Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of the putative SAICAR synthetase (PH0239) from Pyrococcus horikoshii OT3

The study of proteins involved in de novo biosynthesis of purine nucleotides is central in the development of antibiotics and anticancer drugs. In view of this, a protein from the hyperthermophile Pyrococcus horikoshii OT3 was isolated, purified and crystallized using the microbatch method. Its primary structure was found to be similar to that of SAICAR synthetase, which catalyses the seventh step of de novo purine biosynthesis. A diffraction-quality crystal was obtained using Hampton Research Crystal Screen II condition No. 34, consisting of 0.05 M cadmium sulfate hydrate, 0.1 M HEPES buffer pH 7.5 and 1.0 M sodium acetate trihydrate, with 40%(v/v) 1,4-butanediol as an additive. The crystal belonged to space group P3(1), with unit-cell parameters a = b = 95.62, c = 149.13 angstrom. Assuming the presence of a hexamer in the asymmetric unit resulted in a Matthews coefficient (V-M) of 2.3 angstrom(3) Da(-1), corresponding to a solvent content of about 46%. A detailed study of this protein will yield insights into structural stability at high temperatures and should be highly relevant to the development of antibiotics and anticancer drugs targeting the biosynthesis of purine nucleotides.

X-ray Crystallographic Analysis of the Complexes of Enoyl Acyl Carrier Protein Reductase of Plasmodium falciparum with Triclosan Variants to Elucidate the Importance of Different Functional Groups in Enzyme Inhibition

Triclosan, a well-known inhibitor of Enoyl Acyl Carrier Protein Reductase (ENR) from several pathogenic organisms, is a promising lead compound to design effective drugs. We have solved the X-ray crystal structures of Plasmodium falciparum ENR in complex with triclosan variants having different substituted and unsubstituted groups at different key functional locations. The structures revealed that 4 and 2' substituted compounds have more interactions with the protein, cofactor, and solvents when compared with triclosan. New water molecules were found to interact with some of these inhibitors. Substitution at the 2' position of triclosan caused the relocation of a conserved water molecule, leading to an additional hydrogen bond with the inhibitor. This observation can help in conserved water-based inhibitor design. 2' and 4' unsubstituted compounds showed a movement away from the hydrophobic pocket to compensate for the interactions made by the halogen groups of triclosan. This compound also makes additional interactions with the protein and cofactor which compensate for the lost interactions due to the unsubstitution at 2' and 4'. In cell culture, this inhibitor shows less potency, which indicates that the chlorines at 2' and 4' positions increase the ability of the inhibitor to cross multilayered membranes. This knowledge helps us to modify the different functional groups of triclosan to get more potent inhibitors. (C) 2010 IUBMB IUBMB Life, 62(6): 467-476.

X-Ray structure of a ternary complex, copper(II)–lnosine 5-monophosphate–benzimidazole. The first example for the absence of direct metal–nucleotide interaction

The unprecedented absence of direct metal–nucleotide interaction has been observed in the X-ray structure of the ternary metal nucleotide system [Cu(bzim)(H2O)5]2+[IMP]2–·3H2O [IMP = inosine 5-monophosphate(2–), bzim = benzimidazole). The complex crystallizes in the space group P21 with a= 7.013(2), b= 13.179(9), c= 14.565(9)Å, = 94.82(4)°, and Z= 2. The structure was solved by the heavy-atom method and refined by full-matrix least squares on the basis of 1 761 observed (I? 3i) reflections to final R and R values of 0.034 and 0.036 respectively. The CuII has a distorted octahedral co-ordination with a nitrogen of the bzim ligand [Cu–N 1.947(5)Å] and three oxygens of water molecules in the basal plane [mean Cu–O 2.017(3)Å] and two more water oxygens at axial positions [Cu–O 2.194(6) and 2.732(5)Å]. The nucleotide base stacks with the bzim ligand at an average distance of 3.5 Å and an angle of 22°. In the lattice, N(7) of the base is linked to a lattice water through a hydrogen bond, while all the phosphate oxygens are involved in hydrogen bonds with co-ordinated as well as lattice water molecules. The co-ordination behaviour of IMP to CuII is compared in structures containing different -aromatic amines in order to assess the influence of the ternary ligand in complex formation. The present results indicate that, apart from the commonly observed phosphate binding, other modes of co-ordination are possible, these being influenced mainly by the -accepting properties of the ternary ligand.

Synthesis, X-ray structure and catalytic properties of a copper(II) Schiff base complex modeling the activity of the Cu-B site of dopamine beta-hydroxylase

The copper(II) complex [Cu(salgly) (bpy)] . 4H(2)O (1), where salgly is a tridentate glycinatosalicylaldimine Schiffbase Ligand, is prepared and structurally characterized. The complex is found to be catalytically active in the oxidation of ascorbic acid by dioxygen and the process is also effective in the presence of benzylamine giving benzaldehyde as a product, thus modeling the activity of the Cu-B site of dopamine beta-hydroxylase. (C) 2000 Elsevier Science S.A. All rights reserved.

Dynamics and local structure of colossal magnetoresistance manganites

We report Extended X-ray Absorption Fine Structure and anelastic spectroscopy measurements on on hole doped manganese oxides La1-xCaxMnO3 which present the colossal magnetoresistance effect. EXAFS measurements were realized both in the absence and presence of an applied magnetic field of 1.1 Tesla, in a wide temperature range (between 330 and 77 K) and at various dopings (x = 0.25 and x = 0.33). The magnetic field orders the magnetic moments so favouring the electron mobility and the reduction of Mn-O octahedra distortions. We observe the presence of four short and two long Mn-O distances (1.93 and 2.05 Angstrom respectively) above and also below the metal-insulator phase transition. The overall distortion decreases but does not completely disappear in the metallic phase suggesting the possible coexistence of metallic and insulating regions at low temperatures. The magnetic field reduces the lattice distortions showing evidence of a microscopic counterpart of the macroscopic colossal magnetoresistance. We also present preliminary anelastic relaxation spectra in a wide temperature range from 900 K to 1 K on a sample with x = 0.40, in order to study the structural phase transitions and the lattice dynamics. A double peak has been observed at the metal-insulator transition in the imaginary part of Young's modulus. This double peak indicates that the metal-insulator transition could be a more complex phenomenon than a simple second order phase transition. In particular the peak at lower temperatures can be connected with the possible presence of inhomogeneous phase structures. Another intense dissipation peak has been observed corresponding to the structural orthorhombic-trigonal transition around 750 K.

Crystallization and preliminary X-ray crystallographic analysis of a galactose-specific lectin from Dolichos lablab

The galactose-specific lectin from the seeds of Dolichos lablab has been crystallized using the hanging-drop vapour-diffusion technique. The crystals belong to space group P1, with unit-cell parameters a = 73.99, b = 84.13, c = 93.15 angstrom, alpha = 89.92, beta = 76.01, gamma = 76.99 degrees. X-ray diffraction data to a resolution of 3.0 angstrom have been collected under cryoconditions ( 100 K) using a MAR imaging-plate detector system mounted on a rotating-anode X-ray generator. Molecular-replacement calculations carried out using the available structures of legume lectins as search models revealed that the galactose-specific lectin from D. lablab forms a tetramer similar to soybean agglutinin; two such tetramers are present in the asymmetric unit.

Photo induced optical changes in Sb/As2S3 multilayered film and (As2S3)(0.93)Sb-0.07 film of equal thickness

The increase in optical band gap (photo bleaching) due to light illumination was studied at room temperature as well as at low (4.2 K) temperature for Sb/As2S3 multilayered film of 640 nm thickness by Fourier Transform Infrared Technique. The interdiffusion of Sb into As2S3 matrix results the formation of Sb-As2S3 ternary solid solutions which is explained by the change in optical band gap (E-g), absorption coefficient (alpha), Tauc parameter (B-1/2), Urbach edge (E-e). At the same time, photo darkening phenomena was observed in (As2S3)(0.93)Sb-0.07 film of same thickness both at low and room temperatures. From our X-ray Photoelectron Spectroscopy measurements,we are able to show that some of the As-As, S-S and Sb-Sb bonds are converted into As-S and S-Sb bonds in case of multilayers. We found that the energetically favoured heteropolar bond formation take place by a phonon-assisted mechanism using the lone pair pi electrons of S-2(0). But in case of (As2S3)(0.93)Sb-0.02 film, the homopolar bonds are playing a major role. (C) 2010 Elsevier B.V. All rights reserved.