis, cell shape and turgor under conditions in which potassium is limiting1. This membrane complex, called KdpFABC, has one channel-like subunit (KdpA) belonging to the superfamily of potassium transporters and another pump-like subunit (KdpB) belonging to the superfamily of P-type ATPases. Although there is considerable structural and functional information about members of both superfamilies, the mechanism by which uphill potassium transport through KdpA is coupled with ATP hydrolysis by KdpB remains poorly understood. Here we report the 2.9 Å X-ray structure of the complete Escherichia coli KdpFABC complex with a potassium ion within the selectivity filter of KdpA and a water molecule at a canonical cation site in the transmembrane domain of KdpB. The structure also reveals two structural elements that appear to mediate the coupling between these two subunits. Specifically, a protein-embedded tunnel runs between these potassium and water sites and a helix controlling the cytoplasmic gate of KdpA is linked to the phosphorylation domain of KdpB. On the basis of these observations, we propose a mechanism that repurposes protein channel architecture for active transport across biomembranes.

  8. Crystal Structure of Heparinase II from Pedobacter Heparinus and its Complex with a Disaccharide Product

    Energy Technology Data Exchange (ETDEWEB)

    Shaya,D.; Tocilj, A.; Li, Y.; Myette, J.; Venkatarman, G.; Sasisekharan, R.; Cygler, M.

    2006-01-01

    Heparinase II depolymerizes heparin and heparan sulfate glycosaminoglycans, yielding unsaturated oligosaccharide products through an elimination degradation mechanism. This enzyme cleaves the oligosaccharide chain on the nonreducing end of either glucuronic or iduronic acid, sharing this characteristic with a chondroitin ABC lyase. We have determined the first structure of a heparin-degrading lyase, that of heparinase II from Pedobacter heparinus (formerly Flavobacterium heparinum), in a ligand-free state at 2.15Angstroms resolution and in complex with a disaccharide product of heparin degradation at 2.30Angstroms resolution. The protein is composed of three domains: an N-terminal {alpha}-helical domain, a central two-layered {beta}-sheet domain, and a C-terminal domain forming a two-layered {beta}-sheet. Heparinase II shows overall structural similarities to the polysaccharide lyase family 8 (PL8) enzymes chondroitin AC lyase and hyaluronate lyase. In contrast to PL8 enzymes, however, heparinase II forms stable dimers, with the two active sites formed independently within each monomer. The structure of the N-terminal domain of heparinase II is also similar to that of alginate lyases from the PL5 family. A Zn2+ ion is bound within the central domain and plays an essential structural role in the stabilization of a loop forming one wall of the substrate-binding site. The disaccharide binds in a long, deep canyon formed at the top of the N-terminal domain and by loops extending from the central domain. Based on structural comparison with the lyases from the PL5 and PL8 families having bound substrates or products, the disaccharide found in heparinase II occupies the '+1' and '+2' subsites. The structure of the enzyme-product complex, combined with data from previously characterized mutations, allows us to propose a putative chemical mechanism of heparin and heparan-sulfate degradation.

  9. Crystal structures of the G protein Gi alpha 1 complexed with GDP and Mg2+: a crystallographic titration experiment.

    Science.gov (United States)

    Coleman, D E; Sprang, S R

    1998-10-13

    The effect of Mg2+ binding on the conformation of the inactive GDP-bound complex of the heterotrimeric G protein alpha subunit Gi alpha 1 has been investigated by X-ray crystallography. Crystal structures of the Gi alpha 1.GDP complex were determined after titration with 5, 10, 100, and 200 mM Mg2+. Comparison of these structures with that of the Mg2+-free complex revealed Mg2+ bound at the same site as observed in the structure of the active, Gi alpha 1. GTP gamma S.Mg2+-bound complex of Gi alpha 1, with a similar coordination scheme except for the substitution of a water molecule for an oxygen ligand of the gamma-phosphate of Gi alpha 1.GTP gamma S. Mg2+. In contrast to the GDP.Mg2+ complex of Gt alpha and of other G proteins, switch I residues of Gi alpha 1 participate in Mg2+ binding and undergo conformational changes as a consequence of Mg2+ binding. Partial order is induced in switch II, which is disordered in the Mg2+-free complex, but no order is observed in the switch III region. This contrasts with the GDP.Mg2+ complex of Gt alpha in which both switch II and III switch are ordered. Mg2+ binding also induces binding of an SO42- molecule to the active site in a manner which may mimic a Gi alpha 1.GDP.PO42-.Mg2+ product complex. Implications of these findings are discussed.

  10. Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Manchi C.M.; Kuppan, Gokulan; Shetty, Nishant D.; Owen, Joshua L.; Ioerger, Thomas R.; Sacchettini, James C. (TAM)

    2009-12-01

    S-adenosylhomocysteine hydrolase (SAHH) is a ubiquitous enzyme that plays a central role in methylation-based processes by maintaining the intracellular balance between S-adenosylhomocysteine (SAH) and S-adenosylmethionine. We report the first prokaryotic crystal structure of SAHH, from Mycobacterium tuberculosis (Mtb), in complex with adenosine (ADO) and nicotinamide adenine dinucleotide. Structures of complexes with three inhibitors are also reported: 3{prime}-keto aristeromycin (ARI), 2-fluoroadenosine, and 3-deazaadenosine. The ARI complex is the first reported structure of SAHH complexed with this inhibitor, and confirms the oxidation of the 3{prime} hydroxyl to a planar keto group, consistent with its prediction as a mechanism-based inhibitor. We demonstrate the in vivo enzyme inhibition activity of the three inhibitors and also show that 2-fluoradenosine has bactericidal activity. While most of the residues lining the ADO-binding pocket are identical between Mtb and human SAHH, less is known about the binding mode of the homocysteine (HCY) appendage of the full substrate. We report the 2.0 {angstrom} resolution structure of the complex of SAHH cocrystallized with SAH. The most striking change in the structure is that binding of HCY forces a rotation of His363 around the backbone to flip out of contact with the 5{prime} hydroxyl of the ADO and opens access to a nearby channel that leads to the surface. This complex suggests that His363 acts as a switch that opens up to permit binding of substrate, then closes down after release of the cleaved HCY. Differences in the entrance to this access channel between human and Mtb SAHH are identified.

  11. Synthesis and crystal structures of two new tin bis(carboranylamidinate complexes

    Directory of Open Access Journals (Sweden)

    Nicole Harmgarth

    2017-10-01

    Full Text Available Reaction of 2 equiv. of the lithium carboranylamidinate Li[o-(C2H10B10C(NCy(NHCy] with SnCl2 in THF afforded the stannylene compound bis(N,N′-dicyclohexylamidinatocarboranatetin(II, SnII[o-(C2H10B10C(NCy(NHCy]2 (1. A similar reaction of SnCl4 with 2 equiv. of Li[o-(C2H10B10C(NiPr(NHiPr] unexpectedly afforded the known solvated pentachloridostannate(IV salt [Li(THF4][SnCl5(THF] as the main reaction product. Small amounts of the new chlorido-tin(IV bis(carboranylamidinate bis(N,N′-diisopropylamidinatocarboranatechloridotin(IV, SnIVCl[o-(C2H10B10C(NiPr(NHiPr][o-(C2H10B10C(NiPr2] (2, were isolated as a by-product. Single-crystal X-ray structure analysis revealed a κC,κN-chelating coordination of the carboranylamidinate ligands in both 1 and 2. The Sn atom in 1 adopts a pseudo-trigonal–bipyramidal coordination under participation of a stereoactive lone pair. In 2, a trigonal–bipyramidal coordination of Sn is completed by a chlorido ligand.

  12. Crystal Structures, Properties and Reactivity of Selected Macrocyclic and Chelate Complexes of Ni(II)

    OpenAIRE

    Churchard, Andrew James

    2012-01-01

    In this dissertation we describe the structure, properties and decomposition reactions of a series of Ni(II) coordination complexes formed from reaction of the appropriate macrocyclic or chelating ligand with a simple nickel salt. The ligands used were 12aneS4 (1,4,7,10-tetrathiacyclododecane), 14aneS4 (1,4,8,11-tetrathiacyclotetradecane), cyclam (1,4,8,11-tetraazacyclotetradecane), dppe (1,2- (diphenylphosphino)ethane), and PP3 (tris-(2-(diphenylphosphino)ethyl)phosphine). The wo...

  13. Synthesis, crystal structures, and properties of oxovanadium(IV)-lanthanide(III) heteronuclear complexes.

    Science.gov (United States)

    Shi, Wei; Chen, Xiao-Yan; Zhao, Yan-Nan; Zhao, Bin; Cheng, Peng; Yu, Ao; Song, Hai-Bin; Wang, Hong-Gen; Liao, Dai-Zheng; Yan, Shi-Ping; Jiang, Zong-Hui

    2005-08-19

    A new series of oxovanadium(IV)-lanthanide(III) heteronuclear complexes [Yb(H2O)8]2[(VO)2(TTHA)](3)21 H2O (1), {[Ho(H2O)7(VO)2(TTHA)][(VO)2(TTHA)](0.5)} 8.5 H2O (2), {[Gd(H2O)7(VO)2(TTHA)][(VO)2(TTHA)](0.5)}8.5 H2O (3), {[Eu(H2O)7][(VO)2(TTHA)](1.5)} 10.5 H2O (4), and [Pr2(H2O)6(SO4)2][(VO)2(TTHA)] (5) (H6TTHA=triethylenetetraaminehexaacetic acid) were prepared by using the bulky flexible organic acid H(6)TTHA as structure-directing agent. X-ray crystallographic studies reveal that they contain the same [(VO)2(TTHA)]2- unit as building block, but the Ln3+ ion lies in different coordination environments. Although the lanthanide ions always exhibit similar chemical behavior, the structures of the complexes are not homologous. Compound 1 is composed of a [Yb(H2O)8]3+ ion and a [(VO)2(TTHA)]2- ion. Compounds 2 and 3 are isomorphous; both contain a trinuclear [Ln(H2O)7(VO)2(TTHA)]+ (Ln=Ho for 2 and Gd for 3) ion and a [(VO)2(TTHA)]2- ion. Compound 4 is an extended one-dimensional chain, in which each Eu3+ ion links two [(VO)2(TTHA)]2- ions. For 5, the structure is further assembled into a three-dimensional network with an interesting framework topology comprising V2Pr2 and V4Pr2 heterometallic lattices. Moreover, 4 and 5 are the first oxovanadium(IV)-lanthanide(III) coordination polymers and thus enlarge the realm of 3d-4f complexes. The IR, UV/Vis, and EPR spectra and the magnetic properties of the heterometallic complexes were studied. Notably, 2 shows unusual ferromagnetic interactions between the VO2+ and Ho3+ ions.

  14. Crystal structure of quinone reductase 2 in complex with cancer prodrug CB1954.

    Science.gov (United States)

    Fu, Yue; Buryanovskyy, Leonid; Zhang, Zhongtao

    2005-10-14

    CB1954 is a cancer pro-drug that can be activated through reduction by Escherichia coli nitro-reductases and quinone reductases. Human quinone reductase 2 is very efficient in the activation of CB1954, approximately 3000 times more efficient than human QR1 in terms of k(cat)/K(m). We have solved the three-dimensional structure of QR2 in complex with CB1954 to a nominal resolution of 1.5A. The complex structure indicates the essentiality of the two nitro groups: one nitro group forms hydrogen bonds with the side-chain of Asn161 of QR2 to hold the other nitro group in position for the reduction. We further conclude that residue 161, an Asn in QR2 and a His in QR1, is critical in differentiating the substrate specificities of these two enzymes. Mutation of Asn161 to His161 in QR2 resulted in the total loss of the enzymatic activity towards activation of CB1954, whereas the rates of reduction towards menadione are not altered.

  15. Crystal structure of the Trypanosoma cruzi trypanothione reductase.mepacrine complex.

    Science.gov (United States)

    Jacoby, E M; Schlichting, I; Lantwin, C B; Kabsch, W; Krauth-Siegel, R L

    1996-01-01

    The three-dimensional structure of the complex between Trypanosoma cruzi trypanothione reductase (TR) (EC 1.6.4.8) and the antiparasitic drug mepacrine (quinacrine) has been solved at 2.9 angstoms resolution. Mepacrine is a competitive inhibitor of TR but does not affect human glutathione reductase (GR), a closely related host enzyme. Of particular importance for inhibitor binding are four amino acid residues in the disulfide substrate-binding site of TR that are not conserved in human GR, namely, Glu-18 (Ala-34 in GR), Trp-21 (Arg-37), Ser-109 (Ile-113), and Met-113 (Asn-117). The acridine ring of mepacrine is fixed at the active site close to the hydrophobic wall formed by Trp-21 and Met-113. Specific pairwise interactions between functional groups of the drug and amino acid side chains include the ring nitrogen and Met-113, the chlorine atom and Trp-21, and the oxymethyl group and Ser-109. The alkylamino chain of mepacrine points into the inner region of the active site and is held in position by a solvent-mediated hydrogen bond to Glu-18. The structure of the complex shows for the first time the atomic interactions between TR and an inhibitory ligand. This is a crucial step towards the rational design of inhibitors that might be suited as drugs against Chagas' disease.

  16. Nephelines from the Somma-Vesuvius volcanic complex (Southern Italy): crystal-chemical, structural and genetic investigations

    Science.gov (United States)

    Balassone, Giuseppina; Kahlenberg, Volker; Altomare, Angela; Mormone, Angela; Rizzi, Rosanna; Saviano, Michele; Mondillo, Nicola

    2014-02-01

    Sixteen nephelines from different geological occurrences were sampled at the type-locality, the Somma-Vesuvius volcanic complex (southern Italy), and investigated for their chemistry and crystal structure obtained by both single-crystal and powder X-ray diffraction. Nepheline-bearing samples are metamorphic or from magmatic ejecta and pumice deposits. The lower K contents characterize the pumice- and some metamorphic-derived nephelines, whereas the higher ones are found in some samples from magmatic nodules. The amount of the anorthite molecule, quite low on average, can be more variable in the metamorphic nephelines. The crystal-structure investigations on Somma-Vesuvius samples compare well with previous studies of natural nephelines. All 16 nepheline samples adopt space group P63. The observed lattice parameters vary between 9.9768-9.9946 Å (for a) and 8.3614-8.3777 Å (for c), respectively. Furthermore, chemical analysis revealed that all specimens exhibit an excess of Si relative the ideal Si:Al ratio of 1:1. The analysis of the T-O distances in our samples clearly indicates a distinct ordering process of aluminium and silicon on the tetrahedral sites which is an agreement with Loewenstein's rule. A linear correlation between the distance of symmetry equivalent split atoms O(1)-O(1)' and the T(1)-O(1)- T(2) tilt angle was observed. The average ( B = Na) distances of all crystals are very similar which is consistent with the outcome of the site population refinement indicating full occupancy with sodium. Oriented precession-type sections of reciprocal space indicated the presence of at least the most intense family of satellite peaks, demonstrating that this group of satellite reflections can occur not only in nephelines from pegmatites and ijolites but also in rocks from completely different petrological settings.

  17. Crystal structure of tabtoxin resistance protein complexed with acetyl coenzyme A reveals the mechanism for {beta}-lactam acetylation.

    Energy Technology Data Exchange (ETDEWEB)

    He, H.; Ding, Y.; Bartlam, M.; Sun, F.; Le, Y.; Qin, X.; Tang, H.; Zhang, R.; Joachimiak, A.; Liu, J.; Zhao, N.; Rao, Z.; Biosciences Division; Tsinghua Univ.; Chinese Academy of Science

    2003-01-31

    Tabtoxin resistance protein (TTR) is an enzyme that renders tabtoxin-producing pathogens, such as Pseudomonas syringae, tolerant to their own phytotoxins. Here, we report the crystal structure of TTR complexed with its natural cofactor, acetyl coenzyme A (AcCoA), to 1.55 {angstrom} resolution. The binary complex forms a characteristic 'V' shape for substrate binding and contains the four motifs conserved in the GCN5-related N-acetyltransferase (GNAT) superfamily, which also includes the histone acetyltransferases (HATs). A single-step mechanism is proposed to explain the function of three conserved residues, Glu92, Asp130 and Tyr141, in catalyzing the acetyl group transfer to its substrate. We also report that TTR possesses HAT activity and suggest an evolutionary relationship between TTR and other GNAT members.

  18. Crystal Structure of 12-Lipoxygenase Catalytic-Domain-Inhibitor Complex Identifies a Substrate-Binding Channel for Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Shu; Mueser, Timothy C.; Marnett, Lawrence J.; Funk, Jr., Max O. (Toledo); (Vanderbilt)

    2014-10-02

    Lipoxygenases are critical enzymes in the biosynthesis of families of bioactive lipids including compounds with important roles in the initiation and resolution of inflammation and in associated diseases such as diabetes, cardiovascular disease, and cancer. Crystals diffracting to high resolution (1.9 {angstrom}) were obtained for a complex between the catalytic domain of leukocyte 12-lipoxygenase and the isoform-specific inhibitor, 4-(2-oxapentadeca-4-yne)phenylpropanoic acid (OPP). In the three-dimensional structure of the complex, the inhibitor occupied a new U-shaped channel open at one end to the surface of the protein and extending past the redox-active iron site that is essential for catalysis. In models, the channel accommodated arachidonic acid, defining the binding site for the substrate of the catalyzed reaction. There was a void adjacent to the OPP binding site connecting to the surface of the enzyme and providing a plausible access channel for the other substrate, oxygen.

  19. Synthesis, crystal structure and properties of two ternary rare earth complexes with aromatic acid and 1,10-phenanthroline

    Energy Technology Data Exchange (ETDEWEB)

    Zhao Na; Wang Shuping; Ma Ruixia; Gao Zhihua [Department of Chemistry, Hebei Normal University, Shijiazhuang 050016 (China); Wang Ruifen [Department of Chemistry, Hebei Normal University, Shijiazhuang 050016 (China)], E-mail: wruifen@mail.hebtu.edu.cn; Zhang Jianjun [Experimental Center, Hebei Normal University, Shijiazhuang 050016 (China)

    2008-09-08

    Two dimeric rare-earth complexes [Eu(o-MOBA){sub 3}phen]{sub 2}.2H{sub 2}O (1), [Tb(o-MOBA){sub 3}phen]{sub 2}.2H{sub 2}O (2), (where o-MOBA = o-methoxybenzoate, phen 1,10-phenanthroline) were synthesized and structurally characterized. Both of them consist of neutral dimeric molecules, crystallize in triclinic system, space group P1-bar. Each RE(III) ion is nine-coordinated with one 1,10-phenanthroline molecule, one bidentate chelating carboxylate group, two bidentate bridging carboxylate groups and two tridentate bridging carboxylate groups. Complex 1 shows bright red luminescence, 2 shows green luminescence under UV light at room temperature, respectively. The thermal analysis indicates that they are all quite stable to heat.

  20. Iron(II) tris(3-bromo-1,10-phenanthroline) complex:synthesis, crystal structure and electropolymerization

    CERN Document Server

    Lee, K J; Lee, S S; Lee, B Y

    2002-01-01

    The complex of iron(II) tris(3-Br-phen)(3-Br-phen; 3-bromo-1,10-phenanthroline) was prepared as a precursor of electropolymerization and the crystal structure of [Fe(3-Br-phen) sub 3](PF sub 6) sub 2 centre dot CH sub 3 CN with a distorted octahedral geometry has been investigated. The reductive electropolymerization of [Fe(3-Br-phen) sub 3] sup 2 sup + complex onto the surface of a glassy carbon electrode and indium tin oxide (ITO) optically transparent electrode were performed in acetonitrile at room temperature. Thin film of poly-[Fe(3-Br-phen) sub 3] sup 2 sup + formed was adherent, electroactive and stably deposited on a glassy carbon disk electrode. The thin metallopolymeric film formed was also confirmed by absorption spectroscopy.

  1. Unsaturated Mn complex decorated hybrid thioarsenates: Syntheses, crystal structures and physical properties

    Energy Technology Data Exchange (ETDEWEB)

    Yue, Cheng-Yang [Key Laboratory of Inorganic Chemistry in Universities of Shandong, Department of Chemistry and Chemical Engineering, Jining University, Qufu, Shandong 273155 (China); State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002 (China); Lei, Xiao-Wu, E-mail: xwlei_jnu@163.com [Key Laboratory of Inorganic Chemistry in Universities of Shandong, Department of Chemistry and Chemical Engineering, Jining University, Qufu, Shandong 273155 (China); Tian, Ya-Wei; Xu, Jing; Bai, Yi-Qun; Wang, Fei; Zhou, Peng-Fei; Liu, Xiao-Fan [Key Laboratory of Inorganic Chemistry in Universities of Shandong, Department of Chemistry and Chemical Engineering, Jining University, Qufu, Shandong 273155 (China); Yi, Fei-Yan, E-mail: yifeiyan@nbu.edu.cn [Faculty of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211 (China)

    2016-03-15

    The incorporation of unsaturated [Mn(1,2-dap)]{sup 2+}, [Mn(1,2-dap){sub 2}]{sup 2+}, [Mn(2,2-bipy)]{sup 2+} (1,2-dap=1,2-diaminopropane) complex cations with thioarsenate anions of [As{sup III}S{sub 3}]{sup 3−} and [As{sup V}S{sub 4}]{sup 3−} led to three new hybrid manganese thioarsenates, namely, [Mn(1,2-dap)]{sub 2}MnAs{sub 2}S{sub 6} (1), [Mn(1,2-dap){sub 2}]{[Mn(1,2-dap)]_2As_2S_8} (2) and (NH{sub 4})[Mn(2,2-bipy){sub 2}]AsS{sub 4} (3). In compound 1, the unsaturated [Mn(1,2-dap)]{sup 2+} complexes, [MnS{sub 4}]{sup 6−} tetrahedra and [As{sup III}S{sub 3}]{sup 3−} trigonal-pyramids are condensed to form the 1D [Mn(1,2-dap)]{sub 2}MnAs{sub 2}S{sub 6} chain, whereas compound 2 features 2D layer composed of [Mn(1,2-dap)]{sup 2+} and [Mn(1,2-dap){sub 2}]{sup 2+} complexes as well as [As{sup V}S{sub 4}]{sup 3−} tetrahedral units. For compound 3, two [As{sup V}S{sub 4}]{sup 3−} anions bridge two [Mn(2,2-bipy)]{sup 2+} complex cations into a butterfly like {[Mn(2,2-bipy)]_2As_2S_8}{sup 2−} anionic unit. Magnetic measurements indicate the ferrimagnetic behavior for compound 1 and antiferromagnetic (AF) behaviors for compounds 2–3. The UV–vis diffuse-reflectance measurements and electronic structural calculations based on density functional theory (DFT) revealed the title compounds belong to semiconductors with band gaps of 2.63, 2.21, and 1.97 eV, respectively. The narrow band-gap of compound 3 led to the efficient and stable photocatalytic degradation activity over organic pollutant than N-doped P25 under visible light irradiation. - Highlights: Three new hybrid manganese thioarsenates have been prepared and structurally characterized. These hybrid phases feature interesting magnetic and visible light responding photocatalytic properties.

  2. Crystal structure of I-Ak in complex with a dominant epitope of lysozyme.

    Science.gov (United States)

    Fremont, D H; Monnaie, D; Nelson, C A; Hendrickson, W A; Unanue, E R

    1998-03-01

    We have determined the structure of murine MHC class II I-Ak in complex with a naturally processed peptide from hen egg lysozyme (HEL residues 50-62) at 1.9 A resolution. These results provide a structural basis for the I-Ak peptide-binding motif. Binding is established by the deep burial of five anchor side chains into specific pockets of the I-Ak binding groove, with a zen-like fit of an aspartic acid in the P1 pocket. We also show that in the I-Ak alpha chain, a bulge occurs in the first strand of the peptide-binding platform, an insertion probably common to all I-A and HLA-DQ alleles. The I-Ak beta chain has a deletion in the helical region adjacent to the P7 pocket and an insertion in the helical region neighboring the P1 pocket. As a result of these structural features, the extended HEL peptide dips low into the center of the I-Ak groove and reaches toward solvent at its C-terminal end.

  3. Crystal structures of multidrug-resistant HIV-1 protease in complex with two potent anti-malarial compounds

    Energy Technology Data Exchange (ETDEWEB)

    Yedidi, Ravikiran S.; Liu, Zhigang; Wang, Yong; Brunzelle, Joseph S.; Kovari, Iulia A.; Woster, Patrick M.; Kovari, Ladislau C.; Gupta, Deepak (LECOM); (WSI); (NWU); (MUSC); (WSU)

    2012-06-19

    Two potent inhibitors (compounds 1 and 2) of malarial aspartyl protease, plasmepsin-II, were evaluated against wild type (NL4-3) and multidrug-resistant clinical isolate 769 (MDR) variants of human immunodeficiency virus type-1 (HIV-1) aspartyl protease. Enzyme inhibition assays showed that both 1 and 2 have better potency against NL4-3 than against MDR protease. Crystal structures of MDR protease in complex with 1 and 2 were solved and analyzed. Crystallographic analysis revealed that the MDR protease exhibits a typical wide-open conformation of the flaps (Gly48 to Gly52) causing an overall expansion in the active site cavity, which, in turn caused unstable binding of the inhibitors. Due to the expansion of the active site cavity, both compounds showed loss of direct contacts with the MDR protease compared to the docking models of NL4-3. Multiple water molecules showed a rich network of hydrogen bonds contributing to the stability of the ligand binding in the distorted binding pockets of the MDR protease in both crystal structures. Docking analysis of 1 and 2 showed a decrease in the binding affinity for both compounds against MDR supporting our structure-function studies. Thus, compounds 1 and 2 show promising inhibitory activity against HIV-1 protease variants and hence are good candidates for further development to enhance their potency against NL4-3 as well as MDR HIV-1 protease variants.

  4. Crystal structure of a Zn complex with terephthalate and 1,6-bis(1,2,4-triazol-1-ylhexane

    Directory of Open Access Journals (Sweden)

    Taisiya S. Sukhikh

    2018-01-01

    Full Text Available A new zinc coordination polymer with rigid benzene-1,4-dicarboxylate (bdc and flexible 1,6-bis(1,2,4-triazol-1-ylhexane (btrh, namely poly[[(μ2-benzene-1,4-dicarboxylato[μ2-1,6-bis(1,2,4-triazol-1-ylhexane]zinc] dimethylformamide monosolvate], [Zn(C8H4O4(C10H16N6]·C3H7NO, was synthesized. According to the single-crystal XRD analysis, the product crystallizes in the P-1 space group and has a layered structure. Analysis of the layered structure reveals {Zn(bdc} chains which are connected by pairs of btrh ligands. The layers are packed tightly perpendicular to the [1-22] direction, separated by one non-disordered dimethylformamide solvent molecule per formula unit. According to thermogravimetric analysis, the product completely loses this solvent at 453 K; the desolvated compound is stable up to 503 K. As a result of the lack of hydrogen-donor groups, hydrogen bonds are not observed in the structure of the complex; however, an intermolecular C—H...π contact of 3.07 Å occurs.

  5. Crystal structure, DNA interaction and thermal analysis data of two new antimicrobial active binuclear cadmium and mercury complexes

    Science.gov (United States)

    Musavi, S. A.; Montazerozohori, M.; Masoudiasl, A.; Naghiha, R.; Joohari, S.; Assoud, A.

    2017-10-01

    Two new binuclear Schiff base complexes with the general formula [CdLBr(μ-Br)]2 (1) and [Hg2L(μ-I)2I2] (2) were prepared by the reaction of 2,2-dimethyl-N,N'- bis-(3-phenyl-allylidene)-propane-1,3-diamine (L), CdBr2 and HgI2. The crystal structure of two complexes was determined by X-ray crystallography. The common structures for four-coordinated compounds are square planar or the tetrahedral geometries, which is evaluated by the Houser angular index (τ4). In [CdLBr(μ-Br)]2 (1), each cadmium center is five-coordinated by two iminic nitrogen atoms from Schiff base ligand, two μ2-bridging bromide anions and one terminal coordinating bromide anion. The metal center in this centrosymmetric dimer has a distorted square-pyramidal geometry. [Hg2L(μ-I)2I2] (2) consists of two four-coordinated mercury centers with different coordination spheres (HgN2I2 for Hg1 and HgI4 for Hg2). The TG/DTG diagrams showed that both complexes were completely decomposed under a nitrogen atmosphere. Furthermore, antibacterial activities of compounds have been screened against various bacteria and fungi by Disk diffusion method. Mercury complex inhibited the growth of the microorganisms more efficient than cadmium complex. DNA cleavage potential of compounds was evaluated by agarose gel electrophoresis method. Finally, nano-structure cadmium complex was sono-chemically synthesized and applied as precursor for preparation of cadmium oxide nanoparticles.

  6. Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate.

    Science.gov (United States)

    Josts, Inokentijs; Almeida Hernandez, Yasser; Andreeva, Antonina; Tidow, Henning

    2016-07-21

    Energy coupling factor (ECF) transporters are responsible for the uptake of essential scarce nutrients in prokaryotes. This ATP-binding cassette transporter family comprises two subgroups that share a common architecture forming a tripartite membrane protein complex consisting of a translocation component and ATP hydrolyzing module and a substrate-capture (S) component. Here, we present the crystal structure of YkoE from Bacillus subtilis, the S component of the previously uncharacterized group I ECF transporter YkoEDC. Structural and biochemical analyses revealed the constituent residues of the thiamine-binding pocket as well as an unexpected mode of vitamin recognition. In addition, our experimental and bioinformatics data demonstrate major differences between YkoE and group II ECF transporters and indicate how group I vitamin transporter S components have diverged from other group I and group II ECF transporters. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Crystal structure of archaeal chromatin protein Alba2-double-stranded DNA complex from Aeropyrum pernix K1.

    Science.gov (United States)

    Tanaka, Tomoyuki; Padavattan, Sivaraman; Kumarevel, Thirumananseri

    2012-03-23

    All thermophilic and hyperthermophilic archaea encode homologs of dimeric Alba (Sac10b) proteins that bind cooperatively at high density to DNA. Here, we report the 2.0 Å resolution crystal structure of an Alba2 (Ape10b2)-dsDNA complex from Aeropyrum pernix K1. A rectangular tube-like structure encompassing duplex DNA reveals the positively charged residues in the monomer-monomer interface of each dimer packing on either side of the bound dsDNA in successive minor grooves. The extended hairpin loop connecting strands β3 and β4 undergoes significant conformational changes upon DNA binding to accommodate the other Alba2 dimer during oligomerization. Mutational analysis of key interacting residues confirmed the specificity of Alba2-dsDNA interactions.

  8. Crystal Structure of Archaeal Chromatin Protein Alba2-Double-stranded DNA Complex from Aeropyrum pernix K1*

    Science.gov (United States)

    Tanaka, Tomoyuki; Padavattan, Sivaraman; Kumarevel, Thirumananseri

    2012-01-01

    All thermophilic and hyperthermophilic archaea encode homologs of dimeric Alba (Sac10b) proteins that bind cooperatively at high density to DNA. Here, we report the 2.0 Å resolution crystal structure of an Alba2 (Ape10b2)-dsDNA complex from Aeropyrum pernix K1. A rectangular tube-like structure encompassing duplex DNA reveals the positively charged residues in the monomer-monomer interface of each dimer packing on either side of the bound dsDNA in successive minor grooves. The extended hairpin loop connecting strands β3 and β4 undergoes significant conformational changes upon DNA binding to accommodate the other Alba2 dimer during oligomerization. Mutational analysis of key interacting residues confirmed the specificity of Alba2-dsDNA interactions. PMID:22334696

  9. Crystal structure of the Lassa virus nucleoprotein-RNA complex reveals a gating mechanism for RNA binding.

    Science.gov (United States)

    Hastie, Kathryn M; Liu, Tong; Li, Sheng; King, Liam B; Ngo, Nhi; Zandonatti, Michelle A; Woods, Virgil L; de la Torre, Juan Carlos; Saphire, Erica Ollmann

    2011-11-29

    Arenaviruses cause disease in industrialized and developing nations alike. Among them, the hemorrhagic fever virus Lassa is responsible for ~300,000-500,000 infections/y in Western Africa. The arenavirus nucleoprotein (NP) forms the protein scaffold of the genomic ribonucleoprotein complexes and is critical for transcription and replication of the viral genome. Here, we present crystal structures of the RNA-binding domain of Lassa virus NP in complex with ssRNA. This structure shows, in contrast to the predicted model, that RNA binds in a deep, basic crevice located entirely within the N-terminal domain. Furthermore, the NP-ssRNA structures presented here, combined with hydrogen-deuterium exchange/MS and functional studies, suggest a gating mechanism by which NP opens to accept RNA. Directed mutagenesis and functional studies provide a unique look into how the arenavirus NPs bind to and protect the viral genome and also suggest the likely assembly by which viral ribonucleoprotein complexes are organized.

  10. A novel cationic cobalt(III) Schiff base complex: Preparation, crystal structure, Hirshfeld surface analysis, antimicrobial activities and molecular docking.

    Science.gov (United States)

    Yousef Ebrahimipour, S; Machura, Barbara; Mohamadi, Maryam; Khaleghi, Moj

    2017-12-01

    A novel Co(III) complex, [Co(L)(Imi)3]Cl incorporating 2-((3-methoxy-2-oxidobenzylidene)amino)-4-methylphenolate (L2-), as a dibasic deprotonated Schiff base ligand and imidazole (Imi) was synthesized and fully characterized using physicochemical and spectroscopic techniques including elemental analysis, conductance measurement, FT-IR, UV-Vis and X-ray single crystal diffraction. As the conductivity data showed, the synthesized complex had a 1:1 ionic nature. The structure of the complex was found to be distorted octahedral in which, O/N donor atoms of the Schiff base ligand and N atoms of three imidazole groups were involved. Antimicrobial activity of the Co(III) complex as well as the its parent Schiff base ligand against two Gram-positive bacteria (S. Aureus and M. luteus), two Gram-negative bacteria (E. coli and P. aeruginosa) and a fungus (C. Albicans) was studied. Moreover, the antimicrobial activity of [Co(L)(Imi)3]Cl was investigated using molecular docking of the complex with GlcN-6-P synthase. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Anion complexation with cyanobenzoyl substituted first and second generation tripodal amide receptors: crystal structure and solution studies.

    Science.gov (United States)

    Hoque, Md Najbul; Gogoi, Abhijit; Das, Gopal

    2015-09-14

    Anion complexation properties of two new tripodal amide receptors have been extensively studied here. Two tripodal receptors have been synthesized from the reaction of cyanobenzoyl acid chloride with two tri-amine building blocks such as (i) tris(2-aminoethyl)amine and (ii) tris(2-(4-aminophenoxy)ethyl)amine, which resulted in the first (L1) and second (L2) generation tripodal amides respectively. A detailed comparison of their coordination behavior with anions is also described by crystallographic and solution state experiments. The crystal structure demonstrates various types of spatial orientations of tripodal arms in two receptors and concomitantly interacts with anions distinctively. Intramolecular H-bonding between amide N–H and CO prevents opening of the receptor cavity in the crystal, which leads to a locked conformation of L1 having C(3v) symmetry and makes amide hydrogen unavailable for the anion which results in side cleft anion binding. However, in L2 we conveniently shift the anion binding sites to a distant position which increases cavity size as well as rules out any intramolecular H-bonding between amide N–H and CO. The crystal structure shows a different orientation of the arms in L2; it adopts a quasi-planar arrangement with C(2v) symmetry. In the crystal structure two arms are pointed in the same direction and while extending the contact the third arm is H-bonded with the apical N-atom through a –CN group, making a pseudo capsular cavity where the anion interacts. Most importantly spatial reorientation of the receptor L2 from a C(2v) symmetry to a folded conformation with a C(3v) symmetry was observed only in the presence of an octahedral SiF6(2-) anion and forms a sandwich type complex. Receptors L1 and L2 are explored for their solution state anion binding abilities. The substantial changes in chemical shifts were observed for the amide (-NH) and aromatic hydrogen (-CH) (especially for F(-)), indicating the role of these hydrogens in

  12. The crystal structure of the secreted aspartic protease 1 from Candida parapsilosis in complex with pepstatin A

    Energy Technology Data Exchange (ETDEWEB)

    Dostál, Ji& #345; í; Brynda, Ji& #345; í; Hrušková-Heidingsfeldová, Olga; Sieglová, Irena; Pichová, Iva; & #344; ezá& #269; ová, Pavlína; (ASCR-ICP)

    2010-09-01

    Opportunistic pathogens of the genus Candida cause infections representing a major threat to long-term survival of immunocompromised patients. Virulence of the Candida pathogens is enhanced by production of extracellular proteolytic enzymes and secreted aspartic proteases (Saps) are therefore studied as potential virulence factors and possible targets for therapeutic drug design. Candida parapsilosis is less invasive than C. albicans, however, it is one of the leading causative agents of yeast infections. We report three-dimensional crystal structure of Sapp1p from C. parapsilosis in complex with pepstatin A, the classical inhibitor of aspartic proteases. The structure of Sapp1p was determined from protein isolated from its natural source and represents the first structure of Sap from C. parapsilosis. Overall fold and topology of Sapp1p is very similar to the archetypic fold of monomeric aspartic protease family and known structures of Sap isoenzymes from C. albicans and Sapt1p from C. tropicalis. Structural comparison revealed noticeable differences in the structure of loops surrounding the active site. This resulted in differential character, shape, and size of the substrate binding site explaining divergent substrate specificities and inhibitor affinities. Determination of structures of Sap isoenzymes from various species might contribute to the development of new Sap-specific inhibitors.

  13. Gold(III) bis-thiosemicarbazonato complexes: synthesis, characterization, radiochemistry and X-ray crystal structure analysis.

    Science.gov (United States)

    Bottenus, Brienne N; Kan, Para; Jenkins, Tyler; Ballard, Beau; Rold, Tammy L; Barnes, Charles; Cutler, Cathy; Hoffman, Timothy J; Green, Mark A; Jurisson, Silvia S

    2010-01-01

    A variety of (bis)thiosemicarbazone-based ligand systems have been investigated as chelating agents for Au(III) complexes with potential radiotherapeutic applications. Ligand systems containing an ethyl, propyl or butyl backbone between the two imine N donors have been synthesized to evaluate chelate ring size effects on the resultant Au(III) complex stability at the macroscopic and radiotracer levels. The Au(III) complexes were synthesized and characterized by NMR, electrospray ionization mass spectra, elemental analysis and X-ray crystallography. The (198)Au complexes were evaluated in vitro at the tracer level for stability in phosphate-buffered saline at pH 7.4 and 37 degrees C. One of these complexes [(198)Au(3,4-HxTSE)] showed high in vitro stability and was further evaluated in vivo in normal mice. [Au(ATSM)]AuCl(4).2CH(3)OH, (ATSM=diacetyl-bis(N(4)-methylthiosemicarbazone)) H(14)C(8)N(6)O(2)S(2)Cl(4)Au(2).2CH(3)OH, crystallized from methanol in the monoclinic space group P21/n with a=14.7293(13) A, b=7.7432(7) A, c=20.4363(18) A, beta=100.140(2) degrees, V=2294.4 (4) A(3), Z=4; [Au(3,4-HxTSE)]Cl.CH(3)CH(2)OH/AuCl(2), (3,4-HxTSE=3,4-hexanedione-bis(N(4)-ethylthiosemicarbazone)) H(26)C(13.6)N(6)O(0.8)S(2)Cl(1.2)Au(1.2), crystallized from ethanol in the monoclinic space group P21/c with a=10.1990(10) A, b=13.8833(14) A, c=15.1752(15) A, beta=99.353(2) degrees , V=2120.2 (4) A(3), Z=4. These studies revealed poor stability of the [(198)Au][Au(3,4-HxTSE)](+) complex; however, crystal structure data suggest potential alterations to the ligand backbone may increase stability. Copyright 2010 Elsevier Inc. All rights reserved.

  14. Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803.

    Science.gov (United States)

    Mazor, Yuval; Nataf, Daniel; Toporik, Hila; Nelson, Nathan

    2013-01-01

    Oxygenic photosynthesis supports virtually all life forms on earth. Light energy is converted by two photosystems-photosystem I (PSI) and photosystem II (PSII). Globally, nearly 50% of photosynthesis takes place in the Ocean, where single cell cyanobacteria and algae reside together with their viruses. An operon encoding PSI was identified in cyanobacterial marine viruses. We generated a PSI that mimics the salient features of the viral complex, named PSI(PsaJF). PSI(PsaJF) is promiscuous for its electron donors and can accept electrons from respiratory cytochromes. We solved the structure of PSI(PsaJF) and a monomeric PSI, with subunit composition similar to the viral PSI, providing for the first time a detailed description of the reaction center and antenna system from mesophilic cyanobacteria, including red chlorophylls and cofactors of the electron transport chain. Our finding extends the understanding of PSI structure, function and evolution and suggests a unique function for the viral PSI. DOI: http://dx.doi.org/10.7554/eLife.01496.001.

  15. Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA

    Science.gov (United States)

    Sarafianos, Stefan G.; Das, Kalyan; Tantillo, Chris; Clark, Arthur D.; Ding, Jianping; Whitcomb, Jeannette M.; Boyer, Paul L.; Hughes, Stephen H.; Arnold, Edward

    2001-01-01

    We have determined the 3.0 Å resolution structure of wild-type HIV-1 reverse transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT). The PPT is resistant to ribonuclease H (RNase H) cleavage and is used as a primer for second DNA strand synthesis. The ‘RNase H primer grip’, consisting of amino acids that interact with the DNA primer strand, may contribute to RNase H catalysis and cleavage specificity. Cleavage specificity is also controlled by the width of the minor groove and the trajectory of the RNA:DNA, both of which are sequence dependent. An unusual ‘unzipping’ of 7 bp occurs in the adenine stretch of the PPT: an unpaired base on the template strand takes the base pairing out of register and then, following two offset base pairs, an unpaired base on the primer strand re-establishes the normal register. The structural aberration extends to the RNase H active site and may play a role in the resistance of PPT to RNase H cleavage. PMID:11250910

  16. Picolinic acid based Cu(II) complexes with heterocyclic bases--crystal structure, DNA binding and cleavage studies.

    Science.gov (United States)

    Pulimamidi, Rabindra Reddy; Nomula, Raju; Pallepogu, Raghavaiah; Shaik, Hussain

    2014-05-22

    In view of the importance of picolinic acid (PA) in preventing cell growth and arresting cell cycle, new PA based metallonucleases were designed with a view to study their DNA binding and cleavage abilities. Three new Cu(II) complexes [Cu(II)(DPPA)].4H2O (1),[Cu(II)(DPPA)(bpy)].5H2O (2) and [Cu(II)(DPPA)(phen)].5H2O (3), were synthesized using a picolinic acid based bifunctional ligand (DPPA) and heterocyclic bases (where DPPA: Pyridine-2-carboxylic acid {2-phenyl-1-[(pyridin-2-ylmethyl)-carbonyl]-ethyl}-amide; bpy: 2, 2'-bipyridine and phen: 1, 10-phenanthroline). DPPA was obtained by coupling 2-picolinic acid and 2-picolyl amine with l-phenylalanine through amide bond‌‌. Complexes were structurally characterized by a single crystal X-ray crystallography. The molecular structure of 1 shows Cu(II) center essentially in a square planar coordination geometry, while complex 2 shows an approximate five coordinated square-pyramidal geometry. Eventhough we could not isolate single crystal for complex (3), its structure was established based on other techniques. The complex (3) also exhibits five coordinate square pyramidal geometry. The complexes show good binding affinity towards CT-DNA. The binding constants (Kb) decrease in the order 1.35 ± 0.01 × 10(5) (3) > 1.23 ± 0.01 × 10(5) (2) > 8.3 ± 0.01 × 10(4) (1) M(-1). They also exhibit efficient nuclease activity towards supercoiled pUC19 DNA both in the absence and presence of external agent (H2O2). The kinetic studies reveal that the hydrolytic cleavage reactions follow the pseudo first-order rate constant and the hydrolysis rates are in the range of (5.8-8.0) × 10(7) fold rate enhancement compared to non-catalyzed double stranded DNA (3.6 × 10(-8) h(-1)). Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  17. Crystal structure of a lipoxygenase in complex with substrate: the arachidonic acid-binding site of 8R-lipoxygenase.

    Science.gov (United States)

    Neau, David B; Bender, Gunes; Boeglin, William E; Bartlett, Sue G; Brash, Alan R; Newcomer, Marcia E

    2014-11-14

    Lipoxygenases (LOX) play critical roles in mammalian biology in the generation of potent lipid mediators of the inflammatory response; consequently, they are targets for the development of isoform-specific inhibitors. The regio- and stereo-specificity of the oxygenation of polyunsaturated fatty acids by the enzymes is understood in terms of the chemistry, but structural observation of the enzyme-substrate interactions is lacking. Although several LOX crystal structures are available, heretofore the rapid oxygenation of bound substrate has precluded capture of the enzyme-substrate complex, leaving a gap between chemical and structural insights. In this report, we describe the 2.0 Å resolution structure of 8R-LOX in complex with arachidonic acid obtained under anaerobic conditions. Subtle rearrangements, primarily in the side chains of three amino acids, allow binding of arachidonic acid in a catalytically competent conformation. Accompanying experimental work supports a model in which both substrate tethering and cavity depth contribute to positioning the appropriate carbon at the catalytic machinery. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. High-resolution crystal structure of human Mapkap kinase 3 in complex with a high affinity ligand.

    Science.gov (United States)

    Cheng, Robert; Felicetti, Brunella; Palan, Shilpa; Toogood-Johnson, Ian; Scheich, Christoph; Barker, John; Whittaker, Mark; Hesterkamp, Thomas

    2010-01-01

    The Mapkap kinases 2 and 3 (MK2 and MK3) have been implicated in intracellular signaling pathways leading to the production of the pro-inflammatory cytokine tumor necrosis factor alpha. MK2 has been pursued by the biopharmaceutical industry for many years for the development of a small molecule anti-inflammatory treatment and drug-like inhibitors have been described. The development of some of these compounds, however, has been slowed by the absence of a high-resolution crystal structure of MK2. Herein we present a high-resolution (1.9 A) crystal structure of the highly homologous MK3 in complex with a pharmaceutical lead compound. While all of the canonical features of Ser/Thr kinases in general and MK2 in particular are recapitulated in MK3, the detailed analysis of the binding interaction of the drug-like ligand within the adenine binding pocket allows relevant conclusions to be drawn for the further design of potent and selective drug candidates.

  19. Crystal Structure of Lymnaea stagnalis AChBP Complexed with the Potent nAChR Antagonist DHßE Suggests a Unique Mode of Antagonism

    DEFF Research Database (Denmark)

    Shahsavar, Azadeh; Kastrup, Jette S; Nielsen, Elsebet Ø.

    2012-01-01

    for the active conformation of nAChRs in complex with agonists whereas an open C-loop reflects an antagonist-bound (closed) state. In this work, we have determined the crystal structure of AChBP from the water snail Lymnaea stagnalis (Ls) in complex with dihydro-ß-erythroidine (DHßE), which is a potent...

  20. Crystal structures at 2.5 Angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate

    DEFF Research Database (Denmark)

    Belrhali, H.; Yaremchuk, A.; Tukalo, M.

    1994-01-01

    Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 Angstrom resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monophosphate), produced enzymatically...

  1. Crystal structure of an affinity-matured prolactin complexed to its dimerized receptor reveals the topology of hormone binding site 2

    DEFF Research Database (Denmark)

    Broutin, Isabelle; Jomain, Jean-Baptiste; Tallet, Estelle

    2010-01-01

    We report the first crystal structure of a 1:2 hormone.receptor complex that involves prolactin (PRL) as the ligand, at 3.8-A resolution. Stable ternary complexes were obtained by generating affinity-matured PRL variants harboring an N-terminal tail from ovine placental lactogen, a closely related...

  2. Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits of the BLM Complex

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Feng; Yang, Yuting; Singh, Thiyam Ramsing; Busygina, Valeria; Guo, Rong; Wan, Ke; Wang, Weidong; Sung, Patrick; Meetei, Amom Ruhikanta; Lei, Ming (Yale-MED); (NIH); (Michigan-Med); (UCIN-MED)

    2010-11-05

    Mutations in BLM, a RecQ-like helicase, are linked to the autosomal recessive cancer-prone disorder Bloom's syndrome. BLM associates with topoisomerase (Topo) III{alpha}, RMI1, and RMI2 to form the BLM complex that is essential for genome stability. The RMI1-RMI2 heterodimer stimulates the dissolution of double Holliday junction into non-crossover recombinants mediated by BLM-Topo III{alpha} and is essential for stabilizing the BLM complex. However, the molecular basis of these functions of RMI1 and RMI2 remains unclear. Here we report the crystal structures of multiple domains of RMI1-RMI2, providing direct confirmation of the existence of three oligonucleotide/oligosaccharide binding (OB)-folds in RMI1-RMI2. Our structural and biochemical analyses revealed an unexpected insertion motif in RMI1N-OB, which is important for stimulating the dHJ dissolution. We also revealed the structural basis of the interaction between RMI1C-OB and RMI2-OB and demonstrated the functional importance of the RMI1-RMI2 interaction in genome stability maintenance.

  3. The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function.

    OpenAIRE

    Rowland, P.; Björnberg, O.; Nielsen, F. S.; Jensen, K. F.; Larsen, S.

    1998-01-01

    Dihydroorotate dehydrogenases (DHODs) catalyze the oxidation of (S)-dihydroorotate to orotate, the fourth step and only redox reaction in the de novo biosynthesis of pyrimidine nucleotides. A description is given of the crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A (DHODA) complexed with the product of the enzyme reaction orotate. The structure of the complex to 2.0 A resolution has been compared with the structure of the native enzyme. The active site of DHODA is kno...

  4. Kinetics of Torpedo californica acetylcholinesterase inhibition by bisnorcymserine and crystal structure of the complex with its leaving group.

    Science.gov (United States)

    Bartolucci, Cecilia; Stojan, Jure; Yu, Qian-sheng; Greig, Nigel H; Lamba, Doriano

    2012-06-01

    Natural and synthetic carbamates act as pseudo-irreversible inhibitors of AChE (acetylcholinesterase) as well as BChE (butyrylcholinesterase), two enzymes involved in neuronal function as well as in the development and progression of AD (Alzheimer's disease). The AChE mode of action is characterized by a rapid carbamoylation of the active-site Ser(200) with release of a leaving group followed by a slow regeneration of enzyme action due to subsequent decarbamoylation. The experimental AD therapeutic bisnorcymserine, a synthetic carbamate, shows an interesting activity and selectivity for BChE, and its clinical development is currently being pursued. We undertook detailed kinetic studies on the activity of the carbamate bisnorcymserine with Tc (Torpedo californica) AChE and, on the basis of the results, crystallized the complex between TcAChE and bisnorcymserine. The X-ray crystal structure showed only the leaving group, bisnoreseroline, trapped at the bottom of the aromatic enzyme gorge. Specifically, bisnoreseroline interacts in a non-covalent way with Ser(200) and His(440), disrupting the existing interactions within the catalytic triad, and it stacks with Trp(84) at the bottom of the gorge, giving rise to an unprecedented hydrogen-bonding contact. These interactions point to a dominant reversible inhibition mechanism attributable to the leaving group, bisnoreseroline, as revealed by kinetic analysis.

  5. Synthesis, Crystal Structure, Stacking Effect and Antibacterial Studies of a Novel Quaternary Copper (II Complex with Quinolone

    Directory of Open Access Journals (Sweden)

    Longguan Zhu

    2003-02-01

    Full Text Available The structural properties of a new copper (II complex [Cu2(cip2(bpy2(pip]·6H2O (bpy=2,2’-bipyridyl, cip=1-cyclopropyl-6-4-oxo-1,4-dihydroquinoline-3-carboxylic acid, pip= piperazinyl anion, obtained during the synthesis of the copper complex with ciprofloxacin (cpf, has been investigated. The complex crystallizes in the triclinic system, space group P-1. The cell dimensions are: a=6.874(2 Å, b= 10.761(3 Å, c= 17.969(5 Å, α =80.071(6°, β= 85.253(6°, γ=79.109(6°,V=1284.5(6 Å3, and Z=2. The Cu (II ion displays a five-coordinate square pyramidal coordination with two nitrogen donors from bpy, the 4-keto and 3-carboxylate oxygen donors of cip, and the third nitrogen atom of the pip anion occupying the fifth site. There is a stack effect between cip ring and bpy ring from another molecule, where the stacking distance is about 3.5 Å. The results of elemental analysis and FT-IR measurement are also included. Both ligand and complex were assayed against gram-positive and gram-negative bacteria by the doubling dilutions method. The complex shows the same minimal inhibitory concentration (MIC against S. Aureus and E. Coli bacteria as the corresponding ligand.

  6. A Novel Phenanthridionone Based Scaffold As a Potential Inhibitor of the BRD2 Bromodomain: Crystal Structure of the Complex.

    Directory of Open Access Journals (Sweden)

    Shailesh Tripathi

    Full Text Available Bromodomain containing proteins recognize the level of histone acetylation and regulate epigenetically controlled processes like gene transcription and chromatin modification. The BET (bromodomain and extra-terminal family proteins, which are transcriptional co-regulators, have been implicated in the pathogenesis of cancer, neurodegenerative disorders, and defects in embryonic stem cell differentiation. Inhibitors selectively targeting the BET bromodomains can pave the path for new drug discovery against several forms of major diseases. By a rational structure-based approach, we have identified a new inhibitor (NSC127133 of the second bromodomain (BD2 of the BET family protein BRD2 using the NCI Diversity Set III library. A high-resolution crystal structure of the BRD2-BD2 in complex with this compound and in apo- form is refined to 0.91 and 0.94 Å, respectively. The compound, which is a phenanthridinone derivative, binds well to the acetyl-lysine binding pocket of BD2 and displays significant hydrophobic and hydrophilic interactions. Moreover, the atomic resolution data obtained in this study allowed us to visualize certain structural features of BD2 which remained unobserved so far. We propose that the discovered compound may be a potential molecule to develop a new library for inhibiting the BRD2-BD2 function.

  7. Crystal structure of RNase H3–substrate complex reveals parallel evolution of RNA/DNA hybrid recognition

    Science.gov (United States)

    Figiel, Małgorzata; Nowotny, Marcin

    2014-01-01

    RNases H participate in the replication and maintenance of genomic DNA. RNase H1 cleaves the RNA strand of RNA/DNA hybrids, and RNase H2 in addition hydrolyzes the RNA residue of RNA–DNA junctions. RNase H3 is structurally closely related to RNases H2, but its biochemical properties are similar to type 1 enzymes. Its unique N-terminal substrate-binding domain (N-domain) is related to TATA-binding protein. Here, we report the first crystal structure of RNase H3 in complex with its RNA/DNA substrate. Just like RNases H1, type 3 enzyme recognizes the 2′-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation. Moreover, the N-domain recognizes RNA and DNA in a manner that is highly similar to the hybrid-binding domain of RNases H1. Our structure demonstrates a remarkable example of parallel evolution of the elements used in the specific recognition of RNA and DNA. PMID:25016521

  8. Crystal structures of three complexes of zinc chloride with tri-tert-butylphosphane

    Directory of Open Access Journals (Sweden)

    Aaron D. Finke

    2016-01-01

    Full Text Available Under anhydrous conditions and in the absence of a Lewis-base solvent, a zinc chloride complex with tri-tert-butylphosphane as the μ-bridged dimer is formed, viz. di-μ-chlorido-bis[chloridobis(tri-tert-butylphosphanezinc], [ZnCl4(C12H27P2], (1, which features a nearly square-shaped (ZnCl2 cyclic core and whose Cl atoms interact weakly with C—H groups on the phosphane ligand. In the presence of THF, monomeric dichlorido(tetrahydrofuran-κO(tri-tert-butylphosphane-κPzinc, [ZnCl2(C4H8O(C12H27P] or [P(tBu3(THFZnCl2], (2, is formed. This slightly distorted tetrahedral Zn complex has weak C—H...Cl interactions between the Cl atoms and phosphane and THF C—H groups. Under ambient conditions, the hydrolysed complex tri-tert-butylphosphonium aquatrichloridozincate 1,2-dichloroethane monosolvate, (C12H28P[ZnCl3(H2O]·C2H4Cl2 or [HPtBu3]+ [(H2OZnCl3]−·C2H4Cl2, (3, is formed. This complex forms chains of [(H2OZnCl3]− anions from hydrogen-bonding interactions between the water H atoms and Cl atoms that propagate along the b axis.

  9. Crystal structures of bis- and hexakis[(6,6′-dihydroxybipyridinecopper(II] nitrate coordination complexes

    Directory of Open Access Journals (Sweden)

    Deidra L. Gerlach

    2015-12-01

    Full Text Available Two multinuclear complexes synthesized from Cu(NO32 and 6,6′-dihydroxybipyridine (dhbp exhibit bridging nitrate and hydroxide ligands. The dinuclear complex (6,6′-dihydroxybipyridine-2κ2N,N′[μ-6-(6-hydroxypyridin-2-ylpyridin-2-olato-1:2κ3N,N′:O2](μ-hydroxido-1:2κ2O:O′(μ-nitrato-1:2κ2O:O′(nitrato-1κOdicopper(II, [Cu2(C10H7N2O2(OH(NO32(C10H8N2O2] or [Cu(6-OH-6′-O-bpy(NO3(μ-OH(μ-NO3Cu(6,6′-dhbp], (I, with a 2:1 ratio of nitrate to hydroxide anions and one partially deprotonated dhbp ligand, forms from a water–ethanol mixture at neutral pH. The hexanuclear complex bis(μ3-bipyridine-2,2′-diolato-κ3O:N,N′:O′tetrakis(6,6′-dihydroxybipyridine-κ2N,N′tetrakis(μ-hydroxido-κ2O:O′bis(methanol-κOtetrakis(μ-nitrato-κ2O:O′hexacopper(II, [Cu6(C10H6N2O22(CH4O2(OH4(NO34(C10H8N2O24] or [Cu(6,6′-dhbp(μ-NO32(μ-OHCu(6,6′-O-bpy(μ-OHCu(6,6′dhbp(CH3OH]2, (II, with a 1:1 NO3–OH ratio and two fully protonated and fully deprotonated dhbp ligands, was obtained by methanol recrystallization of material obtained at pH 3. Complex (II lies across an inversion center. Complexes (I and (II both display intramolecular O—H...O hydrogen bonding. Intermolecular O—H...O hydrogen bonding links symmetry-related molecules forming chains along [100] for complex (I with π-stacking along [010] and [001]. Complex (II forms intermolecular O—H...O hydrogen-bonded chains along [010] with π-stacking along [100] and [001].

  10. Synthesis and X-ray crystal structure determination of the first Copper(II) complexes of tetraazamacrocycle-glyoxal condensates.

    Science.gov (United States)

    Hubin, Timothy J; Alcock, Nathaniel W; Seib, Lawrence L; Busch, Daryle H

    2002-12-30

    Novel Cu(II) complexes CuLCl(2) (L = 1-4) have been synthesized containing the metal bound to a well-known type of tetracyclic bisaminal formed from the condensation of glyoxal and tetraazamacrocycles (1 = cyclam-glyoxal condensate, 2 = [13]aneN4-glyoxal condensate, 3 = cyclen-glyoxal condensate, 4 = isocyclam-glyoxal condensate). The four-coordinate complexes were characterized by X-ray crystallography, electronic spectroscopy, solid-state magnetic moments, and electron spin resonance spectroscopy. The tetracyclic bisaminals, although having four potential donor atoms, are bound in a cis-bidentate fashion to Cu(II) with two additional cis-chloride donors. The ligands take up folded conformations, and with the exception of ligand 4, only nonadjacent nitrogen atoms coordinate. As expected, ligand 2 in Cu(2)Cl(2) has a folded structure similar to those of the previously characterized 1 and 3. The conformation of 4 in the complex Cu(4)Cl(2) differs from 1-3 in that three nitrogens direct their lone pairs to one side of the folded tetracycle, with adjacent nitrogen atoms coordinated to Cu(II). This difference is probably caused by the presence of the more flexible seven-membered ring rather than the five- to six-membered rings in 1-3. Air oxidation of Cu(I) in the presence of 1 or 3 results in bis(mu-hydroxo) dimers as characterized by X-ray crystal structures, suggesting dioxygen binding, followed by O-O bond splitting to give the Cu(2)O(2) diamond core.

  11. Synthesis, crystal structure and reactivity studies of iron complexes with pybox ligands

    KAUST Repository

    Chen, Tao

    2014-11-01

    Iron(II) complexes, [Fe(2,6-bis(4,4-dimethyl-1,3-oxazolin-2-yl)pyridine)Cl2] ((Fe(Me2-pybox)Cl2), 3) and [Fe(2,6-bis(4,4-diphenyl-1,3-oxazolin-2-yl)pyridine)Cl2] ((Fe(Ph2-pybox)Cl2), 4), have been synthesized and characterized by X-ray crystallographic analysis. Upon treatment of complex 3 with silver triflate and 4 with acetonitrile, [Fe(Me2-pybox)(CH3CN)OTf2] (5) and [Fe(Ph2-pybox)(CH3CN)2Cl][FeCl3] (6) were obtained, respectively. The bulkier phenyl substitutes were found not only to cause the elongation of the N-Fe bonds but also influence the reactivity of the Fe center.

  12. Rhenium(IV)-copper(II) heterobimetallic complexes with a bridge malonato ligand. Synthesis, crystal structure, and magnetic properties.

    Science.gov (United States)

    Cuevas, Alicia; Chiozzone, Raúl; Kremer, Carlos; Suescun, Leopoldo; Mombrú, Alvaro; Armentano, Donatella; De Munno, Giovanni; Lloret, Francesc; Cano, Juan; Faus, Juan

    2004-11-29

    The Re(IV) complex [ReCl4(mal)]2-, in the form of two slightly different salts, (AsPh4)1.5(HNEt3)0.5[ReCl4(mal)] (1a) and (AsPh4)(HNEt3)[ReCl4(mal)] (1b), and the Re(IV)-Cu(II) bimetallic complexes [ReCl4(mu-mal)Cu(phen)2].CH3CN (2), [ReCl4(mu-mal)Cu(bpy)2] (3), and [ReCl4(mu-mal)Cu(terpy)] (4) (mal=malonate dianion, AsPh4=tetraphenylarsonium cation, HNEt3=triethylammonium cation, phen=1,10-phenanthroline, bpy=2,2'-bipyridine and terpy=2,2':6',2' '-terpyridine) have been synthesized and the structures of 1a, 1b, 2, and 3 determined by single-crystal X-ray diffraction. The structures of 1a and 1b are made up of discrete [ReCl4(mal)]2- anions and AsPh4+ and HNEt3+ cations, held together by electrostatic forces and hydrogen bonds. The Re(IV) atom is surrounded by four chloride anions and a bidentate malonate group, in a distorted octahedral environment. The structure of 2 consist of neutral dinuclear units [ReCl4(mu-mal)Cu(phen)2], with the metal ions united through a bridge carboxilato. The environment of Re(IV) is nearly identical to that in the mononuclear complex, and Cu(II) is five coordinate, being surrounded by four nitrogen atoms of two bidentate phen ligands and one oxygen atom of the malonato ligand. In 3, there are also dinuclear units, [ReCl4(mu-mal)Cu(bpy)2], but the Cu(II) ions complete a distorted octahedral coordination by binding with the free malonato oxygen atom of a neighbor unit, resulting in an infinite chain. The magnetic properties of 1-4 were also investigated in the temperature range 2.0-300 K. The magnetic behavior of 1a and 1b is as expected for a Re(IV) complex with a large value of the zero-field splitting (2D ca. 110 cm(-1)). For the bimetallic complexes, the magnetic coupling between Re(IV) and Cu(II) is antiferromagnetic in 2 (J=-0.39 cm(-1)), ferromagnetic in 4 (J=+1.51 cm(-1)), and nearly negligible in 3 (J=-0.09 cm(-1)).

  13. Crystal Structures of the Glycopeptide Sulfotransferase Teg12 Complexed with the Teicoplanin Aglycone

    Science.gov (United States)

    Bick, Matthew J.; Banik, Jacob J.; Darst, Seth A.; Brady, Sean F.

    2010-01-01

    The TEG gene cluster, a glycopeptide biosynthetic gene cluster that is predicted to encode the biosynthesis of a polysulfated glycopeptide congener, was recently cloned from DNA extracted directly from desert soil. This predicted glycopeptide gene cluster contains three closely related sulfotransferases (Teg12, 13, and 14) that sulfate teicoplanin-like glycopeptides at three unique sites. Here we report a series of structures including: an apo structure of Teg12, Teg12 bound to the desulfated co-substrate 3'-phosphoadenosine 5'-phosphate and Teg12 bound to the teicoplanin aglycone. Teg12 appears to undergo a series of significant conformational rearrangements during glycopeptide recruitment, binding and catalysis. Loop regions that exhibit the most conformational flexibility show the least sequence conservation between TEG sulfotransferases. Site directed mutagenesis guided by our structural studies confirmed the importance of key catalytic residues as well as the importance of residues found throughout the conformationally flexible loop regions. PMID:20361791

  14. Crystal Structures of the Glycopeptide Sulfotransferase Teg12 in a Complex with the Teicoplanin Aglycone

    Energy Technology Data Exchange (ETDEWEB)

    Bick, Matthew J.; Banik, Jacob J.; Darst, Seth A.; Brady, Sean F. (Rockefeller)

    2010-06-25

    The TEG gene cluster, a glycopeptide biosynthetic gene cluster that is predicted to encode the biosynthesis of a polysulfated glycopeptide congener, was recently cloned from DNA extracted directly from desert soil. This predicted glycopeptide gene cluster contains three closely related sulfotransferases (Teg12, -13, and -14) that sulfate teicoplanin-like glycopeptides at three unique sites. Here we report a series of structures: an apo structure of Teg12, Teg12 bound to the desulfated cosubstrate 3{prime}-phosphoadenosine 5{prime}-phosphate, and Teg12 bound to the teicoplanin aglycone. Teg12 appears to undergo a series of significant conformational rearrangements during glycopeptide recruitment, binding, and catalysis. Loop regions that exhibit the most conformational flexibility show the least sequence conservation between TEG sulfotransferases. Site-directed mutagenesis guided by our structural studies confirmed the importance of key catalytic residues as well as the importance of residues found throughout the conformationally flexible loop regions.

  15. Relationship between Crystal Structures and Photoluminescent Properties of Novel functionalized Carbazole Silver(I) Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Nam; Lee, Young-A [Chonbuk National University, Jeonju (Korea, Republic of); Kim, Jeong Gyun [Pusan National University, Pusan (Korea, Republic of)

    2016-04-15

    We investigated the anion effects on the formation and PL of a series of silver(I) complexes containing new carbazole-decorated L. Nitrate anion acts as an anionic tectonic for the 1D coordination polymeric skeleton whereas other anions act as simple counteranions in the discrete [Ag(L){sub 2}] skeletons. Furthermore, the PL intensity of the present coordination polymers has been known to be sensitive to the size of counteranions. More systematic researches, including modification of the related Ls, will provide more detailed information on the rational development of functional emitting materials sensitive to the external stimuli.

  16. Crystal Structure of Human Factor VIII: Implications for the Formation of the Factor IXa-Factor VIIIa Complex

    Energy Technology Data Exchange (ETDEWEB)

    Chi Ki Ngo,J.; Huang, M.; Roth, D.; Furie, B.; Furie, B.

    2008-01-01

    Factor VIII is a procofactor that plays a critical role in blood coagulation, and is missing or defective in hemophilia A. We determined the X-ray crystal structure of B domain-deleted human factor VIII. This protein is composed of five globular domains and contains one Ca(2+) and two Cu(2+) ions. The three homologous A domains form a triangular heterotrimer where the A1 and A3 domains serve as the base and interact with the C2 and C1 domains, respectively. The structurally homologous C1 and C2 domains reveal membrane binding features. Based on biochemical studies, a model of the factor IXa-factor VIIIa complex was constructed by in silico docking. Factor IXa wraps across the side of factor VIII, and an extended interface spans the factor VIII heavy and light chains. This model provides insight into the activation of factor VIII and the interaction of factor VIIIa with factor IXa on the membrane surface.

  17. Crystal Structure of Human Factor VIII: Implications for the Formation of the Factor IXa-Factor VIIIa Complex

    Energy Technology Data Exchange (ETDEWEB)

    Ngo, J.C.; Huang, M.; Roth, D.A.; Furie, B.C.; Furie, B. (Wyeth); (MBL)

    2008-06-03

    Factor VIII is a procofactor that plays a critical role in blood coagulation, and is missing or defective in hemophilia A. We determined the X-ray crystal structure of B domain-deleted human factor VIII. This protein is composed of five globular domains and contains one Ca{sup 2+} and two Cu{sup 2+} ions. The three homologous A domains form a triangular heterotrimer where the A1 and A3 domains serve as the base and interact with the C2 and C1 domains, respectively. The structurally homologous C1 and C2 domains reveal membrane binding features. Based on biochemical studies, a model of the factor IXa-factor VIIIa complex was constructed by in silico docking. Factor IXa wraps across the side of factor VIII, and an extended interface spans the factor VIII heavy and light chains. This model provides insight into the activation of factor VIII and the interaction of factor VIIIa with factor IXa on the membrane surface.

  18. Crystal Structure of Novel Metallocarboxypeptidase Inhibitor from Marine Mollusk Nerita versicolor in Complex with Human Carboxypeptidase A4*

    Science.gov (United States)

    Covaleda, Giovanni; Alonso del Rivero, Maday; Chávez, María A.; Avilés, Francesc X.; Reverter, David

    2012-01-01

    NvCI is a novel exogenous proteinaceous inhibitor of metallocarboxypeptidases from the marine snail Nerita versicolor. The complex between human carboxypeptidase A4 and NvCI has been crystallized and determined at 1.7 Å resolution. The NvCI structure defines a distinctive protein fold basically composed of a two-stranded antiparallel β-sheet connected by three loops and the inhibitory C-terminal tail and stabilized by three disulfide bridges. NvCI is a tight-binding inhibitor that interacts with the active site of the enzyme in a substrate-like manner. NvCI displays an extended and novel interface with human carboxypeptidase A4, responsible for inhibitory constants in the picomolar range for some members of the M14A subfamily of carboxypeptidases. This makes NvCI the strongest inhibitor reported so far for this family. The structural homology displayed by the C-terminal tails of different carboxypeptidase inhibitors represents a relevant example of convergent evolution. PMID:22294694

  19. Crystal structure of novel metallocarboxypeptidase inhibitor from marine mollusk Nerita versicolor in complex with human carboxypeptidase A4.

    Science.gov (United States)

    Covaleda, Giovanni; del Rivero, Maday Alonso; Chávez, María A; Avilés, Francesc X; Reverter, David

    2012-03-16

    NvCI is a novel exogenous proteinaceous inhibitor of metallocarboxypeptidases from the marine snail Nerita versicolor. The complex between human carboxypeptidase A4 and NvCI has been crystallized and determined at 1.7 Å resolution. The NvCI structure defines a distinctive protein fold basically composed of a two-stranded antiparallel β-sheet connected by three loops and the inhibitory C-terminal tail and stabilized by three disulfide bridges. NvCI is a tight-binding inhibitor that interacts with the active site of the enzyme in a substrate-like manner. NvCI displays an extended and novel interface with human carboxypeptidase A4, responsible for inhibitory constants in the picomolar range for some members of the M14A subfamily of carboxypeptidases. This makes NvCI the strongest inhibitor reported so far for this family. The structural homology displayed by the C-terminal tails of different carboxypeptidase inhibitors represents a relevant example of convergent evolution.

  20. Crystal Structures of Staphylococcus aureus Ketol-Acid Reductoisomerase in Complex with Two Transition State Analogues that Have Biocidal Activity.

    Science.gov (United States)

    Patel, Khushboo M; Teran, David; Zheng, Shan; Kandale, Ajit; Garcia, Mario; Lv, You; Schembri, Mark A; McGeary, Ross P; Schenk, Gerhard; Guddat, Luke W

    2017-10-04

    Ketol-acid reductoisomerase (KARI) is an NAD(P)H and Mg2+ -dependent enzyme of the branched-chain amino acid (BCAA) biosynthesis pathway. Here, the first crystal structures of Staphylococcus aureus (Sa) KARI in complex with two transition state analogues, cyclopropane-1,1-dicarboxylate (CPD) and N-isopropyloxalyl hydroxamate (IpOHA) are reported. These compounds bind competitively and in multi-dentate manner to KARI with Ki values of 2.73 μm and 7.9 nm, respectively; however, IpOHA binds slowly to the enzyme. Interestingly, intact IpOHA is present in only ≈25 % of binding sites, whereas its deoxygenated form is present in the remaining sites. This deoxy form of IpOHA binds rapidly to Sa KARI, but with much weaker affinity (Ki =21 μm). Thus, our data pinpoint the origin of the slow binding mechanism of IpOHA. Furthermore, we propose that CPD mimics the early stage of the catalytic reaction (preceding the reduction step), whereas IpOHA mimics the late stage (after the reduction took place). These structural insights will guide strategies to design potent and rapidly binding derivatives of these compounds for the development of novel biocides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. A new cadmium(II) complex with bridging dithiolate ligand: Synthesis, crystal structure and antifungal activity study

    Science.gov (United States)

    Singh, Mahesh Kumar; Sutradhar, Sanjit; Paul, Bijaya; Adhikari, Suman; Laskar, Folguni; Butcher, Raymond J.; Acharya, Sandeep; Das, Arijit

    2017-07-01

    A new polymeric complex of Cd(II) with 1,1-dicyanoethylene- 2,2-dithiolate [ i-MNT2- = {S2C:C(CN)2}2- ] as a bridging ligand has been synthesized and characterized on the basis of spectroscopy and single-crystal X-ray diffraction analysis. Single crystal X-ray diffraction analysis reveals that the Cadmium (II) complex is six coordinated 1D polymeric in nature. Biological screening effects in vitro of the synthesized polymeric complex has been tested against five fungi Synchitrium endobioticum, Pyricularia oryzae, Helminthosporium oryzae, Candida albicans(ATCC10231), Trichophyton mentagrophytes by the disc diffusion method. In vitro antifungal screening indicates that the complex exhibits fungistatic and fungicidal antifungal activity whereas K2i-MNT.H2O became silent on Synchitrium endobioticum, Pyricularia oryzae, Helminthosporium oryzae, Candida albicans (ATCC10231), Trichophyton mentagrophytes.

  2. A new tetraiminodiphenol macrocyclic ligand and its two dicopper(II) complexes: Syntheses, crystal structures, electrochemistry and magnetochemistry

    Science.gov (United States)

    Majumder, Samit; Fleck, Michel; Lucas, C. Robert; Mohanta, Sasankasekhar

    2012-08-01

    This paper deals with the diprotonated salt, [H4L](ClO4)2 (1), of the tetraiminodiphenolate macrocyclic ligand, H2L which is the [2 + 2] condensation product of 4-ethyl-2,6-diformylphenol and 2,2'-dimethyl-1,3-diaminopropane, and two diphenoxo-bridged dicopper(II) complexes [Cu2L(ClO4)2] (2) and [Cu2L(ClO4)](ClO4) (3). The syntheses, characterization and crystal structures of 1-3 and the magnetic and electrochemical properties of the metal complexes 2 and 3 are presented. The cationic macrocycle [H4L]2+ is stabilized by four intramolecular and symmetric Nsbnd H…O…Hsbnd N hydrogen bonds involving phenoxo oxygen and imino nitrogen atoms. One metal center in 3 is tetracoordinated and in a square planar geometry. The second metal ion of 3 and both the metal ions in 2 are pentacoordinated and in a square pyramidal geometry; one perchlorate oxygen atom occupies the apical position in each case. Both 2 and 3 exhibit quasireversible two-step one-electron couples in the reduction window. The E½ (ΔEp) values (in mV) for the CuIICuII/CuIICuI couple is -0.466 V (0.067 V) for 2 and -0.490 V (0.076 V) for 3, while the E½ (ΔEp) values (in mV) for the CuIICuI/CuICuI couple is -0.953 V (0.060 V) for 2 and -0.985 V (0.069 V) for 3. Variable-temperature (2-300 K) magnetic susceptibility measurements of the two compounds reveal that the metal centers in both of the complexes are coupled by strong antiferromagnetic interactions with 2J values (H = -JS1·S2) of -780 and -820 cm-1 for 2 and 3, respectively.

  3. Synthesis and Crystal Structure of Binuclear and Pentanuclear Nickel(II Complexes Containing 4-(salicylaldiminatoantipyrine Schiff base

    Directory of Open Access Journals (Sweden)

    Mohamed N. EL-Kaheli

    2015-11-01

    Full Text Available The new title binuclear Ni (II compound  (1 and the novel pentanuclear Ni (II cluster {[   } (2 are formed from the reaction of an asymmetric Schiff base ligand L (L = 4-(salicylaldiminatoantipyrine with Ni .4  in the former or Ni(ClO42.6H2O in presence of malonate in the later.  Complex (1 consists of ( ]+ cation and one uncoordinated tetraphenylborate anion.  The cation adopts a distorted octahedral arrangement around each metal center.  In the binuclear unit both Ni(II ions are linked through two phenolate (µ2-O oxygen atoms of L, and two oxygen atoms of a  bridging carboxylate group. Each Ni (II coordinates to four oxygen atoms at the basal plane, two oxygen atoms from two bridging phenolate groups, one from pyrazolone ring and the last of an aqua molecule, and at the axial positions to a bridging carboxylate-O atom and an azomethine nitrogen atom.  In the pentanuclear cluster (2 consisting of [ ]+2 cation and two tetraphenylborate anions, the core of the cation is assembled by four [Ni( ] units, linked to the central Ni-ion by two bridging water molecules. The resulting coordination sphere for the external symmetry related nickel ions is a pseudo octahedron.  The central Ni-atom unusually adopts dodecahedron geometry through its coordination to eight bridging water molecules. In complex (1 each Ni-atom is coordinated to one tridentate L ligand and in complex (2 each [Ni ( ] unit is coordinated to two bidentate L ligands.  Inter-and intramolecular hydrogen bonds are present in both crystal structures.

  4. The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex.

    Science.gov (United States)

    Dym, Orly; Song, Wanling; Felder, Clifford; Roth, Esther; Shnyrov, Valery; Ashani, Yacov; Xu, Yechun; Joosten, Robbie P; Weiner, Lev; Sussman, Joel L; Silman, Israel

    2016-06-01

    Structure-based drug design utilizes apoprotein or complex structures retrieved from the PDB. >57% of crystallographic PDB entries were obtained with polyethylene glycols (PEGs) as precipitant and/or as cryoprotectant, but design, since data for ligand-protein complexes with polyethylene glycol as precipitant may not reflect the ligand's position in its absence, and could result in selecting incorrect drug discovery leads. Docking methylene blue into the structure obtained with PEG200, but omitting the ethyleneglycols, yields results agreeing poorly with the crystal structure; excellent agreement is obtained if they are included. Many proteins display features in which precipitants might lodge. It will be important to investigate presence of precipitants in published crystal structures, and whether it has resulted in misinterpreting electron density maps, adversely affecting drug design. © 2016 The Protein Society.

  5. Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer.

    Science.gov (United States)

    Lin, Jason L J; Wu, Chyuan-Chuan; Yang, Wei-Zen; Yuan, Hanna S

    2016-12-01

    Endonuclease G (EndoG) is an evolutionarily conserved mitochondrial protein in eukaryotes that digests nucleus chromosomal DNA during apoptosis and paternal mitochondrial DNA during embryogenesis. Under oxidative stress, homodimeric EndoG becomes oxidized and converts to monomers with diminished nuclease activity. However, it remains unclear why EndoG has to function as a homodimer in DNA degradation. Here, we report the crystal structure of the Caenorhabditis elegans EndoG homologue, CPS-6, in complex with single-stranded DNA at a resolution of 2.3 Å. Two separate DNA strands are bound at the ββα-metal motifs in the homodimer with their nucleobases pointing away from the enzyme, explaining why CPS-6 degrades DNA without sequence specificity. Two obligatory monomeric CPS-6 mutants (P207E and K131D/F132N) were constructed, and they degrade DNA with diminished activity due to poorer DNA-binding affinity as compared to wild-type CPS-6. Moreover, the P207E mutant exhibits predominantly 3'-to-5' exonuclease activity, indicating a possible endonuclease to exonuclease activity change. Thus, the dimer conformation of CPS-6 is essential for maintaining its optimal DNA-binding and endonuclease activity. Compared to other non-specific endonucleases, which are usually monomeric enzymes, EndoG is a unique dimeric endonuclease, whose activity hence can be modulated by oxidation to induce conformational changes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Crystal structure of the HIV-1 integrase core domain in complex with sucrose reveals details of an allosteric inhibitory binding site

    Energy Technology Data Exchange (ETDEWEB)

    Wielens, Jerome; Headey, Stephen J.; Jeevarajah, Dharshini; Rhodes, David I.; Deadman, John; Chalmers, David K.; Scanlon, Martin J.; Parker, Michael W. (SVIMR-A); (Avea); (Monash IPS)

    2010-04-19

    HIV integrase (IN) is an essential enzyme in HIV replication and an important target for drug design. IN has been shown to interact with a number of cellular and viral proteins during the integration process. Disruption of these important interactions could provide a mechanism for allosteric inhibition of IN. We present the highest resolution crystal structure of the IN core domain to date. We also present a crystal structure of the IN core domain in complex with sucrose which is bound at the dimer interface in a region that has previously been reported to bind integrase inhibitors.

  7. Synthesis, crystal structure and computational chemistry research of a Zinc(II complex: [Zn(Pt(Biim2

    Directory of Open Access Journals (Sweden)

    Teng Fei

    2012-01-01

    Full Text Available The title metal-organic coordination complex [Zn(pt(Biim2] (pt=phthalic acid, benzene-1,2-dicarboxylate, Biim=2,2'-biimidazole 1 has been obtained by using hydrothermal synthesis and characterized by single-crystal X-ray diffraction. The complex crystallizes in monoclinic, space group P21/n with a = 8.5466(15 Å, b = 11.760(2 Å, c = 20.829(4 Å, β = 95.56(2º, V = 2083.5(6 Å3, Mr =497.78, Dc = 1.587 g/cm3, μ(MoKα = 1.226 mm−1, F(000 = 1016, Z = 4, the final R = 0.0564 and wR = 0.1851 for 3656 observed reflections (I > 2σ(I. The elemental analysis, IR, TG and the theoretical calculation were also investigated.

  8. Synthesis and crystal structure of Cu(II and Co(II complexes with 1,3-dimethyl-pyrazole-5-carboxylic acid ligand

    Directory of Open Access Journals (Sweden)

    Jaćimović Željko K.

    2015-01-01

    Full Text Available In the reaction of 1,3-dimethyl-pyrazole-5-carboxylic acid (HL with M(OAc2•4H2O, (M = Cu, Co two novel complexes have been prepared, square-planar [CuL2(H2O2] and octahedral [CoL2(MeOH4]. The crystal structures have been determined by single-crystal X-ray diffraction. In both complexes the deprotonated acid displays monodentate coordination to the metal ions. According to the results of CSD survey this is the first structural report on the metal complexes with N1-substituted pyrazole-5-carboxylic ligand. [Projekat Ministarstva nauke Republike Srbije, br. 172014 i br. 172035

  9. Synthesis, crystal structure, fluorescence and electrochemical studies of a new tridentate Schiff base ligand and its nickel(II) and palladium(II) complexes.

    Science.gov (United States)

    Shafaatian, Bita; Soleymanpour, Ahmad; Kholghi Oskouei, Nasim; Notash, Behrouz; Rezvani, Seyyed Ahmad

    2014-07-15

    A new unsymmetrical tridentate Schiff base ligand was derived from the 1:1M condensation of ortho-vanillin with 2-mercaptoethylamine. Nickel and palladium complexes were obtained by the reaction of the tridentate Schiff base ligand with nickel(II) acetate tetrahydrate and palladium(II) acetate in 2:1M ratio. In nickel and palladium complexes the ligand was coordinated to metals via the imine N and enolic O atoms. The S groups of Schiff bases were not coordinated to the metals and S-S coupling was occured. The complexes have been found to possess 1:2 Metal:Ligand stoichiometry and the molar conductance data revealed that the metal complexes were non-electrolytes. The complexes exhibited octahedral coordination geometry. The emission spectra of the ligand and its complexes were studied in methanol. Electrochemical properties of the ligand and its metal complexes were investigated in the CH3CN solvent at the 100 mV s(-1) scan rate. The ligand and metal complexes showed both reversible and quasi-reversible processes at this scan rate. The Schiff base and its complexes have been characterized by IR, (1)H NMR, UV/Vis, elemental analyses and conductometry. The crystal structure of nickel complex has been determined by single crystal X-ray diffraction. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Synthesis, Crystal Structure and Theoretical Calculation of a Novel Nickel(II) Complex with Dibromotyrosine and 1,10-Phenanthroline

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Guimei; Zhang, Xia; Fan, Yuhua; Bi, Caifeng; Yan, Xingchen; Zhang, Zhongyu; Zhang, Nan [Ocean Univ. of China, Qingdao (China)

    2013-10-15

    A new complex [Ni(phen)(C{sub 9}H{sub 8}Br{sub 2}NO{sub 3}){sub 2}·2CH{sub 3}OH·2H{sub 2}O] [phen: 1,10-phenanthroline C{sub 9}H{sub 8}Br{sub 2}NO{sub 3}: 3,5-dibromo-L-tyrosine] was synthesized and characterized by IR, elemental analysis and single crystal X-ray diffraction. X-ray crystallography shows that Ni(II) ion is six-coordinated. The Ni(II) ion coordinates with four nitrogen atoms and two oxygen atoms from three ligands, forming a mononuclear Ni(II) complex. The crystal crystallizes in the Orthorhombic system, space group P2{sub 1}2{sub 1}2 with a = 12.9546 A, b = 14.9822 A, c = 9.9705 A, V = 1935.2 A, Z = 1, F(000) = 1008, S = 0.969, ρ{sub calcd} = 1.742 g·cm{sup -3}, μ = 4.688 mm{sup -1}, R{sub 1} = 0.0529 and wR{sub 2} = 0.0738 for 3424 observed reflections (I > 2σ(I)). Theoretical study of the title complex was carried out by density functional theory (DFT) method and the B3LYP method employing the 6-3l+G{sup *} basis set. The energy gap between HOMO and LUMO indicates that this complex is prone to interact with DNA. CCDC: 908041.

  11. Syntheses, crystal structures and properties of novel copper(II) complexes obtained by reactions of copper(II) sulfate pentahydrate with tripodal ligands.

    Science.gov (United States)

    Zhao, Wei; Fan, Jian; Song, You; Kawaguchi, Hiroyuki; Okamura, Taka-aki; Sun, Wei-Yin; Ueyama, Norikazu

    2005-04-21

    Three novel metal-organic frameworks (MOFs), [Cu(1)SO4].H2O (4), [Cu2(2)2(SO4)2].4H2O (5) and [Cu(3)(H2O)]SO4.5.5H2O (6), were obtained by hydrothermal reactions of CuSO4.5H2O with the corresponding ligands, which have different flexibility. The structures of the synthesized complexes were determined by single-crystal X-ray diffraction analyses. Complex 4 has a 2D network structure with two types of metallacycles. Complex 5 also has a 2D network structure in which each independent 2D sheet contains two sub-layers bridged by oxygen atoms of the sulfate anions. Complex 6 has a 2D puckered structure in which the sulfate anions serve as counter anions, which are different from those in complexes 4 (terminators) and 5 (bridges). The different structures of complexes 4, 5 and 6 indicate that the nature of organic ligands affected the structures of the assemblies greatly. The magnetic behavior of complex 5 and anion-exchange properties of complex 6 were investigated.

  12. Crystal structure of an essential enzyme in seed starch degradation - barley limit dextrinase in complex with cyclodextrins

    DEFF Research Database (Denmark)

    Vester-Christensen, Malene Bech; Abou Hachem, Maher; Svensson, Birte

    2010-01-01

    Barley limit dextrinase [Hordeum vulgare limit dextrinase (HvLD)] catalyzes the hydrolysis of α-1,6 glucosidic linkages in limit dextrins. This activity plays a role in starch degradation during germination and presumably in starch biosynthesis during grain filling. The crystal structures of Hv...... provide new insight into cation sites and the concerted action of the battery of hydrolytic enzymes in starch degradation....

  13. High-resolution crystal structure of Streptococcus pyogenes β-NAD{sup +} glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin [Seoul National University, Seoul 151-747 (Korea, Republic of); Kim, Hyoun Sook [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-742 (Korea, Republic of); Lee, Sang Jae [Seoul National University, Seoul 151-742 (Korea, Republic of); Im, Ha Na; Jang, Jun Young [Seoul National University, Seoul 151-747 (Korea, Republic of); Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-747 (Korea, Republic of)

    2013-11-01

    The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD{sup +} glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD{sup +} glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN{sub ct}–IFS complex, which consists of the SPN C-terminal domain (SPN{sub ct}; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN{sub ct} and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope.

  14. Structural implications of drug-resistant mutants of HIV-1 protease: high-resolution crystal structures of the mutant protease/substrate analogue complexes.

    Science.gov (United States)

    Mahalingam, B; Louis, J M; Hung, J; Harrison, R W; Weber, I T

    2001-06-01

    Emergence of drug-resistant mutants of HIV-1 protease is an ongoing problem in the fight against AIDS. The mechanisms governing resistance are both complex and varied. We have determined crystal structures of HIV-1 protease mutants, D30N, K45I, N88D, and L90M complexed with peptide inhibitor analogues of CA-p2 and p2-NC cleavage sites in the Gag-pol precursor in order to study the structural mechanisms underlying resistance. The structures were determined at 1.55-1.9-A resolution and compared with the wild-type structure. The conformational disorder seen for most of the hydrophobic side-chains around the inhibitor binding site indicates flexibility of binding. Eight water molecules are conserved in all 9 structures; their location suggests that they are important for catalysis as well as structural stability. Structural differences among the mutants were analyzed in relation to the observed changes in protease activity and stability. Mutant L90M shows steric contacts with the catalytic Asp25 that could destabilize the catalytic loop at the dimer interface, leading to its observed decreased dimer stability and activity. Mutant K45I reduces the mobility of the flap and the inhibitor and contributes to an enhancement in structural stability and activity. The side-chain variations at residue 30 relative to wild-type are the largest in D30N and the changes are consistent with the altered activity observed with peptide substrates. Polar interactions in D30N are maintained, in agreement with the observed urea sensitivity. The side-chains of D30N and N88D are linked through a water molecule suggesting correlated changes at the two sites, as seen with clinical inhibitors. Structural changes seen in N88D are small; however, water molecules that mediate interactions between Asn88 and Thr74/Thr31/Asp30 in other complexes are missing in N88D. Copyright 2001 Wiley-Liss, Inc.

  15. Synthesis, spectra and crystal structure of 2-(?[3-(methyl?3-[(2-hydroxybenzylidene)amino]propyl? amino)propyl]imino?methyl)phenol copper(II) complex

    Science.gov (United States)

    Yilmaz, Veysel T.; Degirmencioglu, Ismail; Andac, Omer; Karabocek, Serdar; Slawin, Alexandra M. Z.

    2003-06-01

    A copper(II) complex, [Cu(salenN3], [salenN3H2=2-({[3-(methyl{3-[(2-hydroxybenzylidene)amino]propyl}amino)propyl]imino}methyl)phenol] was synthesized and characterized by elemental analyses, FTIR spectra and single crystal X-ray diffraction. The complex crystallizes in the monoclinic space group P21/ c with a=6.877(3), b=14.109(6), c=20.106(8) Å, β=92.231(14)°, V=1949.5(14) Å 3. The salen ligand loses two phenolic hydrogens being a dianion and coordinates to the copper(II) ion as a pentadentate ligand through its two O and three N atoms. The copper(II) complex is five-coordinate, lying between perfect square pyramidal and trigonal-bipyramidal extremes. Use of the structural index parameter ( τ) for five coordinate metal complexes indicated that the copper(II) complex exhibits a grater tendency toward trigonal-based-pyramidal geometry ( τ>0.5). The individual molecules in the crystal are held together by C-H⋯π and H⋯H interactions. The IR and electronic spectra of the complex were discussed in detail.

  16. Synthesis, crystal structure and photophysical properties of a series of metal complexes MI{sub 2}L{sub 2} (M = Zn, Cd, Hg) from an imidazole derivative

    Energy Technology Data Exchange (ETDEWEB)

    Fei, Wen-wen; Hu, Gui-ju; Li, Rui; Yang, Long-mei; Li, Sheng-li; Tian, Lei; Yang, Jia-xiang; Wu, Jie-ying [Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, 230039 Hefei (China); Tian, Yu-peng, E-mail: yptian@ahu.edu.cn [Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, 230039 Hefei (China); State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093 (China)

    2013-05-15

    A series of novel metal complexes, ZnL{sub 2}I{sub 2}, CdL{sub 2}I{sub 2}, and HgL{sub 2}I{sub 2} (L: 1-[Trans-4-(4-diethylaminostyryl) phenyl] imidazole), have been prepared and fully characterized. The structure of HgL{sub 2}I{sub 2} was confirmed by single crystal X-ray diffraction analysis, which exhibits that Hg atom is coordinated by two iodine atoms and two nitrogen atoms from the ligand to form a distorted tetrahedral environment. The variable temperature {sup 1}H NMR spectra proved that the metal complexes exhibit well stability in solution. Linear and nonlinear optical properties of them were described on the basis of density functional theory (DFT) calculations. Interestingly, we found that the complexation of the ligands with metal ion extends the electronic delocalization in the metal complexes, leading to dramatically enhanced two-photon absorption. - Highlights: ► Three d{sup 10}-metal complexes with two-photon absorption (TPA) are reported. ► The crystal structure of HgL{sub 2}I{sub 2} was determined. ► The complexes exhibit dramatically enhanced TPA related to its ligand. ► The connections between structure and properties for them were investigated.

  17. Crystal structure of the Escherichia coli regulator of σ70, Rsd, in complex with σ70 domain 4

    OpenAIRE

    Patikoglou, Georgia A; Westblade, Lars F.; Campbell, Elizabeth A.; Lamour, Valérie; Lane, William J; Darst, Seth A

    2007-01-01

    The Escherichia coli Rsd protein binds tightly and specifically to the RNA polymerase (RNAP) σ70 factor. Rsd plays a role in alternative σ factor-dependent transcription by biasing the competition between σ70 and alternative σ factors for the available core RNAP. Here, we determined the 2.6 Å-resolution X-ray crystal structure of Rsd bound to σ70 domain 4 (σ704), the primary determinant for Rsd binding within σ70. The structure reveals that Rsd binding interferes with the two primary function...

  18. Synthesis, crystal structure, catalytic and anti-Trypanosoma cruzi activity of a new chromium(III) complex containing bis(3,5-dimethylpyrazol-1-yl)methane

    Science.gov (United States)

    Hurtado, John; Ibarra, Laura; Yepes, David; García-Huertas, Paola; Macías, Mario A.; Triana-Chavez, Omar; Nagles, Edgar; Suescun, Leopoldo; Muñoz-Castro, Alvaro

    2017-10-01

    The reaction of CrCl36H2O with the ligand bis(3,5-dimethylpyrazol-1-yl)methane (L) yielded the cationic complex [(Cr(L)(H2O)2Cl2]+, which crystallized as the chloride trihydrate [(Cr(L)(H2O)2Cl2]Cl·3H2O. The chromium complex was characterized by elemental analysis, electrical conductivity, Infrared and Ultraviolet/Visible spectroscopy. The crystal structure determination using single-crystal X-ray diffraction showed a chromium center in a distorted octahedral coordination sphere. In the crystal, the packing was directed by Osbnd H⋯(O,Cl) hydrogen bonds and weak Csbnd H⋯O interactions to build a monoclinic P21/c supramolecular structure. The complex showed excellent properties as an initiator for the ring opening polymerization of є-caprolactone (CL) under solvent-free conditions. The obtained polymer showed high crystallinity (89.9%) and a decomposition temperature above 475 °C. In addition, the new complex was evaluated against epimastigotes from Trypanosoma cruzi (T. cruzi) strains. The results indicated that this complex has a high activity against this parasite with a minimum inhibitory concentration 50 (MIC50) of 1.08 μg/mL. Interestingly, this compound showed little effect on erythrocytes, indicating that it is not cytotoxic. These results provide interesting contributions to the design of metal complexes by using simple and accessible ligands with activity against T. cruzi and with potential applications in the polymerization of CL.

  19. SYNTHESIS, CRYSTAL AND MOLECULAR-STRUCTURES, UV-VIS SPECTROSCOPY AND ELECTROCHEMICAL PROPERTIES OF 2 IRON(III) PHENOLATE COMPLEXES

    NARCIS (Netherlands)

    LUBBEN, M; MEETSMA, A; VANBOLHUIS, F; FERINGA, BL; HAGE, R

    The synthesis and molecular structures of two iron(III) phenolate complexes [(L(1))FeCl] (1) and [(L(2))(2)Fe][BPh(4)] (2) are described, where L(1)H(2) is 2,3-dimethyl-2,3-bis(3-tert-butylsalicylideneamino) butane and L(2)H is 2-(2-pyridyl)-1-salicylideneaminoethane. The complexes have been

  20. The Role of Coulomb Interactions for Spin Crossover Behaviors and Crystal Structural Transformation in Novel Anionic Fe(III Complexes from a π-Extended ONO Ligand

    Directory of Open Access Journals (Sweden)

    Suguru Murata

    2016-05-01

    Full Text Available To investigate the π-extension effect on an unusual negative-charged spin crossover (SCO FeIII complex with a weak N2O4 first coordination sphere, we designed and synthesized a series of anionic FeIII complexes from a π-extended naphthalene derivative ligand. Acetonitrile-solvate tetramethylammonium (TMA salt 1 exhibited an SCO conversion, while acetone-solvate TMA salt 2 was in a high-spin state. The crystal structural analysis for 2 revealed that two-leg ladder-like cation-anion arrays derived from π-stacking interactions between π-ligands of the FeIII complex anion and Coulomb interactions were found and the solvated acetone molecules were in one-dimensional channels between the cation-anion arrays. A desolvation-induced single-crystal-to-single-crystal transformation to desolvate compound 2’ may be driven by Coulomb energy gain. Furthermore, the structural comparison between quasi-polymorphic compounds 1 and 2 revealed that the synergy between Coulomb and π-stacking interactions induces a significant distortion of coordination structure of 2.

  1. Crystal Structures of the Iron–Sulfur Cluster-Dependent Quinolinate Synthase in Complex with Dihydroxyacetone Phosphate, Iminoaspartate Analogues, and Quinolinate

    Energy Technology Data Exchange (ETDEWEB)

    Fenwick, Michael K. [Cornell Univ., Ithaca, NY (United States); Ealick, Steven E. [Cornell Univ., Ithaca, NY (United States)

    2016-07-12

    The quinolinate synthase of prokaryotes and photosynthetic eukaryotes, NadA, contains a [4Fe-4S] cluster with unknown function. We report crystal structures of Pyrococcus horikoshii NadA in complex with dihydroxyacetone phosphate (DHAP), iminoaspartate analogues, and quinolinate. DHAP adopts a nearly planar conformation and chelates the [4Fe-4S] cluster via its keto and hydroxyl groups. The active site architecture suggests that the cluster acts as a Lewis acid in enediolate formation, like zinc in class II aldolases. The DHAP and putative iminoaspartate structures suggest a model for a condensed intermediate. The ensemble of structures suggests a two-state system, which may be exploited in early steps.

  2. Crystal structures of three mercury(II complexes [HgCl2L] where L is a bidentate chiral imine ligand

    Directory of Open Access Journals (Sweden)

    Guadalupe Hernández

    2015-12-01

    Full Text Available The crystal structures of three complexes [HgCl2L] were determined, namely, (S-(+-dichlorido[1-phenyl-N-(pyridin-2-ylmethylideneethylamine-κ2N,N′]mercury(II, [HgCl2(C14H14N2], (S-(+-dichlorido[1-(4-methylphenyl-N-(pyridin-2-ylmethylideneethylamine-κ2N,N′]mercury(II, [HgCl2(C15H16N2], and (1S,2S,3S,5R-(+-dichlorido[N-(pyridin-2-ylmethylideneisopinocampheylamine-κ2N,N′]mercury(II, [HgCl2(C16H22N2]. The complexes consist of a bidentate chiral imine ligand coordinating to HgCl2 and crystallize with four independent molecules in the first complex and two independent molecules in the other two. The coordination geometry of mercury is tetrahedral, with strong distortion towards a disphenoidal geometry, as a consequence of the imine bite angle being close to 70°. The Cl—Hg—Cl angles span a large range, 116.0 (2–138.3 (3°, which is related to the aggregation state in the crystals. For small Cl—Hg—Cl angles, complexes have a tendency to form dimers, via intermolecular Hg...Cl contacts. These contacts become less significant in the third complex, which features the largest intramolecular Cl—Hg—Cl angles.

  3. Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif.

    Science.gov (United States)

    Oshima, Kosuke; Gao, Xuzhu; Hayashi, Seiichiro; Ueda, Toshifumi; Nakashima, Takashi; Kimura, Makoto

    2018-01-01

    A characteristic feature of archaeal ribonuclease P (RNase P) RNAs is that they have extended helices P12.1 and P12.2 containing kink-turn (K-turn) motifs to which the archaeal RNase P protein Rpp38, a homologue of the human RNase P protein Rpp38, specifically binds. PhoRpp38 from the hyperthermophilic archaeon Pyrococcus horikoshii is involved in the elevation of the optimum temperature of the reconstituted RNase P by binding the K-turns in P12.1 and P12.2. Previously, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was determined at 3.4 Å resolution. In this study, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was improved to 2.1 Å resolution and the structure of PhoRpp38 in complex with the K-turn in P12.1 was also determined at a resolution of 3.1 Å. Both structures revealed that Lys35, Asn38 and Glu39 in PhoRpp38 interact with characteristic G·A and A·G pairs in the K-turn, while Thr37, Asp59, Lys84, Glu94, Ala96 and Ala98 in PhoRpp38 interact with the three-nucleotide bulge in the K-turn. Moreover, an extended stem-loop containing P10-P12.2 in complex with PhoRpp38, as well as PhoRpp21 and PhoRpp29, which are the archaeal homologues of the human proteins Rpp21 and Rpp29, respectively, was affinity-purified and crystallized. The crystals thus grown diffracted to a resolution of 6.35 Å. Structure determination of the crystals will demonstrate the previously proposed secondary structure of stem-loops including helices P12.1 and P12.2 and will also provide insight into the structural organization of the specificity domain in P. horikoshii RNase P RNA.

  4. Crystal structures of manganese- and cobalt-substituted myoglobin in complex with NO and nitrite reveal unusual ligand conformations.

    Science.gov (United States)

    Zahran, Zaki N; Chooback, Lilian; Copeland, Daniel M; West, Ann H; Richter-Addo, George B

    2008-02-01

    Nitrite is now recognized as a storage pool of bioactive nitric oxide (NO). Hemoglobin (Hb) and myoglobin (Mb) convert, under certain conditions, nitrite to NO. This newly discovered nitrite reductase activity of Hb and Mb provides an attractive alternative to mammalian NO synthesis from the NO synthase pathway that requires dioxygen. We recently reported the X-ray crystal structure of the nitrite adduct of ferric horse heart Mb, and showed that the nitrite ligand binds in an unprecedented O-binding (nitrito) mode to the d(5) ferric center in Mb(III)(ONO) [D.M. Copeland, A. Soares, A.H. West, G.B. Richter-Addo, J. Inorg. Biochem. 100 (2006) 1413-1425]. We also showed that the distal pocket in Mb allows for different conformations of the NO ligand (120 degrees and 144 degrees ) in Mb(II)NO depending on the mode of preparation of the compound. In this article, we report the crystal structures of the nitrite and NO adducts of manganese-substituted hh Mb (a d(4) system) and of the nitrite adduct of cobalt-substituted hh Mb (a d(6) system). We show that the distal His64 residue directs the nitrite ligand towards the rare nitrito O-binding mode in Mn(III)Mb and Co(III)Mb. We also report that the distal pocket residues allow a stabilization of an unprecendented bent MnNO moiety in Mn(II)MbNO. These crystal structural data, when combined with the data for the aquo, methanol, and azide MnMb derivatives, provide information on the role of distal pocket residues in the observed binding modes of nitrite and NO ligands to wild-type and metal-substituted Mb.

  5. Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

    Science.gov (United States)

    Zhang, Xianjun; Zhao, Fei; Wu, Yiran; Yang, Jun; Han, Gye Won; Zhao, Suwen; Ishchenko, Andrii; Ye, Lintao; Lin, Xi; Ding, Kang; Dharmarajan, Venkatasubramanian; Griffin, Patrick R.; Gati, Cornelius; Nelson, Garrett; Hunter, Mark S.; Hanson, Michael A.; Cherezov, Vadim; Stevens, Raymond C.; Tan, Wenfu; Tao, Houchao; Xu, Fei

    2017-05-01

    The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combining the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.

  6. Chemical modeling of mixed occupations and site preferences in anisotropic crystal structures: case of complex intermetallic borides.

    Science.gov (United States)

    Deringer, Volker L; Goerens, Christian; Esters, Marco; Dronskowski, Richard; Fokwa, Boniface P T

    2012-05-21

    Transition-metal borides show not only promising physical properties but also a rich variety of crystal structures. In this context, quantum-chemical tools can shed light on important facets of the chemistry within such intermetallic borides. Using density-functional theory (DFT), we analyze in detail two phases of significant structural-chemical importance: the recently synthesized Ti(1+x)Os(2-x)RuB(2) and the isotypical Ti(1+x)Os(3-x)B(2). Starting from the observation of different Ti/Os occupations in X-ray crystal structure analysis, we assess suitable computational models and rationalize how the interplay of Ti-Ti, Ti-Os, and Os-Os bonds drives the site preferences. Then, we move on to a systematic investigation of the metal-boron bonds which embed the characteristic, trigonal-planar B(4) units within their metallic surroundings. Remarkably, the different Ti-B bonds in Ti(1+x)Os(2-x)RuB(2) (and also in its ternary derivative) are of vastly different strength, and the strength of these bonds does not correlate with their length. The tools presented in this work are based on simple and insightful chemical arguments together with DFT, and may subsequently be transferred to other intermetallic phases--transition-metal borides and beyond.

  7. Synthesis, Crystal Structure, Luminescence, Electrochemical and Antimicrobial Properties of Bis(salamo-Based Co(II Complex

    Directory of Open Access Journals (Sweden)

    Li Wang

    2017-09-01

    Full Text Available A newly designed Co(II complex, [Co3(L(OAc2(CH3OH2]·CH3OH, by the reaction of a bis(salamo-type tetraoxime ligand (H4L with Co(II acetate tetrahydrate was synthesized and characterized by elemental analyses, IR, UV-vis spectra and single-crystal X-ray crystallography. The UV-vis titration experiment manifested that a trinuclear (L:M = 1:3 complex was formed. It is worth noting that the two terminal Co(II (Co1 and Co3 atoms of the Co(II complex have different coordination modes and geometries unreported earlier. Furthermore, through intermolecular interactions (C–H···O, C–H···π and O–H···O, a 2D layer-like network is constructed. In addition, the fluorescence behaviors, antimicrobial activities and electrochemical properties of H4L and its Co(II complex were investigated.

  8. Synthesis, crystal structures and antitumor activities of copper(II) complexes with a 2-acetylpyrazine isonicotinoyl hydrazone ligand

    Science.gov (United States)

    Xu, Jun; Zhou, Tao; Xu, Zhou-Qing; Gu, Xin-Nan; Wu, Wei-Na; Chen, Hong; Wang, Yuan; Jia, Lei; Zhu, Tao-Feng; Chen, Ru-Hua

    2017-01-01

    Five complexes, [Cu(L)2]·4.5H2O (1), [Cu(HL)2](NO3)2·CH3OH (2) {[Cu2(L)2(NO3)(H2O)2]·(NO3)}n (3), [Cu2(HL)2(SO4)2]·2CH3OH (4) and [Cu4(L)4Cl4]·5H2O (5) based on HL (where HL = 2-acetylpyrazine isonicotinoyl hydrazone) have been synthesized and characterized by X-ray diffraction analyses. The counter anion and organic base during the synthesis procedure influence the structures of the complexes efficiently, which generate five complexes as mono-, bi-, tetra-nuclear and one-dimensional structures. The antitumor activities of the complexes 1-5 (except for complex 3 with the poor solubility) against the Patu8988 human pancreatic cancer, ECA109 human esophagus cancer and SGC7901 human gastric cancer cell lines are screened by MTT assay. The results indicate that the chelation of Cu(II) with the ligand is responsible for the observed high cytotoxicity of the copper(II) complexes and the 1:2 copper species 1 and 2 demonstrate lower antitumor activities than that of the 1:1 copper species 4 and 5. In addition, the in vitro apoptosis inducing activity of the copper(II) complex 5 against SGC7901 cell line is determined. And the results show that the complex can bring about apoptosis of the cancerous cells in vitro.

  9. Inorganic Crystal Structure Database (ICSD)

    Science.gov (United States)

    SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

  10. Synthesis, crystal and molecular structures, UV–Vis spectroscopy and electrochemical properties of two iron(III) phenolate complexes

    NARCIS (Netherlands)

    Lubben, Marcel; Meetsma, Auke; Bolhuis, Fré van; Feringa, Bernard

    1994-01-01

    The synthesis and molecular structures of two iron(III) phenolate complexes [(L1)FeCl] (1) and [(L2)2Fe][BPh4] (2) are described, where L1H2 is 2,3-dimethyl-2,3-bis(3-tert-butylsalicylideneamino)butane and L2H is 2-(2-pyridyl)-1-salicylideneaminoethane. The complexes have been characterized by

  11. Synthesis, crystal structure, spectroscopic investigations and DFT calculations of the copper(II) complex of 4-(Trifluoromethyl)pyridine-2-carboxylic acid

    Science.gov (United States)

    Vural, Hatice; Orbay, Metin

    2017-10-01

    A novel polymeric complex of Cu(II) ion, [Cu(tfpc)2]n [tfpc: 4-(Trifluoromethyl)pyridine-2-carboxylate] has been prepared and characterized spectroscopically (by FT-IR) and structurally (by single-crystal XRD). The geometry around the Cu(II) center can be described as square planar made by tfpc ligand having nitrogen and oxygen atoms. Additionally, the Cu(II) complex has a one-dimensional double-bridged polymeric structure in which Cu(II) ions are bridged by two oxygen atoms of adjacent planes. The crystal packing has been stabilized by Csbnd H⋯O intra and intermolecular hydrogen bonds. The molecular structure of the Cu(II) complex has been optimized using the Density Functional Theory (DFT) B3LYP, B3PW91 and PBEPBE levels with 6-311+G(d,p) basis set. The calculated electronic spectra have been explained using the time dependent DFT (TD-DFT) method by applying the polarized continuum model (PCM). The vibrational spectral data have been calculated and compared with experimental ones. The non-linear optical (NLO) properties of the title compound have been investigated using the DFT method with three different levels. Natural Bond Orbital (NBO) property of the Cu(II) complex has been performed by the B3LYP density functional and the 6-311+G(d,p) basis set.

  12. A Hirshfeld surface analysis, crystal structure and spectroscopic properties of new Zn(II) complex with N-aminoethylpiperazine ligand

    Science.gov (United States)

    El Glaoui, Maroua; El Glaoui, Maher; Jelsch, Christian; Aubert, Emmanuel; Lefebvre, Frédéric; Ben Nasr, Chérif

    2017-04-01

    A new organic-inorganic hybrid material, 1-amonioethylpiperazine-1, 4-diium tetrachloridozincate(II) chloride, (C6H18N3)[ZnCl4]Cl, has been synthesized and characterized by various physicochemical techniques including UV-visible absorption, Infra-Red (IR), Raman and NMR spectroscopies. The compound crystallizes in the monoclinic system and P21 space group with Z = 2 and the following unit cell dimensions: a = 7.1728 (6), b = 12.4160 (11), c = 8.0278 (7) Å, β = 97.513 (1)°, V = 708.80 (11) Å3. In this structure, the Zn2+ ion, surrounded by four chlorides, adopts a distorted tetrahedral coordination geometry. The structure of this compound consists of monomeric 1-amonioethylpiperazine-1, 4-diium trications and monomeric [ZnCl4]2- and Cl- anions. These entities are interconnected by means of hydrogen bonding contacts [Nsbnd H⋯Cl, Csbnd H⋯Cl], forming a three-dimensional network. Intermolecular interactions were investigated by Hirshfeld surfaces. More than three quarters of the interaction surface in the crystal packing is constituted by attractive and favored H⋯Cl hydrogen bonds. The 13C and 15N CP-MAS NMR spectra are discussed and the vibrational absorption bands were identified by infrared and Raman spectroscopy.

  13. Synthesis, crystal structure, and magnetic studies of one-dimensional cyano-bridged Ln3+-Cr3+ complexes with bpy as a blocking ligand.

    Science.gov (United States)

    Estrader, Marta; Ribas, Joan; Tangoulis, Vassilis; Solans, Xavier; Font-Bardía, Merce; Maestro, Miguel; Diaz, Carmen

    2006-10-02

    The reaction of Ln(NO3)3.aq with K3[Cr(CN)6] and 2,2'-bipyridine (bpy) in a water/ethanol solution led to two families of complexes: 4 one-dimensional (1D) complexes of the formula trans-[Cr(CN)4(mu-CN)2Ln(H2O)3(bpy)2]n.4nH2O.3.5nbpy (Ln3+ = La, Ce, Pr, and Nd) and 10 1D complexes of the formula trans-[Cr(CN)4(mu-CN)2Ln(H2O)4(bpy)]n.3.5nH2O.1.5nbpy (Ln3+ = Nd, Sm, Eu, Tb, Dy, Ho, Er, Tm, Yb, and Lu). The structures for the fourteen complexes [LaCr]n (1), [CeCr]n (2), [PrCr]n (3), [NdCr]n (4), [NdCr]n (4'), [SmCr]n (5), [EuCr]n (6), [TbCr]n (7), [DyCr]n (8), [HoCr]n (9), [ErCr]n (10), [TmCr]n (11), [YbCr]n (12), and [LuCr]n (13) have been solved. Complexes 1-4 crystallize in the orthorhombic space group Pbam and are isomorphous; complexes 4'-13 crystallize in the triclinic space group PI and are isomorphous. The X-ray structural characterization of complexes 1-4 shows the presence of a discrete decameric water cluster built around a cyclic hexameric core stabilized by the solid-state structure, which represents another new mode of association of water molecules. The Ln3+-Cr3+ magnetic interaction is negligible in 6 and 12, antiferromagnetic in 2, 4', 7, 8, 9, 10, and 11, and unresolved for 3. The complex 5 is a ferrimagnet because its magnetic studies suggest the onset of a very weak ferromagnetic three-dimensional ordering.

  14. Crystal Structure of Mouse Thymidylate Synthase in Tertiary Complex with dUMP and Raltitrexed Reveals N-Terminus Architecture and Two Different Active Site Conformations

    Directory of Open Access Journals (Sweden)

    Anna Dowierciał

    2014-01-01

    Full Text Available The crystal structure of mouse thymidylate synthase (mTS in complex with substrate dUMP and antifolate inhibitor Raltitrexed is reported. The structure reveals, for the first time in the group of mammalian TS structures, a well-ordered segment of 13 N-terminal amino acids, whose ordered conformation is stabilized due to specific crystal packing. The structure consists of two homodimers, differing in conformation, one being more closed (dimer AB and thus supporting tighter binding of ligands, and the other being more open (dimer CD and thus allowing weaker binding of ligands. This difference indicates an asymmetrical effect of the binding of Raltitrexed to two independent mTS molecules. Conformational changes leading to a ligand-induced closing of the active site cleft are observed by comparing the crystal structures of mTS in three different states along the catalytic pathway: ligand-free, dUMP-bound, and dUMP- and Raltitrexed-bound. Possible interaction routes between hydrophobic residues of the mTS protein N-terminal segment and the active site are also discussed.

  15. Crystal structure of mouse thymidylate synthase in tertiary complex with dUMP and raltitrexed reveals N-terminus architecture and two different active site conformations.

    Science.gov (United States)

    Dowierciał, Anna; Wilk, Piotr; Rypniewski, Wojciech; Rode, Wojciech; Jarmuła, Adam

    2014-01-01

    The crystal structure of mouse thymidylate synthase (mTS) in complex with substrate dUMP and antifolate inhibitor Raltitrexed is reported. The structure reveals, for the first time in the group of mammalian TS structures, a well-ordered segment of 13 N-terminal amino acids, whose ordered conformation is stabilized due to specific crystal packing. The structure consists of two homodimers, differing in conformation, one being more closed (dimer AB) and thus supporting tighter binding of ligands, and the other being more open (dimer CD) and thus allowing weaker binding of ligands. This difference indicates an asymmetrical effect of the binding of Raltitrexed to two independent mTS molecules. Conformational changes leading to a ligand-induced closing of the active site cleft are observed by comparing the crystal structures of mTS in three different states along the catalytic pathway: ligand-free, dUMP-bound, and dUMP- and Raltitrexed-bound. Possible interaction routes between hydrophobic residues of the mTS protein N-terminal segment and the active site are also discussed.

  16. The crystal structure of human dipeptidyl peptidase I (cathepsin C) in complex with the inhibitor Gly-Phe-CHN2

    DEFF Research Database (Denmark)

    Mølgaard, Anne; Arnau, Jose; Lauritzen, C.

    2007-01-01

    hDDPI (human dipeptidyl peptidase I) is a lysosomal cysteine protease involved in zymogen activation of granule-associated proteases, including granzymes A and B from cytotoxic T-lymphocytes and natural killer cells, cathepsin G and neutrophil elastase, and mast cell tryptase and chymase. In the ......hDDPI (human dipeptidyl peptidase I) is a lysosomal cysteine protease involved in zymogen activation of granule-associated proteases, including granzymes A and B from cytotoxic T-lymphocytes and natural killer cells, cathepsin G and neutrophil elastase, and mast cell tryptase and chymase...... to 2.05 angstrom resolution to resolve apparent discrepancies between the complex structure and the previously published structure of the native enzyme. The new structure of the native enzyme is, within the experimental error, identical with the structure of the enzyme-inhibitor complex presented here...

  17. Crystal structures of two mononuclear complexes of terbium(III) nitrate with the tripodal alcohol 1,1,1-tris-(hy-droxy-meth-yl)propane.

    Science.gov (United States)

    Gregório, Thaiane; Giese, Siddhartha O K; Nunes, Giovana G; Soares, Jaísa F; Hughes, David L

    2017-02-01

    Two new mononuclear cationic complexes in which the TbIII ion is bis-chelated by the tripodal alcohol 1,1,1-tris-(hy-droxy-meth-yl)propane (H3LEt, C6H14O3) were prepared from Tb(NO3)3·5H2O and had their crystal and mol-ecular structures solved by single-crystal X-ray diffraction analysis after data collection at 100 K. Both products were isolated in reasonable yields from the same reaction mixture by using different crystallization conditions. The higher-symmetry complex dinitratobis[1,1,1-tris-(hy-droxy-meth-yl)propane]-terbium(III) nitrate di-meth-oxy-ethane hemisolvate, [Tb(NO3)2(H3LEt)2]NO3·0.5C4H10O2, 1, in which the lanthanide ion is 10-coordinate and adopts an s-bicapped square-anti-prismatic coordination geometry, contains two bidentate nitrate ions bound to the metal atom; another nitrate ion functions as a counter-ion and a half-mol-ecule of di-meth-oxy-ethane (completed by a crystallographic twofold rotation axis) is also present. In product aqua-nitratobis[1,1,1-tris-(hy-droxy-meth-yl)propane]-terbium(III) dinitrate, [Tb(NO3)(H3LEt)2(H2O)](NO3)2, 2, one bidentate nitrate ion and one water mol-ecule are bound to the nine-coordinate terbium(III) centre, while two free nitrate ions contribute to charge balance outside the tricapped trigonal-prismatic coordination polyhedron. No free water mol-ecule was found in either of the crystal structures and, only in the case of 1, di-meth-oxy-ethane acts as a crystallizing solvent. In both mol-ecular structures, the two tripodal ligands are bent to one side of the coordination sphere, leaving room for the anionic and water ligands. In complex 2, the methyl group of one of the H3LEt ligands is disordered over two alternative orientations. Strong hydrogen bonds, both intra- and inter-molecular, are found in the crystal structures due to the number of different donor and acceptor groups present.

  18. Diphenylacetylene complexes of niobium, molybdenum, tungsten, and rhenium. Crystal structure of (NbCl/sub 3/(Ph-C triple bond C-Ph))/sub 4/

    Energy Technology Data Exchange (ETDEWEB)

    Hey, E.; Weller, F.; Dehnicke, K. (Marburg Univ. (Germany, F.R.). Fachbereich Chemie)

    1984-07-01

    Synthesis and IR spectra of diphenylacetylene complexes of niobium, molybdenum, tungsten, and rhenium are reported. The chloro complexes are formed in the reactions of the pentachlorides of niobium, molybdenum, rhenium, and tungsten hexachloride, respectively, with diphenyl acetylene. The bromo and iodo complexes are obtained by halogen exchange with boron halides, and further derivatives are obtained by reactions of PPh/sub 4/Cl or AsPh/sub 4/Cl and PPh/sub 3/ with the corresponding starting materials. The crystal structure of the niobium complex was determined by the aid of X-ray diffraction data (R = 5.9% for 1548 independent, observed reflexions). The complex crystallizes triclinic in the space group P1 with one tetrameric molecule (NbCl/sub 3/(Ph-C triple bond C-Ph))/sub 4/ per unit cell. The cell dimensions at 20/sup 0/C are a = 1074 pm, b = 1390 pm, c = 1299 pm, ..cap alpha.. = 104.3/sup 0/, ..beta.. = 108.0/sup 0/, ..gamma.. = 108.7/sup 0/. The complex occurs as a centrosymmetric tetramer, which can be regarded as a distorted double hexahedron with two corners missing. Association is effected by chloro bridges in which the chlorine atoms have coordination number two and three. The diphenylacetylene ligands are bonded to the niobium atoms side-on with almost equal Nb-C bond lengths of average value 205 pm. Thus the Nb atoms achieve coordination number seven.

  19. DFT studies of copper(II) complexes of cis-1,2-diaminocyclohexane (Dach) and crystal structure of [Cu(Dach)2(H2O)]Cl2

    Science.gov (United States)

    Nawaz, Sidra; Ghaffar, Abdul; Zierkiewicz, Wiktor; Monim-ul-Mehboob, Muhammad; Khurram; Tahir, Muhammad Nawaz; Isab, Anvarhusein A.; Ahmad, Saeed

    2017-06-01

    A copper(II) complex, [Cu(Dach)2(H2O)]Cl2 (1) (Dach = cis-1,2-Diaminocyclohexane) has been prepared and characterized by IR spectroscopy and X-ray crystallography. The crystal structure of complex 1 is ionic consisting of [Cu(Dach)2(H2O)]2+ cation and two chloride counter ions. The copper atom in the complex ion assumes a distorted square pyramidal geometry with water occupying the apical position. The adjacent molecules are joined by hydrogen bonding to form irregular chains. The structures of [Cu(Dach)2(H2O)]Cl2 (1) and three of its analogues, [Cu(Dach)2Cl]Cl·H2O (2), [Cu(Dach)2(H2O)Cl]Cl (3) and [Cu(Dach)2Cl2]·H2O (4) were predicted by DFT calculations. The DFT results reveal that in the gas phase, the structure 1 is less stable in comparison to the calculated structure, [Cu(Dach)2Cl2]·H2O (4). The additional calculations were performed for the complexes investigated in solution (water) using the polarizable continuum model. According to these calculations, the electronic energies (stabilities) of the complexes 1 and 4 in the solvent are comparable to each other. The atomic charges and second-order interaction energies between orbitals for complexes 1-4 were calculated with natural bond orbital (NBO) analysis.

  20. Mre11-Rad50 complex crystals suggest molecular calisthenics

    NARCIS (Netherlands)

    C. Wyman (Claire); J.H.G. Lebbink (Joyce); R. Kanaar (Roland)

    2011-01-01

    textabstractRecently published crystal structures of different Mre11 and Rad50 complexes show the arrangement of these proteins and imply dramatic ligand-induced rearrangements with important functional consequences.

  1. Mre11-Rad50 complex crystals suggest molecular calisthenics

    OpenAIRE

    Wyman, Claire; Lebbink, Joyce; Kanaar, Roland

    2011-01-01

    Recently published crystal structures of different Mre11 and Rad50 complexes show the arrangement of these proteins and imply dramatic ligand-induced rearrangements with important functional consequences.

  2. Crystal structure of fipronil

    Directory of Open Access Journals (Sweden)

    Hyunjin Park

    2017-10-01

    Full Text Available The title compound, C12H4Cl2F6N4OS {systematic name: 5-amino-1-[2,6-dichloro-4-(trifluoromethylphenyl]-4-[(trifluoromethanesulfinyl]-1H-pyrazole-3-carbonitrile}, is a member of the phenylpyrazole group of acaricides, and one of the phenylpyrazole group of insecticides. The dihedral angle between the planes of the pyrazole and benzene rings is 89.03 (9°. The fluorine atoms of the trifluoromethyl substituent on the benzene ring are disordered over two sets of sites, with occupancy ratios 0.620 (15:0.380 (15. In the crystal, C—N...π interactions [N...ring centroid = 3.607 (4 Å] together with N—H...N and C—H...F hydrogen bonds form a looped chain structure along [10\\overline{1}]. Finally, N—H...O hydrogen bonds and C—Cl...π interactions [Cl...ring centroid = 3.5159 (16 Å] generate a three-dimensional structure. Additionally, there are a short intermolecular F... F contacts present.

  3. Synthesis, characterization, crystal structure, DNA/BSA binding ability and antibacterial activity of asymmetric europium complex based on 1,10- phenanthroline

    Science.gov (United States)

    Alfi, Nafiseh; Khorasani-Motlagh, Mozhgan; Rezvani, Ali Reza; Noroozifar, Meissam; Molčanov, Krešimir

    2017-06-01

    A heteroleptic europium coordination compound formulated as [Eu(phen)2(OH2)2(Cl)2](Cl)(H2O) (phen = 1,10-phenanthroline), has been synthesized and characterized by elemental analysis, FT-IR spectroscopy, and single-crystal X-ray diffractometer. Crystal structure analysis reveals the complex is crystallized in orthorhombic system with Pca21 space group. Electronic absorption and various emission methods for investigation of the binding system of europium(III) complex to Fish Salmon deoxyribonucleic acid (FS-DNA) and Bovamin Serum Albumin (BSA) have been explored. Furthermore, the binding constants, binding sites and the corresponding thermodynamic parameters of the interaction system based on the van't Hoff equation for FS-DNA and BSA were calculated. The thermodynamic parameters reflect the exothermic nature of emission process (ΔH°DNA by non-intercalative mode which the groove binding is preferable mode. Also, the complex exhibits a brilliant antimicrobial activity in vitro against standard bacterial strains.

  4. Synthesis, crystal structure, spectroscopic characterization and nonlinear optical properties of manganese (II) complex of picolinate: A combined experimental and computational study

    Science.gov (United States)

    Tamer, Ömer; Avcı, Davut; Atalay, Yusuf; Çoşut, Bünyemin; Zorlu, Yunus; Erkovan, Mustafa; Yerli, Yusuf

    2016-02-01

    A novel manganese (II) complex with picolinic acid (pyridine 2-carboxylic acid, Hpic), namely, [Mn(pic)2(H2O)2] was prepared and its crystal structure was fully characterized by using single crystal X-ray diffraction. Picolinate (pic) ligands were coordinated to the central manganese(II) ion as bidentate N,O-donors through the nitrogen atoms of pyridine rings and the oxygen atoms of carboxylate groups forming five-membered chelate rings. The spectroscopic characterization of Mn(II) complex was performed by the applications of FT-IR, Raman, UV-vis and EPR techniques. In order to support these studies, density functional theory (DFT) calculations were carried out by using B3LYP level. IR and Raman spectra were simulated at B3LYP level, and obtained results indicated that DFT calculations generally give compatible results to the experimental ones. The electronic structure of the Mn(II) complex was predicted using time dependent DFT (TD-DFT) method with polarizable continuum model (PCM). Molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength were investigated by applying natural bond orbital (NBO) analysis. Nonlinear optical properties of Mn(II) complex were investigated by the determining of molecular polarizability (α) and hyperpolarizability (β) parameters.

  5. Synthesis, characterization, crystal structure and antibacterial activities of transition metal(II) complexes of the schiff base 2-[(4-methylphenylimino)methyl]-6-methoxyphenol.

    Science.gov (United States)

    Yu, Yu-Ye; Xian, Hui-Duo; Liu, Jian-Feng; Zhao, Guo-Liang

    2009-05-07

    Five transition metal(II) complexes, [ML(2)Cl(2)] 1 approximately 5, were synthesized from the reaction of MCl(2) x nH(2)O (M = Mn, Co, Ni, Cu, Cd) and the Schiff base ligand 2-[(4-methylphenylimino)methyl]-6-methoxyphenol (C(15)H(15)NO(2), L), obtained by condensation of o-vanillin (2-hydroxy-3-methoxybenzaldehyde) with p-toluidine. They were characterized by elemental analysis, molar conductance, FT-IR spectra, thermal analysis. The structure of complex 1 was determined by single-crystal X-ray diffraction. Its crystal structure is of monoclinic system, space group P2(1)/c with a = 9.0111(18) A, b = 11.222(2) A, c =28.130 (6) A, alpha = 90 masculine, beta = 92.29(3) masculine, gamma = 90 masculine, V = 2867.6(10) A(3), Z = 4. The Mn atom is six-coordinate and displays distorted octahedral geometry.The Schiff base ligand and its complexes have been tested in vitro to evaluate their antibacterial activity against bacteria, viz., Escherichia coli, Staphylococcus aureus and Bacillus subtilis. It has been found that the complexes have higher activity than the corresponding free Schiff base ligand against the same bacteria.

  6. Synthesis, Characterization, Crystal Structure and Antibacterial Activities of Transition Metal(II Complexes of the Schiff Base 2-[(4-Methylphenyliminomethyl]-6-methoxyphenol

    Directory of Open Access Journals (Sweden)

    Guo-Liang Zhao

    2009-05-01

    Full Text Available Five transition metal(II complexes, [ML2Cl2] 1~5, were synthesized from the reaction of MCl2·nH2O (M = Mn, Co, Ni, Cu, Cd and the Schiff base ligand 2-[(4-methylphenyliminomethyl]-6-methoxyphenol (C15H15NO2, L, obtained by condensation of o-vanillin (2-hydroxy-3-methoxybenzaldehyde with p-toluidine. They were characterized by elemental analysis, molar conductance, FT-IR spectra, thermal analysis. The structure of complex 1 was determined by single-crystal X-ray diffraction. Its crystal structure is of monoclinic system, space group P21/c with a = 9.0111(18 Å, b = 11.222(2 Å, c =28.130 (6 Å, α = 90 º, β = 92.29(3 º, γ = 90 º, V = 2867.6(10 Å3, Z = 4. The Mn atom is six-coordinate and displays distorted octahedral geometry.The Schiff base ligand and its complexes have been tested in vitro to evaluate their antibacterial activity against bacteria, viz., Escherichia coli, Staphylococcus aureus and Bacillus subtilis. It has been found that the complexes have higher activity than the corresponding free Schiff base ligand against the same bacteria.

  7. Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4.

    Science.gov (United States)

    Patikoglou, Georgia A; Westblade, Lars F; Campbell, Elizabeth A; Lamour, Valérie; Lane, William J; Darst, Seth A

    2007-09-21

    The Escherichia coli Rsd protein binds tightly and specifically to the RNA polymerase (RNAP) sigma(70) factor. Rsd plays a role in alternative sigma factor-dependent transcription by biasing the competition between sigma(70) and alternative sigma factors for the available core RNAP. Here, we determined the 2.6 A-resolution X-ray crystal structure of Rsd bound to sigma(70) domain 4 (sigma(70)(4)), the primary determinant for Rsd binding within sigma(70). The structure reveals that Rsd binding interferes with the two primary functions of sigma(70)(4), core RNAP binding and promoter -35 element binding. Interestingly, the most highly conserved Rsd residues form a network of interactions through the middle of the Rsd structure that connect the sigma(70)(4)-binding surface with three cavities exposed on distant surfaces of Rsd, suggesting functional coupling between sigma(70)(4) binding and other binding surfaces of Rsd, either for other proteins or for as yet unknown small molecule effectors. These results provide a structural basis for understanding the role of Rsd, as well as its ortholog, AlgQ, a positive regulator of Pseudomonas aeruginosa virulence, in transcription regulation.

  8. Crystal structure of the Escherichia coli regulator of σ70, Rsd, in complex with σ70 domain 4

    Science.gov (United States)

    Patikoglou, Georgia A.; Westblade, Lars F.; Campbell, Elizabeth A.; Lamour, Valérie; Lane, William J.; Darst, Seth A.

    2007-01-01

    Summary The Escherichia coli Rsd protein binds tightly and specifically to the RNA polymerase (RNAP) σ70 factor. Rsd plays a role in alternative σ factor-dependent transcription by biasing the competition between σ70 and alternative σ factors for the available core RNAP. Here, we determined the 2.6 Å-resolution X-ray crystal structure of Rsd bound to σ70 domain 4 (σ704), the primary determinant for Rsd binding within σ70. The structure reveals that Rsd binding interferes with the two primary functions of σ704, core RNAP binding and promoter –35 element binding. Interestingly, the most highly conserved Rsd residues form a network of interactions through the middle of the Rsd structure that connect the σ704-binding surface with three cavities exposed on distant surfaces of Rsd, suggesting functional coupling between σ704 binding and other binding surfaces of Rsd, either for other proteins or for as yet unknown small molecule effectors. These results provide a structural basis for understanding the role of Rsd, as well as its ortholog, AlgQ, a positive regulator of Pseudomonas aeruginosa virulence, in transcription regulation. PMID:17681541

  9. Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides.

    Science.gov (United States)

    Doan, Thanh Thi Ngoc; Kim, Jin-Kwang; Ngo, Ho-Phuong-Thuy; Tran, Huyen-Thi; Cha, Sun-Shin; Min Chung, Kyung; Huynh, Kim-Hung; Ahn, Yeh-Jin; Kang, Lin-Woo

    2014-03-01

    D-Alanine-D-alanine ligase (DDL) catalyzes the biosynthesis of d-alanyl-d-alanine, an essential bacterial peptidoglycan precursor, and is an important drug target for the development of antibacterials. We determined four different crystal structures of DDL from Xanthomonas oryzae pv. oryzae (Xoo) causing Bacteria Blight (BB), which include apo, ADP-bound, ATP-bound, and AMPPNP-bound structures at the resolution between 2.3 and 2.0 Å. Similarly with other DDLs, the active site of XoDDL is formed by three loops from three domains at the center of enzyme. Compared with d-alanyl-d-alanine and ATP-bound TtDDL structure, the γ-phosphate of ATP in XoDDL structure was shifted outside toward solution. We swapped the ω-loop (loop3) of XoDDL with those of Escherichia coli and Helicobacter pylori DDLs, and measured the enzymatic kinetics of wild-type XoDDL and two mutant XoDDLs with the swapped ω-loops. Results showed that the direct interactions between ω-loop and other two loops are essential for the active ATP conformation for D-ala-phosphate formation. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. X-ray crystal structure and theoretical study of a new dinuclear Cu(II) complex with two different geometry centers bridged with an oxo group

    Science.gov (United States)

    Golbedaghi, Reza; Azimi, Saeid; Molaei, Atefeh; Hatami, Masoud; Notash, Behrouz

    2017-10-01

    A new Schiff base ligand HL, 1,3-bis(2-((Z)-(2-aminoethylimino)methyl)phenoxy)ethylene di amine, has been synthesized from the reaction of a new aldehyde and ethylenediamine. After preparation the Schiff base, a new dinuclear Cu(II) complex with two different geometry for each metal ion was synthesized. Single crystal X-ray structure analysis of the complex Cu(II) showed that the complex is binuclear and all nitrogen and oxygen atoms of ligand (N4O3) are coordinated to two Cu(II) center ions. The crystal structure studying shows, a perchlorate ion has been coordinated to the two Cu(II) metal centers as bridged and another perchlorate coordinated to the one of Cu(II) ion as terminal. However, two interesting structures square pyramidal and distorted octahedral Cu(II) ions are bridged asymmetrically by a perchlorate ion and oxygen of hydroxyl group of Schiff base ligand. In addition, we had a theoretical study to have a comparison of experimental and theoretical results we determined the HOMO and LUMO orbitals.

  11. Synthesis, crystal structure and biological evaluation of a new dasatinib copper(II) complex as telomerase inhibitor.

    Science.gov (United States)

    Qin, Qi-Pin; Meng, Ting; Tan, Ming-Xiong; Liu, Yan-Cheng; Luo, Xu-Jian; Zou, Bi-Qun; Liang, Hong

    2018-01-01

    A new copper(II) complex of dasatinib (DAS) was synthesized and characterized via ESI-MS, UV-Vis, IR, single-crystal X-ray diffraction analysis, 1 H and 13 C NMR spectroscopy, and elemental analysis. The composition of the new complex (1) was found to be [Cu(DAS + H)(NO 3 ) 2 (H 2 O)]NO 3 ·(H 2 O)·(CH 3 OH). Through MTT assay, it was found that 1 had high cytotoxicity towards A549, HeLa, BEL-7402, Hep-G2, NCI-H460, and MGC80-3 tumor cell lines, with IC 50 values in 4.04-13.04 μM. The Hep-G2 cells were the most sensitive to 1. It is worth noting that compared with DAS and cisplatin, 1 not only had higher in vitro anticancer activity but also exhibited greater selective toxicity towards Hep-G2 cells than for normal HL-7702 cells. Experimental results from cell apoptosis analysis, cellular uptake, TRAP-silver staining assay, RT-PCR, western blot, and transfection assays showed that 1 was most likely a telomerase inhibitor that targeted c-myc G-quadruplex DNA. The high cytotoxicity and biological behaviors of 1 could be correlated with the central copper(II) atom in the coordinated mode with DAS. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  12. Crystal structure of the novel complex formed between zinc alpha2-glycoprotein (ZAG) and prolactin-inducible protein (PIP) from human seminal plasma.

    Science.gov (United States)

    Hassan, Md Imtaiyaz; Bilgrami, Sameeta; Kumar, Vijay; Singh, Nagendra; Yadav, Savita; Kaur, Punit; Singh, T P

    2008-12-19

    This is the first report on the formation of a complex between zinc alpha2-glycoprotein (ZAG) and prolactin-inducible protein (PIP). The complex was purified from human seminal plasma and crystallized using 20% polyethylene glycol 9000 and 5% hexaethylene glycol. The structure of the complex has been determined using X-ray crystallographic method and refined to an R(cryst) of 0.199 (R(free)=0.239). The structure of ZAG is broadly similar to the structure of serum ZAG. The scaffolding of PIP consists of seven beta-strands that are organized in the form of two antiparallel beta-pleated sheets, resulting in the formation of a sandwiched beta-sheet. The amino acid sequence of PIP contains one potential N-glycosylation site at Asn77, and the same is found glycosylated with four sugar residues. The structure of the complex shows that the beta-structure of PIP is ideally aligned with the beta-structure of domain alpha3 of ZAG to form a long interface between two proteins. The proximal beta-strands at the long interface are arranged in an antiparallel manner. There are 12 hydrogen bonds and three salt bridges between ZAG and PIP. At the two ends of vertical interface, two salt bridges are formed between pairs of Lys41-Asp233 and Lys68-Glu229. On the perpendicular interface involving alpha1-alpha2 domains of ZAG and a loop of PIP, another salt bridge is formed. The internal space at the corner of the L-shaped structure is filled with solvent molecules including a carbonate ion. The overall buried area in the complex is approximately 914 A(2), which is considerably higher than the 660 A(2) reported for the class I major histocompatibility complex structures.

  13. Electrochemical synthesis, crystal structure, and photomagnetic properties of a three-dimensional cyano-bridged copper-molybdenum complex.

    Science.gov (United States)

    Hozumi, Toshiya; Hashimoto, Kazuhito; Ohkoshi, Shin-ichi

    2005-03-23

    A single crystal of Cs(I)2Cu(II)7[Mo(IV)CN8]4.6H2O was electrochemically prepared on a Pt wire electrode with a constant potential of +500 mV vs Ag/AgCl electrode. X-ray single-crystal structural analysis showed that this compound consists of a three-dimensional cyano-bridged Cu-Mo bimetallic assembly with a tetragonal structure of I4/mmm. The coordination geometry of Mo(IV) is bicapped trigonal prism, and that of Cu(II) is five-coordinate of square pyramidal or four-coordinate of square planar. This compound was also prepared as a 0.2-3.0 microm thick film on a SnO2-coated glass in the same electrochemical manner. When the sample, which shows paramagnetism due to Cu(II) (S = 1/2), was irradiated with 450-500 nm light at 5 K, spontaneous magnetization with a Curie temperature of 23 K was observed. This photoinduced change was recovered by a thermal treatment. In the infrared (IR) and electron spin resonance (ESR) spectra after light irradiation, variations in the stretching IR peak of CN bridged to Mo(IV) and the paramagnetic ESR peak of Cu(II) were observed, respectively. The data indicate that this photomagnetism is caused by the electron transfer from Mo(IV) to Cu(II) and the ferromagnetic ordering between Cu(II) (S = 1/2) and Mo(V) (S = 1/2).

  14. Synthesis, crystal structure and interaction of L-valine Schiff base divanadium(V) complex containing a V2O3 core with DNA and BSA

    Science.gov (United States)

    Guo, Qiong; Li, Lianzhi; Dong, Jianfang; Liu, Hongyan; Xu, Tao; Li, Jinghong

    2013-04-01

    A divanadium(V) complex, [V2O3(o-van-val)2] (o-van-val = Schiff base derived from o-vanillin and L-valine), has been synthesized and structurally characterized. The crystal structure shows that both of the vanadium centers in the complex have a distorted octahedral coordination environment composed of tridentate Schiff base ligand. A V2O3 core in molecular structure adopts intermediate between cis and trans configuration with the O1dbnd V1⋯V1Adbnd O1A torsion angle 115.22 (28)° and the V1⋯V1A distance 3.455 Å. The binding properties of the complex with calf thymus DNA (CT-DNA) have been investigated by UV-vis absorption, fluorescence, CD spectra and viscosity measurement. The results indicate that the complex binds to CT-DNA in non-classical intercalative mode. Meanwhile, the interaction of the complex with bovine serum albumin (BSA) has been studied by UV-vis absorption, fluorescence and CD spectra. Results indicated that the complex can markedly quench the intrinsic fluorescence of BSA via a static quenching process, and cause its conformational change. The calculated apparent binding constant Kb was 1.05 × 106 M-1 and the binding site number n was 1.18.

  15. Prediction of molecular crystal structures

    CERN Document Server

    Beyer, T

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of parac...

  16. Crystal structures, DFT calculations and Hirshfeld surface analyses of three new cobalt(III) Schiff base complexes derived from meso-1,2-diphenyl-1,2-ethylenediamine

    Science.gov (United States)

    Masoudi, Mohaddeseh; Behzad, Mahdi; Arab, Ali; Tarahhomi, Atekeh; Rudbari, Hadi Amiri; Bruno, Giuseppe

    2016-10-01

    Three new Cobalt(III) Schiff base complexes were synthesized and characterized by spectroscopic methods and x-ray crystallography. The DFT optimized structures of the complexes agreed well with the corresponding x-ray structures. According to the calculated vibrational normal modes, the observed signals in the IR spectra of the complexes were assigned. The experimental UV-Vis spectra of the complexes were also discussed considering the calculated excited states and molecular orbitals. Hirshfeld surface analysis was carried out to study the inter-contact interactions in these complexes. These studies provided comprehensive description of such inter-contact interactions by means of an appealing graphical approach using 3D Hirshfeld surfaces and 2D fingerprint plots derived from the surfaces. It indicated the dominant role of various hydrogen intermolecular interactions such as H⋯H (above 60%), C⋯H/H⋯C (near 15%-20%), O⋯H/H⋯O (about 16% or 17% for structures with counter ion ClO4-) and H⋯F (17% for structure with counter ion PF6-) contacts into the crystal packing which are discussed in details.

  17. The crystal structures of native hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 and of substrate and inhibitor complexes.

    Science.gov (United States)

    Ferraroni, Marta; Da Vela, Stefano; Kolvenbach, Boris A; Corvini, Philippe F X; Scozzafava, Andrea

    2017-05-01

    The crystal structure of hydroquinone 1,2-dioxygenase, a Fe(II) ring cleaving dioxygenase from Sphingomonas sp. strain TTNP3, which oxidizes a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes, has been solved by Molecular Replacement, using the coordinates of PnpCD from Pseudomonas sp. strain WBC-3. The enzyme is a heterotetramer, constituted of two subunits α and two β of 19 and 38kDa, respectively. Both the two subunits fold as a cupin, but that of the small α subunit lacks a competent metal binding pocket. Two tetramers are present in the asymmetric unit. Each of the four β subunits in the asymmetric unit binds one Fe(II) ion. The iron ion in each β subunit is coordinated to three protein residues, His258, Glu264, and His305 and a water molecule. The crystal structures of the complexes with the substrate methylhydroquinone, obtained under anaerobic conditions, and with the inhibitors 4-hydroxybenzoate and 4-nitrophenol were also solved. The structures of the native enzyme and of the complexes present significant differences in the active site region compared to PnpCD, the other hydroquinone 1,2-dioxygenase of known structure, and in particular they show a different coordination at the metal center. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Crystal structure of CotA laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhongchuan; Xie, Tian [Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of (China); Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu 610041, People’s Republic of (China); Zhong, Qiuping [Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of (China); Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu 610041, People’s Republic of (China); University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of (China); Wang, Ganggang, E-mail: wanggg@cib.ac.cn [Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of (China); Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu 610041, People’s Republic of (China)

    2016-03-24

    The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) in a hole motif has been solved; this novel binding site could be a potential structure-based target for protein engineering of CotA laccase. The CotA laccase from Bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. The crystal structure of CotA complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in a hole motif has been solved. The novel binding site was about 26 Å away from the T1 binding pocket. Comparison with known structures of other laccases revealed that the hole is a specific feature of CotA. The key residues Arg476 and Ser360 were directly bound to ABTS. Site-directed mutagenesis studies revealed that the residues Arg146, Arg429 and Arg476, which are located at the bottom of the novel binding site, are essential for the oxidation of ABTS and syringaldazine. Specially, a Thr480Phe variant was identified to be almost 3.5 times more specific for ABTS than for syringaldazine compared with the wild type. These results suggest this novel binding site for ABTS could be a potential target for protein engineering of CotA laccases.

  19. Crystal structure of oxamyl

    Directory of Open Access Journals (Sweden)

    Eunjin Kwon

    2016-12-01

    Full Text Available The title compound, C7H13N3O3S [systematic name: (Z-methyl 2-dimethylamino-N-(methylcarbamoyloxy-2-oxoethanimidothioate], is an oxime carbamate acaride, insecticide and nematicide. The asymmetric unit comprises two independent molecules, A and B. The dihedral angles between the mean planes [r.m.s. deviations = 0.0017 (A and 0.0016 Å (B] of the acetamide and oxyimino groups are 88.80 (8° for A and 87.05 (8° for B. In the crystal, N/C—H...O hydrogen bonds link adjacent molecules, forming chains along the a axis. The chains are further linked by C—H...O hydrogen bonds, resulting in a three-dimensional network with alternating rows of A and B molecules in the bc plane stacked along the a-axis direction. The structure was refined as an inversion twin with a final BASF parameter of 0.16 (9.

  20. Crystal structure of vaccinia viral A27 protein reveals a novel structure critical for its function and complex formation with A26 protein.

    Directory of Open Access Journals (Sweden)

    Tao-Hsin Chang

    Full Text Available Vaccinia virus envelope protein A27 has multiple functions and is conserved in the Orthopoxvirus genus of the poxvirus family. A27 protein binds to cell surface heparan sulfate, provides an anchor for A26 protein packaging into mature virions, and is essential for egress of mature virus (MV from infected cells. Here, we crystallized and determined the structure of a truncated form of A27 containing amino acids 21-84, C71/72A (tA27 at 2.2 Å resolution. tA27 protein uses the N-terminal region interface (NTR to form an unexpected trimeric assembly as the basic unit, which contains two parallel α-helices and one unusual antiparallel α-helix; in a serpentine way, two trimers stack with each other to form a hexamer using the C-terminal region interface (CTR. Recombinant tA27 protein forms oligomers in a concentration-dependent manner in vitro in gel filtration. Analytical ultracentrifugation and multi-angle light scattering revealed that tA27 dimerized in solution and that Leu47, Leu51, and Leu54 at the NTR and Ile68, Asn75, and Leu82 at the CTR are responsible for tA27 self-assembly in vitro. Finally, we constructed recombinant vaccinia viruses expressing full length mutant A27 protein defective in either NTR, CTR, or both interactions; the results demonstrated that wild type A27 dimer/trimer formation was impaired in NTR and CTR mutant viruses, resulting in small plaques that are defective in MV egress. Furthermore, the ability of A27 protein to form disulfide-linked protein complexes with A26 protein was partially or completely interrupted by NTR and CTR mutations, resulting in mature virion progeny with increased plasma membrane fusion activity upon cell entry. Together, these results demonstrate that A27 protein trimer structure is critical for MV egress and membrane fusion modulation. Because A27 is a neutralizing target, structural information will aid the development of inhibitors to block A27 self-assembly or complex formation against

  1. Crystal and geometry-optimized structure, Hirshfeld surface analysis and physicochemical studies of a new Co(II) complex with the ligand 2-amino-6-methoxypyrimidine

    Science.gov (United States)

    Nbili, W.; Soudani, S.; Kaabi, K.; Wojtaś, M.; Ferretti, V.; Lefebvre, F.; Jelsch, C.; Ben Nasr, C.

    2017-10-01

    The crystal structure of the new complex [Co(C5H7N3O)2(H2O)4](NO3)2ṡ4H2O synthesized in aqueous solution has been determined by single crystal X-ray diffraction. The compound crystallizes in the triclinic space group P 1 bar with lattice parameters: a = 7.3056(2), b = 8.4065(2), c = 10.4724(3) Å, α = 103.9470(19), β = 105.6600(14), γ = 91.1350(18)°, V = 598.54(3) Å3 and Z = 1. The Co(II) central ion is in a slightly distorted octahedral coordination geometry formed by two nitrogen atoms of two 2-amino-6-methoxypyrimidine ligands and four oxygen atoms of coordinated water molecules. The crystal packing is stabilized by intermolecular Osbnd H⋯O, Nsbnd H⋯O and Csbnd H⋯O hydrogen bonds which link the molecules into a three-dimensional network. Intermolecular interactions were investigated by Hirshfeld surfaces. Electronic properties such as HOMO and LUMO energies were derived. The vibrational absorption bands were identified by infrared spectroscopy. The compound was characterized by thermal analysis to determine its thermal behavior with respect to temperature.

  2. p-halo N4-phenyl substituted thiosemicarbazones: Crystal structure, supramolecular architecture, characterization and bio-assay of their Co(III) and Ni(II) complexes

    Science.gov (United States)

    Kotian, Avinash; Kumara, Karthik; Kamat, Vinayak; Naik, Krishna; Kokare, Dhoolesh G.; Nevrekar, Anupama; Lokanath, Neratur Krishnappagowda; Revankar, Vidyanand K.

    2018-03-01

    In the present work, three potential metal ion chelating ligands, p-halo N4-phenyl substituted thiosemicarbazones are synthesized and characterized. The molecular structure of all (E)-4-(4-halophenyl)-1-(3-hydroxyiminobutan-2-ylidene) thiosemicarbazones (halo = F/Cl/Br) are determined by single crystal X-ray diffraction method. All the molecules have crystallized in monoclinic crystal system with P21/n space group. The ligands show Csbnd H⋯S and Nsbnd H⋯S intermolecular interactions, which are responsible to form the supramolecular self-assemblies through R22(8), R22(12) and R22(14) ring motifs. Hirshfeld surface analysis is carried out to explore the intermolecular interactions. A series of Co(III) and Ni(II) mononuclear transition metal complexes derived from these ligands have been synthesized and characterized by various spectro-analytical methods. The metal to ligand stoichiometry has been found to be 1:2 in all the complexes. The synthesized compounds have been investigated for their in vitro antimicrobial potencies. The compounds are found to be more active than the standard used, in the case of E. coli and A. niger. Additionally, they are also screened for their in vitro antitubercular activity.

  3. Syntheses, crystal structures, and characterization of three 1D, 2D and 3D complexes based on mixed multidentate N- and O-donor ligands

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Huai-Xia, E-mail: yanghuaixia886@163.com [Pharmacy College, Henan University of Traditional Chinese Medicine, Zhengzhou 450008 (China); Liang, Zhen; Hao, Bao-Lian [Pharmacy College, Henan University of Traditional Chinese Medicine, Zhengzhou 450008 (China); Meng, Xiang-Ru, E-mail: mxr@zzu.edu.cn [The College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001 (China)

    2014-10-15

    Three new 1D to 3D complexes, namely, ([Ni(btec)(Himb){sub 2}(H{sub 2}O){sub 2}]·6H{sub 2}O){sub n} (1), ([Cd(btec){sub 0.5}(imb)(H{sub 2}O)]·1.5H{sub 2}O){sub n} (2), and ([Zn(btec){sub 0.5}(imb)]·H{sub 2}O){sub n} (3) (H{sub 4}btec=1,2,4,5-benzenetetracarboxylic acid, imb=2-(1H-imidazol-1-methyl)-1H-benzimidazole) have been synthesized by adjusting the central metal ions. Single-crystal X-ray diffraction analyses reveal that complex 1 possesses a 1D chain structure which is further extended into the 3D supramolecular architecture via hydrogen bonds. Complex 2 features a 2D network with Schla¨fli symbol (5{sup 3}·6{sup 2}·7)(5{sup 2}·6{sup 4}). Complex 3 presents a 3D framework with a point symbol of (4·6{sup 4}·8)(4{sup 2}·6{sup 2}·8{sup 2}). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature. - Graphical abstract: Three new 1D to 3D complexes with different structural and topological motifs have been obtained by modifying the central metal ions. Additionally, their IR, TG analyses and fluorescent properties are also investigated. - Highlights: • Three complexes based on mixed multidentate N- and O-donor ligands. • The complexes are characterized by IR, luminescence and TGA techniques. • Benzenetetracarboxylates display different coordination modes in complexes 1–3. • Changing the metal ions can result in complexes with completely different structures.

  4. The 1.4 Å Crystal Structure of the Class D [beta]-Lactamase OXA-1 Complexed with Doripenem

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Kyle D.; Karpen, Mary E.; Bonomo, Robert A.; Leonard, David A.; Powers, Rachel A.; (Grand Valley); (Case Western U.-Med)

    2010-01-12

    The clinical efficacy of carbapenem antibiotics depends on their resistance to the hydrolytic action of {beta}-lactamase enzymes. The structure of the class D {beta}-lactamase OXA-1 as an acyl complex with the carbapenem doripenem was determined to 1.4 {angstrom} resolution. Unlike most class A and class C carbapenem complexes, the acyl carbonyl oxygen in the OXA-1-doripenem complex is bound in the oxyanion hole. Interestingly, no water molecules were observed in the vicinity of the acyl linkage, providing an explanation for why carbapenems inhibit OXA-1. The side chain amine of K70 remains fully carboxylated in the acyl structure, and the resulting carbamate group forms a hydrogen bond to the alcohol of the 6{alpha}-hydroxyethyl moiety of doripenem. The carboxylate attached to the {beta}-lactam ring of doripenem is stabilized by a salt bridge to K212 and a hydrogen bond with T213, in lieu of the interaction with an arginine side chain found in most other {beta}-lactamase-{beta}-lactam complexes (e.g., R244 in the class A member TEM-1). This novel set of interactions with the carboxylate results in a major shift of the carbapenem's pyrroline ring compared to the structure of the same ring in meropenem bound to OXA-13. Additionally, bond angles of the pyrroline ring suggest that after acylation, doripenem adopts the {Delta}{sup 1} tautomer. These findings provide important insights into the role that carbapenems may have in the inactivation process of class D {beta}-lactamases.

  5. Synthesis, crystal structure and spectroscopic and electrochemical properties of bridged trisbenzoato copper-zinc heterobinuclear complex of 2,2‧-bipyridine

    Science.gov (United States)

    Koch, Angira; Kumar, Arvind; Singh, Suryabhan; Borthakur, Rosmita; Basumatary, Debajani; Lal, Ram A.; Shangpung, Sankey

    2015-03-01

    The synthesis of the heterobinuclear copper-zinc complex [CuZn(bz)3(bpy)2]ClO4 (bz = benzoate) from benzoic acid and bipyridine is described. Single crystal X-ray diffraction studies of the heterobinuclear complex reveals the geometry of the benzoato bridged Cu(II)-Zn(II) centre. The copper or zinc atom is pentacoordinate, with two oxygen atoms from bridging benzoato groups and two nitrogen atoms from one bipyridine forming an approximate plane and a bridging oxygen atom from a monodentate benzoate group. The Cu-Zn distance is 3.345 Å. The complex is normal paramagnetic having μeff value equal to 1.75 BM, ruling out the possibility of Cu-Cu interaction in the structural unit. The ESR spectrum of the complex in CH3CN at RT exhibit an isotropic four line spectrum centred at g = 2.142 and hyperfine coupling constants Aav = 63 × 10-4 cm-1, characteristic of a mononuclear square-pyramidal copper(II) complexes. At LNT, the complex shows an isotropic spectrum with g|| = 2.254 and g⊥ = 2.071 and A|| = 160 × 10-4 cm-1. The Hamiltonian parameters are characteristic of distorted square pyramidal geometry. Cyclic voltammetric studies of the complex have indicated quasi-reversible behaviour in acetonitrile solution.

  6. Synthesis, crystal structure, EPR properties, and anti-convulsant activities of binuclear and mononuclear 1,10-phenanthroline and salicylate ternary copper(II) complexes.

    Science.gov (United States)

    Lemoine, Pascale; Viossat, Bernard; Morgant, Georges; Greenaway, Frederick T; Tomas, Alain; Dung, Nguyen Huy; Sorenson, John R J

    2002-04-10

    Two ternary Cu(II) complexes of 1,10-phenanthroline (phen) and singly (Hsal(-)) or dideprotonated (sal(2-)) salicylate ligands were synthesized, their X-ray crystal structure and electron paramagnetic resonance spectral characteristics determined, and evaluated for anti-convulsant activities in the maximal electroshock (MES) and Metrazol models of seizure and Rotorod toxicity. The X-ray crystal structure of [bis(1,10-phenanthroline)-mu-bis(salicylato-O,O')dicopper(II)] dihydrate, 1, ([Cu(II)(2)(phen)(2)(sal)(2)].2[H(2)O]), shows it to be binuclear. This dimer consists of two centrosymmetrically related pseudo-five coordinate Cu(II) atoms 3.242(2) A apart and bridged by two dideprotonated salicylate ligands. The X-ray crystal structure of [bis(1,10-phenanthroline)(salicylato)copper(II)][salicylate] monohydrate, 2, ([Cu(II)(phen)(2)(Hsal)](+)[Hsal](-)[H(2)O]), shows it to be mononuclear. This complex cation exhibits a highly irregular distorted square pyramidal geometry about the Cu(II) atom, (4+1+1*). Each salicylate is singly deprotonated and one of them is ligand bonded in an asymmetric chelating mode. EPR results for 2 indicate that in concentrated DMF solution phen remains bonded to copper but salicylate is likely monodentate in contrast to the situation for 1. However, in dilute DMF solution, both 1 and 2 form the same species, which accounts for the similarity in anti-convulsant activity of the two compounds. Both 1 and 2 were found to be effective in preventing MES-induced seizures and ineffective in preventing Metrazol-induced seizures. Rotorod toxicity, consistent with central nervous system depression, paralleled the observed anti-convulsant activity. It is suggested that the observed anti-convulsant activity is consistent with central nervous system depression as a physiological mechanism in overcoming MES-induced seizures due to MES-induced brain inflammatory disease.

  7. Crystal Structure of Thrombin in Complex with S-Variegin: Insights of a Novel Mechanism of Inhibition and Design of Tunable Thrombin Inhibitors

    Science.gov (United States)

    Koh, Cho Yeow; Kumar, Sundramurthy; Kazimirova, Maria; Nuttall, Patricia A.; Radhakrishnan, Uvaraj P.; Kim, Seongcheol; Jagadeeswaran, Pudur; Imamura, Takayuki; Mizuguchi, Jun; Iwanaga, Sadaaki; Swaminathan, Kunchithapadam; Kini, R. Manjunatha

    2011-01-01

    The inhibition of thrombin is one of the important treatments of pathological blood clot formation. Variegin, isolated from the tropical bont tick, is a novel molecule exhibiting a unique ‘two-modes’ inhibitory property on thrombin active site (competitive before cleavage, noncompetitive after cleavage). For the better understanding of its function, we have determined the crystal structure of the human α-thrombin:synthetic-variegin complex at 2.4 Å resolution. The structure reveals a new mechanism of thrombin inhibition by disrupting the charge relay system. Based on the structure, we have designed 17 variegin variants, differing in potency, kinetics and mechanism of inhibition. The most active variant is about 70 times more potent than the FDA-approved peptidic thrombin inhibitor, hirulog-1/bivalirudin. In vivo antithrombotic effects of the variegin variants correlate well with their in vitro affinities for thrombin. Our results encourage that variegin and the variants show strong potential for the development of tunable anticoagulants. PMID:22053189

  8. An unexpected phosphate binding site in Glyceraldehyde 3-Phosphate Dehydrogenase: Crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme

    Directory of Open Access Journals (Sweden)

    Chattopadhyay Debasish

    2009-02-01

    Full Text Available Abstract Background The structure, function and reaction mechanism of glyceraldehyde 3-phosphate dehydrogenase (GAPDH have been extensively studied. Based on these studies, three anion binding sites have been identified, one 'Ps' site (for binding the C-3 phosphate of the substrate and two sites, 'Pi' and 'new Pi', for inorganic phosphate. According to the original flip-flop model, the substrate phosphate group switches from the 'Pi' to the 'Ps' site during the multistep reaction. In light of the discovery of the 'new Pi' site, a modified flip-flop mechanism, in which the C-3 phosphate of the substrate binds to the 'new Pi' site and flips to the 'Ps' site before the hydride transfer, was proposed. An alternative model based on a number of structures of B. stearothermophilus GAPDH ternary complexes (non-covalent and thioacyl intermediate proposes that in the ternary Michaelis complex the C-3 phosphate binds to the 'Ps' site and flips from the 'Ps' to the 'new Pi' site during or after the redox step. Results We determined the crystal structure of Cryptosporidium parvum GAPDH in the apo and holo (enzyme + NAD state and the structure of the ternary enzyme-cofactor-substrate complex using an active site mutant enzyme. The C. parvum GAPDH complex was prepared by pre-incubating the enzyme with substrate and cofactor, thereby allowing free movement of the protein structure and substrate molecules during their initial encounter. Sulfate and phosphate ions were excluded from purification and crystallization steps. The quality of the electron density map at 2Å resolution allowed unambiguous positioning of the substrate. In three subunits of the homotetramer the C-3 phosphate group of the non-covalently bound substrate is in the 'new Pi' site. A concomitant movement of the phosphate binding loop is observed in these three subunits. In the fourth subunit the C-3 phosphate occupies an unexpected site not seen before and the phosphate binding loop remains in

  9. Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition

    Energy Technology Data Exchange (ETDEWEB)

    Chaptal, Vincent; Kwon, Seunghyug; Sawaya, Michael R.; Guan, Lan; Kaback, H. Ronald; Abramson, Jeff (UCLA); (TTU)

    2011-08-29

    Lactose permease of Escherichia coli (LacY) with a single-Cys residue in place of A122 (helix IV) transports galactopyranosides and is specifically inactivated by methanethiosulfonyl-galactopyranosides (MTS-gal), which behave as unique suicide substrates. In order to study the mechanism of inactivation more precisely, we solved the structure of single-Cys122 LacY in complex with covalently bound MTS-gal. This structure exhibits an inward-facing conformation similar to that observed previously with a slight narrowing of the cytoplasmic cavity. MTS-gal is bound covalently, forming a disulfide bond with C122 and positioned between R144 and W151. E269, a residue essential for binding, coordinates the C-4 hydroxyl of the galactopyranoside moiety. The location of the sugar is in accord with many biochemical studies.

  10. Bowl adamanzanes-bicyclic tetraamines: syntheses and crystal structures of complexes with cobalt(III) and chelating coordinated oxo-anions

    DEFF Research Database (Denmark)

    Broge, Louise; Søtofte, Inger; Jensen, Kristian

    2007-01-01

    Seven cobalt(III) complexes of the macrobicyclic tetraamine ligand [2(4).3(1)]adamanzane ([2(4).3(1)]adz) are reported along with the crystal structure of six of these complexes. The solid state and solution structures are discussed, and a detailed assignment of the NMR spectra of the sulfato...... measured, yielding half lives of 20 min, 10 min and 3 h for the sulfato, formiato and carbonato species respectively. The corresponding reaction for the nitrato complex occurs with a half life of less than 3 min. The concentration acid dissociation constant for the Co([ 2(4).3(1)] adz)( HCO3)(2+) ion has...... been measured to K-a = 0.33 mol dm(-3) [ 25 degrees C, I = 2 mol dm(-3)] and K-a = 0.15 mol dm(-3) [ 25 degrees C, I = 5 mol dm(-3)]. The propensity for coordination of sulfate was found to be large enough for a quantitative conversion of the carbonato complex to the sulfato complex to occur in 3 mol...

  11. X-ray Crystal Structures of Monomeric and Dimeric Peptide Inhibitors in Complex with the Human Neonatal Fc Receptor, FcRn

    Energy Technology Data Exchange (ETDEWEB)

    Mezo, Adam R.; Sridhar, Vandana; Badger, John; Sakorafas, Paul; Nienaber, Vicki (Zenobia); (Biogen)

    2010-10-28

    The neonatal Fc receptor, FcRn, is responsible for the long half-life of IgG molecules in vivo and is a potential therapeutic target for the treatment of autoimmune diseases. A family of peptides comprising the consensus motif GHFGGXY, where X is preferably a hydrophobic amino acid, was shown previously to inhibit the human IgG:human FcRn protein-protein interaction (Mezo, A. R., McDonnell, K. A., Tan Hehir, C. A., Low, S. C., Palombella, V. J., Stattel, J. M., Kamphaus, G. D., Fraley, C., Zhang, Y., Dumont, J. A., and Bitonti, A. J. (2008) Proc. Natl. Acad. Sci. U.S.A., 105, 2337-2342). Herein, the x-ray crystal structure of a representative monomeric peptide in complex with human FcRn was solved to 2.6 {angstrom} resolution. The structure shows that the peptide binds to human FcRn at the same general binding site as does the Fc domain of IgG. The data correlate well with structure-activity relationship data relating to how the peptide family binds to human FcRn. In addition, the x-ray crystal structure of a representative dimeric peptide in complex with human FcRn shows how the bivalent ligand can bridge two FcRn molecules, which may be relevant to the mechanism by which the dimeric peptides inhibit FcRn and increase IgG catabolism in vivo. Modeling of the peptide:FcRn structure as compared with available structural data on Fc and FcRn suggest that the His-6 and Phe-7 (peptide) partially mimic the interaction of His-310 and Ile-253 (Fc) in binding to FcRn, but using a different backbone topology.

  12. Supramolecular complexes of Co(II), Ni(II) and Zn(II) p-hydroxybenzoates with caffeine: Synthesis, spectral characterization and crystal structure

    Science.gov (United States)

    Taşdemir, Erdal; Özbek, Füreya Elif; Sertçelik, Mustafa; Hökelek, Tuncer; Çelik, Raziye Çatak; Necefoğlu, Hacali

    2016-09-01

    Three novel complexes Co(II), Ni(II) and Zn(II) containing p-hydroxybenzoates and caffeine ligands were synthesized and characterized by elemental analysis, FT-IR and UV-vis Spectroscopy, molar conductivity and single crystal X-ray diffraction methods. The thermal properties of the synthesized complexes were investigated by TGA/DTA. The general formula of the complexes is [M(HOC6H4COO)2(H2O)4]·2(C8H10N4O2)·8H2O (where: M: Co, Ni and Zn). The IR studies showed that carboxylate groups of p-hydroxybenzoate ligands have monodentate coordination mode. The M2+ ions are octahedrally coordinated by two p-hydroxybenzoate ligands, four water molecules leading to an overall MO6 coordination environment. The medium-strength hydrogen bondings involving the uncoordinated caffeine ligands and water molecules, coordinated and uncoordinated water molecules and p-hydroxybenzoate ligands lead to three-dimensional supramolecular networks in the crystal structures.

  13. Crystal structures of Burkholderia cenocepacia dihydropteroate synthase in the apo-form and complexed with the product 7,8-dihydropteroate.

    Science.gov (United States)

    Morgan, Rachel E; Batot, Gaëlle O; Dement, Jennifer M; Rao, Vincenzo A; Eadsforth, Thomas C; Hunter, William N

    2011-05-09

    The enzyme dihydropteroate synthase (DHPS) participates in the de novo synthesis of folate cofactors by catalyzing the formation of 7,8-dihydropteroate from condensation of p-aminobenzoic acid with 6-hydroxymethyl-7,8-dihydropteroate pyrophosphate. DHPS is absent from humans, who acquire folates from diet, and has been validated as an antimicrobial therapeutic target by chemical and genetic means. The bacterium Burkholderia cenocepacia is an opportunistic pathogen and an infective agent of cystic fibrosis patients. The organism is highly resistant to antibiotics and there is a recognized need for the identification of new drugs against Burkholderia and related Gram-negative pathogens. Our characterization of the DHPS active site and interactions with the enzyme product are designed to underpin early stage drug discovery. An efficient recombinant protein expression system for DHPS from B. cenocepacia (BcDHPS) was prepared, the dimeric enzyme purified in high yield and crystallized. The structure of the apo-enzyme and the complex with the product 7,8-dihydropteroate have been determined to 2.35 Å and 1.95 Å resolution respectively in distinct orthorhombic crystal forms. The latter represents the first crystal structure of the DHPS-pterin product complex, reveals key interactions involved in ligand binding, and reinforces data generated by other structural studies. Comparisons with orthologues identify plasticity near the substrate-binding pocket and in particular a range of loop conformations that contribute to the architecture of the DHPS active site. These structural data provide a foundation for hit discovery. An intriguing observation, an artifact of the analysis, that of a potential sulfenamide bond within the ligand complex structure is mentioned. Structural similarities between BcDHPS and orthologues from other Gram-negative species are evident as expected on the basis of a high level of sequence identity. The presence of 7,8-dihydropteroate in the binding

  14. Crystal structures of Burkholderia cenocepacia dihydropteroate synthase in the apo-form and complexed with the product 7,8-dihydropteroate

    Directory of Open Access Journals (Sweden)

    Eadsforth Thomas C

    2011-05-01

    Full Text Available Abstract Background The enzyme dihydropteroate synthase (DHPS participates in the de novo synthesis of folate cofactors by catalyzing the formation of 7,8-dihydropteroate from condensation of p-aminobenzoic acid with 6-hydroxymethyl-7,8-dihydropteroate pyrophosphate. DHPS is absent from humans, who acquire folates from diet, and has been validated as an antimicrobial therapeutic target by chemical and genetic means. The bacterium Burkholderia cenocepacia is an opportunistic pathogen and an infective agent of cystic fibrosis patients. The organism is highly resistant to antibiotics and there is a recognized need for the identification of new drugs against Burkholderia and related Gram-negative pathogens. Our characterization of the DHPS active site and interactions with the enzyme product are designed to underpin early stage drug discovery. Results An efficient recombinant protein expression system for DHPS from B. cenocepacia (BcDHPS was prepared, the dimeric enzyme purified in high yield and crystallized. The structure of the apo-enzyme and the complex with the product 7,8-dihydropteroate have been determined to 2.35 Å and 1.95 Å resolution respectively in distinct orthorhombic crystal forms. The latter represents the first crystal structure of the DHPS-pterin product complex, reveals key interactions involved in ligand binding, and reinforces data generated by other structural studies. Comparisons with orthologues identify plasticity near the substrate-binding pocket and in particular a range of loop conformations that contribute to the architecture of the DHPS active site. These structural data provide a foundation for hit discovery. An intriguing observation, an artifact of the analysis, that of a potential sulfenamide bond within the ligand complex structure is mentioned. Conclusion Structural similarities between BcDHPS and orthologues from other Gram-negative species are evident as expected on the basis of a high level of sequence

  15. Metal-promoted synthesis, characterization, crystal structure and RNA cleavage ability of 2,6-diacetylpyridine bis(2-aminobenzoylhydrazone) lanthanide complexes.

    Science.gov (United States)

    Kozłowski, Michał; Kierzek, Ryszard; Kubicki, Maciej; Radecka-Paryzek, Wanda

    2013-09-01

    New 2,6-diacetylpyridine bis(2-aminobenzoylhydrazone) lanthanide complexes were formed in the metal-induced one-step [1+2] condensation reaction between 2,6-diacetylpyridine and 2-aminobenzoylhydrazide in the presence of lanthanide (La(3+), Pr(3+), Nd(3+), Sm(3+), Eu(3+), Gd(3+), Tb(3+), Dy(3+), Ho(3+), Er(3+), Tm(3+) or Yb(3+)) nitrates as template agents. The analytical and spectral characterizations of all the compounds were correlated with the single crystal X-ray structural determination of Eu(3+), Gd(3+), Tb(3+), Dy(3+) and Er(3+) nitrate complexes. The Eu(3+), Gd(3+), Tb(3+)and Dy(3+) complexes of pentadentate 2,6-diacetylpyridine bis(2-aminobenzoylhydrazone) with the N3O2 set of donor atoms display a high and relatively rare coordination number of 11, whereas the Er(3+) ion complex is 9-coordinated, which is consistent with the lanthanide contraction phenomenon. The scission of 21-mer RNA was assessed for Eu(3+), Gd(3+) and Tb(3+) nitrate complexes. Lanthanide complexes not covalently attached to the oligonucleotide are able to cleave RNA at the target site in a sequence-selective or non-selective manner depending on the presence of protecting 12-mer 2'OMe RNA. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. A new coordination mode of (E)-3-(3-hydroxyl-phenyl)-acrylic acid in copper complex: Crystal structure and magnetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Xin; Zhou, Pei; Zheng, Chunying [Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry, Beijing Institute of Technology, Beijing 100081 (China); Li, Hui, E-mail: lihui@bit.edu [Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry, Beijing Institute of Technology, Beijing 100081 (China)

    2015-05-15

    A copper complex ([Cu(py){sub 2}(L){sub 2}]·2CH{sub 3}OH){sub n} (HL=(E)-3-(3-hydroxyl-phenyl)-acrylic acid) (1) with acrylic acid ligand was synthesized and structurally analyzed by IR, elemental analysis, TGA and the single-crystal X-ray diffraction methods. It is the first time to find that phenolic hydroxyl of L coordinates to Cu(II). Complex 1 exhibits 1D chain by a double-bridge of ligands, and the 3D supramolecular framework in complex 1 is constructed by π–π stacking interactions and van der Waals Contacts among the 1D chains. The magnetic properties of complex 1 have been studied. - Graphical abstract: A copper complex based on (E)-3-(3-hydroxyl-phenyl)-acrylic acid in a novel coordinated way was synthesized and a ferromagnetic exchange interactions between neighboring Cu(II) ions has be achieved. - Highlights: • A new copper complex with acrylic acid ligand was synthesized and analyzed. • We find the phenolic hydroxyl of MCA ligand coordinates to metal ion firstly. • A ferromagnetic exchange interactions between Cu(II) ions has been achieved.

  17. Synthesis and X-ray crystal structure of a novel organometallic (µ(3)-oxido)(µ(3)-imido) trinuclear iridium complex

    DEFF Research Database (Denmark)

    Schau-Magnussen, Magnus; Malcho, Phillip; Herbst, Konrad

    2011-01-01

    be isolated both in the double salt ((t)BuNH(3))[(Cp*Ir)(3)(O)(N(t)Bu)](CF(3)SO(3))(3) (1) and in the simple triflate [(Cp*Ir)(3)(O)(N(t)Bu)](CF(3)SO(3))(2) (2). The double salt is stabilized by hydrogen bonding between the tert-butylammonium ion and the three triflate anions. It is the first time......Reaction of the organometallic aqua ion [Cp*Ir(H(2)O)(3)](2+) with tert-butyl(trimethylsilyl)amine in acetone yielded a novel trinuclear (µ(3)-oxido)(µ(3)-imido)pentamethylcyclopentadienyliridium(iii) complex, [(Cp*Ir)(3)(O)(N(t)Bu)](2+). Single crystal structure analyses show the complex can...

  18. Prediction of molecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Theresa

    2001-07-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  19. Nickel(II) complexes with methyl(2-pyridyl)ketone oxime: Synthesis, crystal structures and DFT calculations

    Science.gov (United States)

    Martínez, Lorena; Gancheff, Jorge S.; Hahn, F. Ekkehardt; Burrow, Robert A.; González, Ricardo; Kremer, Carlos; Chiozzone, Raúl

    2013-03-01

    The synthesis and structural characterization of the three novel nickel(II) complexes [Ni(OOCPh)2(mpkoH)2] (1), [Ni(NO3)2(mpkoH)2] (2) and [Ni(mpkoH)3](NO3)2ṡ½H2O (3ṡ½H2O), with mpkoH = methyl(2-pyridyl)ketone oxime is reported. Geometry optimization and population analyses were performed by means of DFT calculations for the previously mentioned compounds as well as for [NiCl2(mpkoH)2] (4). Electronic UV-vis spectra were also simulated in the TD-DFT framework to assign the origin of the absorption bands and in doing so, to have a clear picture of the absorptive features of the coordination compounds under investigation.

  20. Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site

    Energy Technology Data Exchange (ETDEWEB)

    Patel, Asmita; Yakovleva, Lyudmila; Shuman, Stewart; Mondragón, Alfonso (NWU); (SKI)

    2010-10-22

    Type IB DNA topoisomerases (TopIB) are monomeric enzymes that relax supercoils by cleaving and resealing one strand of duplex DNA within a protein clamp that embraces a {approx}21 DNA segment. A longstanding conundrum concerns the capacity of TopIB enzymes to stabilize intramolecular duplex DNA crossovers and form protein-DNA synaptic filaments. Here we report a structure of Deinococcus radiodurans TopIB in complex with a 12 bp duplex DNA that demonstrates a secondary DNA binding site located on the surface of the C-terminal domain. It comprises a distinctive interface with one strand of the DNA duplex and is conserved in all TopIB enzymes. Modeling of a TopIB with both DNA sites suggests that the secondary site could account for DNA crossover binding, nucleation of DNA synapsis, and generation of a filamentous plectoneme. Mutations of the secondary site eliminate synaptic plectoneme formation without affecting DNA cleavage or supercoil relaxation.

  1. Phenoxo bridged dinuclear Zn(II) Schiff base complex as new precursor for preparation zinc oxide nanoparticles: Synthesis, characterization, crystal structures and photoluminescence studies

    Energy Technology Data Exchange (ETDEWEB)

    Saeednia, S., E-mail: sami_saeednia@yahoo.com [Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan 77188-97111 (Iran, Islamic Republic of); Iranmanesh, P. [Department of physics, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan 77188-97111 (Iran, Islamic Republic of); Ardakani, M. Hatefi; Mohammadi, M.; Norouzi, Gh. [Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan 77188-97111 (Iran, Islamic Republic of)

    2016-06-15

    Highlights: • A novel nano-scale Zn(II) complex was synthesized by solvothermal method. • Chemical structure of the nanostructures was characterized as well as bulk complex. • The photoluminescence property of the complex was investigated at room temperature. • The thermogravimetry and differential thermal analysis were carried out. • Thermal decomposition of the nanostructures was prepared zinc oxide nanoparticles. - Abstract: Nanoparticles of a novel Zn(II) Schiff base complex, [Zn(HL)NO{sub 3}]{sub 2} (1), (H{sub 2}L = 2-[(2-hydroxy-propylimino) methyl] phenol), was synthesized by using solvothermal method. Shape, morphology and chemical structure of the synthesized nanoparticles were characterized by scanning electron microscopy (SEM), X-ray powder diffraction (XRD), Fourier Transform Infrared Spectoscopy (FT-IR) and UV–vis spectroscopy. Structural determination of compound 1 was determined by single-crystal X-ray diffraction. The results were revealed that the zinc complex is a centrosymmetric dimer in which deprotonated phenolates bridge the two five-coordinate metal atoms and link the two halves of the dimer. The thermal stability of compound 1 was analyzed by thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC). The effect of the initial substrates concentration and reaction time on size and morphology of compound 1 nanostructure was investigated as well. Furthermore, the luminescent properties of the complex 1 were examined. ZnO nanoparticles with diameter between 15 and 20 nm were simply synthesized by solid-state transformation of compound 1 at 700 °C.

  2. Crystal and solution structures of an odorant-binding protein from the southern house mosquito complexed with an oviposition pheromone

    Energy Technology Data Exchange (ETDEWEB)

    Mao, Yang; Xu, Xianzhong; Xu, Wei; Ishida, Yuko; Leal, Walter S.; Ames, James B.; Clardy, Jon (Harvard-Med); (UCD)

    2010-11-15

    Culex mosquitoes introduce the pathogens responsible for filariasis, West Nile virus, St. Louis encephalitis, and other diseases into humans. Currently, traps baited with oviposition semiochemicals play an important role in detection efforts and could provide an environmentally friendly approach to controlling their populations. The odorant binding proteins (OBPs) in the female's antenna play a crucial, if yet imperfectly understood, role in sensing oviposition cues. Here, we report the X-ray crystallography and NMR 3D structures of OBP1 for Culex quinquefasciatus (CquiOBP1) bound to an oviposition pheromone (5R,6S)-6-acetoxy-5-hexadecanolide (MOP). In both studies, CquiOBP1 had the same overall six-helix structure seen in other insect OBPs, but a detailed analysis revealed an important previously undescribed feature. There are two models for OBP-mediated signal transduction: (i) direct release of the pheromone from an internal binding pocket in a pH-dependent fashion and (ii) detection of a pheromone-induced conformational change in the OBP {center_dot} pheromone complex. Although CquiOBP1 binds MOP in a pH-dependent fashion, it lacks the C terminus required for the pH-dependent release model. This study shows that CquiOBP binds MOP in an unprecedented fashion using both a small central cavity for the lactone head group and a long hydrophobic channel for its tail.

  3. Strategies in the crystallization of glycoproteins and protein complexes

    Science.gov (United States)

    Stura, Enrico A.; Nemerow, Glen R.; Wilson, Ian A.

    1992-08-01

    Modern biochemical and molecular biological techniques have provided new opportunities to investigate the structure of more complex biomolecules and have opened new paths for the crystallization of complexes. Desialation, deglycosylation and modification of glycoproteins are techniques being investigated as a means of making glycosylated more amenable for crystallization. A simple solubility screen based on a limited set of precipitants has been extensively used in the comparison of various protein preparations and in the crystallization of macromolecular complexes. Antibodies, or their Fabs or Fab' fragments, can also be utilized in the crystallization of glycoproteins or other proteins which have proved difficult to crystallize by themselves. Fab complexes can provide different surfaces for lattices to form and may increase the likelihood of crystallizing a given protein. This method can be extended by the addition of an epitope tag, such as a short peptide sequence, to a protein by genetic engineering methods. The same panel of anti-peptide antibodies can then be utilized in both the purification and crystallization of different expressed proteins, making this a potential general method for protein crystallization.

  4. The meloxicam complexes of Co(II) and Zn(II): Synthesis, crystal structures, photocleavage and in vitro DNA-binding

    Science.gov (United States)

    Sanatkar, Tahereh Hosseinzadeh; Hadadzadeh, Hassan; Simpson, Jim; Jannesari, Zahra

    2013-10-01

    Two neutral mononuclear complexes of Co(II) and Zn(II) with the non-steroidal anti-inflammatory drug meloxicam (H2mel, 4-hydroxy-2-methyl-N-(5-methyl-2-thiazolyl)-2H-1,2-benzothiazine-3-carboxammide-1,1-dioxide), [Co(Hmel)2(EtOH)2] (1), and [Zn(Hmel)2(EtOH)2] (2), were synthesized and characterized by elemental analysis, IR and UV-Vis spectroscopy and their solid-state structures were studied by single-crystal diffraction. The complexes have a distorted octahedral geometry around the metal atom. The experimental data indicate that the meloxicam acts as a deprotonated bidentate ligand (through the amide oxygen and the nitrogen atom of the thiazolyl ring) in the complexes, and a strong intramolecular hydrogen bond between the amide N-H function and the enolate O atom stabilizes the ZZZ conformation of meloxicam ligands. Absorption, fluorescence spectroscopy and cyclic voltammetry have been used to investigate the binding of the complexes with fish sperm DNA (FS-DNA). Additionally, the photocleavage studies have been also used to investigate the binding of the complexes with plasmid DNA. The interaction of the complexes with DNA was monitored by a blue shift and hyperchromism in the UV-Vis spectra attributed to an electrostatic binding mode. A competitive study with ethidium bromide (EB) has shown that the complexes can displace the DNA-bound EB indicating that they bind to DNA in strong competition with EB. The experimental results show that the complexes can cleave pUC57 plasmid DNA.

  5. Synthesis, Characterization, Crystal Structure and Antimicrobial Activity of Copper(II Complexes with the Schiff Base Derived from 2-Hydroxy-4-Methoxybenzaldehyde

    Directory of Open Access Journals (Sweden)

    Elena Pahonțu

    2015-04-01

    Full Text Available A novel Schiff base, ethyl 4-[(E-(2-hydroxy-4-methoxyphenylmethylene-amino]benzoate (HL, was prepared and structurally characterized on the basis of elemental analyses, 1H NMR, 13C NMR, UV-Vis and IR spectral data. Six new copper(II complexes, [Cu(L(NO3(H2O2] (1, [Cu(L2] (2, [Cu(L(OAc] (3, [Cu2 (L2Cl2(H2O4] (4, [Cu(L(ClO4(H2O] (5 and [Cu2(L2S(ClO4(H2O]ClO4·H2O (6 have been synthesized. The characterization of the newly formed compounds was done by IR, UV-Vis, EPR, FAB mass spectroscopy, elemental and thermal analysis, magnetic susceptibility measurements and molar electric conductivity. The crystal structures of Schiff base and the complex [Cu2(L2S(ClO4(H2O]ClO4·H2O (6 have been determined by single crystal X-ray diffraction studies. Both copper atoms display a distorted octahedral coordination type [O4NS]. This coordination is ensured by three phenol oxygen, two of which being related to the µ-oxo-bridge, the nitrogen atoms of the azomethine group and the sulfur atoms that come from the polydentate ligand. The in vitro antimicrobial activity against Escherichia coli ATCC 25922, Salmonella enteritidis, Staphylococcus aureus ATCC 25923, Enterococcus and Candida albicans strains was studied and compared with that of free ligand. The complexes 1, 2, 5 showed a better antimicrobial activity than the Schiff base against the tested microorganisms.

  6. Crystal structure of cafenstrole

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

    Full Text Available The title compound (systematic name: N,N-diethyl-3-mesitylsulfonyl-1H-1,2,4-triazole-1-carboxamide, C16H22N4O3S, is a triazole herbicide. The dihedral angle between the planes of the triazole and benzene ring planes is 88.14 (10°. In the crystal, C—H...O hydrogen bonds and weak C—H...π interactions link adjacent molecules, forming one-dimensional chains along the a axis.

  7. Crystal structures of covalent complexes of β-lactam antibiotics with E. coli penicillin-binding protein 5: toward an understanding of antibiotic specificity†

    Science.gov (United States)

    Nicola, George; Tomberg, Joshua; Pratt, R. F.; Nicholas, Robert A.; Davies, Christopher

    2010-01-01

    Penicillin-binding proteins (PBPs) are the molecular target for the widely used β-lactam class of antibiotics, but how these compounds act at the molecular level is not fully understood. We have determined crystal structures of E. coli PBP5 as covalent complexes with imipenem, cloxacillin and cefoxitin. These antibiotics exhibit very different second order rates of acylation for the enzyme. In all three structures, there is excellent electron density for the central portion of the β-lactam, but weak or absent density for the R1 or R2 side chains. Areas of contact between the antibiotics and PBP 5 do not correlate with the rates of acylation. The same is true for conformational changes because although shift of a loop leading to an electrostatic interaction between Arg248 and the β-lactam carboxylate, which occurs completely with cefoxitin, partially with imipenem and is absent with cloxacillin, is consistent with the different rates of acylation, mutagenesis of Arg248 only decreased cefoxitin acylation two fold. Together, these data suggest that structures of post-covalent complexes of PBP 5 are unlikely to be useful vehicles for design of new covalent inhibitors of PBPs. Finally, superimposition of the imipenem-acylated complex with PBP5 in complex with a boronic acid peptidemimetic shows that the position corresponding to the hydrolytic water molecule is occluded by the ring nitrogen of the β-lactam. Since the ring nitrogen occupies a similar position in all three complexes, this supports the hypothesis that deacylation is blocked by the continued presence of the leaving group after opening of the β-lactam ring. PMID:20726582

  8. Crystal Structures of Covalent Complexes of [beta]-Lactam Antibiotics with Escherichia coli Penicillin-Binding Protein 5: Toward an Understanding of Antibiotic Specificity

    Energy Technology Data Exchange (ETDEWEB)

    Nicola, George; Tomberg, Joshua; Pratt, R.F.; Nicholas, Robert A.; Davies, Christopher (SC); (UNC); (Wesleyan)

    2010-12-07

    Penicillin-binding proteins (PBPs) are the molecular targets for the widely used {beta}-lactam class of antibiotics, but how these compounds act at the molecular level is not fully understood. We have determined crystal structures of Escherichia coli PBP 5 as covalent complexes with imipenem, cloxacillin, and cefoxitin. These antibiotics exhibit very different second-order rates of acylation for the enzyme. In all three structures, there is excellent electron density for the central portion of the {beta}-lactam, but weak or absent density for the R1 or R2 side chains. Areas of contact between the antibiotics and PBP 5 do not correlate with the rates of acylation. The same is true for conformational changes, because although a shift of a loop leading to an electrostatic interaction between Arg248 and the {beta}-lactam carboxylate, which occurs completely with cefoxitin and partially with imipenem and is absent with cloxacillin, is consistent with the different rates of acylation, mutagenesis of Arg248 decreased the level of cefoxitin acylation only 2-fold. Together, these data suggest that structures of postcovalent complexes of PBP 5 are unlikely to be useful vehicles for the design of new covalent inhibitors of PBPs. Finally, superimposition of the imipenem-acylated complex with PBP 5 in complex with a boronic acid peptidomimetic shows that the position corresponding to the hydrolytic water molecule is occluded by the ring nitrogen of the {beta}-lactam. Because the ring nitrogen occupies a similar position in all three complexes, this supports the hypothesis that deacylation is blocked by the continued presence of the leaving group after opening of the {beta}-lactam ring.

  9. Antivitamin B12 Inhibition of the Human B12 -Processing Enzyme CblC: Crystal Structure of an Inactive Ternary Complex with Glutathione as the Cosubstrate.

    Science.gov (United States)

    Ruetz, Markus; Shanmuganathan, Aranganathan; Gherasim, Carmen; Karasik, Agnes; Salchner, Robert; Kieninger, Christoph; Wurst, Klaus; Banerjee, Ruma; Koutmos, Markos; Kräutler, Bernhard

    2017-06-19

    B12 antivitamins are important and robust tools for investigating the biological roles of vitamin B12 . Here, the potential antivitamin B12 2,4-difluorophenylethynylcobalamin (F2PhEtyCbl) was prepared, and its 3D structure was studied in solution and in the crystal. Chemically inert F2PhEtyCbl resisted thermolysis of its Co-C bond at 100 °C, was stable in bright daylight, and also remained intact upon prolonged storage in aqueous solution at room temperature. It binds to the human B12 -processing enzyme CblC with high affinity (KD =130 nm) in the presence of the cosubstrate glutathione (GSH). F2PhEtyCbl withstood tailoring by CblC, and it also stabilized the ternary complex with GSH. The crystal structure of this inactivated assembly provides first insight into the binding interactions between an antivitamin B12 and CblC, as well as into the organization of GSH and a base-off cobalamin in the active site of this enzyme. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. The crystal structure of the active domain of Anopheles anti-platelet protein, a powerful anti-coagulant, in complex with an antibody.

    Science.gov (United States)

    Sugiyama, Kanako; Iyori, Mitsuhiro; Sawaguchi, Asuka; Akashi, Satoko; Tame, Jeremy R H; Park, Sam-Yong; Yoshida, Shigeto

    2014-06-06

    Blood clotting is a vitally important process that must be carefully regulated to prevent blood loss on one hand and thrombosis on the other. Severe injury and hemophilia may be treated with pro-coagulants, whereas risk of obstructive clotting or embolism may be reduced with anti-coagulants. Anti-coagulants are an extremely important class of drug, one of the most widely used types of medication, but there remains a pressing need for novel treatments, however, as present drugs such as warfarin have significant drawbacks. Nature provides a number of examples of anti-coagulant proteins produced by blood-sucking animals, which may provide templates for the development of new small molecules with similar physiological effects. We have, therefore, studied an Anopheles anti-platelet protein from a malaria vector mosquito and report its crystal structure in complex with an antibody. Overall the protein is extremely sensitive to proteolysis, but the crystal structure reveals a stable domain built from two helices and a turn, which corresponds to the functional region. The antibody raised against Anopheles anti-platelet protein prevents it from binding collagen. Our work, therefore, opens new avenues to the development of both novel small molecule anti-clotting agents and anti-malarials. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Crystal Structure of the Thermus thermophilus 16 S rRNA Methyltransferase RsmC in Complex with Cofactor and Substrate Guanosine

    Energy Technology Data Exchange (ETDEWEB)

    Demirci, H.; Gregory, S; Dahlberg, A; Jogl, G

    2008-01-01

    Post-transcriptional modification is a ubiquitous feature of ribosomal RNA in all kingdoms of life. Modified nucleotides are generally clustered in functionally important regions of the ribosome, but the functional contribution to protein synthesis is not well understood. Here we describe high resolution crystal structures for the N{sup 2}-guanine methyltransferase RsmC that modifies residue G1207 in 16 S rRNA near the decoding site of the 30 S ribosomal subunit. RsmC is a class I S-adenosyl-l-methionine-dependent methyltransferase composed of two methyltransferase domains. However, only one S-adenosyl-l-methionine molecule and one substrate molecule, guanosine, bind in the ternary complex. The N-terminal domain does not bind any cofactor. Two structures with bound S-adenosyl-l-methionine and S-adenosyl-l-homocysteine confirm that the cofactor binding mode is highly similar to other class I methyltransferases. Secondary structure elements of the N-terminal domain contribute to cofactor-binding interactions and restrict access to the cofactor-binding site. The orientation of guanosine in the active site reveals that G1207 has to disengage from its Watson-Crick base pairing interaction with C1051 in the 16 S rRNA and flip out into the active site prior to its modification. Inspection of the 30 S crystal structure indicates that access to G1207 by RsmC is incompatible with the native subunit structure, consistent with previous suggestions that this enzyme recognizes a subunit assembly intermediate.

  12. Crystal Structure of the HLA-DM - HLA-DR1 Complex Defines Mechanisms for Rapid Peptide Selection

    Science.gov (United States)

    Pos, Wouter; Sethi, Dhruv K.; Call, Melissa J.; Schulze, Monika-Sarah E. D.; Anders, Anne-Kathrin; Pyrdol, Jason; Wucherpfennig, Kai W.

    2012-01-01

    Summary HLA-DR molecules bind microbial peptides in an endosomal compartment and present them on the cell surface for CD4 T cell surveillance. HLA-DM plays a critical role in the endosomal peptide selection process. The structure of the HLA-DM – HLA-DR complex shows major rearrangements of the HLA-DR peptide binding groove. Flipping of a tryptophan away from the HLA-DR1 P1 pocket enables major conformational changes that position hydrophobic HLA-DR residues into the P1 pocket. These conformational changes accelerate peptide dissociation and stabilize the empty HLA-DR peptide binding groove. Initially, incoming peptides have access to only part of the HLA-DR groove and need to compete with HLA-DR residues for access to the P2 site and the hydrophobic P1 pocket. This energetic barrier creates a rapid and stringent selection process for the highest-affinity binders. Insertion of peptide residues into the P2 and P1 sites reverses the conformational changes, terminating selection through DM dissociation. PMID:23260142

  13. A cyanide-bridged trinuclear Fe(II)-Ru(II)-Fe(II) complex with three stable states: synthesis, crystal structures, electronic couplings and magnetic properties.

    Science.gov (United States)

    Ma, Xiao; Hu, Sheng-Min; Tan, Chun-Hong; Wen, Yue-Hong; Zhu, Qi-Long; Shen, Chao-Jun; Sheng, Tian-Lu; Wu, Xin-Tao

    2012-10-21

    Treatment of trans-(Ph-tpy)Ru(PPh(3))(CN)(2) (Ph-tpy = 4'-phenyl-2,2':6',2''-terpyridine, PPh(3) = triphenylphosphine) with 2 equiv of Cp(dppe)Fe(NCCH(3))Br (dppe = bis(diphenylphosphino)ethane) in the presence of NH(4)PF(6) produced a trinuclear cyanide-bridged complex, trans-[Cp(dppe)Fe(CN)(Ph-tpy)Ru(PPh(3))(CN)Fe(dppe)Cp][PF(6)](2) (1[PF(6)](2)). Its one-electron oxidation product (1[PF(6)](3)) and two-electron-oxidation product (1[PF(6)](4)) were obtained by oxidation with (Cp)(2)FePF(6) and AgPF(6), respectively. Firstly, the crystal structures of the cyanide-bridged complexes with three stable states were fully characterized. The reversible electrochemistry measurement of 1(2)(+) shows the presence of a long range intervalence interaction between the external iron centres. Both 1(3)(+) and 1(4)(+) were considered to be Class II mixed valence complexes according to the classification of Robin and Day. Magnetic analysis indicated the presence of a moderately strong antiferromagnetic coupling between the two remote Fe(III) ions across the Fe-NC-Ru-CN-Fe array in 1(4)(+). This proves that the Ru(II)-dicyano complex is a bridging ligand that can transmit electro- and magneto-communication.

  14. The crystal structure of the complex of Zea mays alpha subunit with a fragment of human beta subunit provides the clue to the architecture of protein kinase CK2 holoenzyme

    DEFF Research Database (Denmark)

    Battistutta, R; Sarno, S; De Moliner, E

    2000-01-01

    The crystal structure of a complex between the catalytic alpha subunit of Zea mays CK2 and a 23-mer peptide corresponding the C-terminal sequence 181-203 of the human CK2 regulatory beta subunit has been determined at 3.16-A resolution. The complex, composed of two alpha chains and two peptides...

  15. Crystal structure of the NADP+and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis.

    Science.gov (United States)

    Yoneda, Kazunari; Sakuraba, Haruhiko; Araki, Tomohiro; Ohshima, Toshihisa

    2018-01-20

    A gene encoding L-serine dehydrogenase (L-SerDH) that exhibits extremely low sequence identity to the Agrobacterium tumefaciens L-SerDH was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The predicted amino acid sequence showed 36% identity with that of Pseudomonas aeruginosa L-SerDH, suggesting that P. calidifontis L-SerDH is a novel type of L-SerDH, like Ps. aeruginosa L-SerDH. The overexpressed enzyme appears to be the most thermostable L-SerDH described to date, and no loss of activity was observed by incubation for 30 min at temperatures up to 100 °C. The enzyme showed substantial reactivity towards D-serine, in addition to L-serine. Two different crystal structures of P. calidifontis L-SerDH were determined using the Se-MAD and MR method: the structure in complex with NADP + /sulfate ion at 1.18 Å and the structure in complex with NADP + /L-tartrate (substrate analog) at 1.57 Å. The fold of the catalytic domain showed similarity with that of Ps. aeruginosa L-SerDH. However, the active site structure significantly differed between the two enzymes. Based on the structure of the tartrate, L- and D-serine and 3-hydroxypropionate molecules were modeled into the active site and the substrate binding modes were estimated. A structural comparison suggests that the wide cavity at the substrate binding site is likely responsible for the high reactivity of the enzyme toward both L- and D-serine enantiomers. This is the first description of the structure of the novel type of L-SerDH with bound NADP + and substrate analog, and it provides new insight into the substrate binding mechanism of L-SerDH. The results obtained here may be very informative for the creation of L- or D-serine-specific SerDH by protein engineering.

  16. Crystal Structures of GII.10 and GII.12 Norovirus Protruding Domains in Complex with Histo-Blood Group Antigens Reveal Details for a Potential Site of Vulnerability

    Energy Technology Data Exchange (ETDEWEB)

    Hansman, Grant S.; Biertümpfel, Christian; Georgiev, Ivelin; McLellan, Jason S.; Chen, Lei; Zhou, Tongqing; Katayama, Kazuhiko; Kwong, Peter D. (NIH); (NIID-Japan)

    2011-10-10

    Noroviruses are the dominant cause of outbreaks of gastroenteritis worldwide, and interactions with human histo-blood group antigens (HBGAs) are thought to play a critical role in their entry mechanism. Structures of noroviruses from genogroups GI and GII in complex with HBGAs, however, reveal different modes of interaction. To gain insight into norovirus recognition of HBGAs, we determined crystal structures of norovirus protruding domains from two rarely detected GII genotypes, GII.10 and GII.12, alone and in complex with a panel of HBGAs, and analyzed structure-function implications related to conservation of the HBGA binding pocket. The GII.10- and GII.12-apo structures as well as the previously solved GII.4-apo structure resembled each other more closely than the GI.1-derived structure, and all three GII structures showed similar modes of HBGA recognition. The primary GII norovirus-HBGA interaction involved six hydrogen bonds between a terminal {alpha}fucose1-2 of the HBGAs and a dimeric capsid interface, which was composed of elements from two protruding subdomains. Norovirus interactions with other saccharide units of the HBGAs were variable and involved fewer hydrogen bonds. Sequence analysis revealed a site of GII norovirus sequence conservation to reside under the critical {alpha}fucose1-2 and to be one of the few patches of conserved residues on the outer virion-capsid surface. The site was smaller than that involved in full HBGA recognition, a consequence of variable recognition of peripheral saccharides. Despite this evasion tactic, the HBGA site of viral vulnerability may provide a viable target for small molecule- and antibody-mediated neutralization of GII norovirus.

  17. Crystal structure of pyriproxyfen

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

    Full Text Available In the title compound {systematic name: 4-phenoxyphenyl (RS-2-[(pyridin-2-yloxy]propyl ether}, C20H19NO3, which is a juvenile hormone mimic and insecticide, the dihedral angles between the plane of the central benene ring and those of the pendant pyridine ring and phenyl ring are 78.09 (6 and 82.14 (8°, respectively. The conformation of the O—C—C—O linkage is gauche [torsion angle = −75.0 (2°]. In the crystal, weak aromatic π–π stacking interactions [centroid–centroid separation = 3.8436 (13 Å] and C—H...π interactions link adjacent molecules, forming a three-dimensional network.

  18. Crystal structure of Lymnaea stagnalis AChBP complexed with the potent nAChR antagonist DHβE suggests a unique mode of antagonism.

    Directory of Open Access Journals (Sweden)

    Azadeh Shahsavar

    Full Text Available Nicotinic acetylcholine receptors (nAChRs are pentameric ligand-gated ion channels that belong to the Cys-loop receptor superfamily. These receptors are allosteric proteins that exist in different conformational states, including resting (closed, activated (open, and desensitized (closed states. The acetylcholine binding protein (AChBP is a structural homologue of the extracellular ligand-binding domain of nAChRs. In previous studies, the degree of the C-loop radial extension of AChBP has been assigned to different conformational states of nAChRs. It has been suggested that a closed C-loop is preferred for the active conformation of nAChRs in complex with agonists whereas an open C-loop reflects an antagonist-bound (closed state. In this work, we have determined the crystal structure of AChBP from the water snail Lymnaea stagnalis (Ls in complex with dihydro-β-erythroidine (DHβE, which is a potent competitive antagonist of nAChRs. The structure reveals that binding of DHβE to AChBP imposes closure of the C-loop as agonists, but also a shift perpendicular to previously observed C-loop movements. These observations suggest that DHβE may antagonize the receptor via a different mechanism compared to prototypical antagonists and toxins.

  19. Crystal structures of Leishmania mexicana arginase complexed with α,α-disubstituted boronic amino-acid inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Hai, Yang; Christianson, David W.

    2016-03-16

    Leishmaniaarginase is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme initiatesde novopolyamine biosynthesis by catalyzing the hydrolysis of L-arginine to generate L-ornithine and urea. The product L-ornithine subsequently undergoes decarboxylation to yield putrescine, which in turn is utilized for spermidine biosynthesis. Polyamines such as spermidine are essential for the growth and survival of the parasite, so inhibition of enzymes in the polyamine-biosynthetic pathway comprises an effective strategy for treating parasitic infections. To this end, two X-ray crystal structures ofL. mexicanaarginase complexed with α,α-disubstituted boronic amino-acid inhibitors based on the molecular scaffold of 2-(S)-amino-6-boronohexanoic acid are now reported. Structural comparisons with human and parasitic arginase complexes reveal interesting differences in the binding modes of the additional α-substituents,i.e.the D side chains, of these inhibitors. Subtle differences in the three-dimensional contours of the outer active-site rims among arginases from different species lead to different conformations of the D side chains and thus different inhibitor-affinity trends. The structures suggest that it is possible to maintain affinity while fine-tuning intermolecular interactions of the D side chain of α,α-disubstituted boronic amino-acid inhibitors in the search for isozyme-specific and species-specific arginase inhibitors.

  20. Crystal structure of Lymnaea stagnalis AChBP complexed with the potent nAChR antagonist DHβE suggests a unique mode of antagonism.

    Science.gov (United States)

    Shahsavar, Azadeh; Kastrup, Jette S; Nielsen, Elsebet Ø; Kristensen, Jesper L; Gajhede, Michael; Balle, Thomas

    2012-01-01

    Nicotinic acetylcholine receptors (nAChRs) are pentameric ligand-gated ion channels that belong to the Cys-loop receptor superfamily. These receptors are allosteric proteins that exist in different conformational states, including resting (closed), activated (open), and desensitized (closed) states. The acetylcholine binding protein (AChBP) is a structural homologue of the extracellular ligand-binding domain of nAChRs. In previous studies, the degree of the C-loop radial extension of AChBP has been assigned to different conformational states of nAChRs. It has been suggested that a closed C-loop is preferred for the active conformation of nAChRs in complex with agonists whereas an open C-loop reflects an antagonist-bound (closed) state. In this work, we have determined the crystal structure of AChBP from the water snail Lymnaea stagnalis (Ls) in complex with dihydro-β-erythroidine (DHβE), which is a potent competitive antagonist of nAChRs. The structure reveals that binding of DHβE to AChBP imposes closure of the C-loop as agonists, but also a shift perpendicular to previously observed C-loop movements. These observations suggest that DHβE may antagonize the receptor via a different mechanism compared to prototypical antagonists and toxins.

  1. Crystal Structure and Functional Analysis of the SARS-Coronavirus RNA Cap 2′-O-Methyltransferase nsp10/nsp16 Complex

    Science.gov (United States)

    Decroly, Etienne; Debarnot, Claire; Ferron, François; Bouvet, Mickael; Coutard, Bruno; Imbert, Isabelle; Gluais, Laure; Papageorgiou, Nicolas; Sharff, Andrew; Bricogne, Gérard; Ortiz-Lombardia, Miguel; Lescar, Julien; Canard, Bruno

    2011-01-01

    Cellular and viral S-adenosylmethionine-dependent methyltransferases are involved in many regulated processes such as metabolism, detoxification, signal transduction, chromatin remodeling, nucleic acid processing, and mRNA capping. The Severe Acute Respiratory Syndrome coronavirus nsp16 protein is a S-adenosylmethionine-dependent (nucleoside-2′-O)-methyltransferase only active in the presence of its activating partner nsp10. We report the nsp10/nsp16 complex structure at 2.0 Å resolution, which shows nsp10 bound to nsp16 through a ∼930 Å2 surface area in nsp10. Functional assays identify key residues involved in nsp10/nsp16 association, and in RNA binding or catalysis, the latter likely through a SN2-like mechanism. We present two other crystal structures, the inhibitor Sinefungin bound in the S-adenosylmethionine binding pocket and the tighter complex nsp10(Y96F)/nsp16, providing the first structural insight into the regulation of RNA capping enzymes in (+)RNA viruses. PMID:21637813

  2. Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2'-O-methyltransferase nsp10/nsp16 complex.

    Directory of Open Access Journals (Sweden)

    Etienne Decroly

    2011-05-01

    Full Text Available Cellular and viral S-adenosylmethionine-dependent methyltransferases are involved in many regulated processes such as metabolism, detoxification, signal transduction, chromatin remodeling, nucleic acid processing, and mRNA capping. The Severe Acute Respiratory Syndrome coronavirus nsp16 protein is a S-adenosylmethionine-dependent (nucleoside-2'-O-methyltransferase only active in the presence of its activating partner nsp10. We report the nsp10/nsp16 complex structure at 2.0 Å resolution, which shows nsp10 bound to nsp16 through a ∼930 Ų surface area in nsp10. Functional assays identify key residues involved in nsp10/nsp16 association, and in RNA binding or catalysis, the latter likely through a SN2-like mechanism. We present two other crystal structures, the inhibitor Sinefungin bound in the S-adenosylmethionine binding pocket and the tighter complex nsp10(Y96F/nsp16, providing the first structural insight into the regulation of RNA capping enzymes in +RNA viruses.

  3. Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2'-O-methyltransferase nsp10/nsp16 complex.

    Science.gov (United States)

    Decroly, Etienne; Debarnot, Claire; Ferron, François; Bouvet, Mickael; Coutard, Bruno; Imbert, Isabelle; Gluais, Laure; Papageorgiou, Nicolas; Sharff, Andrew; Bricogne, Gérard; Ortiz-Lombardia, Miguel; Lescar, Julien; Canard, Bruno

    2011-05-01

    Cellular and viral S-adenosylmethionine-dependent methyltransferases are involved in many regulated processes such as metabolism, detoxification, signal transduction, chromatin remodeling, nucleic acid processing, and mRNA capping. The Severe Acute Respiratory Syndrome coronavirus nsp16 protein is a S-adenosylmethionine-dependent (nucleoside-2'-O)-methyltransferase only active in the presence of its activating partner nsp10. We report the nsp10/nsp16 complex structure at 2.0 Å resolution, which shows nsp10 bound to nsp16 through a ∼930 Ų surface area in nsp10. Functional assays identify key residues involved in nsp10/nsp16 association, and in RNA binding or catalysis, the latter likely through a SN2-like mechanism. We present two other crystal structures, the inhibitor Sinefungin bound in the S-adenosylmethionine binding pocket and the tighter complex nsp10(Y96F)/nsp16, providing the first structural insight into the regulation of RNA capping enzymes in +RNA viruses.

  4. Crystal structures of three classes of non-steroidal anti-inflammatory drugs in complex with aldo-keto reductase 1C3.

    Directory of Open Access Journals (Sweden)

    Jack U Flanagan

    Full Text Available Aldo-keto reductase 1C3 (AKR1C3 catalyses the NADPH dependent reduction of carbonyl groups in a number of important steroid and prostanoid molecules. The enzyme is also over-expressed in prostate and breast cancer and its expression is correlated with the aggressiveness of the disease. The steroid products of AKR1C3 catalysis are important in proliferative signalling of hormone-responsive cells, while the prostanoid products promote prostaglandin-dependent proliferative pathways. In these ways, AKR1C3 contributes to tumour development and maintenance, and suggest that inhibition of AKR1C3 activity is an attractive target for the development of new anti-cancer therapies. Non-steroidal anti-inflammatory drugs (NSAIDs are one well-known class of compounds that inhibits AKR1C3, yet crystal structures have only been determined for this enzyme with flufenamic acid, indomethacin, and closely related analogues bound. While the flufenamic acid and indomethacin structures have been used to design novel inhibitors, they provide only limited coverage of the NSAIDs that inhibit AKR1C3 and that may be used for the development of new AKR1C3 targeted drugs. To understand how other NSAIDs bind to AKR1C3, we have determined ten crystal structures of AKR1C3 complexes that cover three different classes of NSAID, N-phenylanthranilic acids (meclofenamic acid, mefenamic acid, arylpropionic acids (flurbiprofen, ibuprofen, naproxen, and indomethacin analogues (indomethacin, sulindac, zomepirac. The N-phenylanthranilic and arylpropionic acids bind to common sites including the enzyme catalytic centre and a constitutive active site pocket, with the arylpropionic acids probing the constitutive pocket more effectively. By contrast, indomethacin and the indomethacin analogues sulindac and zomepirac, display three distinctly different binding modes that explain their relative inhibition of the AKR1C family members. This new data from ten crystal structures greatly broadens

  5. Syntheses, crystal structures, and physical properties of dinuclear copper(I) and tetranuclear mixed-valence copper(I,II) complexes with hydroxylated bipyridyl-like ligands.

    Science.gov (United States)

    Zhang, Xian-Ming; Tong, Ming-Liang; Gong, Meng-Lian; Lee, Hung-Kay; Luo, Li; Li, King-Fai; Tong, Ye-Xiang; Chen, Xiao-Ming

    2002-07-15

    Four copper complexes with hydroxylated bipyridyl-like ligands, namely [Cu(2)(ophen)(2)] (1), [Cu(4)(ophen)(4)(tp)] (2), [Cu(4)(obpy)(4)(tp)] (3), and [Cu(4)(obpy)(4)(dpdc)].2H(2)O (4), (Hophen=2-hydroxy-1,10-phenanthroline, Hobpy=6-hydroxy-2,2'-bipyridine, tp=terephthalate, dpdc=diphenyl-4,4'-dicarboxylate) have been synthesized hydrothermally. X-ray single-crystal structural analyses of these complexes reveal that 1,10-phenanthroline (phen) or 2,2'-bipyridine (bpy) ligands are hydroxylated into ophen or obpy during the reaction, which provides structural evidence for the long-time argued Gillard mechanism. The dinuclear copper(I) complex 1 has three supramolecular isomers in the solid state, in which short copper-copper distances (2.66-2.68 A) indicate weak metal-metal bonding interactions. Each of the mixed-valence copper(i,ii) complexes 2-4 consists of a pair of [Cu(2)(ophen)(2)](+) or [Cu(2)(obpy)(2)](+) fragments bridged by a dicarboxylate ligand into a neutral tetranuclear dumbbell structure. Dinuclear 1 is an intermediate in the formation of 2 and can be converted into 2 in the presence of additional copper(II) salt and tp ligands under hydrothermal conditions. In addition to the ophen-centered pi-->pi* excited-state emission, 1 shows strong emissions at ambient temperature, which may be tentatively assigned as an admixture of copper-centered d-->s,p and MLCT excited states.

  6. The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function.

    Science.gov (United States)

    Rowland, P; Björnberg, O; Nielsen, F S; Jensen, K F; Larsen, S

    1998-06-01

    Dihydroorotate dehydrogenases (DHODs) catalyze the oxidation of (S)-dihydroorotate to orotate, the fourth step and only redox reaction in the de novo biosynthesis of pyrimidine nucleotides. A description is given of the crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A (DHODA) complexed with the product of the enzyme reaction orotate. The structure of the complex to 2.0 A resolution has been compared with the structure of the native enzyme. The active site of DHODA is known to contain a water filled cavity buried beneath a highly conserved and flexible loop. In the complex the orotate displaces the water molecules from the active site and stacks above the DHODA flavin isoalloxazine ring, causing only small movements of the surrounding protein residues. The orotate is completely buried beneath the protein surface, and the orotate binding causes a significant reduction in the mobility of the active site loop. The orotate is bound by four conserved asparagine side chains (Asn 67, Asn 127, Asn 132, and Asn 193), the side chains of Lys 43 and Ser 194, and the main chain NH groups of Met 69, Gly 70, and Leu 71. Of these the Lys 43 side chain makes hydrogen bonds to both the flavin isoalloxazine ring and the carboxylate group of the orotate. Potential interactions with bound dihydroorotate are considered using the orotate complex as a basis for molecular modeling. The role of Cys 130 as the active site base is discussed, and the sequence conservation of the active site residues across the different families of DHODs is reviewed, along with implications for differences in substrate binding and in the catalytic mechanisms between these families.

  7. Host cell recognition by the henipaviruses: Crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Kai; Rajashankar, Kanagalaghatta R.; Chan, Yee-Peng; Himanen, Juha P.; Broder, Christopher C.; Nikolov, Dimitar B. (USUHS); (Cornell); (MSKCC)

    2008-07-28

    Nipah virus (NiV) and Hendra virus are the type species of the highly pathogenic paramyxovirus genus Henipavirus, which can cause severe respiratory disease and fatal encephalitis infections in humans, with case fatality rates approaching 75%. NiV contains two envelope glycoproteins, the receptor-binding G glycoprotein (NiV-G) that facilitates attachment to host cells and the fusion (F) glycoprotein that mediates membrane merger. The henipavirus G glycoproteins lack both hemagglutinating and neuraminidase activities and, instead, engage the highly conserved ephrin-B2 and ephrin-B3 cell surface proteins as their entry receptors. Here, we report the crystal structures of the NiV-G both in its receptor-unbound state and in complex with ephrin-B3, providing, to our knowledge, the first view of a paramyxovirus attachment complex in which a cellular protein is used as the virus receptor. Complex formation generates an extensive protein-protein interface around a protruding ephrin loop, which is inserted in the central cavity of the NiV-G {beta}-propeller. Analysis of the structural data reveals the molecular basis for the highly specific interactions of the henipavirus G glycoproteins with only two members (ephrin-B2 and ephrin-B3) of the very large ephrin family and suggests how they mediate in a unique fashion both cell attachment and the initiation of membrane fusion during the virus infection processes. The structures further suggest that the NiV-G/ephrin interactions can be effectively targeted to disrupt viral entry and provide the foundation for structure-based antiviral drug design.

  8. Crystal structure refinement with SHELXL

    Energy Technology Data Exchange (ETDEWEB)

    Sheldrick, George M., E-mail: gsheldr@shelx.uni-ac.gwdg.de [Department of Structural Chemistry, Georg-August Universität Göttingen, Tammannstraße 4, Göttingen 37077 (Germany)

    2015-01-01

    New features added to the refinement program SHELXL since 2008 are described and explained. The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

  9. Crystal structure of pymetrozine

    Directory of Open Access Journals (Sweden)

    Youngeun Jeon

    2015-07-01

    Full Text Available The title compound, C10H11N5O {systematic name: 6-methyl-4-[(E-(pyridin-3-ylmethylideneamino]-4,5-dihydro-1,2,4-triazin-3(2H-one}, C10H11N5O, is used as an antifeedant in pest control. The asymmetric unit comprises two independent molecules, A and B, in which the dihedral angles between the pyridinyl and triazinyl ring planes [r.m.s. deviations = 0.0132 and 0.0255 ] are 11.60 (6 and 18.06 (4°, respectively. In the crystal, N—H...O, N—H...N, C—H...N and C—H...O hydrogen bonds, together with weak π–π interactions [ring-centroid separations = 3.5456 (9 and 3.9142 (9 Å], link the pyridinyl and triazinyl rings of A molecules, generating a three-dimensional network.

  10. Synthesis, crystal structure, catecholase and phenoxazinone synthase activities of a mononuclear cobalt(III) complex containing in situ formed tridentate N-donor Schiff base

    Science.gov (United States)

    Maji, Ashis Kumar; Chatterjee, Arnab; Khan, Sumitava; Ghosh, Barindra Kumar; Ghosh, Rajarshi

    2017-10-01

    Synthesis and structural characterization of a mononuclear cobalt(III) Schiff base complex is reported. It crystallizes with monoclinic crystal system with P21/n space group with a = 9.9793(4) Å, b = 28.2907(12) Å and c = 13.1233(6) Å, and β = 97.532(3)°. The compound is active to catecholase and phenoxazinone synthase activities in MeOH, and MeOH and MeCN solvents, respectively at room temperature. Each of the reactions was found to be of first order with reaction rate 8.08 × 10-3 min-1 (MeOH) for the catecholase activity and 1.05 × 10-3 min-1 (MeOH) and 3.82 × 10-3 min-1 (MeCN) for the phenoxazinone synthase activity. The turn over numbers for the catecholase activity is 5.02 × 103 h-1 (MeOH) and for the phenoxazinone synthase activity is 4.59 × 103 h-1 (MeOH) and 5.12 × 103 h-1 (MeCN). Substrate-catalyst adduct was tried to be trapped in each case using mass spectrometry.

  11. Synthesis, crystal structure and photophysical properties of europium(III) and terbium(III) complexes with pyridine-2,6-dicarboxamide

    NARCIS (Netherlands)

    Tanase, S.; Gallego, P.M.; Gelder, R. de; Fu, W.T.

    2007-01-01

    The reactions of pyridine-2,6-dicarboxamide with europium(III) and terbium(III) triflates led to the formation of mononuclear complexes of formula [Ln(pcam)(3)](CF3SO3)(3) (Ln = Eu 1, Tb 2; pcam stands for pyridine-2,6-dicarboxamide). From single-crystal X-ray diffraction analysis, the complexes

  12. Synthesis, Crystal Structure, Gas Absorption, and Separation Properties of a Novel Complex Based on Pr and a Three-Connected Ligand

    Directory of Open Access Journals (Sweden)

    Jie Sun

    2017-12-01

    Full Text Available A novel Pr complex, constructed from a rigid three-connected H3TMTA and praseodymium(III ion, has been synthesized in a mixed solvent system and characterized by X-ray single crystal diffraction, infrared spectroscopy, a thermogravimetric analysis, an element analysis, and powder X-ray diffraction, which reveals that complex 1 crystallizes in a three-dimensional porous framework. Moreover, the thermal stabilities and the fluorescent and gas adsorption and separation properties of complex 1 were investigated systematically.

  13. Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate

    DEFF Research Database (Denmark)

    Venskutonyte, Raminta; Frydenvang, Karla; Gajhede, Michael

    2011-01-01

    present the first X-ray crystal structure of the ligand binding domain of GluK3 in complex with glutamate, determined to 1.6Å resolution. The structure reveals a conserved glutamate binding mode, characteristic for iGluRs, and a water molecule network in the glutamate binding site similar to that seen...

  14. Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI(5-24) and adenosine.

    Science.gov (United States)

    Narayana, N; Cox, S; Shaltiel, S; Taylor, S S; Xuong, N

    1997-04-15

    The crystal structure of the hexahistidine-tagged mouse recombinant catalytic subunit (H6-rC) of cAMP-dependent protein kinase (cAPK), complexed with a 20-residue peptide inhibitor from the heat-stable protein kinase inhibitor PKI(5-24) and adenosine, was determined at 2.2 A resolution. Novel crystallization conditions were required to grow the ternary complex crystals. The structure was refined to a final crystallographic R-factor of 18.2% with good stereochemical parameters. The "active" enzyme adopts a "closed" conformation as found in rC:PKI(5-24) [Knighton et al. (1991a,b) Science 253, 407-414, 414-420] and packs in a similar manner with the peptide providing a major contact surface. This structure clearly defines the subsites of the unique nucleotide binding site found in the protein kinase family. The adenosine occupies a mostly hydrophobic pocket at the base of the cleft between the two lobes and is completely buried. The missing triphosphate moiety of ATP is filled with a water molecule (Wtr 415) which replaces the gamma-phosphate of ATP. The glycine-rich loop between beta1 and beta2 helps to anchor the phosphates while the ribose ring is buried beneath beta-strand 2. Another ordered water molecule (Wtr 375) is pentacoordinated with polar atoms from adenosine, Leu 49 in beta-strand 1, Glu 127 in the linker strand between the two lobes, Tyr 330, and a third water molecule, Wtr 359. The conserved nucleotide fold can be defined as a lid comprised of beta-strand 1, the glycine-rich loop, and beta-strand 2. The adenine ring is buried beneath beta-strand 1 and the linker strand (120-127) that joins the small and large lobes. The C-terminal tail containing Tyr 330, a segment that lies outside the conserved core, covers this fold and anchors it in a closed conformation. The main-chain atoms of the flexible glycine-rich loop (residues 50-55) in the ATP binding domain have a mean B-factor of 41.4 A2. This loop is quite mobile, in striking contrast to the other

  15. Crystal structure of the UvrB dimer: insights into the nature and functioning of the UvrAB damage engagement and UvrB–DNA complexes

    Science.gov (United States)

    Webster, Matthew P. J.; Jukes, Rachael; Zamfir, Vlad S.; Kay, Christopher W. M.; Bagnéris, Claire; Barrett, Tracey

    2012-01-01

    UvrB has a central role in the highly conserved UvrABC pathway functioning not only as a damage recognition element but also as an essential component of the lesion tracking machinery. While it has been recently confirmed that the tracking assembly comprises a UvrA2B2 heterotetramer, the configurations of the damage engagement and UvrB–DNA handover complexes remain obscure. Here, we present the first crystal structure of a UvrB dimer whose biological significance has been verified using both chemical cross-linking and electron paramagnetic resonance spectroscopy. We demonstrate that this dimeric species stably associates with UvrA and forms a UvrA2B2–DNA complex. Our studies also illustrate how signals are transduced between the ATP and DNA binding sites to generate the helicase activity pivotal to handover and formation of the UvrB2–DNA complex, providing key insights into the configurations of these important repair intermediates. PMID:22753105

  16. Eight- and six-coordinated Mn(II) complexes of heteroaromatic alcohol and aldehyde: Crystal structure, spectral, magnetic, thermal and antibacterial activity studies

    Science.gov (United States)

    Jabłońska-Wawrzycka, Agnieszka; Barszcz, Barbara; Zienkiewicz, Małgorzata; Hodorowicz, Maciej; Jezierska, Julia; Stadnicka, Katarzyna; Lechowicz, Łukasz; Kaca, Wiesław

    2014-08-01

    Crystal, molecular and electronic structure of new manganese(II) compounds: [Mn(2-CH2OHpy)2(NO3)2] (1), [Mn(4-CHO-5-MeIm)2(NO3)2] (2) and [Mn(4-CHO-5-MeIm)2Cl2] (3), where 2-hydroxymethylpyridine (2-CH2OHpy) and 5(4)-carbaldehyde-4(5)-methylimidazole (5(4)-CHO-4(5)-MeIm), have been characterised using X-ray, spectroscopic, magnetic and TG/DTG data. In compounds 1 and 2, the Mn(II) ion is eight-coordinated forming distorted pseudo-dodecahedron, that is rather unusual for the manganese(II) complexes, whereas in 3 the Mn(II) ion environment is a distorted octahedron. The high coordination number (CN = 8) of 1 and 2 results from bidentate character of the nitrate ligands. The X-band EPR spectra of compounds 2 and 3 exhibit fine structure signals resulting from zero-field splitting (ZFS) of the spin states for high spin d5 Mn(II), whereas for 1 the broad isotropic signals were observed. The estimation of ZFS for individual Mn(II) ions was carried out for all compounds using DFT calculations. The free ligands and their manganese(II) complexes have been tested in vitro against gram-positive and gram-negative bacteria in order to assess their antimicrobial properties.

  17. Synthesis, Structure and Antitumor Activity of Dibutyltin Oxide Complexes with 5-Fluorouracil Derivatives. Crystal Structure of [(5-Fluorouracil-1-CH2CH2COOSn(n-Bu 2]4O2

    Directory of Open Access Journals (Sweden)

    Zhan Shi

    2001-07-01

    Full Text Available Dibutyltin (IV oxide complex reacts with the fluorouracil compounds 5-fluorouracil-1-propanonic or 5-fluorouracil-1-acetic acid (Fu to give the complexes [(5-Fu-1-(CH2nCOOSn(n-Bu2]4O2 (I, n=2; II, n=1 which were characterized by IR and 1H-NMR. The crystal structure of complex I shows that the molecular is a dimer, in which two [(5-Fu-1-CH2CH2COOSn(n-Bu2]2O units are linked by a bridging oxygen atom, and the tin atoms adopt distorted trigonal bipyramids via two carbons from a dibutyl moiety and three oxygen atoms from 5-Fu and bridging oxygen. These complexes have potential anti-tumour activity: in vitro tests showed that complexes I and II exhibit high cytotoxicity against OVCAR-3 and PC-14.

  18. Antibacterial, antibiofilm and antioxidant screening of copper(II)-complexes with some S-alkyl derivatives of thiosalicylic acid. Crystal structure of the binuclear copper(II)-complex with S-propyl derivative of thiosalicylic acid

    Science.gov (United States)

    Bukonjić, Andriana M.; Tomović, Dušan Lj.; Nikolić, Miloš V.; Mijajlović, Marina Ž.; Jevtić, Verica V.; Ratković, Zoran R.; Novaković, Slađana B.; Bogdanović, Goran A.; Radojević, Ivana D.; Maksimović, Jovana Z.; Vasić, Sava M.; Čomić, Ljiljana R.; Trifunović, Srećko R.; Radić, Gordana P.

    2017-01-01

    The spectroscopically predicted structure of the obtained copper(II)-complex with S-propyl derivative of thiosalicylic acid was confirmed by X-ray structural study. The binuclear copper(II)-complex with S-propyl derivative of thiosalicylic acid crystallized in two polymorphic forms with main structural difference in the orientation of phenyl rings relative to corresponding carboxylate groups. The antibacterial activity was tested determining the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) by using microdilution method. The influence on bacterial biofilm formation was determined by tissue culture plate method. In general, the copper(II)-complexes manifested a selective and moderate activity. The most sensitive bacteria to the effects of Cu(II)-complexes was a clinical isolate of Pseudomonas aeruginosa. For this bacteria MIC and biofilm inhibitory concentration (BIC) values for all tested complexes were in the range or better than the positive control, doxycycline. Also, for the established biofilm of clinical isolate Staphylococcus aureus, BIC values for the copper(II)-complex with S-ethyl derivative of thiosalicylic acid,[Cu2(S-et-thiosal)4(H2O)2] (C3) and copper(II)-complex with S-butyl derivative of thiosalicylic acid, [Cu2(S-bu-thiosal)4(H2O)2] (C5) were in range or better than the positive control. All the complexes acted better against Gram-positive bacteria (Staphylococcus aureus and Staphylococcus aureus ATCC 25923) than Gram-negative bacteria (Proteus mirabilis ATCC 12453, Pseudomonas aeruginosa, and P. aeruginosa ATCC 27855). The complexes showed weak antioxidative properties tested by two methods (1,1-diphenyl-2-picrylhydrazyl (DPPH) and reducing power assay).

  19. Non-covalent interactions in 2-methylimidazolium copper(II) complex (MeImH)2[Cu(pfbz)4]: Synthesis, characterization, single crystal X-ray structure and packing analysis

    Science.gov (United States)

    Sharma, Raj Pal; Saini, Anju; Kumar, Santosh; Kumar, Jitendra; Sathishkumar, Ranganathan; Venugopalan, Paloth

    2017-01-01

    A new anionic copper(II) complex, (MeImH)2 [Cu(pfbz)4] (1) where, MeImH = 2-methylimidazolium and pfbz = pentafluorobenzoate has been isolated by reacting copper(II) sulfate pentahydrate, pentafluorobenzoic acid and 2-methylimidazole in ethanol: water mixture in 1:2:2 molar ratio. This complex 1 has been characterized by elemental analysis, thermogravimetric analysis, spectroscopic techniques (UV-Vis, FT-IR) and conductance measurements. The complex salt crystallizes in monoclinic crystal system with space group C2/c. Single crystal X-ray structure determination revealed the presence of discrete ions: [Cu(pfbz)4]2- anion and two 2-methylimidazolium cation (C4H7N2)+. The crystal lattice is stabilized by strong hydrogen bonding and F⋯F interactions between cationic-anionic and the anionic-anionic moieties respectively, besides π-π interactions.

  20. Tris(β-diketonato) Ru(III) complexes as chiral dopants for nematic liquid crystals: the effect of the molecular structure on the helical twisting power.

    Science.gov (United States)

    Yoshida, Jun; Watanabe, Go; Kakizawa, Kaori; Kawabata, Yasuhiro; Yuge, Hidetaka

    2013-10-07

    Doping nematic liquid crystals with optically active compounds transforms them into chiral nematic phases with helical structures. In this phenomenon, the chirality of the dopant molecules is transferred or amplified to the bulk of the liquid crystals. Δ-[Ru(acac)3] (acac = acetylacetonato) is known to work as one of the dopants with a strong helical twisting power (HTP). In this study, we have systematically modified [Ru(acac)3] to clarify the correlation between the molecular structure and HTP; we have designed and synthesized five new Ru(III) complexes, [Ru(acac)2(acacC8)] (RuC8-1, acac = acetylacetonate, acacC8 = 3-(4'-octyloxy-phenylalkynyl)-pentane-2,4-dionato), [Ru(acac)(acacC8)2] (RuC8-2), [Ru(acacC8)3] (RuC8-3), [Ru(acacC0)3] (RuC0-3, acacC0 = 3-(phenylalkynyl)-pentane-2,4-dionato), and [Ru(acacC24)3] (RuC24-3, acacC24 = 3-(3',4',5'-tri(octyloxy)-phenylalkynyl)-pentane-2,4-dionato). All the complexes, except for RuC0-3, could be separated into Δ, Λ isomers by HPLC on a chiral column and were examined as chiral dopants for a nematic liquid crystal, N-(4-methoxybenzilidene)-4-butylaniline (MBBA). The Δ isomers of RuC8-1, RuC8-2, RuC8-3, and RuC24-3 induced a right-handed (P) helix and the magnitudes of the HTPs (/μm(-1)) were determined as follows: RuC8-1 (+60) RuC8-3 (+78) > RuC24-3 (+41). The HTPs of the ruthenium dopants were not simply proportional to their size. The highest HTP observed in biaxial RuC8-2 was attributed to the balance of the molecular helicity and high ordering in MBBA based on the surface chirality model.

  1. Determinants of dual substrate specificity revealed by the crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate·Mg(2+)·NADH.

    Science.gov (United States)

    Takahashi, Kento; Tomita, Takeo; Kuzuyama, Tomohisa; Nishiyama, Makoto

    2016-09-30

    HICDH (Homoisocitrate dehydrogenase) is a member of the β-decarboxylating dehydrogenase family that catalyzes the conversion of homoisocitrate to α-ketoadipate using NAD(+) as a coenzyme, which is the fourth reaction involved in lysine biosynthesis through the α-aminoadipate pathway. Although typical HICDHs from fungi and yeast exhibit strict substrate specificities toward homoisocitrate (HIC), HICDH from a thermophilic bacterium Thermus thermophilus (TtHICDH) catalyzes the reactions using both HIC and isocitrate (IC) as substrates at similar efficiencies. We herein determined the crystal structure of the quaternary complex of TtHICDH with HIC, NADH, and Mg(2+) ion at a resolution of 2.5 Å. The structure revealed that the distal carboxyl group of HIC was recognized by the side chains of Ser72 and Arg85 from one subunit, and Asn173 from another subunit of a dimer unit. Model structures were constructed for TtHICDH in complex with IC and also for HICDH from Saccharomyces cerevisiae (ScHICDH) in complex with HIC. TtHICDH recognized the distal carboxyl group of IC by Arg85 in the model. In ScHICDH, the distal carboxyl group of HIC was recognized by the side chains of Ser98 and Ser108 from one subunit and Asn208 from another subunit of a dimer unit. By contrast, in ScHICDH, which lacks an Arg residue at the position corresponding to Arg85 in TtHICDH, these residues may not interact with the distal carboxyl group of shorter IC. These results provide a molecular basis for the differences in substrate specificities between TtHICDH and ScHICDH. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Crystal structure and solution characterization of the thioredoxin-2 from Plasmodium falciparum, a constituent of an essential parasitic protein export complex.

    Science.gov (United States)

    Peng, Mindy; Cascio, Duilio; Egea, Pascal F

    2015-01-02

    Survival of the malaria parasite Plasmodium falciparum when it infects red blood cells depends upon its ability to export hundreds of its proteins beyond an encasing vacuole. Protein export is mediated by a parasite-derived protein complex, the Plasmodium translocon of exported proteins (PTEX), and requires unfolding of the different cargos prior to their translocation across the vacuolar membrane. Unfolding is performed by the AAA+protein unfoldase HSP101/ClpB2 and the thioredoxin-2 enzyme (TRX2). Protein trafficking is dramatically impaired in parasites with defective HSP101 or lacking TRX2. These two PTEX subunits drive export and are targets for the design of a novel class of antimalarials: protein export inhibitors. To rationalize inhibitor design, we solved the crystal structure of Pfal-TRX2 at 2.2-Å resolution. Within the asymmetric unit, the three different copies of this protein disulfide reductase sample its two redox catalytic states. Size exclusion chromatography and small-angle X-ray scattering (SAXS) analyses demonstrate that Pfal-TRX2 is monomeric in solution. A non-conserved N-terminal extension precedes the canonical thioredoxin-fold; although it is not observed in our structure, our solution analysis suggests it is flexible in contrast to Plasmodium thioredoxin-1. This represents a first step towards the reconstitution of the entire PTEX for mechanistic and structural studies. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Crystal structure and luminescence of complexes of Eu(III) and Tb(III) with furan-2,5-dicarboxylate

    NARCIS (Netherlands)

    Akerboom, S.; Fu, W.T.; Lutz, M.|info:eu-repo/dai/nl/304828971; Bouwman, E.

    2012-01-01

    Four new Ln(III) complexes (Ln = Eu, Tb) with furan-2,5-dicarboxylic acid (H2FDA) as a ligand have been synthesized and characterized in the solid state. Luminescence studies indicate that the compounds exhibit line-like luminescence characteristic of the lanthanide centre upon excitation in the

  4. New asymmetric heptaaza Schiff base macrocyclic complex of Mn(II): Crystal structure, biological and DFT studies

    Science.gov (United States)

    Khanmohammadi, Hamid; Amani, Saeid; Abnosi, Mohammad H.; Khavasi, Hamid R.

    2010-10-01

    A new asymmetric heptaaza Schiff base macrocyclic bis(pendant donor) manganese(II) complex, [MnL 1](ClO 4) 2·CH 3CN ( 1), has been prepared and characterized by X-ray diffraction and spectroscopic methods. The antimicrobial activity of 1 and a series of its familiar symmetric heptaaza [15]pydieneN 5, [16]pydieneN 5, and [17]pydieneN 5-based bis-(2-aminoethyl) pendant armed Schiff base macrocyclic complexes of Mn(II) were tested against Escherichia coli, Staphylococcus aureus and Candida albicans. The results showed that the symmetric heptaaza [16]pydieneN 5, and [17]pydieneN 5-based Schiff base macrocyclic complexes of Mn(II) had remarkable inhibition zone on the culture of S. aureus and E. coli as compared with standard drugs. The optimized geometry of the prepared complex has been obtained from density functional method, DFT, using B3LYP/6-31G* basis set.

  5. The xenograft antigen bound to Griffonia simplicifolia lectin 1-B(4). X-ray crystal structure of the complex and molecular dynamics characterization of the binding site.

    Science.gov (United States)

    Tempel, Wolfram; Tschampel, Sarah; Woods, Robert J

    2002-02-22

    The shortage of organs for transplantation into human patients continues to be a driving force behind research into the use of tissues from non-human donors, particularly pig. The primary barrier to such xenotransplantation is the reaction between natural antibodies present in humans and Old World monkeys and the Gal alpha(1-3)Gal epitope (xenograft antigen, xenoantigen) found on the cell surfaces of the donor organ. This hyperacute immune response leads ultimately to graft rejection. Because of its high specificity for the xenograft antigen, isolectin 1-B(4) from Griffonia simplicifolia (GS-1-B(4)) has been used as an immunodiagnostic reagent. Furthermore, haptens that inhibit natural antibodies also inhibit GS-1-B(4) from binding to the xenoantigen. Here we report the first x-ray crystal structure of the xenograft antigen bound to a protein (GS-1-B(4)). The three-dimensional structure was determined from orthorhombic crystals at a resolution of 2.3 A. To probe the influence of binding on ligand properties, we report also the results of molecular dynamics (MD) simulations on this complex as well as on the free ligand. The MD simulations were performed with the AMBER force-field for proteins augmented with the GLYCAM parameters for glycosides and glycoproteins. The simulations were performed for up to 10 ns in the presence of explicit solvent. Through comparison with MD simulations performed for the free ligand, it has been determined that GS-1-B(4) recognizes the lowest energy conformation of the disaccharide. In addition, the x-ray and modeling data provide clear explanations for the reported specificities of the GS-1-B(4) lectin. It is anticipated that a further understanding of the interactions involving the xenograft antigen will help in the development of therapeutic agents for application in the prevention of hyperacute xenograft rejection.

  6. Efficient hydrolytic cleavage of plasmid DNA by chloro-cobalt(II) complexes based on sterically hindered pyridyl tripod tetraamine ligands: synthesis, crystal structure and DNA cleavage.

    Science.gov (United States)

    Massoud, Salah S; Perkins, Richard S; Louka, Febee R; Xu, Wu; Le Roux, Anne; Dutercq, Quentin; Fischer, Roland C; Mautner, Franz A; Handa, Makoto; Hiraoka, Yuya; Kreft, Gabriel L; Bortolotto, Tiago; Terenzi, Hernán

    2014-07-14

    Four new cobalt(ii) complexes [Co(6-MeTPA)Cl]ClO4/PF6 (2/2a), [Co(6-Me2TPA)Cl]ClO4/PF6 (3/3a), [Co(BPQA)Cl]ClO4/PF6 (4/4a) and [Co(BQPA)Cl]ClO4/PF6 (5/5a) as well as [Co(TPA)Cl]ClO4 (1) where TPA = tris(2-pyridylmethyl)amine, 6-MeTPA = ((6-methyl-2-pyridyl)methyl)bis(2-pyridylmethyl)amine, 6-Me2TPA = bis(6-methyl-2-pyridyl)methyl)-(2-pyridylmethyl)amine, BPQA = bis(2-pyridylmethyl)-(2-quinolylmethyl)-amine and BQPA = bis(2-quinolylmethyl)-(2-pyridylmethyl)amine were synthesized and structurally characterized. Single crystal X-ray crystallography confirmed the distorted trigonal bipyramidal geometries of complexes 2a-5a. Spectrophotometric titrations and conductivity measurements of the complexes in the CH3CN-H2O mixture showed that the chloro complexes exist in equilibrium with the corresponding hydrolyzed aqua species, [Co(L)(H2O)](2+). The pKa values of the coordinated H2O in aqua complexes vary from 8.4 to 8.7 (37 °C). The interactions of the complexes (1-5) with DNA have been investigated at pH = 7.0 and 9.0 (10 mM Tris-HCl buffer) and 37 °C where very high catalytic cleavage was observed. Under pseudo Michaelis-Menten kinetic conditions, the catalytic rate constants, kcat, decrease in the order 4>2>5>1>3. At pH 7.0 (10 mM Tris-HCl buffer) and 37 °C, the kcat value for complex 4 (6.02 h(-1)), where [Co(BPQA)(H2O)](2+) is the major species, corresponds to 170 million rate enhancement over the non-catalyzed DNA. Electrophoretic experiments conducted in the presence and absence of radical scavengers (DMSO, KI, NaN3) ruled out the oxidative mechanistic pathway of the reaction and suggested that the hydrolytic mechanism is the preferred one. This finding was in agreement with the observed increase in the kcat values at pH 9.0 compared to the corresponding values at pH 7.0 as a result of the increased concentration of the reactive hydroxo species, [Co(L)(OH)](+). The reactivity of the synthesized complexes in catalyzing the DNA cleavage is discussed in relation to

  7. Characterization of ternary bivalent metal complexes with bis(2-hydroxyethyl)iminotris(hydroxymethy)methane (Bis?Tris) and the comparison of five crystal structures of Bis?Tris complexes*1

    Science.gov (United States)

    Inomata, Yoshie; Gochou, Yoshihiro; Nogami, Masanobu; Howell, F. Scott; Takeuchi, Toshio

    2004-09-01

    Eleven bivalent metal complexes with bis(2-hydroxyethyl)iminotris(hydroxymethy)methane (Bis-Tris:hihm): [M(hihm)(H 2O)]SO 4· nH 2O (M: Co, Ni, Cu, Zn), [MCl(hihm)]Cl· nH 2O (M: Co, Ni, Cu), and [M(HCOO)(hihm)](HCOO) (M: Co, Ni, Cu, Zn) have been prepared and characterized by using their infrared absorption and powder diffuse reflection spectra, magnetic susceptibility, thermal analysis and powder X-ray diffraction analysis. The crystal structures of [Ni(hihm)(H 2O)]SO 4·H 2O ( 2), [Cu(hihm)(H 2O)]SO 4 ( 3), [NiCl(hihm)]Cl·H 2O ( 6), [CuCl(hihm)]Cl ( 7) and [Co(HCOO)(hihm)](HCOO) ( 8) have been determined by single crystal X-ray diffraction analysis. The crystals of [Ni(hihm)(H 2O)]SO 4·H 2O ( 2) and [Cu(hihm)(H 2O)]SO 4 ( 3) are each orthorhombic with the space group P2 12 12 1 and Pna2 1. For both complexes, the metal atom is in a distorted octahedral geometry, ligated by four hydroxyl oxygen atoms, a nitrogen atom and a water molecule. [NiCl(hihm)]Cl·H 2O ( 6) is monoclinic with the space group P2 1/ n. For complex ( 6), the nickel atom is in a distorted octahedral geometry, ligated by four hydroxyl oxygen atoms, a nitrogen atom and a chloride ion. [CuCl(hihm)]Cl ( 7) is orthorhombic with the space group P2 12 12 1. Although in this copper(II) complex the copper atom is ligated by six atoms, it is more reasonable to think that the copper atom is in a trigonal bipyramidal geometry coordinated with five atoms: three hydroxyl oxygen atoms, a nitrogen atom and a chloride ion if the bond distances and angles surrounding the copper atom are taken into consideration. [Co(HCOO)(hihm)](HCOO) ( 8) is monoclinic with the space group P2 1. In cobalt(II) complex ( 8), the cobalt atom is in a distorted octahedral geometry, ligated by four hydroxyl oxygen atoms, a nitrogen atom and an oxygen atom of a formate ion. The structure of complex ( 8) is the same as the structure of [NiCl(hihm)]Cl·H 2O ( 6) except for the formate ion coordinating instead of the chloride ion. [M

  8. Study on potential antitumor mechanism of a novel Schiff base copper(II) complex: synthesis, crystal structure, DNA binding, cytotoxicity and apoptosis induction activity.

    Science.gov (United States)

    Qiao, Xin; Ma, Zhong-Ying; Xie, Cheng-Zhi; Xue, Fei; Zhang, Yan-Wen; Xu, Jing-Yuan; Qiang, Zhao-Yan; Lou, Jian-Shi; Chen, Gong-Jun; Yan, Shi-Ping

    2011-05-01

    A new cytotoxic copper(II) complex with Schiff base ligand [Cu(II)(5-Cl-pap)(OAc)(H(2)O)]·2H(2)O (1) (5-Cl-pap=N-2-pyridiylmethylidene-2-hydroxy-5-chloro-phenylamine), was synthesized and structurally characterized by X-ray diffraction. Single-crystal analysis revealed that the copper atom shows a 4+1 pyramidal coordination, a water oxygen appears in the apical position, and three of the basal positions are occupied by the NNO tridentate ligand and the fourth by an acetate oxygen. The interaction of Schiff base copper(II) complex 1 with DNA was investigated by UV-visible spectra, fluorescence spectra and agarose gel electrophoresis. The apparent binding constant (K(app)) value of 6.40×10(5) M(-1) for 1 with DNA suggests moderate intercalative binding mode. This copper(II) complex displayed efficient oxidative cleavage of supercoiled DNA, which might indicate that the underlying mechanism involve hydroxyl radical, singlet oxygen-like species, and hydrogen peroxide as reactive oxygen species. In addition, our present work showed the antitumor effect of 1 on cell cycle and apoptosis. Flow cytometric analysis revealed that HeLa cells were arrested in the S phase after treatment with 1. Fluorescence microscopic observation indicated that complex 1 can induce apoptosis of HeLa cells, whose process was mediated by intrinsic mitochondrial apoptotic pathway owing to the activation of caspase-9 and caspase-3. Copyright © 2011 Elsevier Inc. All rights reserved.

  9. Crystal structure of vinculin in complex with vinculin binding site 50 (VBS50), the integrin binding site 2 (IBS2) of talin

    Energy Technology Data Exchange (ETDEWEB)

    Yogesha, S.D.; Rangarajan, Erumbi S.; Vonrhein, Clemens; Bricogne, Gerard; Izard, Tina (Globel Phasing); (Scripps)

    2012-05-10

    The cytoskeletal protein talin activates integrin receptors by binding of its FERM domain to the cytoplasmic tail of {beta}-integrin. Talin also couples integrins to the actin cytoskeleton, largely by binding to and activating the cytoskeletal protein vinculin, which binds to F-actin through the agency of its five-helix bundle tail (Vt) domain. Talin activates vinculin by means of buried amphipathic {alpha}-helices coined vinculin binding sites (VBSs) that reside within numerous four- and five-helix bundle domains that comprise the central talin rod, which are released from their buried locales by means of mechanical tension on the integrin:talin complex. In turn, these VBSs bind to the N-terminal seven-helix bundle (Vh1) domain of vinculin, creating an entirely new helix bundle that severs its head-tail interactions. Interestingly, talin harbors a second integrin binding site coined IBS2 that consists of two five-helix bundle domains that also contain a VBS (VBS50). Here we report the crystal structure of VBS50 in complex with vinculin at 2.3 {angstrom} resolution and show that intramolecular interactions of VBS50 within IBS2 are much more extensive versus its interactions with vinculin. Indeed, the IBS2-vinculin interaction only occurs at physiological temperature and the affinity of VBS50 for vinculin is about 30 times less than other VBSs. The data support a model where integrin binding destabilizes IBS2 to allow it to bind to vinculin.

  10. SYNTHESIS, CRYSTAL STRUCTURE, AND SPECTRAL AND MAGNETIC PROPERTIES OF CHLORO-BRIDGED CHAIN COMPLEX OF DINUCLEAR RUTHENIUM(II,III 3,4,5-TRIETHOXYBENZOATE

    Directory of Open Access Journals (Sweden)

    Hideaki Ishida

    2009-06-01

    Full Text Available A chloro-bridged chain complex constructed from paddlewheel-type dinuclear ruthenium(II,III carboxylate units, [Ru2{3,4,5-(C2H5O3C6H2CO2}4Cl]n·1.2nC2H5OH (1·1.2nC2H5OH, was synthesized and characterized by elemental analysis and IR and UV-vis spectroscopies. The single-crystal X-ray analysis showed that the complex forms a zig-zag chain structure, in which the chloroligands bridge the dinuclear units at the axial positions with the Ru1–Cl–Ru2 angle of 120.38(7°. A broad band around 1144 nm and a band at 475 nm were observed in the diffused reflectance spectra and ascribed to a δ→δ* and a π(RuO, Ru2→π*(Ru2 transitions, respectively. Temperature dependence of magnetic susceptibility showed that the antiferromagnetic interaction between the dinuclear units is weak (zJ = −0.8 cm−1 with D value of 60 cm−1

  11. Crystal structure of a PP2A B56-BubR1 complex and its implications for PP2A substrate recruitment and localization

    Directory of Open Access Journals (Sweden)

    Jiao Wang

    2016-06-01

    Full Text Available ABSTRACT Protein phosphatase 2A (PP2A accounts for the majority of total Ser/Thr phosphatase activities in most cell types and regulates many biological processes. PP2A holoenzymes contain a scaffold A subunit, a catalytic C subunit, and one of the regulatory/targeting B subunits. How the B subunit controls PP2A localization and substrate specificity, which is a crucial aspect of PP2A regulation, remains poorly understood. The kinetochore is a critical site for PP2A functioning, where PP2A orchestrates chromosome segregation through its interactions with BubR1. The PP2A-BubR1 interaction plays important roles in both spindle checkpoint silencing and stable microtubule-kinetochore attachment. Here we present the crystal structure of a PP2A B56-BubR1 complex, which demonstrates that a conserved BubR1 LxxIxE motif binds to the concave side of the B56 pseudo-HEAT repeats. The BubR1 motif binds to a groove formed between B56 HEAT repeats 3 and 4, which is quite distant from the B56 binding surface for PP2A catalytic C subunit and thus is unlikely to affect PP2A activity. In addition, the BubR1 binding site on B56 is far from the B56 binding site of shugoshin, another kinetochore PP2A-binding protein, and thus BubR1 and shugoshin can potentially interact with PP2A-B56 simultaneously. Our structural and biochemical analysis indicates that other proteins with the LxxIxE motif may also bind to the same PP2A B56 surface. Thus, our structure of the PP2A B56-BubR1 complex provides important insights into how the B56 subunit directs the recruitment of PP2A to specific targets.

  12. Hydrothermal syntheses and crystal structures of two 4,4'-biphenyldicarboxylate copper(II) complexes with 1,10-phenanthroline

    Science.gov (United States)

    Zhang, Shu-Yan; Yu, Ming-Xin; Zhu, Long-Guan

    2004-08-01

    Two structurally diverse compounds, [Cu(Hbpdc) 2(phen)] ( 1) and [Cu(bpdc)(phen)(H 2O)] n ( 2) (H 2bpdc=4,4'-biphenyldicarboxylic acid, phen=1,10-phenanthroline), were synthesized under hydrothermal conditions. Copper atom in 1 is four-coordinated to one bidentate phen ligand and two monodentate partly deprotonated 4,4'-biphenyldicarboxylates. As expected, the structure of 1 is a monomeric species and affords an extended two-dimensional hydrogen bonding architecture. Each copper atom in 2 is five-coordinated to one phen, one water molecule, and two bis-monodentate fully deprotonated 4,4'-biphenyldicarboxylates. Therefore, the structure of 2 is a one-dimensional chain.

  13. Crystal structure of human cyclin-dependent kinase-2 complex with MK2 inhibitor TEI-I01800: insight into the selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Fujino, Aiko; Fukushima, Kei; Kubota, Takaharu; Kosugi, Tomomi; Takimoto-Kamimura, Midori, E-mail: m.kamimura@teijin.co.jp [Teijin Pharma Limited, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512 (Japan)

    2013-11-01

    The Gly-rich loop of cyclin-dependent kinase 2 (CDK2) bound to TEI-I01800 as an MK2 specific inhibitor forms a β-sheet which is a common structure in CDK2–ligand complexes. Here, the reason why TEI-I01800 does not become a strong inhibitor against CDK2 based on the conformation of TEI-I01800 is presented. Mitogen-activated protein kinase-activated protein kinase 2 (MK2 or MAPKAP-K2) is a Ser/Thr kinase from the p38 mitogen-activated protein kinase signalling pathway and plays an important role in inflammatory diseases. The crystal structure of the MK2–TEI-I01800 complex has been reported; its Gly-rich loop was found to form an α-helix, not a β-sheet as has been observed for other Ser/Thr kinases. TEI-I01800 is 177-fold selective against MK2 compared with CDK2; in order to understand the inhibitory mechanism of TEI-I01800, the cyclin-dependent kinase 2 (CDK2) complex structure with TEI-I01800 was determined at 2.0 Å resolution. Interestingly, the Gly-rich loop of CDK2 formed a β-sheet that was different from that of MK2. In MK2, TEI-I01800 changed the secondary structure of the Gly-rich loop from a β-sheet to an α-helix by collision between Leu70 and a p-ethoxyphenyl group at the 7-position and bound to MK2. However, for CDK2, TEI-I01800 bound to CDK2 without this structural change and lost the interaction with the substituent at the 7-position. In summary, the results of this study suggest that the reason for the selectivity of TEI-I01800 is the favourable conformation of TEI-I01800 itself, making it suitable for binding to the α-form MK2.

  14. Synthesis, crystal structure and photoluminescence study of green light emitting bis(1[(4-butylphenylimino]methyl naphthalen-2-ol Ni(II complex

    Directory of Open Access Journals (Sweden)

    M. Srinivas

    2016-09-01

    Full Text Available Synthetically feasible and cost effective Ni(II complex phosphor (4 as green organic light emitting diode (OLED was prepared by using Schiff base 1-[(4-butylphenylimino]methyl naphthalen-2-ol (3. The single crystals of Ni(II complex were grown from chloroform and hexane (1:1 v/v solution. The green crystals of the complex were characterized by using single crystal XRD studies and were evaluated for their photophysical properties. From the Diffused Reflectance Spectrum of the complex, the measured band gap energy was found to be 1.83 eV and the PL spectrum of the complex showed emission peak at 519 nm. The excitation peaks at 519 nm were appeared at 394 nm and 465 nm. The Commission Internationale De L'Eclairage (CIE chromaticity diagram indicated that, the complex exhibit green color. Hence, Ni(II complex (4 could be a promising green OLED for developing strong electroluminescent materials for flat panel display applications.

  15. Synthesis, X-ray single crystal structure, likelihood of occurrence of intermolecular contacts, spectroscopic investigation and DFT quantum chemical calculations of zwitterionic complex: 1-Ethylpiperaziniumtrichlorozincate (II)

    Science.gov (United States)

    Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.

    2017-10-01

    The synthesis and the X-ray structure of the Zn(II) zwitterionic complex:1-ethylpiperaziniumtrichlorozincate (II) are described. In the atomic arrangement, the ZnCl3N entities, grouped in pairs, are deployed along the b-axis to form layers. The organic entities are inserted between these layers through Nsbnd H⋯Cl and Csbnd H⋯Cl hydrogen bonds to form infinite three-dimensional network. The 3D Hirshfeld surfaces were investigated for intermolecular interactions. The optimized geometry, Mulliken charge distribution, molecular electrostatic potential (MEP) maps and thermodynamic properties have been calculated using the Lee-Yang-Parr correlation functional B3LYP with the LanL2DZ basis set. The HOMO and LUMO energy gap and chemical reactivity parameters were made. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray crystal structure. The vibrational absorption bands were identified by infrared spectroscopy. DFT calculations allowed the attribution of the NMR peaks and of the IR bands.

  16. Inhibition of DD-peptidases by a specific trifluoroketone: crystal structure of a complex with the Actinomadura R39 DD-peptidase.

    Science.gov (United States)

    Dzhekieva, Liudmila; Adediran, S A; Herman, Raphael; Kerff, Frédéric; Duez, Colette; Charlier, Paulette; Sauvage, Eric; Pratt, R F

    2013-03-26

    Inhibitors of bacterial DD-peptidases represent potential antibiotics. In the search for alternatives to β-lactams, we have investigated a series of compounds designed to generate transition state analogue structures upon reaction with DD-peptidases. The compounds contain a combination of a peptidoglycan-mimetic specificity handle and a warhead capable of delivering a tetrahedral anion to the enzyme active site. The latter includes a boronic acid, two alcohols, an aldehyde, and a trifluoroketone. The compounds were tested against two low-molecular mass class C DD-peptidases. As expected from previous observations, the boronic acid was a potent inhibitor, but rather unexpectedly from precedent, the trifluoroketone [D-α-aminopimelyl(1,1,1-trifluoro-3-amino)butan-2-one] was also very effective. Taking into account competing hydration, we found the trifluoroketone was the strongest inhibitor of the Actinomadura R39 DD-peptidase, with a subnanomolar (free ketone) inhibition constant. A crystal structure of the complex between the trifluoroketone and the R39 enzyme showed that a tetrahedral adduct had indeed formed with the active site serine nucleophile. The trifluoroketone moiety, therefore, should be considered along with boronic acids and phosphonates as a warhead that can be incorporated into new and effective DD-peptidase inhibitors and therefore, perhaps, antibiotics.

  17. Structure Formation of Ultrathin PEO Films at Solid Interfaces—Complex Pattern Formation by Dewetting and Crystallization

    Directory of Open Access Journals (Sweden)

    Hans-Georg Braun

    2013-02-01

    Full Text Available The direct contact of ultrathin polymer films with a solid substrate may result in thin film rupture caused by dewetting. With crystallisable polymers such as polyethyleneoxide (PEO, molecular self-assembly into partial ordered lamella structures is studied as an additional source of pattern formation. Morphological features in ultrathin PEO films (thickness < 10 nm result from an interplay between dewetting patterns and diffusion limited growth pattern of ordered lamella growing within the dewetting areas. Besides structure formation of hydrophilic PEO molecules, n-alkylterminated (hydrophobic PEO oligomers are investigated with respect to self-organization in ultrathin films. Morphological features characteristic for pure PEO are not changed by the presence of the n-alkylgroups.

  18. The crystal structure of protease Sapp1p from Candida parapsilosis in complex with the HIV protease inhibitor ritonavir

    Czech Academy of Sciences Publication Activity Database

    Dostál, Jiří; Brynda, Jiří; Hrušková-Heidingsfeldová, Olga; Pachl, Petr; Pichová, Iva; Řezáčová, Pavlína

    2012-01-01

    Roč. 27, č. 1 (2012), s. 160-165 ISSN 1475-6366 R&D Projects: GA MŠk(CZ) LC531; GA ČR GA310/09/1945; GA ČR GA203/09/0820 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50520514 Keywords : secreted aspartic protease * virulence factor * X-ray structure * candidiasis Subject RIV: CE - Biochemistry Impact factor: 1.495, year: 2012

  19. Predicting complex mineral structures using genetic algorithms.

    Science.gov (United States)

    Mohn, Chris E; Kob, Walter

    2015-10-28

    We show that symmetry-adapted genetic algorithms are capable of finding the ground state of a range of complex crystalline phases including layered- and incommensurate super-structures. This opens the way for the atomistic prediction of complex crystal structures of functional materials and mineral phases.

  20. Structure Formation of Ultrathin PEO Films at Solid Interfaces—Complex Pattern Formation by Dewetting and Crystallization

    Science.gov (United States)

    Braun, Hans-Georg; Meyer, Evelyn

    2013-01-01

    The direct contact of ultrathin polymer films with a solid substrate may result in thin film rupture caused by dewetting. With crystallisable polymers such as polyethyleneoxide (PEO), molecular self-assembly into partial ordered lamella structures is studied as an additional source of pattern formation. Morphological features in ultrathin PEO films (thickness PEO molecules, n-alkylterminated (hydrophobic) PEO oligomers are investigated with respect to self-organization in ultrathin films. Morphological features characteristic for pure PEO are not changed by the presence of the n-alkylgroups. PMID:23385233

  1. Crystal structures of human pyridoxal kinase in complex with the neurotoxins, ginkgotoxin and theophylline: insights into pyridoxal kinase inhibition.

    Science.gov (United States)

    Gandhi, Amit K; Desai, Jigar V; Ghatge, Mohini S; di Salvo, Martino L; Di Biase, Stefano; Danso-Danquah, Richmond; Musayev, Faik N; Contestabile, Roberto; Schirch, Verne; Safo, Martin K

    2012-01-01

    Several drugs and natural compounds are known to be highly neurotoxic, triggering epileptic convulsions or seizures, and causing headaches, agitations, as well as other neuronal symptoms. The neurotoxic effects of some of these compounds, including theophylline and ginkgotoxin, have been traced to their inhibitory activity against human pyridoxal kinase (hPL kinase), resulting in deficiency of the active cofactor form of vitamin B₆, pyridoxal 5'-phosphate (PLP). Pyridoxal (PL), an inactive form of vitamin B₆ is converted to PLP by PL kinase. PLP is the B₆ vitamer required as a cofactor for over 160 enzymatic activities essential in primary and secondary metabolism. We have performed structural and kinetic studies on hPL kinase with several potential inhibitors, including ginkgotoxin and theophylline. The structural studies show ginkgotoxin and theophylline bound at the substrate site, and are involved in similar protein interactions as the natural substrate, PL. Interestingly, the phosphorylated product of ginkgotoxin is also observed bound at the active site. This work provides insights into the molecular basis of hPL kinase inhibition and may provide a working hypothesis to quickly screen or identify neurotoxic drugs as potential hPL kinase inhibitors. Such adverse effects may be prevented by administration of an appropriate form of vitamin B₆, or provide clues of how to modify these drugs to help reduce their hPL kinase inhibitory effects.

  2. Crystal structures of human pyridoxal kinase in complex with the neurotoxins, ginkgotoxin and theophylline: insights into pyridoxal kinase inhibition.

    Directory of Open Access Journals (Sweden)

    Amit K Gandhi

    Full Text Available Several drugs and natural compounds are known to be highly neurotoxic, triggering epileptic convulsions or seizures, and causing headaches, agitations, as well as other neuronal symptoms. The neurotoxic effects of some of these compounds, including theophylline and ginkgotoxin, have been traced to their inhibitory activity against human pyridoxal kinase (hPL kinase, resulting in deficiency of the active cofactor form of vitamin B₆, pyridoxal 5'-phosphate (PLP. Pyridoxal (PL, an inactive form of vitamin B₆ is converted to PLP by PL kinase. PLP is the B₆ vitamer required as a cofactor for over 160 enzymatic activities essential in primary and secondary metabolism. We have performed structural and kinetic studies on hPL kinase with several potential inhibitors, including ginkgotoxin and theophylline. The structural studies show ginkgotoxin and theophylline bound at the substrate site, and are involved in similar protein interactions as the natural substrate, PL. Interestingly, the phosphorylated product of ginkgotoxin is also observed bound at the active site. This work provides insights into the molecular basis of hPL kinase inhibition and may provide a working hypothesis to quickly screen or identify neurotoxic drugs as potential hPL kinase inhibitors. Such adverse effects may be prevented by administration of an appropriate form of vitamin B₆, or provide clues of how to modify these drugs to help reduce their hPL kinase inhibitory effects.

  3. Crystal Structures of Human Pyridoxal Kinase in Complex with the Neurotoxins, Ginkgotoxin and Theophylline: Insights into Pyridoxal Kinase Inhibition

    Science.gov (United States)

    Ghatge, Mohini S.; di Salvo, Martino L.; Di Biase, Stefano; Danso-Danquah, Richmond; Musayev, Faik N.; Contestabile, Roberto; Schirch, Verne; Safo, Martin K.

    2012-01-01

    Several drugs and natural compounds are known to be highly neurotoxic, triggering epileptic convulsions or seizures, and causing headaches, agitations, as well as other neuronal symptoms. The neurotoxic effects of some of these compounds, including theophylline and ginkgotoxin, have been traced to their inhibitory activity against human pyridoxal kinase (hPL kinase), resulting in deficiency of the active cofactor form of vitamin B6, pyridoxal 5′-phosphate (PLP). Pyridoxal (PL), an inactive form of vitamin B6 is converted to PLP by PL kinase. PLP is the B6 vitamer required as a cofactor for over 160 enzymatic activities essential in primary and secondary metabolism. We have performed structural and kinetic studies on hPL kinase with several potential inhibitors, including ginkgotoxin and theophylline. The structural studies show ginkgotoxin and theophylline bound at the substrate site, and are involved in similar protein interactions as the natural substrate, PL. Interestingly, the phosphorylated product of ginkgotoxin is also observed bound at the active site. This work provides insights into the molecular basis of hPL kinase inhibition and may provide a working hypothesis to quickly screen or identify neurotoxic drugs as potential hPL kinase inhibitors. Such adverse effects may be prevented by administration of an appropriate form of vitamin B6, or provide clues of how to modify these drugs to help reduce their hPL kinase inhibitory effects. PMID:22879864

  4. Heteropentanuclear Oxalato-Bridged nd–4f (n=4, 5) Metal Complexes with NO Ligand: Synthesis, Crystal Structures, Aqueous Stability and Antiproliferative Activity

    KAUST Repository

    Kuhn, Paul-Steffen

    2015-08-10

    A series of heteropentanuclear oxalate-bridged Ru(NO)-Ln (4d–4f) metal complexes of the general formula (nBu4N)5[Ln{RuCl3(μ-ox)(NO)}4], where Ln=Y (2), Gd (3), Tb (4), Dy (5) and ox=oxalate anion, were obtained by treatment of (nBu4N)2[RuCl3(ox)(NO)] (1) with the respective lanthanide salt in 4:1 molar ratio. The compounds were characterized by elemental analysis, IR spectroscopy, electrospray ionization (ESI) mass spectrometry, while 1, 2, and 5 were in addition analyzed by X-ray crystallography, 1 by Ru K-edge XAS and 1 and 2 by 13C NMR spectroscopy. X-ray diffraction showed that in 2 and 5 four complex anions [RuCl3(ox)(NO)]2− are coordinated to YIII and DyIII, respectively, with formation of [Ln{RuCl3(μ-ox)(NO)}4]5− (Ln=Y, Dy). While YIII is eight-coordinate in 2, DyIII is nine-coordinate in 5, with an additional coordination of an EtOH molecule. The negative charge is counterbalanced by five nBu4N+ ions present in the crystal structure. The stability of complexes 2 and 5 in aqueous medium was monitored by UV/Vis spectroscopy. The antiproliferative activity of ruthenium-lanthanide complexes 2–5 were assayed in two human cancer cell lines (HeLa and A549) and in a noncancerous cell line (MRC-5) and compared with those obtained for the previously reported Os(NO)-Ln (5d–4f) analogues (nBu4N)5[Ln{OsCl3(ox)(NO)}4] (Ln=Y (6), Gd (7), Tb (8), Dy (9)). Complexes 2–5 were found to be slightly more active than 1 in inhibiting the proliferation of HeLa and A549 cells, and significantly more cytotoxic than 5d–4f metal complexes 6–9 in terms of IC50 values. The highest antiproliferative activity with IC50 values of 20.0 and 22.4 μM was found for 4 in HeLa and A549 cell lines, respectively. These cytotoxicity results are in accord with the presented ICP-MS data, indicating five- to eightfold greater accumulation of ruthenium versus osmium in human A549 cancer cells.

  5. In situ monitoring of structural changes during formation of 30S translation initiation complex by energy dissipation measurement using 27-MHz quartz-crystal microbalance.

    Science.gov (United States)

    Furusawa, Hiroyuki; Tsuyuki, Yumi; Takahashi, Shuntaro; Okahata, Yoshio

    2014-06-03

    Ribosome is a bionanomachine that facilitates an orderly translation process during protein synthesis in living cells. Real-time monitoring of conformational changes in ribosomal subunits in aqueous solution is important to understand the regulatory mechanism of protein synthesis, because conformational changes in ribosome in E. coli have been predicted to operate the switch from translation initiation to an elongation process during translation. We performed an energy dissipation measurement by using a quartz-crystal microbalance-admittance (QCM-A) technique for in situ monitoring of conformational changes in pre-30S translation initiation complex in response to the binding of fMet-tRNA(fMet) in aqueous solution. The addition of fMet-tRNA(fMet) caused changes in the physical property (increased dehydration and elasticity) in 30S ribosomal subunit in the presence of mRNA and IF2/guanosine 5'-triphosphate (GTP) on the QCM plate. Furthermore, two sequential changes triggered by the addition of fMet-tRNA(fMet) were observed in 30S ribosomal subunit bound to mRNA in the presence of IF2/GTP and IF3. These observations suggest that the structural changes in 30S ribosomal subunit caused by the binding of fMet-tRNA(fMet) with IF2/GTP in the presence of IF3 could act as a switch to regulate the orderly processing in the construction of translation initiation complex, because the structural distinction can be a guidepost in the process for the relevant biomolecules.

  6. The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function

    DEFF Research Database (Denmark)

    Rowland, Paul; Bjørnberg, Olof; Nielsen, Finn S.

    1998-01-01

    ) complexed with the product of the enzyme reaction orotate. The structure of the complex to 2.0 A resolution has been compared with the structure of the native enzyme. The active site of DHODA is known to contain a water filled cavity buried beneath a highly conserved and flexible loop. In the complex...

  7. Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly

    National Research Council Canada - National Science Library

    Marx, Ailie; Adir, Noam

    2013-01-01

    ... of complexity and detail. The linker-independent assembly of trimers into hexamers in crystal lattices of previously determined structures has been observed in almost all of the phycocyanin (PC...

  8. Crystal structures of yeast beta-alanine synthase complexes reveal the mode of substrate binding and large scale domain closure movements.

    Science.gov (United States)

    Lundgren, Stina; Andersen, Birgit; Piskur, Jure; Dobritzsch, Doreen

    2007-12-07

    Beta-alanine synthase is the final enzyme of the reductive pyrimidine catabolic pathway, which is responsible for the breakdown of uracil and thymine in higher organisms. The fold of the homodimeric enzyme from the yeast Saccharomyces kluyveri identifies it as a member of the AcyI/M20 family of metallopeptidases. Its subunit consists of a catalytic domain harboring a di-zinc center and a smaller dimerization domain. The present site-directed mutagenesis studies identify Glu(159) and Arg(322) as crucial for catalysis and His(262) and His(397) as functionally important but not essential. We determined the crystal structures of wild-type beta-alanine synthase in complex with the reaction product beta-alanine, and of the mutant E159A with the substrate N-carbamyl-beta-alanine, revealing the closed state of a dimeric AcyI/M20 metallopeptidase-like enzyme. Subunit closure is achieved by a approximately 30 degrees rigid body domain rotation, which completes the active site by integration of substrate binding residues that belong to the dimerization domain of the same or the partner subunit. Substrate binding is achieved via a salt bridge, a number of hydrogen bonds, and coordination to one of the zinc ions of the di-metal center.

  9. Crystal structure of SPSB2 in complex with a rational designed RGD-containing cyclic peptide inhibitor of SPSB2-iNOS interaction.

    Science.gov (United States)

    You, Tingting; Wang, Yuhui; Li, Kefa; Zhang, Danting; Wei, Huan; Luo, Yanhong; Li, Hua; Lu, Yongzhi; Su, Xunchen; Kuang, Zhihe

    2017-07-29

    SPRY domain-containing SOCS box protein 2 (SPSB2) is a negative regulator of inducible nitric oxide synthase (iNOS) that modulates the lifetime of iNOS and thus the levels of nitric oxide (NO) production. Inhibitors that can disrupt the endogenous SPSB2-iNOS interaction and augment NO production have potential as novel antimicrobial and anticancer drugs. In this study, we have designed a cyclic peptide (cR8), containing an RGD motif and the SPSB2 binding motif (DINNNV). ITC and chemical shift perturbation showed that cR8 binds to the iNOS binding site on SPSB2 with a Kd of 671 nM, and saturation transfer difference NMR showed that cR8 binds to αvβ3 integrin-expressing cells. Moreover, we determined the crystal structure of SPSB2 in complex with cR8, at a resolution of 1.34 Å. cR8 forms extensive hydrogen bonding with SPSB2 residues, but loss of an intramolecular hydrogen bond that is present in SPSB2-bound iNOS peptide may destabilize the bound conformation of cR8 and lead to a gentle reduction in SPSB2 binding affinity. These results serve as a useful basis for designing site-directed SPSB2 inhibitors in the future. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Synthesis, crystal structure, weak antiferromagnetic behavior and electronic studies of novel [((-)-sparteine)(PhCO 2)(Cl)]Cu(II) complex

    Science.gov (United States)

    Alcántara-Flores, José Luis; Vázquez-Bravo, José Jaime; Gutiérrez-Pérez, René; Ramírez-Rosales, Daniel; Bernès, Sylvain; Ramírez Bokhimi, José Guadalupe; Zamorano-Ulloa, Rafael; Reyes-Ortega, Yasmi

    2003-09-01

    [((-)-Sparteine)(PhCO 2)(Cl)]Cu(II) 1 complex is obtained by direct synthesis using copper(0). 1 crystallizes in the monoclinic space group P2 1 with a=14.7355(12), b=8.9768(5), c=17.2810(10) Å, β=111.916(5)°, and Z=4. The electronic spectrum of 1 shows a broad band with λ max˜841 nm(ɛ=0.261 mM-1 cm-6) characteristic of a low symmetry and tetragonally distorted square pyramidal local Cu geometry. The far IR spectrum of 1 shows characteristic vibrations of Cu-Cl (260, 267 cm -1), Cu-N (436, 467 cm -1) and Cu-O (457 cm -1) bonds. The 1H NMR spectrum of 1 is typical of magnetic Cu(II) complexes with line broadening due to efficient nuclear relaxation from the metal center. ESR spectra of polycrystalline 1 at 77 K show an axial spectrum with linewidth of 58.6 G and at 300 K of 89.0 G, with areas in the ratio A77/ A300=2.79, indicative of antiferromagnetic order. The linewidth is reduced by 34% on going from 300 to 77 K. Standard magnetization measurements at low temperatures show an Curie-Weiss behavior with θ=-21.67 K, suggesting a weak exchange coupling interaction. The crystalline structure of 1 shows that the lattice is arranged so that the space between molecules is smaller than 40 Å 3, not enough to accommodate solvent molecules. However, the shortest Cu-Cu contact is 7.5912(8) Å.

  11. The Solitary Isomer of C60 H18 Is Proven to Have a C3v Crown Shape: Crystal Structure Determination and Synthesis of Its Triruthenium Cluster Complex.

    Science.gov (United States)

    Chen, Chi-Shian; Chuang, Tsung-Han; Liu, Yi-Hung; Yeh, Wen-Yann

    2015-11-23

    Analytically pure C60 H18 is obtained by a Ru3 cluster complexation and decomplexation method. The crystal structure of C60 H18 consists of one flattened hemisphere, to which all 18 hydrogen atoms are symmetrically bonded, and one curved hemisphere akin to C60 . A benzenoid ring in the flattened hemisphere is isolated from the residual π systems by a belt composed of sp(3) -hybridized CH units. The average out-of-plane distances for carbon atoms attached to the benzenoid ring (0.14 Å) is substantially larger than that found in C60 F18 (0.06 Å). Several long C(sp(3) )C(sp(3) ) single bond lengths [1.61(3)-1.65(3) Å] are observed for C60 H18 . The reaction of [Ru3 (CO)12 ] and C60 H18 produces [Ru3 (CO)9 (μ3 -η(2) ,η(2) ,η(2) -C60 H18 )] (1), where the Ru3 triangle is regiospecifically linked to the hexagon opposite to the benzenoid ring. Compound 1 is the first transition metal complex of a polyhydrofullerene (fullerane). C60 H18 and 1 have been characterized by (1) H and (13) C NMR, UV/Vis, and mass spectroscopies. The HOMO-LUMO gap of C60 H18 is evaluated to be 1.51 V by cyclic voltammetry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Crystal structure of rat heme oxygenase-1 in complex with biliverdin-iron chelate. Conformational change of the distal helix during the heme cleavage reaction.

    Science.gov (United States)

    Sugishima, Masakazu; Sakamoto, Hiroshi; Higashimoto, Yuichiro; Noguchi, Masato; Fukuyama, Keiichi

    2003-08-22

    The crystal structure of rat heme oxygenase-1 in complex with biliverdin-iron chelate (biliverdin(Fe)-HO-1), the immediate precursor of the final product, biliverdin, has been determined at a 2.4-A resolution. The electron density in the heme pocket clearly showed that the tetrapyrrole ring of heme is cleaved at the alpha-meso edge. Like the heme bound to HO-1, biliverdin-iron chelate is located between the distal and proximal helices, but its accommodation state seems to be less stable in light of the disordering of the solvent-exposed propionate and vinyl groups. The middle of the distal helix is shifted away from the center of the active site in biliverdin(Fe)-HO-1, increasing the size of the heme pocket. The hydrogen-bonding interaction between Glu-29 and Gln-38, considered to restrain the orientation of the proximal helix in the heme-HO-1 complex, was lost in biliverdin(Fe)-HO-1, leading to relaxation of the helix. Biliverdin has a distorted helical conformation; the lactam oxygen atom of its pyrrole ring-A interacted with Asp-140 through a hydrogen-bonding solvent network. Because of the absence of a distal water ligand, the iron atom is five-coordinated with His-25 and four pyrrole nitrogen atoms. The coordination geometry deviates considerably from a square pyramid, suggesting that the iron may be readily dissociated. We speculate that the opened conformation of the heme pocket facilitates sequential product release, first iron then biliverdin, and that because of biliverdin's increased flexibility, iron release triggers its slow dissociation.

  13. Decomposition of Intermolecular Interactions in the Crystal Structure of Some Diacetyl Platinum(II Complexes: Combined Hirshfeld, AIM, and NBO Analyses

    Directory of Open Access Journals (Sweden)

    Saied M. Soliman

    2016-12-01

    Full Text Available Intermolecular interactions play a vital role in crystal structures. Therefore, we conducted a topological study, using Hirshfeld surfaces and atom in molecules (AIM analysis, to decompose and analyze, respectively, the different intermolecular interactions in six hydrazone-diacetyl platinum(II complexes. Using AIM and natural bond orbital (NBO analyses, we determined the type, nature, and strength of the interactions. All the studied complexes contain C-H⋯O interactions, and the presence of bond critical points along the intermolecular paths underlines their significance. The electron densities (ρ(r at the bond critical points (0.0031–0.0156 e/a03 fall within the typical range for H-bonding interactions. Also, the positive values of the Laplacian of the electron density (∇2ρ(r revealed the depletion of electronic charge on the interatomic path, another characteristic feature of closed-shell interactions. The ratios of the absolute potential energy density to the kinetic energy density (|V(r|/G(r and ρ(r are highest for the O2⋯H15-N3 interaction in [Pt(COMe2(2-pyCMe=NNH2] (1; hence, this interaction has the highest covalent character of all the O⋯H intermolecular interactions. Interestingly, in [Pt(COMe2(H2NN=CMe-CMe=NNH2] (3, there are significant N-H⋯Pt interactions. Using the NBO method, the second-order interaction energies, E(2, of these interactions range from 3.894 to 4.061 kJ/mol. Furthermore, the hybrid Pt orbitals involved in these interactions are comprised of dxy, dxz, and s atomic orbitals.

  14. Crystal structure of a mixed-ligand dinuclear Ba-Zn complex with 2-meth-oxy-ethanol having tri-phenyl-acetate and chloride bridges.

    Science.gov (United States)

    Utko, Józef; Sobocińska, Maria; Dobrzyńska, Danuta; Lis, Tadeusz

    2015-07-01

    The dinuclear barium-zinc complex, μ-chlorido-1:2κ(2) Cl:Cl-chlorido-2κCl-bis-(2-meth-oxy-ethanol-1κO)bis-(2-meth-oxy-ethanol-1κ(2) O,O')bis-(μ-tri-phenyl-acetato-1:2κ(2) O:O')bariumzinc, [BaZn(C20H15O2)2Cl2(C3H8O2)4], has been synthesized by the reaction of barium tri-phenyl-acetate, anhydrous zinc chloride and 2-meth-oxy-ethanol in the presence of toluene. The barium and zinc metal cations in the dinuclear complex are linked via one chloride anion and carboxyl-ate O atoms of the tri-phenyl-acetate ligands, giving a Ba⋯Zn separation of 3.9335 (11) Å. The irregular nine-coordinate BaO8Cl coordination centres comprise eight O-atom donors, six of them from 2-meth-oxy-ethanol ligands (four from two bidentate O,O'-chelate inter-actions and two from monodentate inter-actions), two from bridging tri-phenyl-acetate ligands and one from a bridging Cl donor. The distorted tetra-hedral coordination sphere of zinc comprises two O-atom donors from the tri-phenyl-acetate ligands and two Cl donors (one bridging and one terminal). In the crystal, O-H⋯Cl, O-H⋯O and C-H⋯Cl inter-molecular inter-actions form a layered structure, lying parallel to (001).

  15. Nuclear structures: Twinning and modulation in crystals

    Science.gov (United States)

    Petříček, Václav; Dušek, Michal

    2017-10-01

    Crystal structure analysis is a standard technique routinely applied to single crystals as well as powders. However the process is not so straightforward if the crystal sample is affected by twinning or if the structure is modulated. In such cases the standard procedures are not directly applicable. The main purpose of this contribution is to show how to solve and refine such difficult structures. While for twinned structures the basic property of crystal - translation symmetry in three dimensional space-remains valid, for modulated crystals a special superspace theory must be exploited in order to describe the atomic structure with crystallographic methods generalized for superspace.

  16. Synthesis, characterization and crystal structures of two pentagonal-bipyramidal Fe(III) complexes with dihydrazone of 2,6-diacetylpyridine and Girard's T reagent. Anticancer properties of various metal complexes of the same ligand.

    Science.gov (United States)

    Anđelković, Katarina; Milenković, Milica R; Pevec, Andrej; Turel, Iztok; Matić, Ivana Z; Vujčić, Miroslava; Sladić, Dušan; Radanović, Dušanka; Brađan, Gabrijela; Belošević, Svetlana; Čobeljić, Božidar

    2017-09-01

    In this work synthesis, characterization and crystal structures of two isothiocyanato Fe(III) complexes with 2,2'-[2,6-pyridinediylbis(ethylidyne-1-hydrazinyl-2-ylidene)]bis[N,N,N-trimethyl-2-oxoethanaminium] dichloride (H2LCl2) ligand, with composition [FeL(NCS)2]SCN·2H2O and [FeL(NCS)2]2[Fe(H2O)(NCS)5]·4H2O, has been reported. Both iron(III) complexes possess the same pentagonal-bipyramidal complex cation, while the nature of their anions depends on mole ratio of NH4SCN and FeCl3·6H2O used in reaction. Cytotoxic activity of new Fe(III) complexes, as well as of previously synthesized isothiocyanato Co(II), Ni(II), Mn(II), Zn(II) and Cd(II) complexes with the same ligand, was tested against five human cancer cell lines (HeLa, MDA-MB-453, K562, LS174 and A549) and normal cell line MRC-5. The best activity was observed in the case of Fe(III), Co(II) and Cd(II) complexes. The investigation of potential of these complexes to induce HeLa and K562 cell cycle perturbations was also evaluated. Mechanism of cell death mode was elucidated on the basis of morphological changes of HeLa cells as well as identification of target caspases. It was established that DNA damage could be responsible for the activity of Fe(III) and Co(II) complexes. Pentagonal-bipyramidal Fe(III) complexes with dihydrazone of 2,6-diacetylpyridine and Girard's T reagent have been synthesized and characterized. Cytotoxic activity of Fe(III) complexes and Co(II), Ni(II), Mn(II), Zn(II) and Cd(II) complexes with the same ligand was tested. The best activity was observed in the case of Fe(III), Co(II) and Cd(II) complexes. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Novel CoIII complexes containing fluorescent coumarin-N-acylhydrazone hybrid ligands: Synthesis, crystal structures, solution studies and DFT calculations

    Science.gov (United States)

    Areas, Esther S.; Bronsato, Bruna Juliana da S.; Pereira, Thiago M.; Guedes, Guilherme P.; Miranda, Fábio da S.; Kümmerle, Arthur E.; da Cruz, Antônio G. B.; Neves, Amanda P.

    2017-12-01

    A series of new CoIII complexes of the type [Co(dien)(L1 -L3)]ClO4 (1-3), containing fluorescent coumarin-N-acylhydrazonate hybrid ligands, (E)-N‧-(1-(7-oxido-2-oxo-2H-chromen-3-yl)ethylidene)-4-R-benzohydrazonate [where R = H (L12 -), OCH3 (L22 -) or Cl (L32 -)], were obtained and isolated in the low spin CoIII configuration. Single-crystal X-ray diffraction showed that the coumarin-N-acylhydrazones act as tridentate ligands in their deprotonated form (L2 -). The cation (+ 1) complexes contain a diethylenetriamine (dien) as auxiliary ligand and their structures were calculated by DFT studies which were also performed for the CoII (S = 1/2 and S = 3/2) configurations. The LS CoII (S = 1/2) concentrated the spin density on the O-Co-O axis while the HS CoII (S = 3/2) exhibited a broad spin density distribution around the metallic center. Cyclic voltammetry studies showed that structural modifications made in the L2 - ligands caused a slight influence on the electronic density of the metal center, and the E1/2 values for the CoIII/CoII redox couple increased following the electronic effect of the R-substituent, in the order: 2 (R = OCH3) < 1 (R = H) < 3 (R = Cl). The theoretical redox potentials (E°) of the process CoIII → CoII were calculated for both CoII spin states (S = 1/2 and S = 3/2) and a better correlation was found for CoIII → CoII (S = 1/2), compared with experimental values vs SHE (E°calc = - 0.37, - 0.36 and - 0.32 V vs E°exp. = - 0.371, - 0.406 and - 0.358 V, for 1-3 respectively). Complexes 1-3 exhibited a very intense absorption band around 470 nm, assigned by DFT calculations as π-π* transitions from the delocalized coumarin-N-acylhydrazone system. 1-3 were very stable in MeOH for several days. Likewise, 1-3 were stable in phosphate buffer containing sodium ascorbate after 15 h, which was attributed to the high chelate effect and σ-donor ability of the L2 - and dien ligands.

  18. The Crystal Structure of Cytochrome P450 4B1 (CYP4B1) Monooxygenase Complexed with Octane Discloses Several Structural Adaptations for ω-Hydroxylation*♦

    Science.gov (United States)

    Hsu, Mei-Hui; Baer, Brian R.; Rettie, Allan E.

    2017-01-01

    P450 family 4 fatty acid ω-hydroxylases preferentially oxygenate primary C–H bonds over adjacent, energetically favored secondary C–H bonds, but the mechanism explaining this intriguing preference is unclear. To this end, the structure of rabbit P450 4B1 complexed with its substrate octane was determined by X-ray crystallography to define features of the active site that contribute to a preference for ω-hydroxylation. The structure indicated that octane is bound in a narrow active-site cavity that limits access of the secondary C–H bond to the reactive intermediate. A highly conserved sequence motif on helix I contributes to positioning the terminal carbon of octane for ω-hydroxylation. Glu-310 of this motif auto-catalytically forms an ester bond with the heme 5-methyl, and the immobilized Glu-310 contributes to substrate positioning. The preference for ω-hydroxylation was decreased in an E310A mutant having a shorter side chain, but the overall rates of metabolism were retained. E310D and E310Q substitutions having longer side chains exhibit lower overall rates, likely due to higher conformational entropy for these residues, but they retained high preferences for octane ω-hydroxylation. Sequence comparisons indicated that active-site residues constraining octane for ω-hydroxylation are conserved in family 4 P450s. Moreover, the heme 7-propionate is positioned in the active site and provides additional restraints on substrate binding. In conclusion, P450 4B1 exhibits structural adaptations for ω-hydroxylation that include changes in the conformation of the heme and changes in a highly conserved helix I motif that is associated with selective oxygenation of unactivated primary C–H bonds. PMID:28167536

  19. The Crystal Structure of Cytochrome P450 4B1 (CYP4B1) Monooxygenase Complexed with Octane Discloses Several Structural Adaptations for ω-Hydroxylation.

    Science.gov (United States)

    Hsu, Mei-Hui; Baer, Brian R; Rettie, Allan E; Johnson, Eric F

    2017-03-31

    P450 family 4 fatty acid ω-hydroxylases preferentially oxygenate primary C-H bonds over adjacent, energetically favored secondary C-H bonds, but the mechanism explaining this intriguing preference is unclear. To this end, the structure of rabbit P450 4B1 complexed with its substrate octane was determined by X-ray crystallography to define features of the active site that contribute to a preference for ω-hydroxylation. The structure indicated that octane is bound in a narrow active-site cavity that limits access of the secondary C-H bond to the reactive intermediate. A highly conserved sequence motif on helix I contributes to positioning the terminal carbon of octane for ω-hydroxylation. Glu-310 of this motif auto-catalytically forms an ester bond with the heme 5-methyl, and the immobilized Glu-310 contributes to substrate positioning. The preference for ω-hydroxylation was decreased in an E310A mutant having a shorter side chain, but the overall rates of metabolism were retained. E310D and E310Q substitutions having longer side chains exhibit lower overall rates, likely due to higher conformational entropy for these residues, but they retained high preferences for octane ω-hydroxylation. Sequence comparisons indicated that active-site residues constraining octane for ω-hydroxylation are conserved in family 4 P450s. Moreover, the heme 7-propionate is positioned in the active site and provides additional restraints on substrate binding. In conclusion, P450 4B1 exhibits structural adaptations for ω-hydroxylation that include changes in the conformation of the heme and changes in a highly conserved helix I motif that is associated with selective oxygenation of unactivated primary C-H bonds. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP- trapped ternary complex of Klentaq1: Insights into nucleotide incorporation and selectivity

    OpenAIRE

    Li,Ying; Waksman, Gabriel

    2001-01-01

    The mechanism by which DNA polymerase I enzymes function has been the subject of extensive biochemical and structural studies. We previously determined the structure of a ternary complex of the large fragment of DNA polymerase I from Thermus aquaticus (Klentaq1) bound to a primer/template DNA and a dideoxycytidine 5′-triphosphate (ddCTP). In this report, we present the details of the 2.3-Å resolution crystal structures of three additional ternary complexes of Klentaq1 bound to a primer/templa...

  1. imide, crystal structure, thermal and dielectric studies

    Indian Academy of Sciences (India)

    IR and Raman spectroscopies and its crystal structure is confirmed by single crystal X-ray diffraction method. The X-ray studies on ... Di-cationic ionic liquids; crystal structure; dielectric; thermal properties. 1. Introduction. The chemistry of ionic ... exposed in various emerging areas as solvents of high tem- perature organic ...

  2. Synthesis, characterization and crystal structure of new nickel ...

    Indian Academy of Sciences (India)

    Abstract. A novel nickel molybdenum complex with the 2,6-pyridine dicarboxylic acid ligand was successfully synthesized and characterized by thermogravimetric analysis and single crystal X-ray crystallography. The single-crystal X-ray data revealed that the structure is a hydrated 1-D polymer with two different Ni sites.

  3. Synthesis and Crystal Structure of a Five-Coordinate Complex of Copper(II) with 4-Nitrobenzenesulfonate and 2, 2'-Bipyridine.

    Science.gov (United States)

    Sharif, Mahboubeh A; Tabatabaee, Masoumeh; Beik, Vahideh; Khavasi, Hamid Reza

    2012-06-01

    [Cu(bipy)2Cl](nbs) (1) (bipy = 2,2'-bipyridine, nbs = 4-nitrobenzenesulfonate) was obtained from the reaction of 4-nitrobenzenesulfonyl chloride and 2-amine-4-methylopyridine with CuCl2 in the presence of 2,2'-bipyridine and characterized by elemental analysis, IR spectra and X-ray single-crystal diffraction. The asymmetric unit of (1) contains the cationic complex [Cu(bipy)2Cl]+ and, in the outer coordination sphere, an (nbs)- counter ion.

  4. Crystal structure of 3-(diethylaminophenol

    Directory of Open Access Journals (Sweden)

    James A. Golen

    2015-12-01

    Full Text Available The title compound, C10H15NO, has two molecules in the asymmetric unit. Each molecule has a near-planar C8NO unit excluding H atoms and the terminal methyl groups on the diethylamino groups, with mean deviations from planarity of 0.036 and 0.063 Å. In the crystal, hydrogen bonding leads to four-membered O—H...O—H...O—H·· rings. No π–π interactions were observed in the structure.

  5. Crystal Structure, Fluorescence Property and Theoretical Calculation of the Zn(II) Complex with o-Aminobenzoic Acid and 1,10-Phenanthroline

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhongyu; Bi, Caifeng; Fan, Yuhua; Zhang, Xia; Zhang, Nan; Yan, Xingchen; Zuo, Jian [Ocean Univ. of China, Qingdao (China)

    2014-06-15

    A novel complex [Zn(phen)(o-AB){sub 2}] [phen: 1,10-phenanthroline o-AB: o-aminobenzoic acid] was synthesized and characterized by elemental analysis and X-ray diffraction single-crystal analysis. The crystal crystallizes in monoclinic, space group P2(1)/c with a = 7.6397(6) A, b = 16.8761(18) A, c = 17.7713(19) A, α = 90 .deg., β = 98.9570(10) .deg., γ = 90 .deg., V = 2.2633(4) nm{sup 3}, Z = 4, F(000) = 1064, S = 1.058, Dc = 1.520 g·cm{sup -3}, R{sub 1} = 0.0412, wR{sub 2} = 0.0948, μ = 1.128 mm{sup -1}. The Zn(II) is six coordinated by two nitrogen and four oxygen atoms from the 1,10-phenanthroline and o-aminobenzoic acid to furnish a distorted octahedron geometry. The complex exhibits intense fluorescence at room temperature. Theoretical studies of the title complex were carried out by density functional theory (DFT) B3LYP method. CCDC: 898291.

  6. Synthesis, crystal structure, theoretical study and luminescence ...

    Indian Academy of Sciences (India)

    phenanthroline) has been synthesized and characterized by elemental analysis, infrared spectroscopy, ultraviolet-visible spectroscopy, X-ray single crystal analysis and fluorescent analysis. Its crystal structure is monoclinic with space group 2/ and ...

  7. Synthesis, spectral, thermal, crystal structure, Hirschfeld analysis of [bis(triamine)Cadimium(II)][Cadimum(IV)tetra-bromide] complexes and their thermolysis to CdO nanoparticles

    National Research Council Canada - National Science Library

    Warad, Ismail; Al-Rimawi, Fuad; Barakat, Assem; Affouneh, Saida; Shivalingegowda, Naveen; Lokanath, Neartur Krishnappagowda; Abu-Reidah, Ibrahim M

    2016-01-01

    ...) complexes in dicationic form with general formula [Cd(dien)2]CdBr4 complex 1 (dien = diethylenetriamine) and [Cd(dipn)2]CdBr4 complex 2 (dipn = diproylenetriamine) were prepared and elucidated there chemical structures by elemental analysis, UV...

  8. Synthesis, crystal structure, and anti-breast cancer activity of a novel metal-porphyrinic complex [YK(TCPP(OH2·(solventsx

    Directory of Open Access Journals (Sweden)

    J-C. Liu

    2017-11-01

    Full Text Available A novel heterometallic metal-porphyrinic framework (MPFs built from Y and K ions as nods and meso-tetra(4-carboxyphenylporphyrin as linkers has been successfully synthesized and characterized. The single crystal X-ray diffraction indicated that this complex 1 exhibited a bilayered architecture of the porphyrins, which is seldom seen in MPFs. In addition, in vitro anticancer activity of complex 1 on three human breast cancer cells (BT474, SKBr-3 and ZR-75-30 was further determined.

  9. synthesis, crystal structure and antimicrobial activity of a hetero ...

    African Journals Online (AJOL)

    B. S. Chandravanshi

    cyanide N atom. The effects of the complex on the antimicrobial activity against Staphylococcus aureus,. Escherichia coli, and Candida albicans were studied. KEY WORDS: Schiff base, Manganese(III) complex, Iron(II) complex, Heteronuclear, Crystal structure. INTRODUCTION. Schiff bases are a kind of important ligands ...

  10. Synthesis, characterization, crystal structure determination and computational study of a new Cu(II) complex of bis [2-{(E)-[2-chloroethyl)imino]methyl}phenolato)] copper(II) Schiff base complex

    Science.gov (United States)

    Grivani, Gholamhossein; Vakili, Mohammad; Khalaji, Aliakbar Dehno; Bruno, Giuseppe; Rudbari, Hadi Amiri; Taghavi, Maedeh

    2016-07-01

    The copper (II) Schiff base complex of [CuL2] (1), HL = 2-{(E)-[2-chloroethyl) imino]methyl}phenol, has been synthesized and characterized by elemental (CHN) analysis, UV-Vis and FT-IR spectroscopy. The molecular structure of 1 was determined by single crystal X-ray diffraction technique. The conformational analysis and molecular structures of CuL2 were investigated by means of density functional theory (DFT) calculations at B3LYP/6-311G* level. An excellent agreement was observed between theoretical and experimental results. The Schiff base ligand of HL acts as a chelating ligand and coordinates via one nitrogen atom and one oxygen atom to the metal center. The copper (II) center is coordinated by two nitrogen atoms and two oxygen atoms from two Schiff base ligands in an approximately square planar trans-[MN2O2] coordination geometry. Thermogravimetric analysis of CuL2 showed that it was decomposed in five stages. In addition, the CuL2 complex thermally decomposed in air at 660 °C and the XRD pattern of the obtained solid showed the formation of CuO nanoparticles with an average size of 34 nm.

  11. Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit D4 in complex with the A20 N-terminal domain.

    Directory of Open Access Journals (Sweden)

    Céline Contesto-Richefeu

    2014-03-01

    Full Text Available Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase E9, the uracil-DNA glycosylase D4 and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase co-factor whose function is essential for processive DNA synthesis. Genetic and biochemical data have established that residues located in the N-terminus of A20 are critical for binding to D4. However, no information regarding the residues of D4 involved in A20 binding is yet available. We expressed and purified the complex formed by D4 and the first 50 amino acids of A20 (D4/A20₁₋₅₀. We showed that whereas D4 forms homodimers in solution when expressed alone, D4/A20₁₋₅₀ clearly behaves as a heterodimer. The crystal structure of D4/A20₁₋₅₀ solved at 1.85 Å resolution reveals that the D4/A20 interface (including residues 167 to 180 and 191 to 206 of D4 partially overlaps the previously described D4/D4 dimer interface. A20₁₋₅₀ binding to D4 is mediated by an α-helical domain with important leucine residues located at the very N-terminal end of A20 and a second stretch of residues containing Trp43 involved in stacking interactions with Arg167 and Pro173 of D4. Point mutations of the latter residues disturb D4/A20₁₋₅₀ formation and reduce significantly thermal stability of the complex. Interestingly, small molecule docking with anti-poxvirus inhibitors selected to interfere with D4/A20 binding could reproduce several key features of the D4/A20₁₋₅₀ interaction. Finally, we propose a model of D4/A20₁₋₅₀ in complex with DNA and discuss a number of mutants described in the literature, which affect DNA synthesis. Overall, our data give new insights into the assembly of the poxvirus DNA polymerase cofactor and may be useful for the design and rational improvement of antivirals targeting the D4/A20 interface.

  12. Crystal structures and thermal behaviour of double complex compounds incorporating the [Cr{CO(NH2)2}6]3+ cation

    Science.gov (United States)

    Pechenyuk, S. I.; Zolotarev, A. A.; Gosteva, A. N.; Domonov, D. P.; Shimkin, A. A.

    2017-11-01

    Double complex compounds (DCC) of the [Cr(ur)6][Fe(CN)6]·4H2O (I), [Cr(ur)6][Co(CN)6]·4H2O (II), [Cr(ur)6][Fe(Ox)3]·2H2O (III), and [Cr(ur)6][Co(Ox)3].3.5H2O (IV) composition, where ur is CO(NH2)2, Ох - С2О42- have been synthesized and their crystal structures have been studied. The DCC I, II and IV are triclinic (Р-1); III is orthorhombic (С2221). The DCC thermal behavior in air and argon atmospheres was analyzed by the following parameters: the temperature interval of total decomposition and the nature of gaseous and solid products. The end solid products in air were FeO and FeCr2O4 for I, a mixture of СоCr2O4 + Со2CrO4 for II and IV and an X-ray amorphous phase with composition CrFeO2.5 for III. The gaseous products were HCN, NH3, HNCO, N2O, СО, СО2, N2, and urea. The temperatures of total decomposition in air were: I, II 400°С, III - 350°С, IV - 460°С. In argon, the solid residue contained, besides the oxides, 7-30% of carbon up to 1000°С.

  13. Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation

    KAUST Repository

    Kim, Jeong Joo

    2016-04-09

    Cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG) is a key regulator of smooth muscle and vascular tone and represents an important drug target for treating hypertensive diseases and erectile dysfunction. Despite its importance, its activation mechanism is not fully understood. To understand the activation mechanism, we determined a 2.5 Å crystal structure of the PKG I regulatory (R) domain bound with cGMP, which represents the activated state. Although we used a monomeric domain for crystallization, the structure reveals that two R domains form a symmetric dimer where the cGMP bound at high-affinity pockets provide critical dimeric contacts. Small-angle X-ray scattering and mutagenesis support this dimer model, suggesting that the dimer interface modulates kinase activation. Finally, structural comparison with the homologous cyclic AMP-dependent protein kinase reveals that PKG is drastically different from protein kinase A in its active conformation, suggesting a novel activation mechanism for PKG. Kim et al. obtain the first crystal structure of the PKG I R domain bound with cGMP representing its activated state. It reveals a symmetric R dimer where cGMP molecules provide dimeric contacts. This R-R interaction prevents the high-affinity inhibitory interaction between R-C domain and sustains activation. © 2016 Elsevier Ltd.

  14. Synthesis and crystal structures of novel copper(II) complexes with glycine and substituted phenanthrolines: reactivity towards DNA/BSA and in vitro cytotoxic and antimicrobial evaluation.

    Science.gov (United States)

    İnci, Duygu; Aydın, Rahmiye; Vatan, Özgür; Sevgi, Tuba; Yılmaz, Dilek; Zorlu, Yunus; Yerli, Yusuf; Çoşut, Bünyemin; Demirkan, Elif; Çinkılıç, Nilüfer

    2017-01-01

    New copper(II) complexes-dimeric-[Cu(nphen)(gly)(H 2 O)] + (1) and [Cu(dmphen)(gly)(NO 3 )(H 2 O)] (2) (nphen = 5-nitro-1,10-phenanthroline, dmphen = 4,7-dimethyl-1,10-phenanthroline, and gly = glycine)-have been synthesized and characterized by CHN analysis, single-crystal X-ray diffraction techniques, FTIR, EPR spectroscopy, and cyclic voltammetry. The CT-DNA-binding properties of these complexes have been investigated by thermal denaturation measurements and both absorption and emission spectroscopy. The DNA cleavage activity of these complexes has been studied on supercoiled pUC19 plasmid DNA by gel electrophoresis experiments in the absence and presence of H 2 O 2 . Furthermore, the interaction of these complexes with bovine serum albumin (BSA) has been investigated using absorption and emission spectroscopy. The thermodynamic parameters, free-energy change (ΔG), enthalpy change (ΔH), and entropy change (ΔS) for BSA + complexes 1 and 2 systems have been calculated by the van't Hoff equation at three different temperatures (293.2, 303.2, and 310.2 K). The distance between the BSA and these complexes has been determined using fluorescence resonance energy transfer (FRET). Conformational changes of BSA have been observed using the synchronous fluorescence technique. In addition, in vitro cytotoxicities of these complexes on tumor cell lines (Caco-2, A549, and MCF-7) and healthy cells (BEAS-2B) have been examined. The antimicrobial activity of the complexes has also been tested on certain bacteria cells. The effect of mono and dimeric in the above complexes is presented and discussed. New copper(II) complexes-dimeric-[Cu(nphen)(gly)(H 2 O)] + (1) and [Cu(dmphen)(gly) (NO 3 )(H 2 O)] (2) (nphen = 5-nitro-1,10-phenanthroline, dmphen = 4,7-dimethyl-1,10-phenanthroline and gly = glycine)-have been synthesized and characterized by CHN analysis, single-crystal X-ray diffraction techniques, FTIR and EPR spectroscopy. They have been tested for their in vitro

  15. Crystal structure of Staphylococcus aureus Cas9

    OpenAIRE

    Nishimasu, Hiroshi; Cong, Le; Yan, Winston X.; Ran, F. Ann; Zetsche, Bernd; Li, Yinqing; Kurabayashi, Arisa; Ishitani, Ryuichiro; Zhang, Feng; Nureki, Osamu

    2015-01-01

    The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. Recently, we harnessed Staphylococcus aureus Cas9 (SaCas9), which is significantly smaller than Streptococcus pyogenes Cas9 (SpCas9), to facilitate efficient in vivo genome editing. Here, we report the crystal structures of SaCas9 in complex with a single guide RNA (sgRNA) and its double-stranded DNA targets, containing the 5′-TTGAAT-3′ PAM and...

  16. Crystal Structure of Human Nicotinamide Riboside Kinase

    Energy Technology Data Exchange (ETDEWEB)

    Khan,J.; Xiang, S.; Tong, L.

    2007-01-01

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD{sup +} as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 {angstrom} resolution and in a ternary complex with ADP and tiazofurin at 2.7 {angstrom} resolution. The active site is located in a groove between the central parallel {beta} sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations.

  17. Crystal structure of human nicotinamide riboside kinase.

    Science.gov (United States)

    Khan, Javed A; Xiang, Song; Tong, Liang

    2007-08-01

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD(+) as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 A resolution and in a ternary complex with ADP and tiazofurin at 2.7 A resolution. The active site is located in a groove between the central parallel beta sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations.

  18. SYNTHESIS, CRYSTAL STRUCTURE AND LUMINESCENT PROPERTY OF A DINUCLEAR Tb(II COMPLEX WITH HOMOPHTHALIC ACID AND 2,2’-BIPYRIDYL

    Directory of Open Access Journals (Sweden)

    LI-HUA WANG

    2015-07-01

    Full Text Available A novel dinuclear Tb(III complex, [Tb(bpy2L2] (bpy = 2,2’-bipyridine, H2L = homophthalic acid, has been synthesized and characterized by elemental analysis and single-crystal X-ray diffraction. The Tb(III complex is monoclinic, space group P21/c with a = 9.368(2 Å, b = 15.948(4 Å, c = 12.216(3 Å, β = 103.023(4º, V= 1778.2(7 Å3, Z = 2, Dc = 1.910 mg·m-3, μ = 4.011 mm-1, F(000 = 996, and final R1 = 0.0602, ωR2 = 0.2192. The result shows that the Tb(III center is seven-coordination with a N2O5 distorted pengonal bipyramidal geometry. The luminescent property of Tb(III complex was investigated.

  19. short communication synthesis and crystal structure of a polymeric ...

    African Journals Online (AJOL)

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    of zinc sulfate, 4-nitrophenylacetic acid, and propane-1,3-diamine (PDA) in water. Structure of the complex has been characterized by single-crystal X-ray diffraction. The complex crystallizes as orthorhombic space group Pnma, with unit cell dimensions a = 15.732(1) Å, b = 23.912(1) Å, c = 5.5565(3) Å, V = 2090.2(2) Å3, ...

  20. Synthesis, solvatochromism and crystal structure of trans-[Cu(Et2NCH2CH2NH2)2.H2O](NO3)2 complex: Experimental with DFT combination

    Science.gov (United States)

    Warad, Ismail; Musameh, Sharif; Badran, Ismail; Nassar, Nashaat N.; Brandao, Paula; Tavares, Carlos Jose; Barakat, Assem

    2017-11-01

    In this study, two dicationic asymmetrical diamine/copper(II) nitrate salt complexes of the general formula trans-[CuII(NN‧)2.H2O](NO3)2 were successfully synthesized using N,N-dimethylethylenediamine and N,N-diethylethylenediamine as asymmetrical diamine ligands. The structure of complex 2 was identified by X-ray single crystal diffraction analysis confirming that the bidentate ligand N,N-dimethylethylenediamine forms a penta-coordinated complex with an H2O molecule located around the copper(II) ion in a trans configuration. It was found that the metal centre is coordinated in a distorted square pyramidal fashion with a τ value of 0.274. The desired complexes were fully characterized using, MS, UV-Vis, CV, FTIR, TG/DTA, and Hirshfeld surface computational analysis. High level theoretical calculations were also performed in order to investigate the complexes structure, conformers, vibrational frequencies, and their excited states.

  1. Effects of the [OC6F5] moiety upon structural geometry: crystal structures of half-sandwich tantalum(V) aryloxide complexes from reaction of Cp*Ta(N(t)Bu)(CH2R)2 with pentafluorophenol.

    Science.gov (United States)

    Cole, Jacqueline M; Chan, Michael C W; Gibson, Vernon C; Howard, Judith A K

    2011-10-01

    The synthesis, chemical and structural characterization of a series of pentamethylcyclopentadienyl (Cp*) tantalum imido complexes and aryloxide derivatives are presented. Specifically, the imido complexes Cp*Ta(N(t)Bu)(CH(2)R)(2), where R = Ph [dibenzyl(tert-butylamido) (η(5)-pentamethylcyclopentadienyl)tantalum(IV) (1)], Me(2)Ph [tert-butylamido)bis(2-methyl-2-phenylpropyl) (η(5)-pentamethylcyclopentadienyl)tantalum(IV) (2)], CMe(3) [(tert-butylamido)bis(2,2-dimethylpropyl) (η(5)-pentamethylcyclopentadienyl)tantalum(IV) (3)], are reported. The crystal structure of (3) reveals α-agostic interactions with the Ta atom. The resulting increase in the tantalum core coordination improves electronic stability. As such it does not react with pentafluorophenol, in contrast to the other two reported imido complexes [(1) and (2)]. Addition of C(6)F(5)OH to (1) yields a dimeric aryl-oxide derivative, [Cp*Ta(CH(2)Ph)(OC(6)H(5))(μ-O)](2) [di-μ-oxido-bis[benzyl(pentafluorophenolato) (η(5)-pentamethylcyclopentadienyl)tantalum(V)] (4)]. Its crystal structure reveals long Ta-O(C(6)H(5)) bonds but short oxo-bridging Ta-O bonds. This is explained by accounting for the fierce electronic competition for the vacant d(π) orbitals of the electrophilic Ta(V) centre. Steric congestion around each metal is alleviated by a large twist angle (77.1°) between the benzyl and pentafluorophenyl ligands and the ordering of each of these groups into stacked pairs. The imido complex (2) reacts with C(6)F(5)OH to produce a mixture of Cp*Ta(OC(6)F(5))(4) [tetrakis(pentafluorophenolato)(η(5)-pentamethylcyclopentadienyl)tantalum(V) (5)] and [Cp*Ta(OC(6)F(5))(2)(μ-O)](2) [di-μ-oxido-bis[bis(pentafluorophenolato)(η(5)-pentamethylcyclopentadienyl)tantalum(V)] (6)]. Steric congestion is offset in both cases by the twisting of its pentafluorophenyl ligands. Particularly strong electronic competition for the empty d(π) metal orbitals in (6) is reflected in its bond geometry, and owes itself to the

  2. Crystal Structure of a Cytochrome P450 2B6 Genetic Variant in Complex with the Inhibitor 4-(4-Chlorophenyl)imidazole at 2.0-Å Resolution

    Science.gov (United States)

    Shah, Manish B.; Talakad, Jyothi C.; Maekawa, Keiko; Roberts, Arthur G.; Wilderman, P. Ross; Sun, Ling; Yang, Jane Y.; Huelga, Stephanie C.; Hong, Wen-Xu; Zhang, Qinghai; Stout, C. David; Halpert, James R.

    2010-01-01

    The structure of the K262R genetic variant of human cytochrome P450 2B6 in complex with the inhibitor 4-(4-chlorophenyl)imidazole (4-CPI) has been determined using X-ray crystallography to 2.0-Å resolution. Production of diffraction quality crystals was enabled through a combination of protein engineering, chaperone coexpression, modifications to the purification protocol, and the use of unique facial amphiphiles during crystallization. The 2B6-4-CPI complex is virtually identical to the rabbit 2B4 structure bound to the same inhibitor with respect to the arrangement of secondary structural elements and the placement of active site residues. The structure supports prior P450 2B6 homology models based on other mammalian cytochromes P450 and is consistent with the limited site-directed mutagenesis studies on 2B6 and extensive studies on P450 2B4 and 2B1. Although the K262R genetic variant shows unaltered binding of 4-CPI, altered binding affinity, kinetics, and/or product profiles have been previously shown with several other ligands. On the basis of new P450 2B6 crystal structure and previous 2B4 structures, substitutions at residue 262 affect a hydrogen-bonding network connecting the G and H helices, where subtle differences could be transduced to the active site. Docking experiments indicate that the closed protein conformation allows smaller ligands such as ticlopidine to bind to the 2B6 active site in the expected orientation. However, it is unknown whether 2B6 undergoes structural reorganization to accommodate bulkier molecules, as previously inferred from multiple P450 2B4 crystal structures. PMID:20061448

  3. Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution.

    Science.gov (United States)

    Gay, Sean C; Shah, Manish B; Talakad, Jyothi C; Maekawa, Keiko; Roberts, Arthur G; Wilderman, P Ross; Sun, Ling; Yang, Jane Y; Huelga, Stephanie C; Hong, Wen-Xu; Zhang, Qinghai; Stout, C David; Halpert, James R

    2010-04-01

    The structure of the K262R genetic variant of human cytochrome P450 2B6 in complex with the inhibitor 4-(4-chlorophenyl)imidazole (4-CPI) has been determined using X-ray crystallography to 2.0-A resolution. Production of diffraction quality crystals was enabled through a combination of protein engineering, chaperone coexpression, modifications to the purification protocol, and the use of unique facial amphiphiles during crystallization. The 2B6-4-CPI complex is virtually identical to the rabbit 2B4 structure bound to the same inhibitor with respect to the arrangement of secondary structural elements and the placement of active site residues. The structure supports prior P450 2B6 homology models based on other mammalian cytochromes P450 and is consistent with the limited site-directed mutagenesis studies on 2B6 and extensive studies on P450 2B4 and 2B1. Although the K262R genetic variant shows unaltered binding of 4-CPI, altered binding affinity, kinetics, and/or product profiles have been previously shown with several other ligands. On the basis of new P450 2B6 crystal structure and previous 2B4 structures, substitutions at residue 262 affect a hydrogen-bonding network connecting the G and H helices, where subtle differences could be transduced to the active site. Docking experiments indicate that the closed protein conformation allows smaller ligands such as ticlopidine to bind to the 2B6 active site in the expected orientation. However, it is unknown whether 2B6 undergoes structural reorganization to accommodate bulkier molecules, as previously inferred from multiple P450 2B4 crystal structures.

  4. Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N⁴-methyl-3-thiosemicarbazone: crystal structure of a novel sulfur bridged copper(II) box-dimer.

    Science.gov (United States)

    Jayakumar, K; Sithambaresan, M; Aiswarya, N; Kurup, M R Prathapachandra

    2015-03-15

    Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N(4)-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, τ=0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g||>g⊥>2.0023 and the g values in frozen DMF are consistent with the d(x2-y2) ground state. The thermal stabilities of some of the complexes were also determined. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N4-methyl-3-thiosemicarbazone: Crystal structure of a novel sulfur bridged copper(II) box-dimer

    Science.gov (United States)

    Jayakumar, K.; Sithambaresan, M.; Aiswarya, N.; Kurup, M. R. Prathapachandra

    2015-03-01

    Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N4-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, τ = 0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)sbnd I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g|| > g⊥ > 2.0023 and the g values in frozen DMF are consistent with the dx2-y2 ground state. The thermal stabilities of some of the complexes were also determined.

  6. Cu(II) bifunctional (N,O,O‧) coordination polymer: A case study for complex ab-initio crystal structure determination from PXRD data

    Science.gov (United States)

    Colombo, Valentina; Cimino, Alessandro; Maspero, Angelo; Tollari, Stefano; Palmisano, Giovanni; Sironi, Angelo

    2017-09-01

    The synthesis of a novel Cu(II) bifunctional (N,O,O‧) coordination polymer, the Cu(PzHP) compound, has been carried out by coupling Cu(II) salts and the newely synthesized H2(PzHP) organic linker (H2(PzHP) = 1-[4-(1H) -pyrazolyl]-2-methyl-3-hydroxy-4(1H)-pyridinone). Despite to the numerous attempts done for the growth of suitable single crystals and to the synthetic trials carried out to ameliorate the crystallinity of the Cu(PzHP) coordination polymer, its diffraction pattern was always characterized by a discouraging, less-than-ideal, crystallinity. Notwithstanding the extended disorder, leading to a higher than required space group symmetry, we succeeded in the description of its relevant structural features by following an unconventional route to ab-initio structure solution. In this process consideration on the coordination ability of the ligand and on the space group symmetry have been taken into account to 'manually' achieve the initial structural model, highlighting that, in some cases, it is still possible to ascertain by PXRD the crystal structure of a material that shows challenging, broad, PXRD pattern.

  7. Synthetic murataite-3C, a complex form for long-term immobilization of nuclear waste. Crystal structure and its comparison with natural analogues

    Energy Technology Data Exchange (ETDEWEB)

    Pakhomova, Anna S.; Krivovichev, Sergey V. [St. Petersburg State Univ. (Russian Federation). Dept. of Crystallography; Yudintsev, Sergey V. [Institute of Geology of Ore Deposits, Petrography, Mineralogy and Geochemistry, St. Petersburg (Russian Federation); Stefanovsky, Sergey V. [MosNPO Radon, Moscow (Russian Federation)

    2013-03-01

    The structure of synthetic murataite-3C intended for long-term immobilization of high-level radioactive waste has been solved using crystals prepared by melting in an electric furnace at 1500 C. The material is cubic, F- anti 43m, a = 14.676(15) A, V = 3161.31(57) A{sup 3}. The structure is based upon a three-dimensional framework consisting of {alpha}-Keggin [Al{sup [4]}Ti{sub 12}{sup [6]}O{sub 40}] clusters linked by sharing the O5 atoms. The Keggin-cluster-framework interpenetrates with the metal-oxide substructure that can be considered as a derivative of the fluorite structure. The crystal chemical formula of synthetic murataite-3C derived from the obtained structure model can be written as {sup [8]}Ca{sub 6}{sup [8]}Ca{sub 4}{sup [6]}Ti{sub 12}{sup [5]}Ti{sub 4}{sup [4]}AlO{sub 42}. Its comparison with the natural murataite shows that the synthetic material has a noticeably less number of vacancies in the cation substructure and contains five instead of four symmetrically independent cation positions. The presence of the additional site essentially increases the capacity of synthetic murataite with respect to large heavy cations such as actinides, rare earth and alkaline earth metals in comparison with the material of natural origin. (orig.)

  8. Transition metal complexes with thiosemicarbazide-based ligands. Part 45. Synthesis, crystal and molecular structure of [2,6-diacetylpyridine bis(S-methylisothiosemicarbazonato]diazide-iron(III

    Directory of Open Access Journals (Sweden)

    REFIK FAZLIC

    2003-05-01

    Full Text Available The template reaction of a warm methanolic solution of FeCl3.6H2O, S-methylisothiosemicarbazidehydroiodide and 2,6-diacetylpyridine in the presence of LiOAc and NaN3 yielded the high-spin complex [Fe(HL(N32], were HL is the monoanion of the ligand 2,6-diacetylpyridine bis(S-methylisothiosemicarbazone. X-Ray analysis of the complex showed its pentagonal-bipyramidal configuration, with pentadenate (N5 HL in the equatorial plane and two monodentate azide groups in the axial positions. Crystal data are: monoclinic, P21/c, a = 1.0263(2, b = 1.2525(2, c = 1.6660(3 nm, b = 98.94°, V = 2.1154 nm3, Z = 4, rx = 1.499 g cm-3, r0 = 1.48 g cm-3, F(000 = 984, m = 9.40 cm-3.

  9. Self-assembly of extended structures through non-coordination intermolecular forces: Synthesis, crystal structures, and properties of metal complexes with 5-methyl-2-pyrazinecarboxylate

    NARCIS (Netherlands)

    Tanase, S.; Son, M. van; Albada, G.A. van; Gelder, R. de; Bouwman, E.; Reedijk, J.

    2006-01-01

    Three new complexes of 5-methyl-2-pyrazinecarboxylate (Hmpca) with cobalt(II), [Co(mpca)(2)(H2O)(2)], nickel(II), [Ni(mpca)(2)(H2O)(2)] and iron(III) [Fe(mpca)(2)(OH)](2) center dot 2H(2)O, have been synthesized and characterized by spectroscopic techniques, X-ray crystallography and low-temperature

  10. Synthesis, structural characterization and antioxidant/anti-inflammatory activity of pentacoordinated bis(isoselenocyanato) and bis(isothiocyanato) Cu II and Ni II complexes with Me 5dien: Crystal structure of [Cu(Me 5dien)(NCSe) 2

    Science.gov (United States)

    Georgousis, Zacharias D.; Christidis, Panayiotis C.; Hadjipavlou-Litina, Dimitra; Bolos, Christos A.

    2007-06-01

    Complexes of the general formula [M(Me 5dien)X 2] [where M = Cu II and Ni II, Me 5dien = N, N, N', N″, N″- pentamethyldiethylenetriamine and X = (SCN -) or (SeCN -)] have been synthesized and characterized by elemental analyses, infrared and electronic spectroscopy, magnetic moment and molar conductivity measurements and X-ray crystallography. The crystal structure of [Cu(Me 5dien)(NCSe) 2] revealed the tridentate coordination of Me 5dien and the N-terminal coordination of two SeCN ligands to the Cu II ion. The latter adopts a distorted square pyramidal geometry, with the basal positions occupied by the three nitrogen atoms of Me 5dien and by the nitrogen atom of one isoselenocyanate ligand. The apical position is occupied by the nitrogen atom of the second isoselenocyanate ligand. Infrared spectra of the complexes confirmed the N-terminal coordination of the pseudohalides and the tridentate coordination of the triamine. Electronic spectra were all consistent with five-coordinate square pyramidal geometries. The complexes are monomeric, paramagnetic and non-electrolytes in MeOH, but 1:1 electrolytes in DMSO. The complexes were tested for antioxidant/anti-inflammatory activity. The presence of a isoselenocyanato (NCSe) group leads to higher reducing activity in comparison to the isothiocyanato (NCS) group. The nature of the metal plays also an important role to this activity. Complex [Ni(Me 5dien)(NCSe) 2] is more potent than the corresponding copper complex and offers 44.7% protection against the carrageenin-induced rat paw edema.

  11. Membrane protein structures without crystals, by single particle electron cryomicroscopy.

    Science.gov (United States)

    Vinothkumar, Kutti R

    2015-08-01

    It is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. However, two major hurdles still remain in the structural biology of membrane proteins. One is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. With single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane proteins and other labile protein complexes can be obtained with very little protein and without the need for crystals. In this review, I highlight recent advances in electron microscopy, detectors and software, which have allowed determination of medium to high-resolution structures of membrane proteins and complexes that have been difficult to study by other structural biological techniques. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  12. Synthesis, crystal structure, thermal analysis and dielectric ...

    Indian Academy of Sciences (India)

    In both the materials, the crystal structure has been determined by X-ray single crystal analysis at room temperature (293 K). The compound structures consist of K + (or NH 4 + ) cations and double chains of CdCl 6 octahedra sharing one edge extending along b -axis. The mixture of KA + /NH 4 + cations are located ...

  13. Crystal structure and hydrogen bonding interactions

    Indian Academy of Sciences (India)

    Giacovazzo C, Guagliardi A, Moliteni A G G, Polidori. G and Spagna R 1997 SIR97 (Release 1.02) - A program for automatic solution and refinement of crystal structure. 10. Sheldrick G M 1997 SHELXL-97, Programs for Crystal. Structure Analysis; University of Göttingen, Germany. 11. ORTEP3 for Windows and Farrugia L J ...

  14. Crystal structure of nonadentate tricompartmental ligand derived from pyridine-2,6-dicarboxylic acid: Spectroscopic, electrochemical and thermal investigations of its transition metal(II) complexes

    Science.gov (United States)

    Vadavi, Ramesh S.; Shenoy, Rashmi V.; Badiger, Dayananda S.; Gudasi, Kalagouda B.; Devi, L. Gomathi; Nethaji, Munirathinam

    2011-07-01

    The coordinating behavior of a new dihydrazone ligand, 2,6-bis[(3-methoxysalicylidene)hydrazinocarbonyl]pyridine towards manganese(II), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) has been described. The metal complexes were characterized by magnetic moments, conductivity measurements, spectral (IR, NMR, UV-Vis, FAB-Mass and EPR) and thermal studies. The ligand crystallizes in triclinic system, space group P-1, with α = 98.491(10)°, β = 110.820(10)° and γ = 92.228(10)°. The cell dimensions are a = 10.196(7) Å, b = 10.814(7) Å, c = 10.017(7) Å, Z = 2 and V = 1117.4(12). IR spectral studies reveal the nonadentate behavior of the ligand. All the complexes are neutral in nature and possess six-coordinate geometry around each metal center. The X-band EPR spectra of copper(II) complex at both room temperature and liquid nitrogen temperature showed unresolved broad signals with giso = 2.106. Cyclic voltametric studies of copper(II) complex at different scan rates reveal that all the reaction occurring are irreversible.

  15. Photonic crystal laser-driven accelerator structures

    CERN Document Server

    Cowan, Benjamin

    2005-01-01

    We discuss simulated photonic crystal structure designs, including two- and three-dimensional planar structures and fibers. The discussion of 2D structures demonstrates guiding of a speed-of-light accelerating mode by a defect in a photonic crystal lattice and reveals design considerations and trade-offs. With a three-dimensional lattice, we introduce a candidate geometry and discuss beam dynamics, coupling, and manufacturing techniques for that structure. In addition we discuss W-band scale tests of photonic crystal structures. The computational methods are also discussed.

  16. Synthesis, characterization, X-ray crystal structure, DFT calculation, DNA binding, and antimicrobial assays of two new mixed-ligand copper(II) complexes

    Science.gov (United States)

    Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Mohamadi, Maryam; Suarez, Sebastian; Baggio, Ricardo; Khaleghi, Moj; Torkzadeh-Mahani, Masoud; Mostafavi, Ali

    2015-05-01

    Two new Cu(II) complexes, [Cu(L)(phen)] (1), [Cu(L)(bipy)] (2), where L2- = (3-methoxy-2oxidobenzylidene)benzohydrazidato, phen = 1,10 phenanthroline, and bipy = 2,2‧ bipyridine, were prepared and fully characterized using elemental analyses, FT-IR, molar conductivity, and electronic spectra. The structures of both complexes were also determined by X-ray diffraction. It was found that, both complexes possessed square pyramidal coordination environment in which, Cu(II) ions were coordinated by donor atoms of HL and two nitrogens of heterocyclic bases. Computational studies were performed using DFT calculations at B3LYP/6-311+G(d,p) level of theory. DNA binding activities of these complexes were also investigated using electronic absorption, competitive fluorescence titration and cyclic voltammetry studies. The obtained results indicated that binding of the complexes to DNA was of intercalative mode. Furthermore, antimicrobial activities of these compounds were screened against microorganisms.

  17. Crystal structure of 2-pentyloxybenzamide

    Directory of Open Access Journals (Sweden)

    Bernhard Bugenhagen

    2014-10-01

    Full Text Available In the title molecule, C12H17NO2, the amide NH2 group is oriented toward the pentyloxy substituent and an intramolecular N—H...O hydrogen bond is formed with the pentyloxy O atom. The benzene ring forms dihedral angles of 2.93 (2 and 5.60 (2° with the amide group and the pentyloxy group mean planes, respectively. In the crystal, molecules are linked by pairs of N—H...O hydrogen bonds, forming inversion dimers with their molecular planes parallel, but at an offset of 0.45 (1 Å to each other. These dimers are ordered into two types of symmetry-related columns extended along the a axis, with the mean plane of one set of dimers in a column approximately parallel to (121 and the other in a column approximately parallel to (1-21. The two planes form a dihedral angle of 85.31 (2°, and are linked via C—H...O hydrogen bonds and C—H...π interactions, forming a three-dimensional framework structure.

  18. Method of fabricating patterned crystal structures

    KAUST Repository

    Yu, Liyang

    2016-12-15

    A method of manufacturing a patterned crystal structure for includes depositing an amorphous material. The amorphous material is modified such that a first portion of the amorphous thin-film layer has a first height/volume and a second portion of the amorphous thin-film layer has a second height/volume greater than the first portion. The amorphous material is annealed to induce crystallization, wherein crystallization is induced in the second portion first due to the greater height/volume of the second portion relative to the first portion to form patterned crystal structures.

  19. 1.2.2.Synthesis, crystal structure and in vitro anti-tumor activity of dibutyltin complex of 2,4-dichloro-5-fluorobenzoic acid

    Directory of Open Access Journals (Sweden)

    Ming Li, Liqin Wang, Zhenlei Zhang, Yue Xin, Laijin Tian*

    2014-04-01

    Full Text Available The dibutyltin complex of 2,4-dichloro-5- fluorobenzoic acid, [(2,4-Cl2 -5-FC6 H2 C(OOSnBu2 2 O]2 (Bu = CH2 CH2 CH2 CH3 (1 , has been synthesized and characterized by elemental analysis, FT-IR, 119 Sn NMR spectroscopy, and Xray single crystal diffraction. Compound 1 is a centrosymmetric dimmer with two distinct types of carboxylate moieties and tin atoms with distorted trigonal bipyramidal geometries. The in vitro  anti-tumor activity of 1 against two human tumor cell lines was found to be higher than that for cis-platin [cis diaminedichloroplatinum( II] used clinically. Supporting information : FT-IR, 119 Sn NMR, X-Ray, Proliferation inhibitory rate, Cif file.

  20. Crystal structure of bis-(1,3-di-meth-oxy-imidazolin-2-yl-idene)silver(I) hexa-fluorido-phosphate, N-heterocyclic carbene (NHC) complex.

    Science.gov (United States)

    Rietzler, Barbara; Laus, Gerhard; Kahlenberg, Volker; Schottenberger, Herwig

    2015-12-01

    The title salt, [Ag(C5H8N2O2)2]PF6, was obtained by deprotonation and metalation of 1,3-di-meth-oxy-imidazolium hexa-fluorido-phosphate using silver(I) oxide in methanol. The C-Ag-C angle in the cation is 178.1 (2)°, and the N-C-N angles are 101.1 (4) and 100.5 (4)°. The meth-oxy groups adopt an anti conformation. In the crystal, anions (A) are sandwiched between cations (C) in a layered arrangement {C…A…C} n stacked along [001]. Within a C…A…C layer, the hexafluoridophosphate anions accept several C-H⋯F hydrogen bonds from the cationic complex.

  1. Porous protein crystals as catalytic vessels for organometallic complexes.

    Science.gov (United States)

    Tabe, Hiroyasu; Abe, Satoshi; Hikage, Tatsuo; Kitagawa, Susumu; Ueno, Takafumi

    2014-05-01

    Porous protein crystals, which are protein assemblies in the solid state, have been engineered to form catalytic vessels by the incorporation of organometallic complexes. Ruthenium complexes in cross-linked porous hen egg white lysozyme (HEWL) crystals catalyzed the enantioselective hydrogen-transfer reduction of acetophenone derivatives. The crystals accelerated the catalytic reaction and gave different enantiomers based on the crystal form (tetragonal or orthorhombic). This method represents a new approach for the construction of bioinorganic catalysts from protein crystals. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Assembling Metal Ions Induced Cyanide-Bridged Heterometallic 1D and Ion-Pair Complexes: Synthesis, Crystal Structures and Magnetic Properties

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Lingqian [Liaocheng Univ., Liaocheng (China); Zhao, Zengdian; Chen, Kexun; Wang, Ping; Zhang, Daopeng [Shandong Univ. of Technology, Zibo (China)

    2013-07-15

    We obtained a heterobimetallic one-dimensional cyanide-bridged Mn(II)-Ni(II) complex and an Co(III)-Ni(II) ion-pair complex with [Ni(CN){sub 4}]{sup 2-} as building block and M(II)-phenanthroline (M = Mn, Co) compounds as assembling segment. The different structural types of complexes 1 and 2 indicate that the property of the metal ions the assembling segment contained have obvious influence on the structure of the cyanide-bridged complex. Investigation over the magnetic properties of complex 1 reveals an overall weak antiferromagnetic coupling between the adjacent Mn(II) ions bridged by the antiferromagnetic [-NC-Ni-CN-] unit. Among of all the molecular magnetism systems, for the well known reasons, cyanide-containing complexes have been widely employed as bridges to assemble homo/hetero-metallic molecular magnetic materials by using the cyanide bridge transferring magnetic coupling between the neighboring paramagnetic ions, in whichsome showed interesting magnetic properties, such as high-Tc magnets, spin crossover materials, single-molecule magnets (SMMs) and single-chain magnets (SCMs)

  3. Mn(II), Zn(II) and Cd(II) Complexes Based on Oxadiazole Backbone Containing Carboxyl Ligand: Synthesis, Crystal Structure, and Photoluminescent Study.

    Science.gov (United States)

    Wang, Li-Na; Fu, Lin; Zhu, Jia-Wei; Xu, Yu; Zhang, Meng; You, Qi; Peng, Wang; Qin, Jie

    2017-01-01

    Three coordination polymers, [Cd(L)2(H2O)2]n (1), [Zn(L)2(H2O)2]n (2) and [Mn(L)2]n (3) were prepared by reacting 5-(3-pyridyl)-1,3,4-oxadiazole-2-thioacetic acid (HL) with corresponding metal acetate in DMF/CH3CN medium under solvothermal condition. The isolated complexes were characterized by elemental analysis and infrared spectroscopy. The X-ray crystallographic analysis revealed double strand structure of 1 and 2, and 3D framework of 3. The different structures of these complexes indicate that the configuration of the ligand and the reaction condition play a key role in self-assemble of complexes 1-3. Furthermore, photoluminescent properties of 1 and 2 were also studied in the solid state.

  4. Synthesis and crystal structure of copper (II) uracil ternary polymeric complex with 1,10-phenanthroline along with the Hirshfeld surface analysis of the metal binding sites for the uracil ligand

    Science.gov (United States)

    Patil, Yogesh Prakash; Nethaji, Munirathinam

    2015-02-01

    The study of models for "metal-enzyme-substrate" interaction has been a proactive area of research owing to its biological and pharmacological importance. In this regard the ternary copper uracil complex with 1,10-phenanthroline represents metal-enzyme-substrate system for DNA binding enzymes. The synthesis of the complex, followed by slow evaporation of the reaction mixture forms two concomitant solvatomorph crystals viz., {[Cu(phen)(μ-ura)(H2O)]n·H2O (1a)} and {[Cu(phen)(μ-ura)(H2O)]n·CH3OH (1b)}. Both complexes are structurally characterized, while elemental analysis, IR and EPR spectra were recorded for 1b (major product). In both complexes, uracil coordinates uniquely via N1 and N3 nitrogen atom acting as a bidentate bridging ligand forming a 1-D polymer. The two solvatomorphs were quantitatively analyzed for the differences with the aid of Hirshfeld surface analysis.

  5. Weak ferromagnetic behavior, crystal structure, and electronic studies of novel [Cu(II)(Br)(PhCO 2)(Sp)] (Sp=(-)-sparteine) complex

    Science.gov (United States)

    Reyes-Ortega, Yasmi; Alcántara-Flores, José Luis; Hernández-Galindo, María del Carmen; Gutiérrez-Pérez, René; Ramírez-Rosales, Daniel; Bernès, Sylvain; Cabrera-Vivas, Blanca Martha; Durán-Hernández, Alejandro; Zamorano-Ulloa, Rafael

    2006-05-01

    Complex [Cu(II)(Br)(PhCO 2)(Sp)] 1 is obtained starting from copper(0), (-)-sparteine (sp) and benzoyl bromide. 1 Crystallizes in the monoclinic space group P2 1 with a=14.8857(11), b=8.9257(9), c=17.4456(14) Å, β=111.689(5)°, and Z=4. The UV-vis spectrum is characteristic of Cu(II) complexes with tetragonally distorted square pyramidal geometry. The far IR spectrum of 1 shows characteristic vibrations of Cu-Br (239 cm -1), Cu-N (437 cm -1) and Cu-O (466 cm -1) bonds. The 1H NMR broad chemical shifts of 1 integrated for a total of 31 protons and are typical of Cu(II) complexes. ESR spectra of polycrystalline 1 at 77 and 300 K show axial spectra with areas in the ratio A77/ A300=4.02, suggesting a very weak Cu-Cu ferromagnetic interaction. Complex 1-doped with Zn(II) gives hfs with hyperfine interaction constant value A∥=112.45×10 -4 cm -1. The magnetization vs temperature data in the 2-299 K range, show that cupric ion pairs interact through a small antiferromagnetic Heisenberg exchange energy— JS1· S2 with a ground singlet state S=0, separated by J=-1.3 cm -1 from the excited triplet state S=1. The sign of the very weak interchange interaction constant, J, does not agree with the ESR spectra areas ratio of 1 at 77 and 300 K, which is a more accurate quantification of the weak ferromagnetic interaction Cu-Cu through the space.

  6. Synthesis, crystal structure and spectroscopy of bioactive Cd(II) polymeric complex of the non-steroidal anti-inflammatory drug diclofenac sodium: Antiproliferative and biological activity

    Science.gov (United States)

    Tabrizi, Leila; Chiniforoshan, Hossein; McArdle, Patrick

    2015-02-01

    The interaction of Cd(II) with the non-steroidal anti-inflammatory drug diclofenac sodium (Dic) leads to the formation of the complex [Cd2(L)41.5(MeOH)2(H2O)]n(L = Dic), 1, which has been isolated and structurally characterized by X-ray crystallography. Diclofenac sodium and its metal complex 1 have also been evaluated for antiproliferative activity in vitro against the cells of three human cancer cell lines, MCF-7 (breast cancer cell line), T24 (bladder cancer cell line), A-549 (non-small cell lung carcinoma), and a mouse fibroblast L-929 cell line. The results of cytotoxic activity in vitro expressed as IC50 values indicated the diclofenac sodium and cadmium chloride are non active or less active than the metal complex of diclofenac (1). Complex 1 was also found to be a more potent cytotoxic agent against T-24 and MCF-7 cancer cell lines than the prevalent benchmark metallodrug, cisplatin, under the same experimental conditions. The superoxide dismutase activity was measured by Fridovich test which showed that complex 1 shows a low value in comparison with Cu complexes. The binding properties of this complex to biomolecules, bovine or human serum albumin, are presented and evaluated. Antibacterial and growth inhibitory activity is also higher than that of the parent ligand compound.

  7. Ligational behaviour of (E)-2-amino-N‧-[1-(2-hydroxyphenyl)ethylidene]benzohydrazide towards later 3d metal ions: X-ray crystal structure of nickel(IV) complex

    Science.gov (United States)

    Gudasi, Kalagouda B.; Patil, Siddappa A.; Bakale, Raghavendra P.; Nethaji, Munirathinum

    2014-05-01

    Ligational behaviour of (E)-2-amino-N‧-[1-(2-hydroxyphenyl)ethylidene]benzohydrazide (Aheb) towards later 3d metal ions[copper(II), cobalt(II), manganese(II), zinc(II), cadmium(II) and nickel(IV)] has been studied. Their structures have been elucidated on the basis of spectral (IR, 1H NMR, UV-Vis, EPR and FAB-mass), elemental analyses, conductance measurements, magnetic moments, and thermal studies. During complexation Ni(II) ion has got oxidized to Ni(IV). The changes in the bond parameters of the ligand on complexation has been discussed by comparing the crystal structure of the ligand with that of its Ni(IV) complex. The X-ray single crystal analysis of [Ni(aheb)2]Cl2·4H2O has confirmed an octahedral geometry around the metal ion. EPR spectra of the Cu(II) complex in polycrystalline state at room (300 K) and liquid nitrogen temperature (77 K) were recorded and their salient features are reported.

  8. Synthesis and crystal structure of binuclear copper(II) complex bridged by N-(2-hydroxyphenyl)-N'-[3-(diethylamino)propyl]oxamide: in vitro anticancer activity and reactivity toward DNA and protein.

    Science.gov (United States)

    Gao, Yang; Li, Yan-Tuan; Wu, Zhi-Yong; Yan, Cui-Wei

    2013-08-01

    A new oxamido-bridged bicopper(II) complex, [Cu2(pdpox)(bpy)(CH3OH)](ClO4), where H3pdpox and bpy stand for N-(2-hydroxyphenyl)-N'-[3-(diethylamino)propyl]oxamide and 2,2'-bipyridine, respectively, has been synthesized and characterized by elemental analyses, molar conductivity measurements, infrared and electronic spectra studies, and X-ray single crystal diffraction. In the crystal structure, the pdpox(3-) ligand bridges two copper(II) ions as cisoid conformation. The inner copper(II) ion has a {N3O} square-planar coordination geometry, while the exo- one is in a {N2O3} square-pyramidal environment. There are two sets of interpenetrating two-dimensional hydrogen bonding networks parallel to the planes (2 1 0) and (21¯0), respectively, to form a three-dimensional supramolecular structure. The bicopper(II) complex exhibits cytotoxic activity against the SMMC7721 and A549 cell lines. The reactivity toward herring sperm DNA and bovine serum albumin revealed that the bicopper(II) complex can interact with the DNA by intercalation mode, and the complex binds to protein BSA responsible for quenching of tryptophan fluorescence by static quenching mechanism. © 2013 Wiley Periodicals, Inc.

  9. Crystal structure and morphology of syndiotactic polypropylene single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Bu, J.Z. [GE Plastics, Washington, WV (United States); Cheng, S.Z.D. [Univ. of Akron, OH (United States)

    1996-12-31

    In the past several years there have been an increased interest in the crystal structure and morphology of s-PP due to the new development of homogeneous metallocene catalysts which can produce s-PP having a high stereoregularity. In this research, the crystal structure and morphology of s-PP single crystals grown from the melt were investigated. A series of ten fractions of s-PP was studied with different molecular weights ranging from 10,300 to 234,000 (g/mol). These fractions all possess narrow molecular weight distributions (around 1.1-1.2) and high syndiotacticities ([r]{approximately}95%). The main techniques employed including transmission electron microscopy (TEM), atomic force microscopy (AFM), wide-angle X-ray diffraction (WAXD), and small-angle X-ray scattering (SAXS).

  10. Synthesis, crystal structure and DFT studies of a Zinc(II) complex of 1,3-diaminopropane (Dap), [Zn(Dap)(NCS)2][Zn(Dap)(NCS)2]n. The additional stabilizing role of S⋯π chalcogen bond

    Science.gov (United States)

    Alotaibi, Mshari A.; Alharthi, Abdulrahman I.; Zierkiewicz, Wiktor; Akhtar, Muhammad; Tahir, Muhammad Nawaz; Mazhar, Muhammad; Isab, Anvarhusein A.; Ahmad, Saeed

    2017-04-01

    A zinc(II) complex of 1,3-diaminopropane (Dap), [Zn(Dap)(NCS)2][Zn(Dap)(NCS)2]n (1) has been prepared and characterized by elemental analysis, IR, 1H &13C NMR spectroscopy, and its crystal structure was determined by X-ray crystallography. The crystal structure of 1 consists of two types of molecules, a discrete monomer and a polymeric one. In the monomeric unit, the zinc atom is bound to one terminal Dap molecule and to two N-bound thiocyanate ions, while in the polymeric unit, Dap acts as a bridging ligand forming a linear chain. The Zn(II) ions in both assume a slightly distorted tetrahedral geometry. The structures of two systems: the [Zn(Dap)(NCS)2][Zn(Dap)(NCS)2]3 complex as a model of 1 and [Zn(Dap)(NCS)2]4 as a simple polymeric structure were optimized with the B3LYP-D3 method. The DFT results support that the experimentally determined structure (1) is more stable in comparison to a simple polymeric structure, [Zn(Dap)(NCS)2]n (2). The interaction energies (ΔE) for NCS anions obtained by B3LYP-D3 method are about -145 kcal mol-1, while the calculated ΔE values for neutral organic ligands are about twice smaller. The X-ray structure of 1 shows that the complex is stabilized mainly by hydrogen bonds. We also found that weak chalcogen bonds play an additional role in stabilization of compound 1. Some of the intermolecular S⋯N distances are smaller than the sum of the van der Waals radii of the corresponding atoms. To the best of our knowledge, this is the first study that shows the structure where the trivalent sulfur is involved in formation of a S⋯π chalcogen bond. The NBO and NCI analyses confirm the existence of this kind of interactions.

  11. Synthesis and crystal structure of a ternary copper(II) complex of 2,2‧-bipyridine and picrate: Molecular docking, reactivity towards DNA and in vitro anticancer activity

    Science.gov (United States)

    Zheng, Kang; Jiang, Man; Li, Yan-Tuan; Wu, Zhi-Yong; Yan, Cui-Wei

    2014-01-01

    A new mononuclear ternary copper(II) complex with mixed ligands of 2,2‧-bipyridine (bpy) and picrate (pic), namely [Cu(bpy)(pic)2], has been synthesized and characterized by elemental analysis, molar conductivity measurement, IR and electronic spectral studies, and single-crystal X-ray diffraction. The crystal structure analysis reveals the presence of two crystallographic independent molecules in an asymmetric unit. The copper(II) atoms are in elongated octahedral coordination geometries. A three-dimensional supermolecular network is formed through non-classical C-H⋯O hydrogen bonds. The DNA-binding properties of the copper(II) complex are investigated both theoretically and experimentally, revealing that the copper(II) complex can interact with HS-DNA in the mode of intercalation, and the molecular docking of the copper(II) complex with the self-complementary DNA duplex of sequence d(ACCGACGTCGGT)2 facilitates the binding events. The in vitro anticancer activities suggest that the copper(II) complex is active against the selected tumor cell lines.

  12. Binding of the Respiratory Chain Inhibitor Antimycin to theMitochondrial bc1 Complex: A New Crystal Structure Reveals an AlteredIntramolecular Hydrogen-Bonding Pattern

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Li-shar; Cobessi, David; Tung, Eric Y.; Berry, Edward A.

    2005-05-10

    Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex.Structure-activity-relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28Angstrom resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cyt b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alpha-A helix.

  13. Synthesis and crystal structure of new dicopper(II) complexes having asymmetric N,N'-bis(substituted)oxamides with DNA/protein binding ability: In vitro anticancer activity and molecular docking studies.

    Science.gov (United States)

    Zheng, Kang; Zhu, Ling; Li, Yan-Tuan; Wu, Zhi-Yong; Yan, Cui-Wei

    2015-08-01

    Two new dicopper(II) complexes bridged by asymmetric N,N'-bis(substituted)oxamide ligands: N-(5-chloro-2-hydroxyphenyl)-N'-[2-(dimethylamino)ethyl]oxamide (H3chdoxd) and N-hydroxypropyl-N'-(2-carboxylatophenyl)oxamide (H3oxbpa), and end-capped with 2,2'-bipyridine (bpy), namely [Cu2(ClO4)(chdoxd)(CH3OH)(bpy)]·H2O (1) and [Cu2(pic)(oxbpa)(CH3OH)(bpy)]·0.5CH3OH (2) (pic denotes picrate anion), have been synthesized and characterized by elemental analysis, molar conductivity measurement, IR and electronic spectral studies, and single-crystal X-ray diffraction. The X-ray diffraction analysis revealed that both the copper(II) ions bridged by the cis-oxamido ligands in dicopper(II) complexes 1 and 2 are all in square-pyramidal environments with the corresponding Cu⋯Cu separations of 5.194(3) and 5.1714(8)Å, respectively. In the crystals of the two complexes, there are abundant hydrogen bonds and π-π stacking interactions contributing to the supramolecular structure. The reactivities toward herring sperm DNA (HS-DNA) and bovine serum albumin (BSA) of the two complexes are studied both theoretically and experimentally, indicating that both the two complexes can interact with the DNA in the mode of intercalation, and effectively bind to BSA via the favored binding sites Trp134 for the complex 1 and Trp213 for the complex 2. Interestingly, the in vitro anticancer activities of the two complexes against the selected tumor cell lines are consistent with their DNA/BSA-binding affinities following the order of 1>2. The effects of coordinated counterions in the two complexes on DNA/BSA-binding ability and in vitro anticancer activity are preliminarily discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Aspirin induces its anti-inflammatory effects through its specific binding to phospholipase A2: crystal structure of the complex formed between phospholipase A2 and aspirin at 1.9 angstroms resolution.

    Science.gov (United States)

    Singh, Rajendra Kumar; Ethayathulla, A S; Jabeen, Talat; Sharma, Sujata; Kaur, Punit; Singh, Tej P

    2005-02-01

    Phospholipase A2 is potentially an important target for structure-based rational drug design. In order to determine the involvement of phospholipase A2 in the action of non-steroidal anti-inflammatory drugs (NSAIDs), the crystal structure of the complex formed between phospholipase A2 and aspirin has been determined at 1.9 angstroms resolution. The structure contains 915 protein atoms, 1 calcium ion, 13 atoms of aspirin and 105 water molecules. The observed electron density of the aspirin molecule in the structure was of very high quality thus allowing the precise determination of its atomic coordinates leading to the clear description of its interactions with the enzyme. The structure of the complex clearly shows that aspirin is literally embedded in the hydrophobic environment of PLA2. It is so placed in the substrate binding channel that it forms several important attractive interactions with calcium ion, His 48 and Asp 49. Thus, the structure of the complex clearly shows that aspirin occupies a favourable place in the specific binding site of PLA2. The binding studies have shown that acetyl salicylate (aspirin) binds to PLA2 enzyme specifically with a dissociation constant of 6.4 x 10(-6) M. The structural details and binding data suggest that the inhibition of PLA2 by aspirin is of pharmacological

  15. Crystal structures of HIV-1 gp120 envelope glycoprotein in complex with NBD analogues that target the CD4-binding site.

    Directory of Open Access Journals (Sweden)

    Young Do Kwon

    Full Text Available Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses para-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing meta-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization.

  16. Synthesis, crystal structure, fluorescent and antioxidation properties of cerium(III) and europium(III) complexes with bis(3-methoxysalicylidene)-3-oxapentane-1,5-diamine

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Xia; Shi, Xinkui; Xu, Yuling; Shen, Kesheng; Mao, Shanshan; Wu, Huilu [School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Gansu (China)

    2017-03-02

    Two aliphatic ether Schiff base lanthanide complexes (Ln = Eu, Ce) with bis(3-methoxysalicylidene)-3-oxapentane-1,5-diamine (Bod), were synthesized and characterized by physicochemical and spectroscopic methods. [Eu(Bod)(NO{sub 3}){sub 3}] (1) is a discrete mononuclear species and [Ce(Bod)(NO{sub 3}){sub 3}DMF]{sub ∞} (2) exhibits an inorganic coordination polymer. In the two complexes, the metal ions both are ten-coordinated and the geometric structure around the Ln{sup III} atom can be described as distorted hexadecahedron. Under excitation at room temperature, the red shift in the fluorescence band of the ligand in the complexes compared with that of the free ligand can be attributed to coordination of the rare earth ions to the ligand. Moreover, the antioxidant activities of the two complexes were investigated. The results demonstrated that the complexes have better scavenging activity than both the ligand and the usual antioxidants on the hydroxyl and superoxide radicals. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  17. Crystal structure and catecholase-like activity of a mononuclear complex [Cu(EDTB)]2+ (EDTB=N,N,N',N'-tetrakis(2'-benzimidazolyl methyl)-1,2-ethanediamine).

    Science.gov (United States)

    Chen, Zhan-Fen; Liao, Zhan-Ru; Li, Dong-Feng; Li, Wu-Ke; Meng, Xiang-Gao

    2004-08-01

    The crystal structure and catecholase-like activity of a mononuclear complex, Cu(EDTB)(NO3)2.C2H5OH (here EDTB stands N,N,N',N'-tetrakis(2'-benzimidazolyl methyl)-1,2-ethanediamine) has been studied in comparison with a binuclear complex Cu2(EDTB)(NO3)4.3H2O. The results show that the reactive rate constants increase with increases of reaction temperature and pH value of intermediate. Electrospray ionization mass spectrum (ESI-MS) shows that tautomerism isomers of catechol with the title complex exist in reaction solution, and catechol is oxidized to quinone, then it is further oxidized resulting in muconic acid and its derivatives via an intradiol mechanism, just like that catalyzed by a mononuclear non-heme iron-containing dioxygenase.

  18. Synthesis and crystal structure of a new homoleptic tetraarylruthenium(IV) complex Ru(2,4,5-Me{sub 3}C{sub 6}H{sub 2}){sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Chang-Jiu; Wu, Xiu-Li; Ma, Xiu-Fang; Jia, Ai-Quan; Zhang, Qian-Feng [Anhui Univ. of Technology, Anhui (China). Inst. of Molecular Engineering and Applied Chemistry and Anhui Province Key Lab. of Metallurgy Engineering and Resources Recycling

    2017-08-01

    Treatment of [Ru(acac){sub 3}] (acac-=acetylacetonate) with (2,4,5-Me{sub 3}C{sub 6}H{sub 2})MgBr, followed by column chromatography in air, afforded the homoleptic tetraaryl-ruthenium(IV) complex [Ru(2,4,5-Me{sub 3}C{sub 6}H{sub 2}){sub 4}] (1) in moderate yield. The product was characterized by proton NMR spectroscopy and microanalyses. Its crystal structure has also been established by X-ray crystallography.

  19. Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials.

    Science.gov (United States)

    Borel, Franck; Barbier, Elodie; Krasutsky, Sergiy; Janthawornpong, Karnjapan; Chaignon, Philippe; Poulter, C Dale; Ferrer, Jean-Luc; Seemann, Myriam

    2017-11-02

    IspH, also called LytB, a protein involved in the biosynthesis of isoprenoids through the methylerythritol phosphate pathway, is an attractive target for the development of new antimicrobial drugs. Here, we report crystal structures of Escherichia coli IspH in complex with the two most potent inhibitors: (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate (TMBPP) and (E)-4-amino-3-methylbut-2-en-1-yl diphosphate (AMBPP) at 1.95 and 1.7 Å resolution, respectively. The structure of the E. coli IspH:TMBPP complex exhibited two conformers of the inhibitor. This unexpected feature was exploited to design and evolve new antimicrobial candidates in silico. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Copper(II) complexes with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid: Syntheses, crystal structures and antifungal activities

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Pingping [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi' an 710069 (China); Li, Jie [Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, Xi' an 710069 (China); Bu, Huaiyu, E-mail: 7213792@qq.com [Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, Xi' an 710069 (China); Wei, Qing [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi' an 710069 (China); Zhang, Ruolin [Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, Xi' an 710069 (China); Chen, Sanping, E-mail: sanpingchen@126.com [Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi' an 710069 (China)

    2014-07-01

    Reaction of Cu(II) with an asymmetric semi-rigid organic ligand 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid (HL), yielded five compounds, [Cu{sub 0.5}L]{sub n} (1), [Cu(HL){sub 2}Cl{sub 2}]{sub n} (2), [Cu(HL){sub 2}Cl{sub 2}(H{sub 2}O)] (3), [Cu(L){sub 2}(H{sub 2}O)]{sub n} (4) and [Cu(L)(phen)(HCO{sub 2})]{sub n} (5), which have been fully characterized by infrared spectroscopy, elemental analysis, and single-crystal X-ray diffraction. As for compounds 1, 2 and 5, Cu(II) is bridged through HL, Cl{sup -}, and formic acid, respectively, featuring 1D chain-structure. In compound 3, Cu(II) with hexahedral coordination sphere is assembled through hydrogen-bonding into 3D supramolecular framework. In compound 4, 1D chain units –Cu–O–Cu–O– are ligand-bridged into a 3D network. All compounds were tested on fungi (Fusarium graminearum, Altemaria solani, Macrophoma kawatsukai, Alternaria alternata and Colletotrichum gloeosporioides). Compound 1 exhibits a better antifungal effect compared to other compounds. An effect of structure on the antifungal activity has also been correlated. - Graphical abstract: Copper(II) compounds with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid, were prepared, structurally characterized and investigated for antifungal activity. - Highlights: • The title compounds formed by thermodynamics and thermokinetics. • The five compounds show higher inhibition percentage than reactants. • The structure effect on the antifungal activity.

  1. Copper(II) complexes with 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid: Syntheses, crystal structures and antifungal activities

    Science.gov (United States)

    Xiong, Pingping; Li, Jie; Bu, Huaiyu; Wei, Qing; Zhang, Ruolin; Chen, Sanping

    2014-07-01

    Reaction of Cu(II) with an asymmetric semi-rigid organic ligand 4-(1H-1, 2, 4-trizol-1-ylmethyl) benzoic acid (HL), yielded five compounds, [Cu0.5L]n (1), [Cu(HL)2Cl2]n (2), [Cu(HL)2Cl2(H2O)] (3), [Cu(L)2(H2O)]n (4) and [Cu(L)(phen)(HCO2)]n (5), which have been fully characterized by infrared spectroscopy, elemental analysis, and single-crystal X-ray diffraction. As for compounds 1, 2 and 5, Cu(II) is bridged through HL, Cl-, and formic acid, respectively, featuring 1D chain-structure. In compound 3, Cu(II) with hexahedral coordination sphere is assembled through hydrogen-bonding into 3D supramolecular framework. In compound 4, 1D chain units -Cu-O-Cu-O- are ligand-bridged into a 3D network. All compounds were tested on fungi (Fusarium graminearum, Altemaria solani, Macrophoma kawatsukai, Alternaria alternata and Colletotrichum gloeosporioides). Compound 1 exhibits a better antifungal effect compared to other compounds. An effect of structure on the antifungal activity has also been correlated.

  2. Characterization of the Deoxynucleotide Triphosphate Triphosphohydrolase (dNTPase) Activity of the EF1143 Protein from Enterococcus faecalis and Crystal Structure of the Activator-Substrate Complex

    Energy Technology Data Exchange (ETDEWEB)

    Vorontsov, Ivan I.; Minasov, George; Kiryukhina, Olga; Brunzelle, Joseph S.; Shuvalova, Ludmilla; Anderson, Wayne F. (NWU)

    2012-06-19

    The EF1143 protein from Enterococcus faecalis is a distant homolog of deoxynucleotide triphosphate triphosphohydrolases (dNTPases) from Escherichia coli and Thermus thermophilus. These dNTPases are important components in the regulation of the dNTP pool in bacteria. Biochemical assays of the EF1143 dNTPase activity demonstrated nonspecific hydrolysis of all canonical dNTPs in the presence of Mn{sup 2+}. In contrast, with Mg{sup 2+} hydrolysis required the presence of dGTP as an effector, activating the degradation of dATP and dCTP with dGTP also being consumed in the reaction with dATP. The crystal structure of EF1143 and dynamic light scattering measurements in solution revealed a tetrameric oligomer as the most probable biologically active unit. The tetramer contains four dGTP specific allosteric regulatory sites and four active sites. Examination of the active site with the dATP substrate suggests an in-line nucleophilic attack on the {alpha}-phosphate center as a possible mechanism of the hydrolysis and two highly conserved residues, His-129 and Glu-122, as an acid-base catalytic dyad. Structural differences between EF1143 apo and holo forms revealed mobility of the {alpha}3 helix that can regulate the size of the active site binding pocket and could be stabilized in the open conformation upon formation of the tetramer and dGTP effector binding.

  3. Crystallization of the Large Membrane Protein Complex Photosystem I in a Microfluidic Channel

    Science.gov (United States)

    Abdallah, Bahige G.; Kupitz, Christopher; Fromme, Petra; Ros, Alexandra

    2014-01-01

    Traditional macroscale protein crystallization is accomplished non-trivially by exploring a range of protein concentrations and buffers in solution until a suitable combination is attained. This methodology is time consuming and resource intensive, hindering protein structure determination. Even more difficulties arise when crystallizing large membrane protein complexes such as photosystem I (PSI) due to their large unit cells dominated by solvent and complex characteristics that call for even stricter buffer requirements. Structure determination techniques tailored for these ‘difficult to crystallize’ proteins such as femtosecond nanocrystallography are being developed, yet still need specific crystal characteristics. Here, we demonstrate a simple and robust method to screen protein crystallization conditions at low ionic strength in a microfluidic device. This is realized in one microfluidic experiment using low sample amounts, unlike traditional methods where each solution condition is set up separately. Second harmonic generation microscopy via Second Order Nonlinear Imaging of Chiral Crystals (SONICC) was applied for the detection of nanometer and micrometer sized PSI crystals within microchannels. To develop a crystallization phase diagram, crystals imaged with SONICC at specific channel locations were correlated to protein and salt concentrations determined by numerical simulations of the time-dependent diffusion process along the channel. Our method demonstrated that a portion of the PSI crystallization phase diagram could be reconstructed in excellent agreement with crystallization conditions determined by traditional methods. We postulate that this approach could be utilized to efficiently study and optimize crystallization conditions for a wide range of proteins that are poorly understood to date. PMID:24191698

  4. Lessons from crystal structures of kainate receptors

    DEFF Research Database (Denmark)

    Møllerud, Stine; Frydenvang, Karla Andrea; Pickering, Darryl S

    2017-01-01

    -length structure has been determined of GluK2 by cryo electron microscopy to 7.6 Å resolution as well as 84 high-resolution crystal structures of N-terminal domains and ligand-binding domains, including agonist and antagonist bound structures, modulatory ions and mutations. However, there are still many unanswered...

  5. Synthesis, crystal structure and spectral characterization of the first Ag+ complex compounds involving O,N,O-coordinated N-acylhydrazones of salicylaldehyde

    Science.gov (United States)

    Repich, H. H.; Orysyk, S. I.; Orysyk, V. V.; Zborovskii, Yu. L.; Pekhnyo, V. I.; Vovk, M. V.

    2017-09-01

    N-acylhydrazones of salicylaldehyde is a well known class of ligands bearing O,N,O tridentate chelate coordination site. But up to now no structurally characterized Ag+ complexes with O,N,O coordinated N-acylhydrazones of salicylaldehyde were known. Therefore three Ag+ coordination compounds with functionally substituted N-acylhydrazones of salicylaldehyde were synthesized and characterized by X-ray diffraction, IR spectroscopy and thermogravimetric studies. In solutions the complexes were studied by 1H NMR and UV-Vis spectroscopy. The influence of the presence and location of additional nitrogen donor atoms in N-acylhydrazones of salicylaldehyde on their coordination modes was investigated. Ligand N'-salicylidenephenylacetohydrazide (contains no additional donor atoms) coordinates to Ag+ in classical O,N,O tridentate chelate manner. Ligand N‧-salicylidene-3-pyridinecarbohydrazide (contains β-N additional donor atom in acyl moiety) involves mixed O,N,O + β-N coordination. Whereas N'-salicylidene-4-pyridinecarbohydrazide (contains γ-N additional donor atom) coordinates to Ag+ in monodentate manner only via γ-N atom of heterocyclic substituent. All the complexes provide high coordination numbers of Ag+ and irregular shapes of coordination polyhedra which are not consistent with classical concepts of Ag+ coordination chemistry. However all the complexes are not thermally stable and easily undergo solvolysis upon dissolution.

  6. Crystal structure, characterization and magnetic properties of a 1D ...

    Indian Academy of Sciences (India)

    A new 1D polymeric copper(II) complex [{Cu(L)(CF3COO)}2]n has been synthesized using a potentially tetradentate Schiff base ... 1D copper(II) polymer; Schiff base; crystal structure; electrochemistry; EPR; magnetic properties. 1. Introduction ... number of copper(II) poly-clusters/assemblies may be mentioned in this regard ...

  7. Synthesis, characterization, X-ray crystal structure, electrochemical ...

    Indian Academy of Sciences (India)

    DOI 10.1007/s12039-015-0978-8. Synthesis, characterization, X-ray crystal structure, electrochemical evaluation and anti-cancer studies of a mixed ligand Cu(II) complex of (E)-N -((2-hydroxynaphthalen-1-yl)methylene)acetohydrazide. IRAN SHEIKHSHOAIEa, S YOUSEF EBRAHIMIPOURa,∗, MAHDIEH SHEIKHSHOAIEa,.

  8. Synthesis, crystal structure and catecholase activity of a Ni (II ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 6. Synthesis, crystal structure and ... The title complex 1 behaves as an effective catalyst towards oxidation of 3,5-ditertiarybutyl catechol (3,5-DTBC) in acetonitrile to its corresponding quinone derivative in air. The reaction follows first-order reaction kinetics ...

  9. Syntheses, characterization and crystal structures of potassium and ...

    Indian Academy of Sciences (India)

    Syntheses, characterization and crystal structures of potassium and barium complexes of a Schiff base ligand with different anions. Bhavesh Parmar Kamal Kumar Bisht Pratyush Maiti Parimal Paul Eringathodi Suresh. Special issue on Chemical Crystallography Volume 126 Issue 5 September 2014 pp 1373-1384 ...

  10. Syntheses, characterization and crystal structures of potassium and ...

    Indian Academy of Sciences (India)

    Syntheses, characterization and crystal structures of potassium and barium complexes of a Schiff base ligand with different anions. BHAVESH PARMARa, KAMAL KUMAR BISHTa,b, PRATYUSH MAITIc, PARIMAL PAULa,b, and ERINGATHODI SURESHa,b,∗. aAnalytical Discipline and Centralized Instrument Facility, ...

  11. Crystal structure of cyclohexylammonium thiocyanate

    OpenAIRE

    Abdulaziz A. Bagabas; Sultan B. Alhoshan; Hazem A. Ghabbour; C. S. Chidan Kumar; Hoong-Kun Fun

    2015-01-01

    In the title salt, C6H11NH3 +?SCN?, the cyclo?hexyl?ammonium ring adopts a slightly distorted chair conformation. The ammonium group occupies an equatorial position to minimize 1,3 and 1,5 diaxial inter?actions. In the crystal, the components are linked by N?H?N and N?H?S hydrogen-bonding inter?actions, resulting in a three-dimensional network.

  12. Crystal structure of cyclohexylammonium thiocyanate

    Directory of Open Access Journals (Sweden)

    Abdulaziz A. Bagabas

    2015-01-01

    Full Text Available In the title salt, C6H11NH3+·SCN−, the cyclohexylammonium ring adopts a slightly distorted chair conformation. The ammonium group occupies an equatorial position to minimize 1,3 and 1,5 diaxial interactions. In the crystal, the components are linked by N—H...N and N—H...S hydrogen-bonding interactions, resulting in a three-dimensional network.

  13. Crystal structure of Deep Vent DNA polymerase.

    Science.gov (United States)

    Hikida, Yasushi; Kimoto, Michiko; Hirao, Ichiro; Yokoyama, Shigeyuki

    2017-01-29

    DNA polymerases are useful tools in various biochemical experiments. We have focused on the DNA polymerases involved in DNA replication including the unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px). Many reports have described the different combinations between unnatural base pairs and DNA polymerases. As an example, for the replication of the Ds-Px pair, Deep Vent DNA polymerase exhibits high efficiency and fidelity, but Taq DNA polymerase shows much lower efficiency and fidelity. In the present study, we determined the crystal structure of Deep Vent DNA polymerase in the apo form at 2.5 Å resolution. Using this structure, we constructed structural models of Deep Vent DNA polymerase complexes with DNA containing an unnatural or natural base in the replication position. The models revealed that the unnatural Ds base in the template-strand DNA clashes with the side-chain oxygen of Thr664 in Taq DNA polymerase, but not in Deep Vent DNA polymerase. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  14. Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of Schiff base formation.

    Science.gov (United States)

    Light, Samuel H; Antanasijevic, Aleksandar; Krishna, Sankar N; Caffrey, Michael; Anderson, Wayne F; Lavie, Arnon

    2014-02-11

    A component of the shikimate biosynthetic pathway, dehydroquinate dehydratase (DHQD) catalyzes the dehydration of 3-dehydroquniate (DHQ) to 3-dehydroshikimate. In the type I DHQD reaction mechanism a lysine forms a Schiff base intermediate with DHQ. The Schiff base acts as an electron sink to facilitate the catalytic dehydration. To address the mechanism of Schiff base formation, we determined structures of the Salmonella enterica wild-type DHQD in complex with the substrate analogue quinate and the product analogue shikimate. In addition, we determined the structure of the K170M mutant (Lys170 being the Schiff base forming residue) in complex with quinate. Combined with nuclear magnetic resonance and isothermal titration calorimetry data that revealed altered binding of the analogue to the K170M mutant, these structures suggest a model of Schiff base formation characterized by the dynamic interplay of opposing forces acting on either side of the substrate. On the side distant from the substrate 3-carbonyl group, closure of the enzyme's β8-α8 loop is proposed to guide DHQ into the proximity of the Schiff base-forming Lys170. On the 3-carbonyl side of the substrate, Lys170 sterically alters the position of DHQ's reactive ketone, aligning it at an angle conducive for nucleophilic attack. This study of a type I DHQD reveals the interplay between the enzyme and substrate required for the correct orientation of a functional group constrained within a cyclic substrate.

  15. Crystal Structure of Human Interferon-[lamda]1 in Complex with Its High-Affinity Receptor Interferon-[lamda]R1

    Energy Technology Data Exchange (ETDEWEB)

    Miknis, Zachary; Magracheva, Eugenia; Li, Wei; Zdanov, Alexander; Kotenko, Sergei V.; Wlodawer, Alexander (NJMS); (NCI)

    2010-12-01

    Interferon (IFN)-{lambda}1 [also known as interleukin (IL)-29] belongs to the recently discovered group of type III IFNs. All type III IFNs initiate signaling processes through formation of specific heterodimeric receptor complexes consisting of IFN-{lambda}R1 and IL-10R2. We have determined the structure of human IFN-{lambda}1 complexed with human IFN-{lambda}R1, a receptor unique to type III IFNs. The overall structure of IFN-{lambda}1 is topologically similar to the structure of IL-10 and other members of the IL-10 family of cytokines. IFN-{lambda}R1 consists of two distinct domains having fibronectin type III topology. The ligand-receptor interface includes helix A, loop AB, and helix F on the IFN site, as well as loops primarily from the N-terminal domain and inter-domain hinge region of IFN-{lambda}R1. Composition and architecture of the interface that includes only a few direct hydrogen bonds support an idea that long-range ionic interactions between ligand and receptor govern the process of initial recognition of the molecules while hydrophobic interactions finalize it.

  16. Crystal structure from one-electron theory

    DEFF Research Database (Denmark)

    Skriver, H. L.

    1985-01-01

    The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated by the the......The authors have studied the crystal structure of all the 3d, 4d, and 5d transition metals at zero pressure and temperature by means of the linear muffin-tin orbital method and Andersen's force theorem. They find that, although the structural energy differences seem to be overestimated...

  17. New cobalt(II) and nickel(II) complexes of benzyl carbazate Schiff bases: Syntheses, crystal structures, in vitro DNA and HSA binding studies.

    Science.gov (United States)

    Nithya, Palanivelu; Helena, Sannasi; Simpson, Jim; Ilanchelian, Malaichamy; Muthusankar, Aathi; Govindarajan, Subbiah

    2016-12-01

    In the present study, new Schiff base complexes with the composition [M(NCS)2(L1)2]·nH2O, where M=Co (n=0) (1) and Ni (n=2) (2); [M(NCS)2(L2)2], M=Co (3) and Ni (4) as well as [M(NCS)2(L3)2], M=Co (5) and Ni (6); (L1=benzyl 2-(propan-2-ylidene)hydrazinecarboxylate, L2=benzyl 2-(butan-2-ylidene)hydrazinecarboxylate and L3=benzyl 2-(pentan-3-ylidene)hydrazinecarboxylate) have been synthesized by a template method. The complexes were characterised by analytical methods, spectroscopic studies, thermal and X-ray diffraction techniques. The structures of all the complexes explore that the metal(II) cation has a trans-planar coordination environment, the monomeric units containing a six-coordinated metal center in octahedral geometry with N-bound isothiocyanate anions coordinated as terminal ligands. Furthermore, the binding of the two Schiff base ligands to the metal centers involves the azomethine nitrogen and the carbonyl oxygen in mutually trans configuration. The binding interactions of all the complexes with Calf thymus-deoxyribonucleic acid (CT-DNA) and human serum albumin (HSA) have been investigated using absorption and emission spectral techniques. The CT-DNA binding properties of these complexes reveal that they bind to CT-DNA through a partial intercalation mode and the binding constant values were calculated using the absorption and emission spectral data. The binding constant values (~10×10(6)moldm(-3)) indicate strong binding of metal complexes with CT-DNA. HSA binding interaction studies showed that the cobalt and nickel complexes can quench the intrinsic fluorescence of HSA through static quenching process. Also, molecular docking studies were supported out to apprehend the binding interactions of these complexes with DNA and HSA which offer new understandings into the experimental model observations. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. A 2.3 A resolution structure of chymosin complexed with a reduced bond inhibitor shows that the active site beta-hairpin flap is rearranged when compared with the native crystal structure

    NARCIS (Netherlands)

    Groves, M R; Dhanaraj, V; Badasso, M; Nugent, P; Pitts, J E; Hoover, D J; Blundell, T L

    1998-01-01

    In the crystal structure of uncomplexed native chymosin, the beta-hairpin at the active site, known as 'the flap', adopts a different conformation from that of other aspartic proteinases. This conformation would prevent the mode of binding of substrates/inhibitors generally found in other aspartic

  19. pH-controlled change of the metal coordination in a dicopper(II) complex of the ligand H-BPMP: crystal structures, magnetic properties, and catecholase activity.

    Science.gov (United States)

    Torelli, S; Belle, C; Gautier-Luneau, I; Pierre, J L; Saint-Aman, E; Latour, J M; Le Pape, L; Luneau, D

    The dinucleating ligand 2,6-bis[(bis(2-pyridylmethyl)amino)methyl]-4-methylphenol (H-BPMP) has been used to synthesize the three dinuclear Cu(II) complexes [Cu2(BPMP)(OH)][ClO4](2).0.5C4H8O (1), [Cu2(BPMP)(H2O)2](ClO4)(3).4H2O (2), and [Cu2(H-BPMP)][(ClO4)4].2CH3CN (3). X-ray diffraction studies reveal that 1 is a mu-hydroxo, mu-phenoxo complex, 2 a diaqua, mu-phenoxo complex, and 3 a binuclear complex with Cu-Cu distances of 2.96, 4.32, and 6.92 A, respectively. Magnetization measurements reveal that 1 is moderately antiferromagnetically coupled while 2 and 3 are essentially uncoupled. The electronic spectra in acetonitrile or in water solutions give results in accordance with the solid-state structures. 1 is EPR-silent, in agreement with the antiferromagnetic coupling between the two copper atoms. The X-band spectrum of powdered 2 is consistent with a tetragonally elongated square pyramid geometry around the Cu(II) ions, in accordance with the solid-state structure, while the spectrum in frozen solution suggests a change in the coordination geometry. The EPR spectra of 3 corroborate the solid-state and UV-visible studies. The 1H NMR spectra also lead to observations in accordance with the conclusions from other spectroscopies. The electrochemical behavior of 1 and 2 in acetonitrile or in water solutions shows that the first reduction (Cu(II)Cu(II)-Cu(II)Cu(I) redox couple) is reversible and the second (formation of Cu(I)Cu(I) irreversible. In water, 1 and 2 are reversibly interconverted upon acid/base titration (pK 4.95). In basic medium a new species, 4, is reversibly formed (pK 12.0), identified as the bishydroxo complex. Only 1 exhibits catecholase activity (oxidation of 3,5-di-tert-butylcatechol to the corresponding quinone, vmax = 1.1 x 10(-6) M-1 s-1 and KM = 1.49 mM). The results indicate that the pH dependence of the catalytic abilities of the complexes is related to changes in the coordination sphere of the metal centers.

  20. Synthesis, crystal structures and supramolecular architectures of square pyramidal Cu(II) complexes containing aromatic chelating N,N’-donor ligands

    National Research Council Canada - National Science Library

    Jennifer, Samson Jegan; Muthiah, Packianathan Thomas

    2014-01-01

    ... on the structure.A series of five copper(II) complexes [Cu(Bipy) (5-TPC) 2(H2O)] (1), [Cu(Phen) (5-TPC) 2(H2O)] (2), [Cu(NO3) (4,7-Phen) (5-TPC) (H2O)].H2O (3), [Cu(Bipy) 2(5-TPC)]2.(ClO4)2 (4), and [Cu2(Bipy)4(H2PO4)] (5) (where Bipy = 2,2'-bipyridine, Phen...

  1. Crystal and molecular structure of a complex formed between the hydrochloride of 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene and 5,5‧-dibromo-2,2‧-biphenol

    Science.gov (United States)

    Bartoszak-Adamska, E.; Wojciechowski, G.; Jaskólski, M.; Brzezinski, B.

    2001-09-01

    A complex of 5,5‧-dibromo-2,2‧-biphenol with 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD) hydrochloride has been studied using X-ray diffraction, FT-IR, and 1H NMR spectroscopy. The compound crystallises in the space group P21/c with a=9.738(2), b=12.100(2), c=18.347(4) Å,β=92.62(3)° (at 100 K), and Z=4. In the crystal structure, the MTBDH+ cation, a chloride anion, and one molecule of 5,5‧-dibromo-2,2‧-biphenol are present. In the solid state the Cl- anion is an acceptor in N+-H⋯Cl-, O-H⋯Cl- and C-H⋯Cl- intermolecular hydrogen bonds. In chloroform the structure of the complex is comparable with that in the solid, whereas in acetonitryle the complex assumes a new structure owing to the almost complete dissociation of the protonated MTBD molecule. The 5,5‧-dibromo-2,2‧-biphenol molecule is hydrogen-bonded with the chloride anion. Within this complex the OH⋯OH hydrogen bond shows very large proton polarisability indicated by the continuous absorption in the FTIR spectrum.

  2. Phase transitions in KDP crystals with the complex organic and inorganic impurities

    Directory of Open Access Journals (Sweden)

    B.Strukov

    2007-01-01

    Full Text Available In this paper we present the results of the study of dielectric and thermal properties of KDP crystals doped with different complex organic and inorganic molecules which decorate different (pyramidal or prismatic crystal growth sectors. It is shown that the properties of stained and transparent parts of the crystal in comparison with the corresponding parts of the nominally pure crystal are different for KDP crystals grown by means of traditional (slow and rapid growth technique. The difference of the domain contribution into dielectric constant of the polar phase and its characteristic hysteresis in pure and dyed crystals, transition temperature position, form of the specific heat anomaly are presented and analyzed. The most probable model of incorporation of the complex impurity molecules into KDP structure is proposed.

  3. Crystal structure of human IRAK1.

    Science.gov (United States)

    Wang, Li; Qiao, Qi; Ferrao, Ryan; Shen, Chen; Hatcher, John M; Buhrlage, Sara J; Gray, Nathanael S; Wu, Hao

    2017-12-19

    Interleukin 1 (IL-1) receptor-associated kinases (IRAKs) are serine/threonine kinases that play critical roles in initiating innate immune responses against foreign pathogens and other types of dangers through their role in Toll-like receptor (TLR) and interleukin 1 receptor (IL-1R) mediated signaling pathways. Upon ligand binding, TLRs and IL-1Rs recruit adaptor proteins, such as myeloid differentiation primary response gene 88 (MyD88), to the membrane, which in turn recruit IRAKs via the death domains in these proteins to form the Myddosome complex, leading to IRAK kinase activation. Despite their biological and clinical significance, only the IRAK4 kinase domain structure has been determined among the four IRAK family members. Here, we report the crystal structure of the human IRAK1 kinase domain in complex with a small molecule inhibitor. The structure reveals both similarities and differences between IRAK1 and IRAK4 and is suggestive of approaches to develop IRAK1- or IRAK4-specific inhibitors for potential therapeutic applications. While the IRAK4 kinase domain is capable of homodimerization in the unphosphorylated state, we found that the IRAK1 kinase domain is constitutively monomeric regardless of its phosphorylation state. Additionally, the IRAK1 kinase domain forms heterodimers with the phosphorylated, but not unphosphorylated, IRAK4 kinase domain. Collectively, these data indicate a two-step kinase activation process in which the IRAK4 kinase domain first homodimerizes in the Myddosome, leading to its trans-autophosphorylation and activation. The phosphorylated IRAK4 kinase domain then forms heterodimers with the IRAK1 kinase domain within the Myddosome, leading to its subsequent phosphorylation and activation.

  4. Crystal structure of dichloridobis(dimethyl N-cyanodithioiminocarbonatezinc

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-03-01

    Full Text Available The ZnII atom in the title complex, [ZnCl2(C4H6N2S22], is coordinated in a distorted tetrahedral manner by two Cl atoms and two terminal N atoms of two dimethyl N-cyanodithioiminocarbonate ligands. In the crystal, the complex molecules are connected through C—H...Cl hydrogen bonds and Cl...S contacts, leading to a two-dimensional structure extending parallel to the ab plane.

  5. Tailoring quantum structures for active photonic crystals

    DEFF Research Database (Denmark)

    Kuznetsova, Nadezda

    This work is dedicated to the tailoring of quantum structures, with particular attention to the integration of selective area grown (SAG) active material into photonic crystal (PhC) slabs. The platform based on active PhC is vital to the realization of highly efficient elements with low energy......; in particular, the emission control of SAG QW matched the operating wavelength of photonic crystals. A strong photoluminescence signal in the slow light regime with the group index of 18 was demonstrated....

  6. Two-dimensional photonic crystal accelerator structures

    Directory of Open Access Journals (Sweden)

    Benjamin M. Cowan

    2003-10-01

    Full Text Available Photonic crystals provide a method of confining a synchronous speed-of-light mode in an all-dielectric structure, likely a necessary feature in any optical accelerator. We explore computationally a class of photonic crystal structures with translational symmetry in a direction transverse to the electron beam. We demonstrate synchronous waveguide modes and discuss relevant parameters of such modes. We then explore how accelerator parameters vary as the geometry of the structure is changed and consider trade-offs inherent in the design of an accelerator of this type.

  7. Crystal structure of enolase from Drosophila melanogaster.

    Science.gov (United States)

    Sun, Congcong; Xu, Baokui; Liu, Xueyan; Zhang, Zhen; Su, Zhongliang

    2017-04-01

    Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

  8. SYNTHESIS, CHARACTERIZATION, AND CRYSTAL STRUCTURE ...

    African Journals Online (AJOL)

    a

    organic coordination networks based on complexes of transition metals and multifunctional bridging ligands, such as polyamine and polyacid, has proven to be a fertile field due to the intriguing network topologies and potential functions as new ...

  9. Crystal structures of human sulfotransferases SULT1B1 and SULT1C1 complexed with the cofactor product adenosine-3'- 5'-diphosphate (PAP)

    Energy Technology Data Exchange (ETDEWEB)

    Dombrovski, Luidmila; Dong, Aiping; Bochkarev, Alexey; Plotnikov, Alexander N. (Toronto)

    2008-09-17

    Cytosolic sulfotransferases (SULTs), often referred as Phase II enzymes of chemical defense, are a superfamily of enzymes that catalyze the transfer of a sulfonate group from 3{prime}-phosphoadenosine 5{prime}-phosphosulfate (PAPS) to an acceptor group of substrates. This reaction modulates the activities of a large array of small endogenous and foreign chemicals including drugs, toxic compounds, steroid hormones, and neurotransmitters. In some cases, however, SULTs activate certain food and environmental compounds to mutagenenic and carcinogenic metabolites. Twelve human SULTs have been identified, which are partitioned into three families: SULT1, SULT2 and SULT4. The SULT1 family is further divided in four subfamilies, A, B, C, and E, and comprises eight members (1A1, 1A2, 1A3, 1B1, 1C1, 1C2, 1C3, and 1E1). Despite sequence and structural similarity among the SULTs, the family and subfamily members appear to have different biological function. SULT1 family shows substrate-binding specificity for simple phenols, estradiol, and thyroid hormones, as well as environmental xenobiotics and drugs. Human SULT1B1 is expressed in liver, colon, small intestine, and blood leukocytes, and shows substrate-binding specificity to thyroid hormones and benzylic alcohols. Human SULT1C1 is expressed in the adult stomach, kidney, and thyroid, as well as in fetal kidney and liver. SULT1C1 catalyzes the sulfonation of p-nitrophenol and N-hydroxy-2-acetylaminofluorene in vitro. However, the in vivo function of the enzyme remains unknown. We intend to solve the structures for all of the SULTs for which structural information is not yet available, and compare the structural and functional features of the entire SULT superfamily. Here we report the structures of two members of SULT1 family, SULT1B1 and SULT1C1, both in complex with the product of the PAPS cofactor, adenosine-3{prime}-5{prime}-diphosphate (PAP).

  10. Synthesis, crystal structure and EPR spectra of tetraaquabis(methylisonicotinate) copper(II) disaccharinate single crystal

    Science.gov (United States)

    Çelik, Yunus; Bozkurt, Esat; Uçar, İbrahim; Karabulut, Bünyamin

    2011-10-01

    The crystal structure of the [Cu(mein)2(H2O)4]·(sac)2 complex (mein: methylisonicotinate, sac: saccharine) was investigated by single crystal X-ray diffraction technique. The vibrational spectrum was also discussed in relation with the other compounds containing methylisonicotinate and saccharinate complexes. The EPR spectra of [Cu(mein)2(H2O)4]·(sac)2 single crystal have been studied in the temperature range between 113 and 300 K in three mutually perpendicular planes and exhibit two sets of four hyperfine lines of Cu2+ ion. The ground state wave function of the Cu2+ ion is an admixture of dx2-y2 and dz2 states.

  11. Crystal structure of levomepromazine maleate

    Directory of Open Access Journals (Sweden)

    Gyula Tamás Gál

    2016-05-01

    Full Text Available The asymmetric unit of the title salt, C19H25N2OS+·C4H3O4− [systematic name: (S-3-(2-methoxyphenothiazin-10-yl-N,N,2-trimethylpropanaminium hydrogen maleate], comprises two (S-levomepromazine cations and two hydrogen maleate anions. The conformations of the two cations are similar. The major difference relates to the orientation of the methoxy substituent at the phenothiazine ring system. The crystal components form a three-dimensional supramolecular network via N—H...O, C—H...O and C—H...π interactions. A comparison of the conformations of the levomepromazine cations with those of the neutral molecule and similar protonated molecules reveals significant conformational flexibility of the phenothiazine ring system and the substituent at the phenothiazine N atom.

  12. Transition Metal Complexes and Radical Anion Salts of 1,10-Phenanthroline Derivatives Annulated with a 1,2,5-Tiadiazole and 1,2,5-Tiadiazole 1,1-Dioxide Moiety: Multidimensional Crystal Structures and Various Magnetic Properties

    Directory of Open Access Journals (Sweden)

    Yoshiaki Shuku

    2014-01-01

    Full Text Available Advances in the molecular variety and the elucidation of the physical properties of 1,10-phenanthroline annulated with 1,2,5-thiadiazole and 1,2,5-thiadiazole 1,1-dioxide moieties have been achieved, and are described herein. A 1,2,5-thiadiazole compound, [1,2,5]thiadiazolo[3,4-f][1,10]phenanthroline (tdap, was used as a ligand to create multidimensional network structures based on S•••S and S•••N intermolecular interactions. A 1,2,5-thiadiazole 1,1-dioxide compound, [1,2,5] thiadiazolo[3,4-f][1,10]phenanthroline, 1,1-dioxide (tdapO2, was designed to create a stable radical anion, as well as good network structures. Single crystal X-ray structure analyses revealed that transition metal complexes of tdap, and radical anion salts of tdapO2 formed multidimensional network structures, as expected. Two kinds of tdap iron complexes, namely [Fe(tdap2(NCS2] and [Fe(tdap2(NCS2]•MeCN exhibited spin crossover transitions, and their transition temperatures showed a difference of 150 K, despite their similar molecular structures. Magnetic measurements for the tdapO2 radical anion salts revealed that the magnetic coupling constants between neighboring radical species vary from strongly antiferromagnetic (J = −320 K to ferromagnetic (J = 24 K, reflecting the differences in their π overlap motifs.

  13. Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action.

    Science.gov (United States)

    Kato, Akira; Yamao, Makiko; Hashihara, Yuta; Ishida, Hiroaki; Itoh, Toshimasa; Yamamoto, Keiko

    2017-10-26

    Vitamin D receptor (VDR) antagonists can be classified into two categories: the first category of VDR antagonists, which do not stabilize the helix 11-12, and the second category of antagonists, which destabilize the helix 6-7 region. To elucidate the mechanism underlying the first category antagonists by using the crystal structure, we designed and synthesized several VDR ligands with a p-hydroxyphenyl group at the C25-position. Of these, 22S-butyl-25-carbonyl analogue 5b and 25-di-p-hydoroxyphenyl analogues 6a,b showed strong antagonistic activity. We succeeded in cocrystallizing the ligand-binding domain of VDR complexed with 5b and found that the structure showed an alternative conformation of the helix 11-12 that explained the mechanism of the first category antagonists. Taking the present and previous studies together, we could elucidate the mechanisms underlying first and second categories antagonists based on individual crystal structures. This study provides significant insights into antagonism against not only VDR but also nuclear receptors.

  14. Phase equilibria, crystal structure, oxygen nonstoichiometry and thermal expansion of complex oxides in the Nd2O3 - SrO - Fe2O3 system

    Science.gov (United States)

    Aksenova, T. V.; Vakhromeeva, A. E.; Elkalashy, Sh. I.; Urusova, A. S.; Cherepanov, V. A.

    2017-07-01

    The phase equilibria in the ½ Nd2O3 - SrO - ½ Fe2O3 system were systematically studied at 1373 K in air. The homogeneity ranges and crystal structure of the solid solutions Nd1-xSrxFeO3-δ with 0.0≤x≤0.6 (sp. gr. Pbnm) and with 0.7≤x≤0.9 (sp. gr. Pm3m), Sr2-yNdyFeO4-δ with 0.7≤y≤0.9 (sp. gr. I4/mmm), Sr3-zNdzFe2O7-δ with 0.0≤z≤0.4 and 1.8≤z≤1.9 (sp. gr. I4/mmm) and Sr4-uNduFe3O10-δ with 0.7≤u≤0.9 (sp. gr. I4/mmm) were determined by X-ray diffraction analysis of quenched samples. The structural parameters of single-phase oxides were refined by the Rietveld profile method. The changes of oxygen content in the solid solutions Nd1-xSrxFeO3-δ (0.2≤x≤0.9), Sr3-zNdzFe2O7-δ (0.0≤z≤0.4 and z=1.9) and Sr4-uNduFe3O10-δ (0.7≤u≤0.9) versus temperature in air were determined by thermogravimetric analysis. Gradual substitution of neodymium by strontium leads to the decrease of the oxygen content. The average thermal expansion coefficients for the Nd1-xSrxFeO3-δ (0.6≤x≤0.8) samples were calculated within the temperature range 298-1373 K in air. The project of isothermal-isobaric phase diagram for the Nd-Sr-Fe-O system to the compositional triangle of metallic components was presented.

  15. New Mn(II, Ni(II, Cd(II, Pb(II complexes with 2-methylbenzimidazole and other ligands. Synthesis, spectroscopic characterization, crystal structure, magnetic susceptibility and biological activity studies

    Directory of Open Access Journals (Sweden)

    Shayma A. Shaker

    2016-11-01

    Full Text Available Synthesis and characterization of Mn(II, Ni(II, Cd(II and Pb(II mixed ligand complexes of 2-methylbenzimidazole with other ligands have been reported. The structure of the ligands and their complexes was investigated using elemental analysis, IR, UV–Vis, (1H, 13C NMR spectroscopy, molar conductivity and magnetic susceptibility measurements. In all the studies of complexes, the 2-methylbenzimidazole behaves as a neutral monodentate ligand which is coordinated with the metal ions through the N atom. While benzotriazole behaves as a neutral bidentate ligand which is coordinated with the Ni(II ion through the two N atoms. Moreover, the N-acetylglycine behaves as a bidentate ligand which is coordinated with the Mn(II, Ni(II and Pb(II ions through the N atom and the terminal carboxyl oxygen atom. The magnetic and spectral data indicate the tetrahedral geometry for Mn(II complex, irregular tetrahedral geometry for Pb(II complex and octahedral geometry for Ni(II complex. The X-ray single crystal diffraction method was used to confirm a centrosymmetric dinuclear Cd(II complex as each two metal ions are linked by a pair of thiocyanate N = S bridge. Two 2-methylbenzimidazole N-atom donors and one terminal thiocyanate N atom complete a highly distorted square pyramid geometry around the Cd atom. Besides, different cell types were used to determine the inhibitory effect of Mn(II, Ni(II, Cd(II and Pb(II complexes on cell growth using MTT assay. Cd(II complex showed cytotoxic effect on various types of cancer cell lines with different EC50 values.

  16. Synthesis and X-ray Crystal Structure of a Stable cis-1,2-bis(diphenylphosphinoethene Monodentate Thiolate Platinum Complex and TGA Studies of its Precursors

    Directory of Open Access Journals (Sweden)

    Vaz Rodrigo H.

    2002-01-01

    Full Text Available The stable Pt(II complex [Pt(SPh2(dppen (4, (dppen, Ph2PCH=CHPPh2 was obtained from [PtCl(SPh2(SnPh3cod] (1 (cod = 1,5-cyclooctadiene by reductive elimination reaction of SnClPh3 and substitution of the cod ligand by the diphosphine, albeit in low yields. Yields of 80% were obtained when [Pt(SPh2cod] (3 was used as the starting material instead. The viability of these reactions was suggested by a TG study, performed on the starting materials. Complex 4 was characterized by multinuclear NMR (195Pt, 31P, ¹H and 13C and IR spectroscopies and elemental analysis. The molecular structure, solved by an X-ray diffraction study, exhibted a slightly distorted square-planar geometry and short C=C and Pt-P bond distances which were interpreted in terms of a p interaction between the double bond and the metal-ligand bond, as observed for other diphosphine compounds described previously.

  17. Isothermal Titration Calorimetry: Assisted Crystallization of RNA-Ligand Complexes.

    Science.gov (United States)

    Da Veiga, Cyrielle; Mezher, Joelle; Dumas, Philippe; Ennifar, Eric

    2016-01-01

    The success rate of nucleic acids/ligands co-crystallization can be significantly improved by performing preliminary biophysical analyses. Among suitable biophysical approaches, isothermal titration calorimetry (ITC) is certainly a method of choice. ITC can be used in a wide range of experimental conditions to monitor in real time the formation of the RNA- or DNA-ligand complex, with the advantage of providing in addition the complete binding profile of the interaction. Following the ITC experiment, the complex is ready to be concentrated for crystallization trials. This chapter describes a detailed experimental protocol for using ITC as a tool for monitoring RNA/small molecule binding, followed by co-crystallization.

  18. Dislocation dynamics during plastic deformations of complex plasma crystals

    Science.gov (United States)

    Durniak, C.; Samsonov, D.; Ralph, J. F.; Zhdanov, S.; Morfill, G.

    2013-11-01

    The internal structures of most periodic crystalline solids contain defects. This affects various important mechanical and thermal properties of crystals. Since it is very difficult and expensive to track the motion of individual atoms in real solids, macroscopic model systems, such as complex plasmas, are often used. Complex plasmas consist of micrometer-sized grains immersed into an ion-electron plasma. They exist in solidlike, liquidlike, and gaseouslike states and exhibit a range of nonlinear and dynamic effects, most of which have direct analogies in solids and liquids. Slabs of a monolayer hexagonal complex plasma were subjected to a cycle of uniaxial compression and decompression of large amplitudes to achieve plastic deformations, both in experiments and simulations. During the cycle, the internal structure of the lattice exhibited significant rearrangements. Dislocations (point defects) were generated and displaced in the stressed lattice. They tended to glide parallel to their Burgers vectors under load. It was found that the deformation cycle was macroscopically reversible but irreversible at the particle scale.

  19. Synthesis, characterization, X-ray crystal structures and antibacterial activities of Schiff base ligands derived from allylamine and their vanadium(IV), cobalt(III), nickel(II), copper(II), zinc(II) and palladium(II) complexes

    Science.gov (United States)

    Amiri Rudbari, Hadi; Iravani, Mohammad Reza; Moazam, Vahid; Askari, Banafshe; Khorshidifard, Mahsa; Habibi, Neda; Bruno, Giuseppe

    2016-12-01

    A new Schiff base ligand, HL2, and four new Schiff base complexes, NiL12, PdL12, NiL22 and ZnL22, have been prepared and characterized by elemental analysis (CHN), FT-IR and UV-Vis spectroscopy. 1H and 13C NMR techniques were employed for characterization of the ligand (HL2) and the diamagnetic complexes (PdL12 and ZnL22). The molecular structures of PdL12, NiL22 and ZnL22 complexes were determined by the single crystal X-ray diffraction technique. The crystallographic data reveal that in these complexes the metal centers are four-coordinated by two phenolate oxygen and two imine nitrogen atoms of two Schiff base ligands. The geometry around the metal center in the PdL12 and NiL22 complexes is square-planar and for ZnL22 it is a distorted tetrahedral.In the end, five new (HL2, NiL12, PdL12, NiL22 and ZnL22) and six reported (HL1, VOL12, CoL13, CuL12, ZnL12 and Zn2L14) Schiff base compounds were tested for their in vitro antimicrobial activity against Staphylococcus aureus and Escherichia coli as examples of Gram-positive and Gram-negative bacterial strains, respectively, by disc diffusion method.

  20. Crystal Structures of the Staphylococcal Toxin SSL5 in Complex With Sialyl-Lewis X Reveal a Conserved Binding Site That Shares Common Features With Viral And Bacterial Sialic Acid-Binding Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Baker, H.M.; Basu, I.; Chung, M.C.; Caradoc-Davies, T.; Fraser, J.D.; Baker, E.N.

    2009-06-02

    Staphylococcus aureus is a significant human pathogen. Among its large repertoire of secreted toxins is a group of staphylococcal superantigen-like proteins (SSLs). These are homologous to superantigens but do not have the same activity. SSL5 is shown here to bind to human granulocytes and to the cell surface receptors for human IgA (Fc alphaRI) and P-selectin [P-selectin glycoprotein ligand-1 (PSGL-1)] in a sialic acid (Sia)-dependent manner. Co-crystallization of SSL5 with the tetrasaccharide sialyl Lewis X (sLe(X)), a key determinant of PSGL-1 binding to P-selectin, led to crystal structures of the SSL5-sLe(X) complex at resolutions of 1.65 and 2.75 A for crystals at two pH values. In both structures, sLe(X) bound to a specific site on the surface of the C-terminal domain of SSL5 in a conformation identical with that bound by P-selectin. Conservation of the key carbohydrate binding residues indicates that this ability to bind human glycans is shared by a substantial subgroup of the SSLs, including SSL2, SSL3, SSL4, SSL5, SSL6, and SSL11. This indicates that the ability to target human glycans is an important property of this group of toxins. Structural comparisons also showed that the Sia binding site in SSL5 contains a substructure that is shared by other Sia binding proteins from bacteria as well as viruses and represents a common binding motif.

  1. The n-propyl 3-azido-2,3-dideoxy-β-D-arabino-hexopyranoside: Syntheses, crystal structure, physical properties and stability constants of their complexes with Cu(II), Ni(II) and VO(II)

    Science.gov (United States)

    Barabaś, Anna; Madura, Izabela D.; Marek, Paulina H.; Dąbrowska, Aleksandra M.

    2017-11-01

    The structure, conformation and configuration of the n-propyl 3-azido-2,3-dideoxy-β-D-arabino-hexopyranoside (BAra-nPr) were determined by 1H NMR, 13C NMR, and IR spectroscopy, as well as by optical rotation. The crystal structure was confirmed by single-crystal X-ray diffraction studies at room temperature. The compound crystallizes in P21 space group symmetry of the monoclinic system. The molecule has a 4C1 chair conformation with azide group in the equatorial position both in a solution as well as in the crystal. The spatial arrangement of azide group is compared to other previously determined azidosugars. The hydrogen bonds between the hydroxyl group of sugar molecules lead to a ribbon structure observed also for the ethyl homolog. The packing of ribbons is dependent on the alkyl substituent length and with the elongation changes from pseudohexagonal to lamellar. Acidity constants for the n-propyl 3-azido-2,3-dideoxy-β-D-arabino-hexopyranoside (BAra-nPr) in an aqueous solution were evaluated by the spectrophotometric and potentiometric titrations methods. Title compound exhibit blue absorption with the maximum wavelengths in the range of 266 nm and 306 nm. Based on these measurements we showed equilibria existing in a particular solution and a distribution of species which have formed during the titration. We also investigated interactions between Cu(II), Ni(II) and VO(II) and title compound (as ligand L) during complexometric titration. On these bases we identified that in [CuII-BAra-nPr]2+ the ratio of the ligand L to metal ion M(II) was 3:1, while in [NiII-BAra-nPr]2+ and [VOII-BAra-nPr]2+ complexes 2:1 ratios were found. The cumulative stability constants (as log β) occurring in an aqueous solution for the complexes of BAra-nPr with Cu(II), Ni(II) and VO(IV) were 14.57; 11.71 and 4.20, respectively.

  2. Structural derivation and crystal chemistry of apatites.

    Science.gov (United States)

    White, T J; ZhiLi, Dong

    2003-02-01

    The crystal structures of the [A(1)(2)][A(2)(3)](BO(4))(3)X apatites and the related compounds [A(1)(2)][A(2)(3)](BO(5))(3)X and [A(1)(2)][A(2)(3)](BO(3))(3)X are collated and reviewed. The structural aristotype for this family is Mn(5)Si(3) (D8(8) type, P6(3)/mcm symmetry), whose cation array approximates that of all derivatives and from which related structures arise through the systematic insertion of anions into tetrahedral, triangular or linear interstices. The construction of a hierarchy of space-groups leads to three apatite families whose high-symmetry members are P6(3)/m, Cmcm and P6(3)cm. Alternatively, systematic crystallographic changes in apatite solid-solution series may be practically described as deviations from regular anion nets, with particular focus on the O(1)-A(1)-O(2) twist angle phi projected on (001) of the A(1)O(6) metaprism. For apatites that contain the same A cation, it is shown that phi decreases linearly as a function of increasing average ionic radius of the formula unit. Large deviations from this simple relationship may indicate departures from P6(3)/m symmetry or cation ordering. The inclusion of A(1)O(6) metaprisms in structure drawings is useful for comparing apatites and condensed-apatites such as Sr(5)(BO(3))(3)Br. The most common symmetry for the 74 chemically distinct [A(1)(2)][A(2)(3)](BO(4))(3)X apatites that were surveyed was P6(3)/m (57%), with progressively more complex chemistries adopting P6(3) (21%), P3; (9%), P6 (4.3%), P2(1)/m (4.3%) and P2(1) (4.3%). In chemically complex apatites, charge balance is usually maintained through charge-coupled cation substitutions, or through appropriate mixing of monovalent and divalent X anions or X-site vacancies. More rarely, charge compensation is achieved through insertion/removal of oxygen to produce BO(5) square pyramidal units (as in ReO(5)) or BO(3) triangular coordination (as in AsO(3)). Polysomatism arises through the ordered filling of [001] BO(4) tetrahedral strings to

  3. Mössbauer investigation of the photoexcited spin states and crystal structure analysis of the spin-crossover dinuclear complex [{Fe(bt)(NCS)(2)}(2)bpym] (bt=2,2'-bithiazoline, bpym=2,2'-bipyrimidine).

    Science.gov (United States)

    Gaspar, Ana B; Ksenofontov, Vadim; Reiman, Sergey; Gütlich, Philipp; Thompson, Amber L; Goeta, Andrés E; Muñoz, M Carmen; Real, José A

    2006-12-13

    The crystal structure of the complex [{Fe(bt)(NCS)(2)}(2)bpym] (1) (bt=2,2'-bithiazoline, bpym=2,2'-bipyrimidine) has been solved at 293, 240, 175 and 30 K. At all four temperatures the crystal remains in the P space group with a=8.7601(17), b=9.450(2), c=12.089(3) A, alpha=72.77(2), beta=79.150(19), gamma=66.392(18) degrees , V=873.1(4) Angstrom(3) (data for 293 K structure). The structure consists of centrosymmetric dinuclear units in which each iron(II) atom is coordinated by two NCS(-) ions in the cis position and two nitrogen atoms of the bridging bpym ligand, with the remaining positions occupied by the peripheral bt ligand. The iron atom is in a severely distorted octahedral FeN(6) environment. The average Fe--N bond length of 2.15(9) Angstrom indicates that compound 1 is in the high-spin state (HS-HS) at 293 K. Crystal structure determinations at 240, 175 and 30 K gave a cell comparable to that seen at 293 K, but reduced in volume. At 30 K, the average Fe--N distance is 1.958(4) Angstrom, showing that the structure is clearly low spin (LS-LS). At 175 K the average Fe--N bond length of 2.052(11) Angstrom suggests that there is an intermediate phase. Mössbauer investigations of the light-induced excited spin state trapping (LIESST) effect (lambda=514 nm, 25 mW cm(-2)) in 1 (4.2 K, H(ext)=50 kOe) show that the excited spin states correspond to the HS-HS and HS-LS pairs. The dynamics of the relaxation of the photoexcited states studied at 4.2 K and H(ext)=50 kOe demonstrate that HS-HS pairs revert with time to both HS-LS and LS-LS configurations. The HS-LS photoexcited pairs relax with time back to the ground LS-LS configuration. Complex [{Fe(0.15)Zn(0.85)(bt)(NCS)(2)}(2)bpym] (2) exhibits a continuous spin transition centred around 158 K in contrast to the two-step transition observed for 1. The different spin-crossover behaviour observed for 2 is due to the decrease of cooperativity (intermolecular interactions) imposed by the matrix of Zn(II) ions. This

  4. A novel structure of gel grown strontium cyanurate crystal and its structural, optical, electrical characterization

    Science.gov (United States)

    Divya, R.; Nair, Lekshmi P.; Bijini, B. R.; Nair, C. M. K.; Gopakumar, N.; Babu, K. Rajendra

    2017-12-01

    Strontium cyanurate crystals with novel structure and unique optical property like mechanoluminescence have been grown by conventional gel method. Transparent crystals were obtained. The single crystal X-ray diffraction analysis reveals the exquisite structure of the grown crystal. The crystal is centrosymmetric and has a three dimensional polymeric structure. The powder X ray diffraction analysis confirms its crystalline nature. The functional groups present in the crystal were identified by Fourier transform infrared spectroscopy. Elemental analysis confirmed the composition of the complex. A study of thermal properties was done by thermo gravimetric analysis and differential thermal analysis. The optical properties like band gap, refractive index and extinction coefficient were evaluated from the UV visible spectral analysis. The etching study was done to reveal the dislocations in the crystal which in turn explains mechanoluminescence emission. The mechanoluminescence property exhibited by the crystal makes it suitable for stress sensing applications. Besides being a centrosymmetric crystal, it also exhibits NLO behavior. Dielectric properties were studied and theoretical calculations of Fermi energy, valence electron plasma energy, penn gap and polarisability have been done.

  5. Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP- trapped ternary complex of Klentaq1: insights into nucleotide incorporation and selectivity.

    Science.gov (United States)

    Li, Y; Waksman, G

    2001-06-01

    The mechanism by which DNA polymerase I enzymes function has been the subject of extensive biochemical and structural studies. We previously determined the structure of a ternary complex of the large fragment of DNA polymerase I from Thermus aquaticus (Klentaq1) bound to a primer/template DNA and a dideoxycytidine 5'-triphosphate (ddCTP). In this report, we present the details of the 2.3-A resolution crystal structures of three additional ternary complexes of Klentaq1 bound to a primer/template DNA and a dideoxyguanosine 5'-triphosphate (ddGTP), a dideoxythymidine 5'-triphosphate (ddTTP), or a dideoxyadenosine 5'-triphosphate (ddATP). Comparison of the active site of the four ternary complexes reveals that the protein residues around the nascent base pair (that formed between the incoming dideoxynucleoside triphosphate [ddNTP] and the template base) form a snug binding pocket into which only a correct Watson-Crick base pair can fit. Except in the ternary complex bound to dideoxyguanosine 5'-triphosphate, there are no sequence specific contacts between the protein side chains and the nascent base pair, suggesting that steric constraints imposed by the protein onto the nascent base pair is the major contributor to nucleotide selectivity at the polymerase active site. The protein around the polymerase active site also shows plasticity, which may be responsible for the substrate diversity of the enzyme. Two conserved side chains, Q754 and R573, form hydrogen bonds with the N3 atom in the purine base and O2 atom in the pyrimidine base at the minor groove side of the base pair formed by the incorporated ddNMP and the corresponding template base in all the four ternary complexes. These hydrogen-bonding interactions may provide a means of detecting misincorporation at this position.

  6. A new Salen-type azo-azomethine ligand and its Ni(II), Cu(II) and Zn(II) complexes: Synthesis, spectral characterization, crystal structure and photoluminescence studies.

    Science.gov (United States)

    Ozkan, Gozde; Kose, Muhammet; Zengin, Huseyin; McKee, Vickie; Kurtoglu, Mukerrem

    2015-11-05

    A novel Salen-type azo-azomethine ligand H2agen, 2,2'-{ethane-1,2-diylbis[nitrilomethylylidene]}bis{4-[ethylphenyldiazenyl]phenol}, formed by the 1:2M condensation of ethane-1,2-diamine with 5-[(4-ethylphenyl)diazenyl]-2-hydroxybenzaldehyde and its nickel(II), copper(II), and zinc(II) complexes were synthesized and characterized by the spectroscopic and analytical methods. The UV-vis spectra of the ligand were investigated in three organic solvents (DMSO, DMF and CHCl3). The ligand shows two absorption bands assigned to π-π(∗) and n-π(∗) transitions in the solvents used. Cu(II), and Ni(II) are tetra-coordinate binding to two phenolic oxygens and two imine nitrogens in approximate square planar geometry. Zn(II) also coordinates using the same sites like other metals but gave tetragonal configuration. Molecular structure of the Cu(II) complex [Cu(agen)] was determined by single crystal X-ray diffraction study. The X-ray data revealed that crystallographic imposed symmetry was absent for the complex molecule. In the structure, the Cu(II) ion is coordinated to two phenolate oxygen atoms and two imine nitrogen atoms of the azo-azomethine ligand with approximate square planar geometry. The ligand H2agen and its metal complexes exhibit strong blue emissions with irradiation. Fluorescence quantum yields and excited-state lifetimes for the ligand and its complexes were obtained. The H2agen ligand had a 35% quantum yield and a 3.27 ns excited-state lifetime. Complexation with metal ions caused reductions in intensities and quantum yields. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Complex investigations of structural and optical homogeneities of low-photorefractivity lithium niobate crystals by the conoscopy and photoinduced and Raman light scattering methods

    Science.gov (United States)

    Sidorov, N. V.; Pikoul, O. Yu.; Kruk, A. A.; Teplyakova, N. A.; Yanichev, A. A.; Palatnikov, M. N.

    2015-02-01

    Using photoinduced light scattering, conoscopy, and Raman spectroscopy methods, we have studied stoichiometric lithium niobate crystals and congruent crystals that were doped with Mg(0.078, 0.89 mas %), Zn(0.03, 0.52, 0.62), Cu(0.015), B(0.12), Gd(0.51), Y(0.46), Gd(0.23):Mg(0.75), Mg(0.86):Fe(0.0036), Ta(1.13):Mg(0.011), and Y(0.24):Mg(0.63) cations. It has been found that, depending on the kind of the pattern of photoinduced light scattering, investigated specimens can be divided into three groups. We have shown that the asymmetry of the indicatrix of photoinduced light scattering of LiNbO3 crystals is caused by birefringence of exciting laser radiation as it propagates perpendicularly to the polar axis of the crystal, whereas the asymmetry of the Raman spectrum arises due to the occurrence of spontaneous polarization, the vector of which is directed along the polar axis, and by birefringence. The pattern of the photoinduced light scattering depends on the difference of the refractive indices Δ n = n o - n e of the ordinary ( n o ) and extraordinary ( n e ) rays and their energies E. If En o {ie259-1} En e , the proportion of the photoinduced light scattering has the shape of a three-layer round spot. For equal energies, the pattern has the shape of a symmetric figure-eight. At En o < En e , the figure-eight is asymmetric. In this case, its large "lobe" is directed in the positive direction of the polar axis of the crystal.

  8. Shear induced structures in crystallizing cocoa butter

    Science.gov (United States)

    Mazzanti, Gianfranco; Guthrie, Sarah E.; Sirota, Eric B.; Marangoni, Alejandro G.; Idziak, Stefan H. J.

    2004-03-01

    Cocoa butter is the main structural component of chocolate and many cosmetics. It crystallizes in several polymorphs, called phases I to VI. We used Synchrotron X-ray diffraction to study the effect of shear on its crystallization. A previously unreported phase (phase X) was found and a crystallization path through phase IV under shear was observed. Samples were crystallized under shear from the melt in temperature controlled Couette cells, at final crystallization temperatures of 17.5^oC, 20^oC and 22.5^oC in Beamline X10A of NSLS. The formation of phase X was observed at low shear rates (90 s-1) and low crystallization temperature (17.5^oC), but was absent at high shear (720 s-1) and high temperature (20^oC). The d-spacing and melting point suggest that this new phase is a mixture rich on two of the three major components of cocoa butter. We also found that, contrary to previous reports, the transition from phase II to phase V can happen through the intermediate phase IV, at high shear rates and temperature.

  9. Crystal structure of a mixed-ligand silver(I complex of the non-steroidal anti-inflammatory drug diclofenac and pyrimidine

    Directory of Open Access Journals (Sweden)

    Sevim Hamamci Alisir

    2016-10-01

    Full Text Available In the title mixed-ligand silver(I coordination polymeric complex with the non-steroidal anti-inflammatory drug diclofenac (C14H11Cl2NO2 (diclH and pyrimidine (pym, namely poly[{μ2-2-[2-(2,6-dichloroanilinophenyl]acetato-κ2O:O′}(μ2-pyrimidine-κ2N1:N3silver(I], [Ag(C14H10Cl2NO2(C4H4N2]n or [Ag(μ-dicl(μ-pym]n, the very distorted tetrahedral AgN2O2 coordination centres comprise two N-atom donors from bridging pym ligands [Ag—N = 2.381 (3 and 2.412 (3 Å] and two carboxylate O-atom donors from dicl ligands [Ag—O = 2.279 (2 and 2.280 (2 Å], which bridge Ag atoms, giving a centrosymmetric dinuclear units with a short Ag...Ag separation [2.8931 (5 Å]. Within the units are short intraligand C—Cl...π(pym interactions [3.6409 (15 Å]. The units are linked through the bridging N atoms of the pym ligand into a two-dimensional sheet–polymer structure lying parallel to (100 and stabilized by inter-ring π–π interactions between the pym ligands [Cg...Cg = 3.4199 (17 Å]. Additional inter-unit C—H...O and C—H...Cg hydrogen-bonding interactions between the sheets give an overall three-dimensional structure.

  10. Crystallization, data collection and processing of the chymotrypsin–BTCI–trypsin ternary complex

    Energy Technology Data Exchange (ETDEWEB)

    Esteves, Gisele Ferreira; Teles, Rozeni Chagas Lima; Cavalcante, Nayara Silva; Neves, David; Ventura, Manuel Mateus [Laboratório de Biofísica, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900 Brasília-DF (Brazil); Barbosa, João Alexandre Ribeiro Gonçalves, E-mail: joao@lnls.br [Center for Structural Molecular Biology (CeBiME), Brazilian Synchrotron Light Laboratory (LNLS), CP 6192, 13083-970 Campinas-SP (Brazil); Freitas, Sonia Maria de, E-mail: joao@lnls.br [Laboratório de Biofísica, Instituto de Ciências Biológicas, Universidade de Brasília, 70910-900 Brasília-DF (Brazil)

    2007-12-01

    A ternary complex of the proteinase inhibitor (BTCI) with trypsin and chymotrypsin was crystallized and its crystal structure was solved by molecular replacement. A ternary complex of the black-eyed pea trypsin and chymotrypsin inhibitor (BTCI) with trypsin and chymotrypsin was crystallized by the sitting-drop vapour-diffusion method with 0.1 M HEPES pH 7.5, 10%(w/v) polyethylene glycol 6000 and 5%(v/v) 2-methyl-2,4-pentanediol as precipitant. BTCI is a small protein with 83 amino-acid residues isolated from Vigna unguiculata seeds and is able to inhibit trypsin and chymotrypsin simultaneously by forming a stable ternary complex. X-ray data were collected from a single crystal of the trypsin–BTCI–chymotrypsin ternary complex to 2.7 Å resolution under cryogenic conditions. The structure of the ternary complex was solved by molecular replacement using the crystal structures of the BTCI–trypsin binary complex (PDB code) and chymotrypsin (PDB code) as search models.

  11. Crystal Structure of the Homo sapiens Kynureninase-3-Hydroxyhippuric Acid Inhibitor Complex: Insights into the Molecular Basis Of Kynureninase Substrate Specificity

    Energy Technology Data Exchange (ETDEWEB)

    Lima,Santiago; Kumar,Sunil; Gawandi,Vijay; Momany,Cory; Phillips,Robert S.; (Georgia)

    2009-02-23

    Homo sapiens kynureninase is a pyridoxal-5'-phosphate dependent enzyme that catalyzes the hydrolytic cleavage of 3-hydroxykynurenine to yield 3-hydroxyanthranilate and L-alanine as part of the tryptophan catabolic pathway leading to the de novo biosynthesis of NAD{sup +}. This pathway results in quinolinate, an excitotoxin that is an NMDA receptor agonist. High levels of quinolinate have been correlated with the etiology of neurodegenerative disorders such as AIDS-related dementia and Alzheimer's disease. We have synthesized a novel kynureninase inhibitor, 3-hydroxyhippurate, cocrystallized it with human kynureninase, and solved the atomic structure. On the basis of an analysis of the complex, we designed a series of His-102, Ser-332, and Asn-333 mutants. The H102W/N333T and H102W/S332G/N333T mutants showed complete reversal of substrate specificity between 3-hydroxykynurenine and L-kynurenine, thus defining the primary residues contributing to substrate specificity in kynureninases.

  12. Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex.

    NARCIS (Netherlands)

    Buchwald, G.; Ebert, J.; Basquin, C.; Sauliere, J.; Jayachandran, U.; Bono, F.; Hir, H. Le; Conti, E.

    2010-01-01

    In mammals, Up-frameshift proteins (UPFs) form a surveillance complex that interacts with the exon junction complex (EJC) to elicit nonsense-mediated mRNA decay (NMD). UPF3b is the component of the surveillance complex that bridges the interaction with the EJC. Here, we report the 3.4 A resolution

  13. Molecular and crystal structure of ivalin

    Energy Technology Data Exchange (ETDEWEB)

    Coetzer, J. (Council for Scientific and Industrial Research, Pretoria (South Africa). National Physical Research Lab.); Kruger, G.J.; Levendis, D.C. (Council for Scientific and Industrial Research, Pretoria (South Africa). National Chemical Research Lab.)

    1982-01-01

    The bromoacetate derivative of ivalin, which is a sesquiterpene lactone, crystallizes in the space group P2/sub 1/, with two molecules in the unit cell. Its structure was solved by standard X-ray methods. Full-matrix least-squares refinement converged at R=0,052. The proposed stereochemistry has been confirmed.

  14. Hydrothermal synthesis, crystal structure and luminescence property ...

    Indian Academy of Sciences (India)

    Hydrothermal synthesis, crystal structure and luminescence property of a three dimensional Sm(III) coordination polymer with. 2,5-pyridinedicarboxylic acid. KRANTHI KUMAR GANGU, ANIMA S DADHICH and. SARATCHANDRA BABU MUKKAMALA. ∗. Department of Chemistry, GITAM University, Visakhapatnam 530 045, ...

  15. Hydrothermal synthesis, crystal structure and luminescence property ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 12. Hydrothermal synthesis, crystal structure and luminescence property of a three dimensional Sm(III) coordination polymer with 2,5-pyridinedicarboxylic acid. Kranthi Kumar Gangu Anima S Dadhich Saratchandra Babu Mukkamala. Volume 127 Issue 12 ...

  16. Synthesis, crystal structure, theoretical study and luminescence ...

    Indian Academy of Sciences (India)

    Synthesis, crystal structure, theoretical study and luminescence property of a butterfly-like W/Cu/S cluster with 1,10-phenanthroline. AI-HUA CHENa,b, SU-CI MENGc,d, JIN-FANG ZHANGb,c and CHI ZHANGb,c,∗. aSchool of Chemical & Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051,.

  17. Theoretical investigation on crystal structure, detonation ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 125; Issue 4. Theoretical investigation on crystal structure, detonation ... The bond dissociation energies and bond orders for the weakest bonds were analysed to investigate the thermal stability of the title compound. The detonation and pressure were evaluated by ...

  18. Solvothermal syntheses, crystal structures, optical and thermal ...

    Indian Academy of Sciences (India)

    Keywords. Selenidogermanates; nickel; solvothermal syntheses; crystal structures; optical properties ... The different coordination environments of Ni²⁺ ions indicate the influence of the denticity of ethylene polyamines on the formation of selenidogermanates in the presence of transition metal ions. Thecompounds 1–3 ...

  19. Synthesis of liquid-crystal vanadyl complex with Schiff base

    Energy Technology Data Exchange (ETDEWEB)

    Galyametdinov, Yu.G.; Ivanova, G.I.; Ovchinnikov, I.V. (AN SSSR, Kazan. Fiziko-Tekhnicheskij Inst.)

    1984-12-01

    The paramagnetic Schiff base vanadyl (4) complex (4-octiloxy-N-(2-hydroxy-4-heptyloxybenziliden aniline) possessing liquid-crystal properties is obtained. The complex is synthesized by heating Schiff base with vanadyl acetate in absolute ethanol with the 65% yield. The IR and EPR spectra are measured.

  20. Crystallization of Mitochondrial Respiratory Complex II fromChicken Heart: A Membrane-Protein Complex Diffracting to 2.0Angstrom

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Li-shar; Borders, Toni M.; Shen, John T.; Wang, Chung-Jen; Berry, Edward A.

    2004-12-17

    Procedure is presented for preparation of diffraction-quality crystals of a vertebrate mitochondrial respiratory Complex II. The crystals have the potential to diffract to at least 2.0 Angstrom with optimization of post-crystal-growth treatment and cryoprotection. This should allow determination of the structure of this important and medically relevant membrane protein complex at near-atomic resolution and provide great detail of the mode of binding of substrates and inhibitors at the two substrate-binding sites.

  1. Molecular structure of a complex formed between hydrobromide of 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene and 5,5'-dibromo-2,2'-biphenol in crystal and solutions

    Science.gov (United States)

    Wojciechowski, Grzegorz; Ratajczak-Sitarz, Małgorzata; Katrusiak, Andrzej; Brzezinski, Bogumil

    2002-08-01

    A complex of 5,5'-dibromo-2,2'-biphenol with 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene hydrobromide has been studied using X-ray diffraction, FT-IR, and 1H NMR spectroscopy. In the crystal structure, a bromide anion is hydrogen-bonded with MTBDH + cation and two hydroxyl groups of two 5,5'-dibromo-2,2'-biphenol molecules. In the solid state, the Br - anion is an acceptor in N +-H⋯Br -, and two O-H⋯Br - intermolecular hydrogen bonds. In chloroform and acetonitrile, the structure of the complex assumes a new structure due to almost complete dissociation of protonated MTBD molecule. In chloroform, the MTBDH + cation is hydrogen-bonded with 5,5'-dibromo-2,2'-biphenol whereas in acetonitrile it is free and solvated by the solvent. In both cases, the 5,5'-dibromo-2,2'-biphenol molecule is hydrogen-bonded to the bromide anion.

  2. Modular crystals as modulated structures

    DEFF Research Database (Denmark)

    Elcoro, L.; Perez-Mato, J.M.; Friese, K.

    2008-01-01

    The use of the superspace formalism is extended to the description and refinement of the homologous series of modular structures with two symmetry-related modules with different orientations. The lillianite homologous series has been taken as a study case. Starting from a commensurate modulated...... and introduce in the starting model the two orientations of the underlying module sublattices. We show that a composite approach with this type of function, which treats the cations and anions as two separate subsystems forming a misfit compound, is the most appropriate and robust method for the refinements....

  3. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Li, Fenglei [Iowa State Univ., Ames, IA (United States)

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition

  4. Photonic Crystal Laser-Driven Accelerator Structures

    Energy Technology Data Exchange (ETDEWEB)

    Cowan, Benjamin M

    2007-08-22

    Laser-driven acceleration holds great promise for significantly improving accelerating gradient. However, scaling the conventional process of structure-based acceleration in vacuum down to optical wavelengths requires a substantially different kind of structure. We require an optical waveguide that (1) is constructed out of dielectric materials, (2) has transverse size on the order of a wavelength, and (3) supports a mode with speed-of-light phase velocity in vacuum. Photonic crystals---structures whose electromagnetic properties are spatially periodic---can meet these requirements. We discuss simulated photonic crystal accelerator structures and describe their properties. We begin with a class of two-dimensional structures which serves to illustrate the design considerations and trade-offs involved. We then present a three-dimensional structure, and describe its performance in terms of accelerating gradient and efficiency. We discuss particle beam dynamics in this structure, demonstrating a method for keeping a beam confined to the waveguide. We also discuss material and fabrication considerations. Since accelerating gradient is limited by optical damage to the structure, the damage threshold of the dielectric is a critical parameter. We experimentally measure the damage threshold of silicon for picosecond pulses in the infrared, and determine that our structure is capable of sustaining an accelerating gradient of 300 MV/m at 1550 nm. Finally, we discuss possibilities for manufacturing these structures using common microfabrication techniques.

  5. Three Co(II) complexes with a sexidentate N2O4-donor bis-Schiff base ligand: Synthesis, crystal structures, DFT studies, urease inhibition and molecular docking studies

    Science.gov (United States)

    Wang, Hu; Zhang, Xia; Zhao, Yu; Zhang, Dongmei; Jin, Fan; Fan, Yuhua

    2017-11-01

    Three new N2O4-donor bis-Schiff base Co(II) complexes, Co(C36H34N2O8)·2CH3OH (1), Co(C28H34N2O8S2)·H2O (2) and Co(C40H36N4O8)·3CH3OH (3) with distorted octahedral six-coordinate Co(II) centers were synthesized and determined by single crystal X-ray analysis. The X-ray crystallography shows that the metal atoms of three complexes are all six-coordinate with two nitrogen atoms from Cdbnd N groups, two oxygen atoms from ether groups and two carboxylic oxygen atoms in the mono-ligand, forming a distorted octahedral geometry. Theoretical studies of the three complexes were carried out by density functional theory (DFT) Becke's three-parameter hybrid (B3LYP) method employing the 6-31G basis set. The DFT studies indicate that the calculation is in accordance with the experimental results. Moreover, inhibition of jack bean urease by Co(II) complexes 1-3 have also been investigated. At the same time, a docking analysis using a DOCK program was conducted to determine the probable binding mode by inserting the complexes into the active site of jack bean urease. The experimental values and docking simulation exhibited that the complex 3 showed strong inhibitory activity (IC50 = 16.43 ± 2.35 μM) and the structure-activity relationships were further discussed.

  6. Nonlinear coherent structures in granular crystals

    Science.gov (United States)

    Chong, C.; Porter, Mason A.; Kevrekidis, P. G.; Daraio, C.

    2017-10-01

    The study of granular crystals, which are nonlinear metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics, and condensed-matter physics. Granular crystals exploit geometrical nonlinearities in their constitutive microstructure to produce properties (such as tunability and energy localization) that are not conventional to engineering materials and linear devices. In this topical review, we focus on recent experimental, computational, and theoretical results on nonlinear coherent structures in granular crystals. Such structures—which include traveling solitary waves, dispersive shock waves, and discrete breathers—have fascinating dynamics, including a diversity of both transient features and robust, long-lived patterns that emerge from broad classes of initial data. In our review, we primarily discuss phenomena in one-dimensional crystals, as most research to date has focused on such scenarios, but we also present some extensions to two-dimensional settings. Throughout the review, we highlight open problems and discuss a variety of potential engineering applications that arise from the rich dynamic response of granular crystals.

  7. Synthesis and crystal structure analysis of uranyl triple acetates

    Energy Technology Data Exchange (ETDEWEB)

    Klepov, Vladislav V., E-mail: vladislavklepov@gmail.com [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Serezhkina, Larisa B.; Serezhkin, Victor N. [Department of Chemistry, Samara National Research University, 443086 Samara (Russian Federation); Alekseev, Evgeny V., E-mail: e.alekseev@fz-juelich.de [Institute for Energy and Climate Research (IEK-6), Forschungszentrum Jülich GmbH, 52428 Jülich (Germany); Institut für Kristallographie, RWTH Aachen University, 52066 Aachen (Germany)

    2016-12-15

    Single crystals of triple acetates NaR[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O (R=Mg, Co, Ni, Zn), well-known for their use as reagents for sodium determination, were grown from aqueous solutions and their structural and spectroscopic properties were studied. Crystal structures of the mentioned phases are based upon (Na[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}){sup 2–} clusters and [R(H{sub 2}O){sub 6}]{sup 2+} aqua-complexes. The cooling of a single crystal of NaMg[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O from 300 to 100 K leads to a phase transition from trigonal to monoclinic crystal system. Intermolecular interactions between the structural units and their mutual packing were studied and compared from the point of view of the stereoatomic model of crystal structures based on Voronoi-Dirichlet tessellation. Using this method we compared the crystal structures of the triple acetates with Na[UO{sub 2}(CH{sub 3}COO){sub 3}] and [R(H{sub 2}O){sub 6}][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} and proposed reasons of triple acetates stability. Infrared and Raman spectra were collected and their bands were assigned. - Graphical abstract: Single crystals of uranium based triple acetates, analytical reagents for sodium determination, were synthesized and structurally, spectroscopically and topologically characterized. The structures were compared with the structures of compounds from preceding families [M(H{sub 2}O){sub 6})][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} (M = Mg, Co, Ni, Zn) and Na[UO{sub 2}(CH{sub 3}COO){sub 3}]. Analysis was performed with the method of molecular Voronoi-Dirichlet polyhedra to reveal a large contribution of the hydrogen bonds into intermolecular interactions which can be a reason of low solubility of studied complexes.

  8. Structural examination of lithium niobate ferroelectric crystals by combining scanning electron microscopy and atomic force microscopy

    Science.gov (United States)

    Efremova, P. V.; Ped'ko, B. B.; Kuznecova, Yu. V.

    2016-02-01

    The structure of lithium niobate single crystals is studied by a complex technique that combines scanning electron microscopy and atomic force microscopy. By implementing the piezoresponse force method on an atomic force microscope, the domain structure of lithium niobate crystals, which was not revealed without electron beam irradiation, is visualized

  9. Synthesis, crystal structure and catecholase activity of a Ni(II ...

    Indian Academy of Sciences (India)

    Synthesis, crystal structure and catecholase activity of a Ni(II) complex derived from a tetradentate ... of the crystal are a = 30.6345(4)Å, b = 8.45340(10)Å, c = 7.75180(10)Å. Structural analysis reveals a tetradentate chelation behaviour of ..... Acc. Chem. Res. 35 183. 7. (a) Abuhijleh A L, Pollitte J and Woods C 1994 Inorg.

  10. Synthesis, crystal structure and Thermogravimetry of ortho-phthalic ...

    Indian Academy of Sciences (India)

    acid bridged coordination polymer of Copper(II) ... Keywords. o-Phthalic acid; coordination polymer; X-ray crystal structure; Copper(II); EPR; TGA. 1. .... 3.2 EPR spectrum of. [{Cu(O2C-μ2-C6H5-μ1-CO2)2}.2H2O]n. The EPR spectrum of the complex was recorded as polycrystalline solid and has been shown in figure 1.

  11. A new copper(II) chelate complex with tridentate ligand: Synthesis, crystal and molecular electronic structure of aqua-(diethylenetriamine-N, N‧, N‧‧)-copper(II) sulfate monohydrate and its fire retardant properties

    Science.gov (United States)

    Lavrenyuk, H.; Mykhalichko, O.; Zarychta, B.; Olijnyk, V.; Mykhalichko, B.

    2015-09-01

    The crystals of a new aqua-(diethylenetriamine-N, N‧, N‧‧)-copper(II) sulfate monohydrate have been synthesized by direct interaction of solid copper(II) sulfate pentahydrate with diethylenetriamine (deta). The crystal structure of [Cu(deta)H2O]SO4ṡH2O (1) has been determined by X-ray diffraction methods at 100 K and characterized using X-ray powder diffraction pattern: space group P 1 bar, a = 7.2819(4), b = 8.4669(4), c = 8.7020(3) Å, α = 83.590(3), β = 89.620(4), γ = 84.946(4)°, Z = 2. The environment of the Cu(II) atom is a distorted, elongated square pyramid which consists of three nitrogen atoms of the deta molecule and oxygen atom of the water molecule in the basal plane of the square pyramid (the average lengths of the in-plane Cu-N and Cu-O bonds are 2.00 Å). The apical position of the coordination polyhedron is occupied by complementary oxygen atom of the sulfate anion (the length of the axial Cu-O bond is 2.421(1) Å). The crystal packing is governed by strong hydrogen bonds of O-H⋯O and N-H⋯O types. The ab initio quantum-chemical calculations have been performed by the restricted Hartree-Fock method with a basis set 6-31∗G using the structural data of [Cu(deta)H2O]SO4ṡH2O. It has been ascertained that the degenerate d-orbitals of the Cu2+ ion split under the co-action of both the square-pyramidal coordination and the chelation. It is significant that visually observed crystals color (blue-violet) of the [Cu(deta)H2O]SO4ṡH2O complex is in good agreement with the calculated value of wavelength of visible light (λ = 5735 Å) which is closely related to the energy of the absorbed photon (Δ = 2.161 eV). Furthermore, the stereo-chemical aspect of influence of the CuSO4 upon combustibility of modified epoxy-amine polymers has been scrutinized.

  12. Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization.

    Science.gov (United States)

    Totir, Monica; Echols, Nathaniel; Nanao, Max; Gee, Christine L; Moskaleva, Alisa; Gradia, Scott; Iavarone, Anthony T; Berger, James M; May, Andrew P; Zubieta, Chloe; Alber, Tom

    2012-01-01

    Structural biology and structural genomics projects routinely rely on recombinantly expressed proteins, but many proteins and complexes are difficult to obtain by this approach. We investigated native source proteins for high-throughput protein crystallography applications. The Escherichia coli proteome was fractionated, purified, crystallized, and structurally characterized. Macro-scale fermentation and fractionation were used to subdivide the soluble proteome into 408 unique fractions of which 295 fractions yielded crystals in microfluidic crystallization chips. Of the 295 crystals, 152 were selected for optimization, diffraction screening, and data collection. Twenty-three structures were determined, four of which were novel. This study demonstrates the utility of native source proteins for high-throughput crystallography.

  13. Prototyping of chemical composition of complex crystals using method of neural networks

    Science.gov (United States)

    Blagin, A. V.; Nefedov, V. V.; Nefedova, N. A.

    2017-10-01

    The traditional methods of study of multi-component crystal heterojunction structures by means of X-ray diffractometry and electroscopy are expensive and complex. The present paper discusses the information technology based on the use of artificial neural networks for identification of the chemical composition of complex semiconductor structures. The obtained results allow supposing the successful use of this method for many multi-component systems.

  14. Five novel lanthanide complexes with 2-chloroquinoline-4-carboxylic acid and 1,10-phenanthroline: Crystal structures, molecular spectra, thermal properties and bacteriostatic activities

    Science.gov (United States)

    Wang, Ye; Jin, Cheng-Wei; He, Shu-Mei; Ren, Ning; Zhang, Jian-Jun

    2016-12-01

    Five novel lanthanide complexes [Ln2(2-ClQL)6(phen)2(H2O)2]·2H2O (Ln = Pr(1), Sm(2), Eu(3), Ho(4), Er(5)); 2-ClQL: 2-chloroquinoline-4-carboxylate; phen: 1,10-phenanthroline; were synthesized by conventional solution method at room temperature and characterized via elemental analysis, powder x-ray diffraction, Infrared spectroscopy and Raman spectrometry. The results indicate that complexes 1-5 are isostructural, and each Ln3+ ion is eight-coordinated adopting a distorted square antiprismatic molecular geometry. Binuclear complex 1 are stitched together via hydrogen bonding interactions to form 1D chains, and further to form 2D sheets by the π-π interactions. Luminescence investigation reveals that complex 3 displays strong red emission. TG/DTG-FTIR, reveal the thermal decomposition processes and products of title complexes. The bacteriostatic activities of the complexes were evaluated against Candida albicans, Escherichia coli, and Staphylococcus aureus.

  15. Structural chemistry and number theory amalgamized: crystal structure of Na11Hg52.

    Science.gov (United States)

    Hornfeck, Wolfgang; Hoch, Constantin

    2015-12-01

    The recently elucidated crystal structure of the technologically important amalgam Na11Hg52 is described by means of a method employing some fundamental concept of number theory, namely modular arithmetical (congruence) relations observed between a slightly idealized set of atomic coordinates. In combination with well known ideas from group theory, regarding lattice-sublattice transformations, these allow for a deeper mutual understanding of both and provide the structural chemist with a slightly different kind of spectacles, thus enabling a distinct viw on complex crystal structures in general.

  16. Structural insights into the exon junction complex.

    Science.gov (United States)

    Le Hir, Hervé; Andersen, Gregers Rom

    2008-02-01

    In higher eukaryotes, the exon junction complex is loaded onto spliced mRNAs at a precise position upstream of exon junctions, where it remains during nuclear export and cytoplasmic localisation until it is removed during the first translation round. The exon junction core complex consists of four proteins that form a dynamic binding platform for a variety of peripheral factors involved in mRNA metabolism. In the complex, mRNA binding is mediated by the DEAD-box protein eIF4AIII, and inhibition of its ATPase activity forms the mechanistic basis for the long-term stability of the complex. Recent crystal structures of the exon junction complex and eIF4AIII have provided the structural framework for investigating the function of the eIF4AIII ATPase and for localisation of surface patches involved in binding peripheral factors. Additionally, by comparison with the structure of a second DEAD-box protein also bound to RNA and ATP, general principles for the ATPase and unwinding/mRNP remodelling activities for this important group of enzymes can be proposed on the basis of atomic structures.

  17. Crystal structure of tris(hydroxylammonium orthophosphate

    Directory of Open Access Journals (Sweden)

    Malte Leinemann

    2015-11-01

    Full Text Available The crystal structure of the title salt, ([H3NOH]+3·[PO4]3−, consists of discrete hydroxylammonium cations and orthophosphate anions. The atoms of the cation occupy general positions, whereas the anion is located on a threefold rotation axis that runs through the phosphorus atom and one of the phosphate O atoms. In the crystal structure, cations and anions are linked by intermolecular O—H...O and N—H...O hydrogen bonds into a three-dimensional network. Altogether, one very strong O—H...O, two N—H...O hydrogen bonds of medium strength and two weaker bifurcated N—H...O interactions are observed.

  18. Synthesis, crystal structure, thermal analysis and dielectric ...

    Indian Academy of Sciences (India)

    providing information about the complete crystal structure at room temperature of the new compounds. These materi- ... Data collection instrument. Kappa-APEX II. Kappa-APEX II. Radiation, graphite ..... graphic method of the mixed compounds K0.57(NH4)0.43CdCl3 and K0.25(NH4)0.75CdCl3. This study is restricted to ...

  19. Chemical composition, crystal structure, and their relationships with the intrinsic properties of spinel-type crystals based on bond valences.

    Science.gov (United States)

    Liu, Xiao; Wang, Hao; Lavina, Barbara; Tu, Bingtian; Wang, Weimin; Fu, Zhengyi

    2014-06-16

    Spinel-type crystals may possess complex and versatile chemical composition and crystal structure, which leads to difficulty in constructing relationships among the chemical composition, crystal structure, and intrinsic properties. In this work, we develop new empirical methods based on bond valences to estimate the intrinsic properties, namely, compressibility and thermal expansion of complex spinel-type crystals. The composition-weighted average of bond force constants in tetrahedral and octahedral coordination polyhedra is derived as a function of the composition-weighted average of bond valences, which can be calculated according to the experimental chemical composition and crystal structural parameters. We discuss the coupled effects of tetrahedral and octahedral frameworks on the aforementioned intrinsic properties. The bulk modulus could be quantitatively calculated from the composition-weighted average of bond force constants in tetrahedral and octahedral coordination polyhedra. In contrast, a quantitative estimation of the thermal expansion coefficient could be obtained from the composition-weighted average of bond force constants in octahedral coordination polyhedra. These empirical methods have been validated by the results obtained for a new complex quaternary spinel-type oxynitride Mg0.268Al2.577O3.733N0.267 as well as MgAl2O4 and Al2.85O3.45N0.55 from the literature. Further, these empirical methods have the potential to be extensively applied in other types of complex crystals.

  20. Coefficient of crystal lattice matching as a parameter of substrate - crystal structure compatibility in silumins

    Directory of Open Access Journals (Sweden)

    J. Piątkowski

    2009-07-01

    Full Text Available Adding high-melting point elements (Mo, Nb, Ni, Ti, W to complex silumins results in hardening of the latter ones, owing to the formation of new intermetallic phases of the AlxMey type, with refinement of dendrites in α solution and crystals in β phase. The hardening is also due to the effect of various inoculants. An addition of the inoculant is expected to form substrates, the crystal lattice of which, or some (privileged lattice planes and interatomic spaces should bear a strong resemblance to the crystal nucleus. To verify this statement, using binary phase equilibria systems, the coefficient of crystal lattice matching, being one of the measures of the crystallographic similarity, was calculated. A compatibility of this parameter (up to 20% may decide about the structure compatibility between the substrate and crystal which, in turn, is responsible for the effectiveness of alloy modification. Investigations have proved that, given the temperature range of their formation, the density, the lattice type, and the lattice parameter, some intermetallic phases of the AlxMey type can act as substrates for the crystallisation of aluminium and silicon, and some of the silumin hardening phases.

  1. Optically induced structural phase transitions in ion Coulomb crystals

    DEFF Research Database (Denmark)

    Horak, Peter; Dantan, Aurelien Romain; Drewsen, Michael

    2012-01-01

    We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures, such as b......We investigate numerically the structural dynamics of ion Coulomb crystals confined in a three-dimensional harmonic trap when influenced by an additional one-dimensional optically induced periodical potential. We demonstrate that transitions between thermally excited crystal structures...

  2. General study on the crystal, electronic and band structures, the morphological characterization, and the magnetic properties of the Sr{sub 2}DyRuO{sub 6} complex perovskite

    Energy Technology Data Exchange (ETDEWEB)

    Triana, C.A.; Landínez Téllez, D.A.; Roa-Rojas, J., E-mail: jroar@unal.edu.co

    2015-01-15

    A comprehensive investigation of the general properties of the Sr{sub 2}DyRuO{sub 6} complex perovskite was undertaken. Crystal structure characterization performed by X-ray diffraction measurements and Rietveld analysis allowed establishing that the material crystallizes in a distorted monoclinic perovskite-like structure belonging to the P2{sub 1}/n (#14) space group, with alternating distribution of Dy{sup 3} {sup +} (2c: 0, 0.5, 0) and Ru{sup 5} {sup +} (2d: 0.5, 0, 0). Because of the mismatch in the ionic radii, the DyO{sub 6} and RuO{sub 6} octahedra are forced to tilt around the cubic directions so as to optimize the Sr–O inter-atomic bond lengths. Morphological characterization carried out by scanning electron microscopy indicated a particle size D = 37.17 nm and an activation energy Q = 109.8 kJ/mol. Semi-quantitative compositional study, performed through energy-dispersive X-ray experiments, corroborated that the pure phase of the Sr{sub 2}DyRuO{sub 6} was correctly obtained. Magnetic properties determined from the fit of the Curie–Weiss law to the curves of magnetic susceptibility as a function of temperature showed that Sr{sub 2}DyRuO{sub 6} exhibits an antiferromagnetic-like behavior at low temperatures as a consequence of a magnetic transition at T = 38 K. Data collected with respect to the field dependence of the magnetization showed the existence of a weak ferromagnetic moment relationship with antiferromagnetic-like behavior. Density functional theory allowed establishing the optimum electronic structure for Sr{sub 2}DyRuO{sub 6}, and the study of the density of states showed that Dy{sup 3} {sup +} and Ru{sup 5} {sup +} are responsible for the magnetic character of the compound, with the prediction that at T = 0 K it behaves as a half-metallic material. The spin magnetic moment of the cell is close to 16 μ{sub B}, and the integer number of Bohr magneton is a signature of half-metallic character. Evolution of crystal structure at high

  3. Crystal structures of the 2:2 complex of 1,1′-(1,2-phenylenebis(3-m-tolylurea and tetrabutylammonium chloride or bromide

    Directory of Open Access Journals (Sweden)

    Chao Huang

    2017-09-01

    Full Text Available The title compounds, tetrabutylammonium chloride–1,1′-(1,2-phenylenebis(3-m-tolylurea (1/1, C16H36N+·Cl−·C22H22N4O2 or [(n-Bu4N+·Cl−(C22H22N4O2] (I and tetrabutylammonium bromide–1,1′-(1,2-phenylenebis(3-m-tolylurea (1/1, C16H36N+·Br−·C22H22N4O2 or [(n-Bu4N+·Br−(C22H22N4O2] (II, both comprise a tetrabutylammonium cation, a halide anion and an ortho-phenylene bis-urea molecule. Each halide ion shows four N—H...X (X = Cl or Br interactions with two urea receptor sites of different bis-urea moieties. A crystallographic inversion centre leads to the formation of a 2:2 arrangement of two halide anions and two bis-urea molecules. In the crystals, the dihedral angle between the two urea groups of the bis-urea molecule in (I [defined by the four N atoms, 165.4 (2°] is slightly smaller than that in (II [167.4 (2°], which is probably due to the smaller ionic radius of chloride compared to bromide.

  4. The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg2+ ion in the active site and a putative RNA-binding site

    Energy Technology Data Exchange (ETDEWEB)

    Min, Andrew B; Miallau, Linda; Sawaya, Michael R; Habel, Jeff; Cascio, Duilio; Eisenberg, David [UCLA; (UCB)

    2013-01-10

    VapBC pairs account for 45 out of 88 identified toxin-antitoxin (TA) pairs in the Mycobacterium tuberculosis (Mtb) H37Rv genome. A working model suggests that under times of stress, antitoxin molecules are degraded, releasing the toxins to slow the metabolism of the cell, which in the case of VapC toxins is via their RNase activity. Otherwise the TA pairs remain bound to their promoters, autoinhibiting transcription. The crystal structure of Rv0301-Rv0300, an Mtb VapBC TA complex determined at 1.49 Å resolution, suggests a mechanism for these three functions: RNase activity, its inhibition by antitoxin, and its ability to bind promoter DNA. The Rv0301 toxin consists of a core of five parallel beta strands flanked by alpha helices. Three proximal aspartates coordinate a Mg2+ ion forming the putative RNase active site. The Rv0300 antitoxin monomer is extended in structure, consisting of an N-terminal beta strand followed by four helices. The last two helices wrap around the toxin and terminate near the putative RNase active site, but with different conformations. In one conformation, the C-terminal arginine interferes with Mg2+ ion coordination, suggesting a mechanism by which the antitoxin can inhibit toxin activity. At the N-terminus of the antitoxin, two pairs of Ribbon-Helix-Helix (RHH) motifs are related by crystallographic twofold symmetry. The resulting hetero-octameric complex is similar to the FitAB system, but the two RHH motifs are about 30 Å closer together in the Rv0301-Rv0300 complex, suggesting either a different span of the DNA recognition sequence or a conformational change.

  5. Crystal structure of the high-affinity Na+,K+-ATPase–ouabain complex with Mg2+ bound in the cation binding site

    DEFF Research Database (Denmark)

    Laursen, Mette; Yatime, Laure; Nissen, Poul

    2013-01-01

    of ouabain and the side chains of αM1, αM2, and αM6. Furthermore, the structure reveals that cation transport site II is occupied by Mg2+, and crystallographic studies indicate that Rb+ and Mn2+, but not Na+, bind to this site. Comparison with the low-affinity [K2]E2–MgFx–ouabain structure [Ogawa et al...

  6. Crystal structure of dichloridobis(dimethyl N-cyanodithioiminocarbonatecobalt(II

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-01-01

    Full Text Available The structure of the mononuclear title complex, [{(H3CS2C=NC[triple-bond] N}2CoCl2], consists of a CoII atom coordinated in a distorted tetrahedral manner by two Cl− ligands and the terminal N atoms of two dimethyl N-cyanodithioiminocarbonate ligands. The two organic ligands are almost coplanar, with a dihedral angle of 5.99 (6° between their least-squares planes. The crystal packing features pairs of inversion-related complexes that are held together through C—H...Cl and C—H...S interactions and π–π stacking [centroid-to-centroid distance = 3.515 (su? Å]. Additional C—H...Cl and C—H...S interactions, as well as Cl...S contacts < 3.6 Å, consolidate the crystal packing.

  7. Structural evolution in the crystallization of rapid cooling silver melt

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Z.A., E-mail: ze.tian@gmail.com [School of Physics and Electronics, Hunan University, Changsha 410082 (China); Laboratory for Simulation and Modelling of Particulate Systems School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052 (Australia); Dong, K.J.; Yu, A.B. [Laboratory for Simulation and Modelling of Particulate Systems School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052 (Australia)

    2015-03-15

    The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald’s rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperature range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid–solid phase transition. - Highlights: • A comprehensive structural analysis is conducted focusing on crystallization. • The involved atoms in our analysis are more than 90% for all samples concerned. • A series of distinct intermediate states are found in crystallization of silver melt. • A novelty icosahedron-saturated state breeds the metastable bcc state.

  8. A palladium(II) complex containing both carbonyl and imine oxime ligands: Crystal structure, experimental and theoretical UV-vis, IR and NMR studies

    Science.gov (United States)

    Kaya, Yunus; Icsel, Ceyda; Yilmaz, Veysel T.; Buyukgungor, Orhan

    2013-05-01

    A new palladium(II) complex, [Pd(ppeieo)(inap)]·DMSO (ppeieo = (1E,2E)-phenyl-[(1-phenylethyl)imino]-ethanal oxime and inap = isonitrosoacetophenone) has been synthesized and characterized by elemental analysis, UV-vis, IR, NMR. X-ray diffraction analysis of the DMSO solvate of the complex shows that the palladium(II) ion is coordinated in a distorted square-planar geometry by ppeieo and inap, which is formed during the hydrolysis of ppeieo. DFT (B3LYP/LANL2DZ) calculations on the complex have been carried out to correlate geometry and spectroscopic properties such as electronic, vibrational and NMR chemical shifts. The complete vibrational frequency assignments were made and the calculation results were applied to simulate infrared spectra of the title compound which shows good agreement with observed spectra. The calculated HOMO and LUMO energies show that several transitions including the π → π* and charge transfer occur within the molecule. The chemical shifts reasonably correspond to the calculated spectra.

  9. Crystal structure of Vδ1 T cell receptor in