Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5

Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 angstrom resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alpha beta alpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

Synthesis of BaSO4 nanoparticles by precipitation method using sodium hexa metaphosphate as a stabilizer

We describe the synthesis and structure of Barium sulfate nanoparticles by precipitation method in the presence of water soluble inorganic stabilizing agent, sodium hexametaphosphate, (NaPO3)(6). The structural parameters were refined by the Rietveld refinement method using powder X-ray diffraction data. Barium sulfate nanoparticles were crystallized in the orthorhombic structure with space group Pbnm (No. 62) having the lattice parameters a = 7.215(1) (angstrom), b = 8.949(1) (angstrom) and c = 5.501 (1) (angstrom) respectively. Transmission electron microscopy study reveals that the nanoparticles are size range, 30-50 nm. Fourier transform infrared spectra showed distinct absorption due to the SO42- moiety at 1115 and 1084 cm(-1) indicating formation of barium sulfate nanoparticles free from the phosphate group from the stabilizer used in the synthesis. (C) 2009 Elsevier Ltd. All rights reserved.

Modular design of synthetic protein mimics. Crystal structure of two seven-residue helical peptide segments linked by .epsilon.-aminocaproic acid

Two seven-residue helical segments, Val-Ala-Leu-Aib-Val-Ala-Leu, were linked synthetically with an epsilon-aminocaproic acid (Acp) linker with the intention of making a stable antiparallel helix-helix motif. The crystal structure of the linked peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Acp-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe (1) shows the two helices displaced laterally from each other by the linker, but the linker has not folded the molecule into a close-packed antiparallel conformation. Two strong intermolecular NH...O = C hydrogen bonds are formed between the top of the lower helix of one molecule and the bottom of the upper helix in a laterally adjacent molecule to give the appearance of an extended single helix. The composite peptide with Boc and OMe end groups, C76H137N15O18.H2O, crystallize in space group P2(1) with a = 8.802 (1) angstrom, b = 20.409 (4) angstrom, c = 26.315 (3) angstrom, and beta = 90.72 (1)degrees; overall agreement R = 7.86% for 5030 observed reflections (\F(o)\ > 3-sigma(F)); resolution = 0.93 angstrom. Limited evidence for a more compact conformation in solution consistent with an antiparallel helix arrangement is obtained by comparison of the HPLC retention times and CD spectra of peptide 1 with well-characterized continuous helices of similar length and sequence.

Erythrocyte-binding studies on an acidic lectin from winged bean (Psophocarpus tetragonolobus)

n acidic lectin (WBA II) was isolated to homogeneity from the crude seed extract of the winged bean (Psophocarpus tetragonolobus) by affinity chromatography on lactosylaminoethyl-Bio-Gel. Binding of WBA II to human erythrocytes of type-A, -B and -O blood groups showed the presence of 10(5) receptors/cell, with high association constants (10(6)-10(8) M-1). Competitive binding studies with blood-group-specific lectins reveal that WBA II binds to H- and T-antigenic determinants on human erythrocytes. Affinity-chromatographic studies using A-, B-, H- and T-antigenic determinants coupled to an insoluble matrix confirm the specificity of WBA II towards H- and T-antigenic determinants. Inhibition of the binding of WBA II by various sugars show that N-acetylgalactosamine and T-antigenic disaccharide (Thomsen-Friedenreich antigen, Gal beta 1-3GalNAc) are the most potent mono- and di-saccharide inhibitors respectively. In addition, inhibition of the binding of WBA II to erythrocytes by dog intestine H-fucolipid prove that the lectin binds to H-antigenic determinant.

Ultrasonic wave characteristics of nanorods via nonlocal strain gradient models

This paper studies an ultrasonic wave dispersion characteristics of a nanorod. Nonlocal strain gradient models (both second and fourth order) are introduced to analyze the ultrasonic wave behavior in nanorod. Explicit expressions are derived for wave numbers and the wave speeds of the nanorod. The analysis shows that the fourth order strain gradient model gives approximate results over the second order strain gradient model for dynamic analysis. The second order strain gradient model gives a critical wave number at certain wave frequency, where the wave speeds are zero. A relation among the number of waves along the nanorod, the nonlocal scaling parameter (e(0)a), and the length of the nanorod is obtained from the nonlocal second order strain gradient model. The ultrasonic wave characteristics of the nanorod obtained from the nonlocal strain gradient models are compared with the classical continuum model. The dynamic response behavior of nanorods is explained from both the strain gradient models. The effect of e(0)a on the ultrasonic wave behavior of the nanorods is also observed. (C) 2010 American Institute of Physics.

A spectroscopic study of the interaction of isoflavones with human serum albumin

Genistein and daidzein, the major isoflavones present in soybeans, possess a wide spectrum of physiological and pharmacological functions. The binding of genistein to human serum albumin (HSA) has been investigated by equilibrium dialysis, fluorescence measurements, CD and molecular visualization. One mole of genistein is bound per mole of HSA with a binding constant of 1.5 +/- 0.2 X 10(5) m(-1). Binding of genistein to HSA precludes the attachment of daidzein. The ability of HSA to bind genistein is found to be lost when the tryptophan residue of albumin is modified with N-bromosuccinimide. At 27 degrees C (pH 7.4), van't Hoff's enthalpy, entropy and free energy changes that accompany the binding are found to be -13.16 kcal.mol(-1), -21 cal.mol(-1)K(-1) and -6.86 kcal.mol(-1), respectively. Temperature and ionic strength dependence and competitive binding measurements of genistein with HSA in the presence of fatty acids and 8-anilino-1-naphthalene sulfonic acid have suggested the involvement of both hydrophobic and ionic interactions in the genistein-HSA binding. Binding measurements of genistein with BSA and HSA, and those in the presence of warfarin and 2,3,5-tri-iodobenzoic acid and Forster energy transfer measurements have been used for deducing the binding pocket on HSA. Fluorescence anisotropy measurements of daidzein bound and then displaced with warfarin, 2,3,5-tri-iodobenzoic acid or diazepam confirm the binding of daidzein and genistein to subdomain IIA of HSA. The ability of HSA to form ternery complexes with other neutral molecules such as warfarin, which also binds within the subdomain IIA pocket, increases our understanding of the binding dynamics of exogenous drugs to HSA.

Interaction of metal ions with 6-oxopurine nucleotides. Part 2. X-Ray structures of ternary nickel(II) complexes with 2'-deoxyguanosine 5'-monophosphate or guanosine 5'-monophosphate

The ternary metal nucleotide complexes [Ni(en)1.3(H2O)1.4(H2O)2][Ni(5?-dGMP)2(en)0.7-(H2O)0.6(H2O)2]·7H2O (1) and [Ni(en)2(H2O)2][Ni(5?-GMP)2(H2O)4]·6H2O (2)(en = ethylenediamine, 5?-dGMP = 2?-deoxyguanosine 5?-monophosphate, 5?-GMP = guanosine 5?-monophosphate) have been prepared and their structures analyzed by X-ray diffraction methods. Both compounds crystallise in the space group C2221 with a= 8.810(1), b= 25.090(4), c= 21.084(1)Å, and Z= 4 for (1) and a= 8.730(1), b= 25.691(4), c= 21.313(5)Å, and Z= 4 for (2). The structures were deduced from the analogous CoIII complexes and refined by full-matrix least-squares methods to final R values of 0.087 and 0.131 for 1 211 and 954 reflections for (1) and (2) respectively. An interesting feature of the deoxyribonucleotide complex (1) is that en is not totally labilized from the metal centre on nucleotide co-ordination, as observed in corresponding ribonucleotide complexes. Apart from extensive intra- and inter-molecular hydrogen bonding, the structures are stabilized by significant intracomplex base�base and base�sugar interactions. The nucleotides in both complexes have an anti base, C(2?)-endo sugar pucker, and gauche�gauche conformation about the C(4?)�C(5?) bond.

The superfluid as a source of all interactions

The superfluid state of fermion-antifermion fields developed in our previous papers is generalized to include higher orbital and spin states. In addition to single-particle excitations, the system is capable of having real and virtual bound or quasibound composite excitations which are akin to bosons of spinJ P equal to0 �, 1�, 2+, etc. These pseudoscalar, vector, and tensor bosons can be massive or massless and provide the vehicles for strong, electromagnetic, weak, and gravitational interactions. The concept that the basic (unmanifest) fermion-antifermion interaction can lead to a multiplicity of manifest interactions seems to provide a basis for a unified field theory.

Structure of 6,5'-anhydro-6-hydroxy-2',3' O-isopropylideneuridine

CI2HI4N206, Mr=282"3, orthorhombic,P21212 t, a = 10.412 (2), b = 14.936 (2), c =16.651(3),/k, V=2589.46A 3, Z--8, Din= 1.450, D x = 1.447 Mg m -3, 2(Cu Kct) = 1.5418/~, # =0.902mm -~, F(000)-- 1184.00, T= 293 K, R = 0.039, wR--0.038 for 2548 unique reflections with F > 3a(F). The two crystallographically independent molecules in the asymmetric unit have similar geome-tries with the ribose ring having an O(4')-exo, C(4')-endo pucker and the uracil base in the anti conformation.The geometry about the exocyclic C(4')-C(5') bond in both molecules is gauche-gauche. The dioxolane ring assumes twist conformations in both molecules.

Synthesis and characterization of Pd(0), PdS, and Pd@PdO core-shell nanoparticles by solventless thermolysis of a Pd-thiolate cluster

Colloids of palladium nanoparticles have been prepared by the solvated metal atom dispersion (SMAD) method. The as-prepared Pd colloid consists of particles with an average diameter of 2.8 +/- 0.1 nm. Digestive ripening of the as-prepared Pd colloid, a process involving refluxing the as-prepared colloid at or near the boiling point of the solvent in the presence of a passivating agent, dodecanethiol resulted in a previously reported Pd-thiolate cluster, Pd(SC12H25)(2)](6) but did not render the expected narrowing down of the particle size distribution. Solventless thermolysis of the Pd-thiolate complex resulted in various Pd systems such as Pd(0), PdS, and Pd@PdO core-shell nanoparticles thus demonstrating its versatility. These I'd nanostructures have been characterized using high-resolution electron microscopy and powder X-ray diffraction methods. (C) 2010 Elsevier Inc. All rights reserved.

Reactions of tetrahalogeno-o-benzoquinones—Part VII. Reaction of alkyl-2-naphthols with tetrachloro-o-benzoquinone

Reaction of 8-methyl-2-naphthol (4a) with the quinone3 gave a mixture of 8-methyl-2,2-(tetrachlorohenylenedioxy)naphthalen-1(2H)-one (1b) and 8-methyl-1,1-(tetrachloro-o-phenylenedioxy)naphthalen-2(1H)-one (2b) in almost equal amounts. Similarly, reaction of the naphthols (4b), (4d) and (4e) with3 gave the corresponding dienones (1c &2c), (1e &2e) and (1f &2f) in almost equal amounts. Reaction of 8-t-butyl-2-naphthol (4c) with3 gave exclusively 8-t-butyl-2,2-(tetrachloro--henylenedioxy)-naphthalen-1(2H)-one (1d). Oxidation of 3-t-butyl-2-naphthol (4f) with3 gave a mixture of 3-t-butyl-2,2-(tetrachloro-o-phenylendioxy) nephthalene-1(2H)-one(1g) and 3-t-butyl-1,1-(tetrachloro--phenylenedioxy)naphthelen-2 (1H)-one (2g) in the ratio 1∶6. Thus, onlyt-butyl group exherts pronounced steric influence on the rearrangement observed in the reaction of β-naphthol with the quinone3. Structures of all the compounds have been established by spectral data.

Crystal structure of the charge-transfer complex promethazine picrate

Promethazine picrate (C23H23N5O7S) crystallises in the triclinic space group P[unk] with a = 8.137(1), b = 8.144(3), c = 19.224(6) Å, α = 87.78(3), β = 79.97(2), γ = 70.57(2)° and two molecules per unit cell. The structure was solved by direct methods (MULTAN 80) using 2438 observed reflections [I > 2.5 σ(I)]. Refinement was carried out by block-diagonal least-squares methods to a final R = 0.052. The picrate group is planar and is almost perpendicular to the promethazine plane. The two groups are joined by a hydrogen bond. The pairs of molecules related by a centre of symmetry make a molecular arrangement where promethazine and picrate groups are packed in sheets in three dimensions.

Crystal and molecular structure of sym-homospermidine monohydrate

Sym-homospermidine, [formula; see text] is a naturally occurring rare-polyamine found in relatively large concentration in sandal leaves. As part of our studies on structure and interactions of polyamines, ym-homospermidine was purified from sandal leaves and its structure was determined by single crystal X-ray diffraction technique. The phosphate salt of the molecule crystallized in the triclinic space group P1- with a = 8.246(1)A, b = 8.775(1)A, c = 15.531(2)A, alpha = 74.20(1) degrees, beta = 88.36(1) degrees and gamma = 65.41(1) degrees. The structure was determined by direct methods and refined to a final R factor of 5.4% for 2087 reflections with magnitude of F(obs) greater than 5 sigma [F(obs)]. The amine exists in its most favourable all trans conformation. For each amine molecule three phosphate groups exist in the crystal structure, suggesting that two of the oxygens of each phosphate group are protonated. There is also a single water molecule in the asymmetric unit in contrast to that of spermidine phosphate which has 3 water molecules. These differences probably reflect the hydrogen bonding properties of mono-ionic and di-ionic phosphate groups. The structure is predominantly stabilized by a network of hydrogen bonds.

Nucleosomes on linear duplex DNA allow homologous pairing but prevent strand exchange promoted by RecA protein

To understand the molecular basis of gene targeting, we have studied interactions of nucleoprotein filaments comprised of single-stranded DNA and RecA protein with chromatin templates reconstituted from linear duplex DNA and histones. We observed that for the chromatin templates with histone/DNA mass ratios of 0.8 and 1.6, the efficiency of homologous pairing was indistinguishable from that of naked duplex DNA but strand exchange was repressed. In contrast, the chromatin templates with a histone/DNA mass ratio of 9.0 supported neither homologous pairing nor strand exchange. The addition of histone H1, in stoichiometric amounts, to chromatin templates quells homologous pairing. The pairing of chromatin templates with nucleoprotein filaments of RecA protein-single-stranded DNA proceeded without the production of detectable networks of DNA, suggesting that coaggregates are unlikely to be the intermediates in homologous pairing. The application of these observations to strategies for gene targeting and their implications for models of genetic recombination are discussed.

Origin of nonmetallicity in PrBa2Cu3O7 from a study of Gd1−xPrxBa2Cu3O7 using soft x-ray absorption at the oxygen K-edge

We present the x-ray absorption data at the oxygen K-edge using total yield technique for Gd1−xPrxba2Cu3O7 (x= 0.0, 0.2, 0.4, 0.6, 0.8, and 1.0). The data clearly to oxygen that the holes doped in the GdBa2Cu3O7 due to oxygen composition are not removed by Pr doping even for the x = 1.0 sample, suggesting that Pr is predominantly in the formally trivalent state. However, the data also clearly indicate the evidence of hybridization effects between the Pr3+ and the adjacent CuO2 layers. This is suggested to be responsible for the progressive suppression of Tc and the metallicity with Pr doping in these systems.