Molecular modeling and small angle X-ray scattering studies of Hoplosternum littorale cathodic haemoglobin

Considerable interest is currently focused on fish haemoglobins in order to identify the structural basis for their diversity of functional behavior. Hoplosternum littorale is a catfish that presents bimodal gill (water)/gut (air) -breathing, which allows this species to survive in waters with low oxygen content. The hemolysate of this fish showed the presence of two main haemoglobins, cathodic and anodic. This work describes structural features analyzed here by integration of molecular modeling with small angle X-ray scattering. Here is described a molecular model for the cathodic haemoglobin in the unliganded and liganded states. The models were determined by molecular modeling based on the high-resolution crystal structure of fish haemoglobins. The structural models for both forms of H. littorale haemoglobin were compared to human haemoglobin. (C) 2004 Elsevier B.V. All rights reserved.

Crystallization and preliminary X-ray diffraction analysis of prephenate dehydratase from Mycobacterium tuberculosis H37Rv

Tuberculosis remains the leading cause of mortality arising from a bacterial pathogen ( Mycobacterium tuberculosis). There is an urgent need for the development of new antimycobacterial agents. The aromatic amino-acid pathway is essential for the survival of this pathogen and represents a target for structure-based drug design. Accordingly, the M. tuberculosis prephenate dehydratase has been cloned, expressed, purified and crystallized by the hanging-drop vapour-diffusion method using PEG 400 as a precipitant. The crystal belongs to the orthorhombic space group I222 or I2(1)2(1)2(1), with unit-cell parameters a = 98.26, b = 133.22, c = 225.01 angstrom, and contains four molecules in the asymmetric unit. A complete data set was collected to 3.2 angstrom resolution using a synchrotron-radiation source.

Crystallization and preliminary X-ray diffraction analysis of XAC1151, a small heat-shock protein from Xanthomonas axonopodis pv. citri belonging to the alpha-crystallin family

The hspA gene (XAC1151) from Xanthomonas axonopodis pv. citri encodes a protein of 158 amino acids that belongs to the small heat-shock protein ( sHSP) family of proteins. These proteins function as molecular chaperones by preventing protein aggregation. The protein was crystallized using the sitting-drop vapour-diffusion method in the presence of ammonium phosphate. X-ray diffraction data were collected to 1.65 angstrom resolution using a synchrotron-radiation source. The crystal belongs to the rhombohedral space group R3, with unit-cell parameters a = b = 128.7, c = 55.3 angstrom. The crystal structure was solved by molecular-replacement methods. Structure refinement is in progress.

Small-angle X-ray scattering study of gelation and aging of Eu3+-doped sol-gel-derived siloxane-poly(oxyethylene) nanocomposites

The aggregation, gelation, and aging of urea-cross-linked siloxane-poly(oxyethylene) nanohybrids [(U600)-n] containing two different amounts of europium triflate initially dissolved in an ethanol-water mixture were investigated by in situ small-angle X-ray scattering (SAXS). For both low (n = [O]/[Eu] = 80) and high (n = 25) europium contents, the SAXS intensity was attributed to the formation of siloxane clusters of about 8-11 Angstrom in size. Siloxane cluster formation and growth is a rapid process in hybrids with low Eu contents and slow in Eu-rich hybrids. An additional contribution to the scattering intensity at very low angles was attributed to the formation of a coarse structure level. At this secondary level, the structure can be described as a set of dense domains containing siloxane clusters embedded in a depleted matrix composed of unfolded polymer chains and solvent. By fitting a theoretical function for this model to the experimental SAXS curves, relevant structural parameters were determined as functions of time during the sol-gel transition and gel aging. For hybrids with low europium contents (n = 80), the size of the siloxane clusters remains essentially invariant, whereas the dense segregation domains progressively grow. In hybrids with high doping contents (n = 25), the preponderant structure variation during the first stages of the sol-gel transformation is the slow growth of siloxane clusters. For these hybrids, the segregation of siloxane clusters forming dense domains occurs only during advanced stages of the process.

Local order around tungsten atoms in tungstate fluorophosphate glasses by X-ray absorption spectroscopy

X-ray absorption spectroscopy was used to study the local environment of tungsten atoms in NaPO3-BaF2,-WO3 glasses and the results were compared with crystalline references Na2WO4 and WO3. XANES measurements at the W-L-1 edge allowed to determine a distorted octahedral environment of tungsten atoms in these glasses similar to the local order of tungsten in monoclinic WO3. Extended X-ray absorption fine structure (EXAFS) has been used as a local probe to monitor the effect of WO3 concentration on the tungsten environment. Based on an analysis of the EXAFS data, we proposed a three-shell model of oxygen atoms around tungsten as in monoclinic WO3. With increasing WO3 concentration, it was found that R-2 decreases from 1.96 to 1.92 angstrom whereas R-3 increases from 2.07 to 2.12 angstrom. (c) 2005 Elsevier B.V. All rights reserved.

X-ray reflectivity of zirconia based sol-gel coatings on borosilicate glasses

In this work the technique of X-ray reflectometry was applied to study zirconiumsulfate films deposited by sol-gel dip-coating process on a borosilicate glass surface. The influence of withdrawal speed and temperature of thermal treatment on the film structure are analyzed. The thermal evolution of the density and thickness of the film was compared with these properties measured for a monolithic xerogel by helium picnometry and thermomechanical analysis. The fitting of experimental curves by classical reflectivity model showed the presence of an additional layer at the top surface of the coating. Layer thickness increases with increase of withdrawal speed in agreement with the Landau-Levich model. The apparent and real densities are similar for coatings fired below 400 degrees C, which shows that the films are free of pores. The shrinkage during firing is anisotropic, occurring essentially perpendicular to the coating surface. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Crystallization and preliminary X-ray diffraction analysis of an anti-H(O) lectin from Lotus tetragonolobus seeds

The seed lectin from Lotus tetragonolobus (LTA) has been crystallized. The best crystals grew over several days and were obtained using the vapour-diffusion method at a constant temperature of 293 K. A complete structural data set was collected at 2.00 angstrom resolution using a synchrotron-radiation source. LTA crystals were found to be monoclinic, belonging to space group P2(1), with unit-cell parameters a = 68.89, b = 65.83, c = 102.53 angstrom, alpha = gamma = 90, beta = 92 degrees. Molecular replacement yielded a solution with a correlation coefficient and R factor of 34.4 and 51.6%, respectively. Preliminary analysis of the molecular-replacement solution indicates a new quaternary association in the LTA structure. Crystallographic refinement is under way.

Crystal and molecular structures of 4-substituted 3,4-dihydropyrimidin-2(1H)-ones studied by X-ray and AM1 and B3LYP calculations

(1) C13H13N3O5, Mr = 291.26, P (1) over bar, a = 7.4629(9), b = 7.9203(9), c = 12.126(2) angstrom, alpha = 86.804(5), beta = 78.471(7), gamma = 69.401(8)degrees, V = 657.3(2)angstrom(3), Z = 2, R-1 = 0.0454; (2) C11H12N2O4, Mr=236.23, Pbca, a=7.2713(9), b=14.234(1), c=20.848(3)angstrom, V= 2157.8(4) angstrom(3), Z=8, R-1=0.0504; (3) C13H13N2O3Cl, Mr = 280.70, P2/n, a = 17.344(2), b = 9.237(1), c = 18.398(2) angstrom; beta = 92.61(2)degrees, V = 2944.4(6) angstrom(3), Z = 8, R-1 = 0.0714. The conformational features of three 4-substituted-3-4-dihydropyrimidin-2(1H)-ones were investigated by computational and single crystal X-ray crystallographic studies. The geometries were optimized using semiempirical (AM1) and first principle calculations (B3LYP/6-31G**) methods, the rotational barriers for important functional groups were studied. In all structures the pyrimidinone rings are in a more or less distorted boat conformation. The phenyl and the furane rings are almost perpendicular to the best least-squares plane through the dihydropyrimidinone ring.

Purification, crystallization and preliminary X-ray analysis of haemoglobin I from the armoured catfish Liposarcus anisitsi

Liposarcus anisitsi is an armoured catfish that presents accessorial air oxygenation through a modified stomach, which allows this species to survive in waters with very low oxygen content. Analysis of its haemolysate has shown the presence of four haemoglobins; this work focuses on the main component, haemoglobin I. It has been crystallized in two different forms and X-ray diffraction data have been collected to 2.77 and 2.86 Angstrom resolution using synchrotron radiation. Crystals were determined to belong to the space groups C2 and P2(1) and preliminary structural analysis revealed the presence of one tetramer in the asymmetric unit in both crystal forms. The structure was determined using a standard molecular-replacement technique.

New X-ray powder diffraction data and Rietveld refinement for Gd2O3 monodispersed fine spherical particles

Nominally pure Gd2O3 C-form structure from basic carbonate fine spherical particles and its differences concerning the XRD data among literature patterns using Rietveld method is reported. Gd2O3: Eu3+ from basic carbonate and Gd2O3 from oxalate were also investigated. All samples, except the one from oxalate precursor, are narrow sized, 100-200 nm. Only non-doped Gd2O3 from basic carbonate presents XRD data with smaller d(hkl) values than the literature ones. From Rietveld refinement, non-doped Gd2O3 from basic carbonate has the smallest crystallite size and from oxalate shows the greatest one. Also, the unit cell parameters indicate a plan contraction of the Gd2O3 from basic carbonate. The presence of Eu3+ increases crystallite size when basic carbonate precursor is used to prepare Gd2O3 and avoids plan contraction. The structural differences observed among Gd2O3 samples obtained are related to the type of precursor and to the presence or not of doping ion. (C) 2003 Elsevier B.V. (USA). All rights reserved.

Crystallization and preliminary X-ray diffraction analysis of the lectin from Canavalia gladiata seeds

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

Crystallization and X-ray diffraction data analysis of human deoxyhaemoglobin A(0) fully stripped of any anions

In this work, initial crystallographic studies of human haemoglobin (Hb) crystallized in isoionic and oxygen-free PEG solution are presented. Under these conditions, functional measurements of the O-2-linked binding of water molecules and release of protons have evidenced that Hb assumes an unforeseen new allosteric conformation. The determination of the high-resolution structure of the crystal of human deoxy-Hb fully stripped of anions may provide a structural explanation for the role of anions in the allosteric properties of Hb and, particularly, for the influence of chloride on the Bohr effect, the mechanism by which Hb oxygen affinity is regulated by pH. X-ray diffraction data were collected to 1.87 Angstrom resolution using a synchrotron-radiation source. Crystals belong to the space group P2(1)2(1)2 and preliminary analysis revealed the presence of one tetramer in the asymmetric unit. The structure is currently being refined using maximum-likelihood protocols.

Small-angle X-ray scattering study of the smart thermo-optical behavior of zirconyl aqueous colloids

The smart thermo-optical systems studied here are based on the unusual thermoreversible sol-gel transition of zirconyl chloride aqueous solution modified by sulfuric acid in the molar ratio Zr/SO4:3/1. The transparency to the visible light changes during heating due to light scattering. This feature is related to the aggregates growth that occurs during gelation. These reversible changes can be controlled by the amount of chloride ions in solution. The thermoreversible sol-gel transition temperature increases from 323 to 343 K by decreasing the molar ratio Cl/Zr from 7.0 to 1.3. In this work the effect of the concentration of chloride ions on the structural characteristics of the system has been analyzed by in situ SAXS measurements during the sol-gel transition carried out at 323 and 333 K. The experimental SAXS curves of sols exhibit three regions at small, medium and high scattering vectors characteristics of Guinier, fractal and Porod regimes, respectively. The radius of primary particles, obtained from the crossover between the fractal and Porod regimes, remains almost invariable with the chloride concentration, and the value (4 Angstrom) is consistent with the size of the molecular precursor. During the sol-gel transition the aggregates grow with a fractal structure and the fractal dimensionality decreases from 2.4 to 1.8. This last value is characteristic of a cluster-cluster aggregation controlled by a diffusion process. Furthermore, the time exponent of aggregate growth presents values of 0.33 and 1, typical of diffusional and hydrodynamic motions. A crossover between these two regimes is observed.

Crystallization, preliminary X-ray analysis and molecular-replacement solution of the carboxy form of haemoglobin I from the fish Brycon cephalus

Haemoglobin, the 'honorary enzyme' [Brunori (1999), Trends Biochem. Sci. 24, 158-161], constitutes a prime prototype for allosteric models. Here, the crystallization and preliminary X-ray analysis of haemoglobin I from the South American fish Brycon cephalus are reported. X-ray diffraction data have been collected to 2.5 Angstrom resolution using synchrotron radiation (LNLS). Crystals were determined to belong to the space group P6(1)22 and preliminary structural analysis revealed the presence of one dimer (alpha beta) in the asymmetric unit. The structure was determined using standard molecular-replacement techniques.

Characterization of tin oxide based sol-gel coatings on borosilicate glasses by X-ray reflectivity

The X-ray reflectivity technique was applied in the study of tin oxide films deposited by sol-gel dip-coating on borosilicate glasses. The influence of the withdrawal speed and temperature of thermal treatment on the film structure was analyzed. We have compared the thermal evolution of the density and the shrinkage of the films with these properties measured for the monolithic xerogel by helium picnometry and thermomechanical analysis. In agreement with the Landau-Levich model, the layer thickness increases by increasing the withdrawal speed. Nevertheless, it decreases with the increase of the thermal treatment temperature, due to the densification process. The values of apparent density are smaller than the skeletal density, which shows that the films are porous. The comparison between the film and the monolith indicates that shrinkage during firing is anisotropic, occurring essentially perpendicular to the coating surface.