Insights into metal ion binding in phospholipases A(2): ultra high-resolution crystal structures of an acidic phospholipase A(2) in the Ca2+ free and bound states

The electrophile Ca2+ is an essential multifunctional co-factor in the phospholipase A(2) mediated hydrolysis of phospholipids. Crystal structures of an acidic phospholipase A(2) from the venom of Bothrops jararacussu have been determined both in the Ca2+ free and bound states at 0.97 and 1.60 angstrom resolutions, respectively. In the Ca2+ bound state, the Ca2+ ion is penta-coordinated by a distorted pyramidal cage of oxygen and nitrogen atoms that is significantly different to that observed in structures of other Group I/II phospholipases A(2). In the absence of Ca2+, a water molecule occupies the position of the Ca2+ ion and the side chain of Asp49 and the calcium-binding loop adopts a different conformation. (c) 2005 Elsevier SAS. All rights reserved.

Crystallization and preliminary X-ray analysis of bucain, a novel toxin from the Malayan krait Bungarus candidus

Bucain is a three-finger toxin, structurally homologous to snake-venom muscarinic toxins, from the venom of the Malayan krait Bungarus candidus. These proteins have molecular masses of approximately 6000-8000 da and encompass the potent curaremimetic neurotoxins which confer lethality to Elapidae and Hydrophidae venoms. Bucain was crystallized in two crystal forms by the hanging-drop vapour-diffusion technique in 0.1 M sodium citrate pH 5.6, 15% PEG 4000 and 0.15 M ammonium acetate. Form I crystals belong to the monoclinic system space group C2, with unit-cell parameters a = 93.73, b = 49.02, c = 74.09 Angstrom, beta = 111.32degrees, and diffract to a nominal resolution of 1.61 Angstrom. Form II crystals also belong to the space group C2, with unit-cell parameters a = 165.04, b = 49.44, c = 127.60 Angstrom, beta = 125.55degrees, and diffract to a nominal resolution of 2.78 Angstrom. The self-rotation function indicates the presence of four and eight molecules in the crystallographic asymmetric unit of the form I and form II crystals, respectively. Attempts to solve these structures by molecular-replacement methods have not been successful and a heavy-atom derivative search has been initiated.

The X-ray crystallographic structure of Escherichia coli branching enzyme

Branching enzyme catalyzes the formation of alpha-1,6 branch points in either glycogen or starch. We report the 2.3-Angstrom crystal structure of glycogen branching enzyme from Escherichia coli. The enzyme consists of three major domains, an NH2-terminal seven-stranded beta-sandwich domain, a COOH-terminal domain, and a central alpha/beta-barrel domain containing the enzyme active site. While the central domain is similar to that of all the other amylase family enzymes, branching enzyme shares the structure of all three domains only with isoamylase. Oligosaccharide binding was modeled or branching enzyme using the enzyme-oligosaccharide complex structures of various alpha-amylases and cyclodextrin glucanotransferase and residues were implicated in oligosaccharide binding. While most of the oligosaccharides modeled well in the branching enzyme structure, an approximate 50degrees rotation between two of the glucose units was required to avoid steric clashes with Trp(298) of branching enzyme. A similar rotation was observed in the mammalian alpha-amylase structure caused by an equivalent tryptophan residue in this structure. It appears that there are two binding modes for oligosaccharides in these structures depending on the identity and location of this aromatic residue.

At the interface: Crystal structures of phospholipases A(2)

The protein content of many snake venoms often includes one or more phospholipases A(2) (PLA(2)). In recent years a growing number of venoms from snakes of Agkistrodon, Bothrops and Trimeresurus species have been shown to contain a catalytically inactive PLA(2)-homologue in which the highly conserved aspartic acid at position 49 (Asp49) is substituted by lysine (Lys49). Although demonstrating little or no catalytic activity, these Lys49-PLA(2)s disrupt membranes by a Ca2+-independent mechanism of action. In addition, this family of PLA(2)s demonstrates myotoxic and cytolytic pharmacological activities, however the structural bases underlying these functional properties are poorly understood. Through the application of X-ray crystallography in combination with biophysical and bioinformatics techniques, we are studying structure/function relationships of Lys49-PLA(2)s. We here present results of a systematic X-ray crystallographic and amino acid sequence analysis study of Lys49-PLA(2)s and propose a model to explain the Ca2+ independent membrane damaging activity. (C) 1998 Elsevier B.V. Ltd. All rights reserved.

Crystal Structure Determination of Mebendazole Form A Using High-Resolution Synchrotron X-Ray Powder Diffraction Data

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Crystal structure of propylthiouracil determined using high-resolution synchrotron X-ray powder diffraction

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Synthesis, spectroscopic characterization and X-ray crystallographic studies of trans-[PtCl2(PEt3)(PySOR)] complexes, where PySOR=(2-methylsulphinyl)-pyridine and (2-n-propylsulphinyl)pyridine

Alkylsulphinylpyridine ligands containing three potential donor centres: N, S and O atoms and two complexes of general formula trans-[PtCl2(PEt3)PySOR)] (R = Me and Pr-n) were prepared and characterized by elemental analysis, i.r. spectroscopy, H-1- and P-31-n.m.r. and X-ray crystallography. The ambidentate ligands act in both situations as monodentate ligands, bonded to the metal exclusively through the nitrogen atom. The crystal structures revealed the occurrence of discrete molecules and, in both complexes, the Pt atoms are coordinated in square planar arrangements by two chloride ions, in a trans configuration, by the pyridine nitrogen atom, and by the phosphine P atom. The oxygen atoms do not take part in the complexation scheme.

Crystal structures and luminescence properties of La3Zr4F25 and alpha-LaZr3F15

During a study of the LaF3-ZrF4 system, both La3Zr4F25 and alpha-LaZr3F15 compounds have been evidenced. Their crystal structures have been determined from single-crystal X-ray diffraction data. La3Zr4F25 crystallises in the cubic system with a= 12.384 Angstrom and I (4) over bar 3d space group (no. 220). Its crystal structure is built up of (ZrF6)(2-) octahedra and (LaF8)(5-) dodecahedra sharing corners. The low temperature form, alpha, of LaZr3F15 is orthorhombic (space group Pmmn, no. 59) with a = 15.721 Angstrom, b = 16.299 Angstrom, c= 8.438 Angstrom. Its structure is built of corner-sharing tricaped trigonal prisms surrounding the La3+ ions and both octahedra and monocapped trigonal prisms encompassing the Zr4+ ions. This structure is characterised by dynamically disordered (ZrF6)(2-) complex anions.The Eu3+ luminescence properties of these phases have been investigated and are discussed in relationship with their crystal structures.

Terbium(III) and dysprosium(III) 8-connected 3D networks containing 2,5-thiophenedicarboxylate anion: Crystal structures and photoluminescence studies

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Crystal structures and luminescence properties of La3Zr4F25 and α-LaZr3F15

During a study of the LaF3-ZrF4 system, both La3Zr4F25 and α-LaZr3F15 compounds have been evidenced. Their crystal structures have been determined from single-crystal X-ray diffraction data. La3Zr4F25 crystallises in the cubic system with a = 12.384 Å and 143d space group (no. 220). Its crystal structure is built up of (ZrF6)2- octahedra and (LaF8)5- dodecahedra sharing corners. The low temperature form, α, of LaZr3F15 is orthorhombic (space group Pmmn, no. 59) with a = 15.721 Å, b = 16.299 Å, c = 8.438 Å. Its structure is built of corner-sharing tricaped trigonal prisms surrounding the La3+ ions and both octahedra and monocapped trigonal prisms encompassing the Zr4+ ions. This structure is characterised by dynamically disordered (ZrF6)2- complex anions. The Eu3+ luminescence properties of these phases have been investigated and are discussed in relationship with their crystal structures.

Crystal structures and magnetic properties of CuX2(pdmp)2 complexes (X = Br, Cl)

We report the synthesis and the structural and magnetic characterization of two new compounds: dibromobis-(pdmp)copper(II), CuBr2C22H24N4 (1), and dichlorobis(pdmp)copper(II), CuCl2C22H24N4 (2), where pdmp = 1-phenyl-3,5-dimethylpyrazole. The structures were refined by full-matrix least-squares techniques to R1 = 0.0620 and 0.0777, respectively. Compound 1 belongs to the space group P21/n with a = 8.165(5) Å, b = 10.432(3) Å, c = 13.385(4) Å, β = 100.12(4)̊, and Z = 2. Compound 2 belongs to the space group P21/c with a = 8.379(2) Å, b = 22.630(2) Å, c = 12.256(2) Å, β= 98.43(3)°, and Z = 4. It has the same molecular formula as a compound reported previously but a different crystal structure. Detailed single-crystal EPR measurements were performed for single-crystal samples of 1 and 2 at 9 and 35 GHz and at room temperature. The positions and line widths of the EPR lines were measured as a function of the magnetic field orientation in three orthogonal planes. The data were used to study the electronic properties of the copper ions and to evaluate the exchange interactions between them. Our results are discussed in terms of the electronic pathways for superexchange between copper ions, which are provided by the stacking of pyrazole and phenyl rings of neighboring molecules and by hydrogen-halogen bonds. © 1999 American Chemical Society.

First crystal structures of lanthanide-hydrocinnamate complexes: Hydrothermal synthesis and photophysical studies

Five new lanthanide(III) complexes of hydrocinnamic acid (Hcin), [Ln(cin)3(H2O)3]·3Hcin (Ln = Tb(III) (1), Dy(III) (2), Er(III) (3), Eu(III) (4) and Gd(III) (5)) have been synthesized and characterized. The X-ray structures of 1-5 reveal that all compounds are isostructural and that each lanthanide ion is nine-coordinated by oxygen atoms in an overall distorted tricapped trigonal-prismatic geometry. Six oxygen atoms are provided by carboxylate moieties, and the other three by water molecules. The supramolecular architectures of 1-5 show the presence of uncoordinated hydrocinnamic acid molecules which induce the formation of numerous hydrogen bonds. The photophysical properties of these complexes in the solid state at room temperature were studied using diffuse reflectance (DR), fluorescence excitation and emission spectra. An energy level diagram was used to establish the most relevant channels involved in the ligand-to-metal energy transfer, indicating that cin- ligands can act as intramolecular energy donors for Tb(III), Dy(III) and Eu(III) ions. © 2012 Elsevier B.V.

Synthesis, crystal structures, antimicrobial, antifungal and antituberculosis activities of mixed ligand silver(I) complexes

The biological activity of some new mixed silver-phosphane-thio-ligand complexes, with 1:1:2, 1:1:1 and 1:2:1 (Ag:phospine:ligand) compositions, have been examined. Ten compounds were prepared using a series of silver(I) salts [AgX, where X = NO3, ClO4, PF6 and Br], tertiary phosphines and the ligands thi-osemicarbazide, 2-(propan-2-ylidene) hydrazinecarbothioamide, and thiazolidine-2-thione. The syntheses were carried out under ambient conditions, and the ten complexes obtained were found to be light stable. All 10 compounds were characterized by elemental analysis, FTIR, and NMR spectroscopy, whereas nine compounds were characterized by X-ray diffraction analysis. The anti-proliferative activities were evaluated by minimum inhibitory concentration (MIC: lg/mL) in an aqueous suspension system and they all show promising potential activity against selective strains of Gram-positive and Gram-negative bacteria, fungous and Mycrobaterium tuberculosis H37Rv. © 2013 Elsevier Ltd. All rights reserved.

Structural bases for a complete myotoxic mechanism: Crystal structures of two non-catalytic phospholipases A(2)-like from Bothrops brazili venom

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Synthesis and biological evaluation of ternary silver compounds bearing N,N-chelating ligands and thiourea: X-ray structure of [{Ag(bpy) (mu-tu)}(2)](NO3)(2) (bpy=2,2 '-bipyridine; tu = thiourea)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)