Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution

Background: Glucosamine 6-phosphate deaminase from Escherichia coli is an allosteric hexameric enzyme which catalyzes the reversible conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate and ammonium ion and is activated by N-acetyl-D-glucosamine 6-phosphate. Mechanistically, it belongs to the group of aldose-ketose isomerases, but its reaction also accomplishes a simultaneous amination/deamination. The determination of the structure of this protein provides fundamental knowledge for understanding its mode of action and the nature of allosteric conformational changes that regulate its function. Results: The crystal structure of glucosamine 6-phosphate deaminase with bound phosphate ions is presented at 2.1 Å resolution together with the refined structures of the enzyme in complexes with its allosteric activator and with a competitive inhibitor. The protein fold can be described as a modified NAD-binding domain. Conclusions: From the similarities between the three presented structures, it is concluded that these represent the enzymatically active R state conformer. A mechanism for the deaminase reaction is proposed. It comprises steps to open the pyranose ring of the substrate and a sequence of general base-catalyzed reactions to bring about isomerization and deamination, with Asp72 playing a key role as a proton exchanger.

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.

Crystal structure of BaBi2Ta2O9

The crystal structure of the Aurivillius compound Bi2BaTa2O9 prepared via the chemical route was determined by direct methods using EXPO97, and refined using the Rietveld method with conventional X-ray diffraction data. The structure was found to be tetragonal (space group I4/mmm, number 139) and Z = 2, isomorphic of the Bi2BaNb2O9 reported by Blake and co-workers in the literature (1997). Two refinements were performed using the two asymmetry functions of DBWS-9807 (release 20/May/99). The unit cell for each case are: a = 3.932 22(6) Å, c = 25.5053(6) Å (RA) and a = 3.93250(7) Å, c = 25.5069(6) Å (RCF). The differences for atom positions, interatomic distances and angles are in the range of one standard deviation. Final agreements factors are: Rwp = 7.97%, S = 1.84, RBragg = 4.28%(RA), Rwp = 7.98%, S = 1.84, RBragg = 4.30% (RCF). The occupancies of Ba and Bi in site 2b were refined but constrained to have their summation equal to 1.00. The same constraints were applied to the Ba and Bi of the 4e site. The results show that on site 2b there are 70% of Ba and 30% of Bi and on the site 4e there are 82% of Bi and 18% of Ba. The charge equilibrium is maintained for one standard deviation of the site occupancies. © 2000 International Centre for Diffraction Data.

Structure and properties of donor doped barium titanate prepared by citrate process

Niobium doped barium titanate was prepared using two procedures. First, doped barium titanate was prepared starting from citrate solutions of all components and second, pure barium titanate powder was obtained from the citrate solutions and after that doped. Besides niobium, a small amount of manganese, as acceptor dopant was added. Phase composition, crystal structure, microstructure and dielectric properties were reported. The influence of powder processing on the properties of niobium doped barium titanate was analysed. The grain growth and the concentration of dopants on the dielectric properties were considered. © 2002 Taylor & Francis.

Carotid arteries in the dog: Structure and histophysiology

Light microscopy analysis of the mural structure of the common carotid artery, internal carotid artery and external carotid artery in mongrel dog revealed variability in the middle values of vascular diameter and thickness of the intimal plus medial coats and adventitial coat. The vascular diameter did not differ between the internal carotid artery and external carotid artery, but was significantly increased in the common carotid artery from which the other two arteries had origin. The increased thickness of the intimal plus medial coats of the common carotid artery revealed the constant mechanical adjustment of the arterial wall and local shearing stress that occurred among the arterial coats. The adventitial coat of the internal carotid artery was significantly thicker than those of the common carotid and external carotid arteries, with no significant difference noted between the latter arteries. These histomorphometric results were related to the qualitative observations regarding the mural structure of the three arteries analyzed, especially regarding to the increased thickness and structural complexity of the adventitial coat of the internal carotid artery. Perhaps it acted as an external protective sheath of the vascular wall during its long course until the carotid channel. © 2006 Sociedad Chilena de Anatomía.

Compositional modulation and surface stability in InGaP films: Understanding and controlling surface properties

We investigate the formation of compositional modulation and atomic ordering in InGaP films. Such bulk properties - as well as surface morphologies - present a strong dependence on growth parameters, mainly the V/III ratio. Our results indicate the importance of surface diffusion and, particularly, surface reconstruction for these processes. Most importantly from the application point of view, we show that the compositional modulation is not necessarily coupled to the surface instabilities, so that smooth InGaP films with periodic compositional variation could be obtained. This opens a new route for the generation of templates for quantum dot positioning and three-dimensional arrays of nanostructures. © 2007 American Institute of Physics.

Structure and properties of Brazilian peat: Analysis by spectroscopy and microscopy

Peat was taken from the Sergipe State, Brazil and characterized by several techniques: elemental and thermal analyses; Fourier infrared (FTIR) and solid state 13C nuclear magnetic resonance (NMR) spectroscopies; scanning electron microscopy (SEM), environmental scanning electron microscopy (ESEM) and X-ray diffractometry (XRD). Also, the Sergipe State peat samples were compared with other peat sample from later from Sao Paulo State, Brazil. The lowest O/C and E 4/E 6 ratios and differential thermal analysis (DTA) curves of the Santo Amaro (SAO) sample indicated that this sample had the highest degree of decomposition. FTIR results showed that Itabaiana (ITA) and São Paulo (SAP) samples presented more prominent peak at 1086 cm -1 attributed the presence of Si-O than SAO sample spectra. The SAO sample showed two more intense peaks at 2920 cm -1 and 2850 cm -1. These results were corroborated by 13C NMR and thermal gravimetric (TG) where the relative abundance of the alkyl-C groups was greater in the SAO sample. The X-ray diffractometry (XRD) of SAO sample is characteristic of amorphous matter however, the SAP and ITA samples revealed the large presence of quartz mineral. The scanning electron microscopy (SEM) and environmental scanning electron microscopy (ESEM) showed that the surface of peat samples have porous granules of organic material. The ITA and SAP peat samples are alike while SAO peat sample is richer in organic material. Only the SAO sample has truthful characteristics of peat. The results of this study showed that the samples are very different due to variable inorganic and organic material contents. ©2007 Sociedade Brasileira de Química.

Electronic structure and magnetic properties of FeWO 4 nanocrystals synthesized by the microwave-hydrothermal method

This communication reports that FeWO 4 nanocrystals were successfully synthesized by the microwave-hydrothermal method at 443 K for 1 h. The structure and shape of these nanocrystals were characterized by X-ray diffraction, Rietveld refinement, and transmission electron microscopy. The experimental results and first principles calculations were combined to explain the electronic structure and magnetic properties. Experimental data were obtained by magnetization measurements for different applied magnetic fields. Theoretical calculations revealed that magnetic properties of FeWO 4 nanocrystals can be assigned to two magnetic orderings with parallel or antiparallel spins in adjacent chains. These factors are crucial to understanding of competition between ferro- and antiferromagnetic behavior. © 2012 Elsevier Inc.

Crystal structure of Jararacussin-I: The highly negatively charged catalytic interface contributes to macromolecular selectivity in snake venom thrombin-like enzymes

Snake venom serine proteinases (SVSPs) are hemostatically active toxins that perturb the maintenance and regulation of both the blood coagulation cascade and fibrinolytic feedback system at specific points, and hence, are widely used as tools in pharmacological and clinical diagnosis. The crystal structure of a thrombin-like enzyme (TLE) from Bothrops jararacussu venom (Jararacussin-I) was determined at 2.48 Å resolution. This is the first crystal structure of a TLE and allows structural comparisons with both the Agkistrodon contortrix contortrix Protein C Activator and the Trimeresurus stejnegeri plasminogen activator. Despite the highly conserved overall fold, significant differences in the amino acid compositions and three-dimensional conformations of the loops surrounding the active site significantly alter the molecular topography and charge distribution profile of the catalytic interface. In contrast to other SVSPs, the catalytic interface of Jararacussin-I is highly negatively charged, which contributes to its unique macromolecular selectivity. © 2012 The Protein Society.

Morphological modifications and surface amorphization in ZnO sonochemically treated nanoparticles

Application of nanoscale materials in photovoltaic and photocatalysis devices and photosensors are dramatically affected by surface morphology of nanoparticles, which plays a fundamental role in the understanding of the physical and chemical properties of nanoscale materials. Zinc oxide nanoparticles with an average size of 20 nm were obtained by the use of a sonochemical technique. X-ray diffraction (XRD) associated to Rietveld refinements and transmission electron microscopy (TEM) were used to study structural and morphological characteristics of the samples. An amorphous shell approximately 10 nm thick was observed in the ultrasonically treated sample, and a large reduction in particle size and changes in the lattice parameters were also observed. © 2012 Elsevier B.V. All rights reserved.

Effect of the ZrO2 phase on the structure and behavior of supported Cu catalysts for ethanol conversion

The effect of amorphous (am-), monoclinic (m-), and tetragonal (t-) ZrO2 phase on the physicochemical and catalytic properties of supported Cu catalysts for ethanol conversion was studied. The electronic parameters of Cu/ZrO2 were determined by in situ XAS, and the surface properties of Cu/ZrO2 were defined by XPS and DRIFTS of CO-adsorbed. The results demonstrated that the kind of ZrO2 phase plays a key role in the determination of structure and catalytic properties of Cu/ZrO 2 catalysts predetermined by the interface at Cu/ZrO2. The electron transfer between support and Cu surface, caused by the oxygen vacancies at m-ZrO2 and am-ZrO2, is responsible for the active sites for acetaldehyde and ethyl acetate formation. The highest selectivity to ethyl acetate for Cu/m-ZrO2 catalyst up to 513 K was caused by the optimal ratio of Cu0/Cu+ species and the high density of basic sites (O2-) associated with the oxygen mobility from the bulk m-ZrO2. © 2013 Elsevier Inc. All rights reserved.

Optical, mechanical and surface properties of amorphous carbonaceous thin films obtained by plasma enhanced chemical vapor deposition and plasma immersion ion implantation and deposition

Diverse amorphous hydrogenated carbon-based films (a-C:H, a-C:H:F, a-C:H:N, a-C:H:Cl and a-C:H:Si:O) were obtained by radiofrequency plasma enhanced chemical vapor deposition (PECVD) and plasma immersion ion implantation and deposition (PIIID). The same precursors were used in the production of each pair of each type of film, such as a-C:H, using both PECVD and PIIID. Optical properties, namely the refractive index, n, absorption coefficient, α, and optical gap, ETauc, of these films were obtained via transmission spectra in the ultraviolet-visible near-infrared range (wavelengths from 300 to 3300 nm). Film hardness, elastic modulus and stiffness were obtained as a function of depth using nano-indentation. Surface energy values were calculated from liquid drop contact angle data. Film roughness and morphology were assessed using atomic force microscopy (AFM). The PIIID films were usually thinner and possessed higher refractive indices than the PECVD films. Determined refractive indices are consistent with literature values for similar types of films. Values of ETauc were increased in the PIIID films compared to the PECVD films. An exception was the a-C:H:Si:O films, for which that obtained by PIIID was thicker and exhibited a decreased ETauc. The mechanical properties - hardness, elastic modulus and stiffness - of films produced by PECVD and PIIID generally present small differences. An interesting effect is the increase in the hardness of a-C:H:Cl films from 1.0 to 3.0 GPa when ion implantation is employed. Surface energy correlates well with surface roughness. The implanted films are usually smoother than those obtained by PECVD. ©2013 Elsevier B.V. All rights reserved.

Development and functional morphology of the larval foregut of two brachyuran species from Northern Brazil

A alimentação é um importante fator para o sucesso no cultivo larval de espécies de caranguejos. Informações sobre as características morfológicas do estômago podem contribuir para revelar o comportamento alimentar larval ou, se há lecitotrofia em algum, ou até mesmo, em todos os estágios do ciclo larval. No presente estudo, o desenvolvimento estrutural do estômago e as funções digestivas foram examinados em larvas de duas espécies de braquiúros, Uca vocator e Panopeus occidentalis, cultivados em laboratório. Durante o desenvolvimento larval, os estômagos das larvas no primeiro e último estágio de zoea e megalopa foram microscopicamente examinados, descritos e ilustrados. Em ambas espécies, o estômago dos estágios de zoea são desenvolvidos e especializados, apresentando uma válvula cardiopilórica e um filtro pilórico funcionais. Oestágio de megalopa possui um moinho gástrico complexo e especializado semelhante àquele encontrado em caranguejos adultos com o aparecimento de estruturas rígidas e calcificadas. Estes resultados apóiam a hipótese de que o comportamento alimentar de cada estágio larval está diretamente relacionado à estrutura morfológica do estômago. Tal fato, fortemente indica que todos os estágios larvais de ambos U. vocator e P. occidentalis necessitam de uma fonte externa de alimento para completar o desenvolvimento larval no ambiente planctônico.

Development and functional morphology of the foreguts of larvae and postlarvae of three crustacean decapods

O desenvolvimento da estrutura do estômago e da função digestiva foi examinada em larvas e pós-larvas de Litopenaeus vannamei, Sesarma rectum e Callichirus major. O estômago do protozoea de L. vannamei é muito simples, sem válvula cárdiopilórica e apresenta um filtro pilórico rudimentar. Em mysis, o filtro pilórico parece ser mais desenvolvido. No juvenil I surgem calhas e dentes laterais pouco desenvolvidos. Os estômagos dos zoeae de S. rectum possuem a válvula cárdiopilórica e o filtro pilórico funcionais. Nos estágios megalopa e juvenil I o moinho gástrico é complexo. Em C. major, os estômagos dos zoeae se mostram especializados exibindo algumas estruturas rígidas, mas não apresentam moinho gástrico. Esta estrutura surge no megalopa e juvenil I. Os resultados suportam suposições anteriores que o comportamento alimentar de larvas e pós-larvas está diretamente relacionado com as características morfológicas dos estômagos.