Intralamellar structural modifications related to the proton exchanging in K(4)Nb(6)O(17) layered phase

Basic structural aspects about the layered hexaniobate of K(4)Nb(6)O(17) composition and its proton-exchanged form were investigated mainly by spectroscopic techniques. Raman spectra of hydrous K(4)Nb(6)O(17) and H(2)K(2)Nb(6)O(17)center dot H(2)O show significant modifications in the 950-800 cm(-1) region (Nb-O stretching mode of highly distorted NbO(6) octahedra). The band at 900 cm(-1) shifts to 940 cm(-1) after the replacement of K(+) ion by proton. Raman spectra of the original materials and the related deuterated samples are similar suggesting that no isotopic effect occurs. Major modifications were observed when H(2)K(2)Nb(6)O(17) was dehydrated: the relative intensity of the band at 940 cm(-1) decreases and new bands seems to be present at about 860-890 cm(-1). The H(+) ions should be shielded by the hydration sphere what preclude the interaction with the layers. Removing the water molecules, H(+) ions can establish a strong interaction with oxygen atoms, decreasing the bond order of Nb-O linkage. X-ray absorption near edge structure studies performed at Nb K-edge indicate that the niobium coordination number and oxidation state remain identical after the replacement of potassium by proton. From the refinement of the fine structure, it appears that the Nb-Nb coordination shell is divided into two main contributions of about 0.33 and 0.39 nm, and interestingly the population, i.e., the number of backscattering atoms is inversed between the two hexaniobate materials. 2009 Elsevier Ltd. All rights reserved.

Structural modifications in stretch-induced crystallization in PVDF films as measured by small-angle X-ray scattering

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

Structural modifications in silica sonogels prepared with additions of poly(vinyl alcohol)

Silica wet gels were prepared from acid sonohydrolysis of tetraethoxysilane (TEOS) and additions of poly(vinyl alcohol) (PVA)-water solution. Aerogels were obtained from supercritical CO(2) extraction. The samples were studied by thermal gravimetric (TG) analysis, small-angle X-ray scattering (SAXS), and nitrogen adsorption. The structure of wet gels can be described as a mass fractal with dimension D equal to 2.0 on the whole length scale experimentally probed by SAXS, from similar to 0.3 to similar to 15 nm. Pure and low-PVA-addition wet gels exhibit an upper cutoff accounting for a finite characteristic length xi of the mass fractal structure. Additions , of PVA increase without modifying D, which was attributed to a steric effect of the polymer in the structure. The pore volume fraction of the aerogels diminishes typically about 11% with respect to that of the wet gels, although nitrogen adsorption could be underestimating some porosity. The pore size distribution of the aerogels is shifted toward the mesopore region with the additions of PVA, in a straight relationship with the increase of xi in the wet gels. The thermal stability of the pore size distribution of the aerogels was studied up to 1000 degrees C.

Age-related functional and structural retinal modifications in the Igf1−/− null mouse

Background. Mutations in the gene encoding human insulin-like growth factor-I (IGF-I) cause syndromic neurosensorial deafness. To understand the precise role of IGF-I in retinal physiology, we have studied the morphology and electrophysiology of the retina of the Igf1−/− mice in comparison with that of the Igf1+/− and Igf1+/+ animals during aging. Methods. Serological concentrations of IGF-I, glycemia and body weight were determined in Igf1+/+, Igf1+/− and Igf1−/− mice at different times up to 360 days of age. We have analyzed hearing by recording the auditory brainstem responses (ABR), the retinal function by electroretinographic (ERG) responses and the retinal morphology by immunohistochemical labeling on retinal preparations at different ages. Results. IGF-I levels are gradually reduced with aging in the mouse. Deaf Igf1−/− mice had an almost flat scotopic ERG response and a photopic ERG response of very small amplitude at postnatal age 360 days (P360). At the same age, Igf1+/− mice still showed both scotopic and photopic ERG responses, but a significant decrease in the ERG wave amplitudes was observed when compared with those of Igf1+/+ mice. Immunohistochemical analysis showed that P360 Igf1−/− mice suffered important structural modifications in the first synapse of the retinal pathway, that affected mainly the postsynaptic processes from horizontal and bipolar cells. A decrease in bassoon and synaptophysin staining in both rod and cone synaptic terminals suggested a reduced photoreceptor output to the inner retina. Retinal morphology of the P360 Igf1+/− mice showed only small alterations in the horizontal and bipolar cell processes, when compared with Igf1+/+ mice of matched age. Conclusions. In the mouse, IGF-I deficit causes an age-related visual loss, besides a congenital deafness. The present results support the use of the Igf1−/− mouse as a new model for the study of human syndromic deaf-blindness.

Ligand-Induced structural changes in TEM‑1 probed by molecular dynamics and relative binding free energy calculations

The TEM family of enzymes has had a crucial impact on the pharmaceutical industry due to their important role in antibiotic resistance. Even with the latest technologies in structural biology and genomics, no 3D structure of a TEM- 1/antibiotic complex is known previous to acylation. Therefore, the comprehension of their capability in acylate antibiotics is based on the protein macromolecular structure uncomplexed. In this work, molecular docking, molecular dynamic simulations, and relative free energy calculations were applied in order to get a comprehensive and thorough analysis of TEM-1/ampicillin and TEM-1/amoxicillin complexes. We described the complexes and analyzed the effect of ligand binding on the overall structure. We clearly demonstrate that the key residues involved in the stability of the ligand (hot-spots) vary with the nature of the ligand. Structural effects such as (i) the distances between interfacial residues (Ser70−Oγ and Lys73−Nζ, Lys73−Nζ and Ser130−Oγ, and Ser70−Oγ−Ser130−Oγ), (ii) side chain rotamer variation (Tyr105 and Glu240), and (iii) the presence of conserved waters can be also influenced by ligand binding. This study supports the hypothesis that TEM-1 suffers structural modifications upon ligand binding.

Desulfovibrio gigas ferredoxin II: redox structural modulation of the [3Fe–4S] cluster

J Biol Inorg Chem (2006) 11: 307–315 DOI 10.1007/s00775-005-0077-2

TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.

Magnetic and topographical modifications of amorphous Co–Fe thin films induced by high energy Ag7+ ion irradiation

We have investigated the effects of swift heavy ion irradiation on thermally evaporated 44 nm thick, amorphous Co77Fe23 thin films on silicon substrates using 100 MeV Ag7+ ions fluences of 1 1011 ions/ cm2, 1 1012 ions/cm2, 1 1013 ions/cm2, and 3 1013 ions/cm2. The structural modifications upon swift heavy irradiation were investigated using glancing angle X-ray diffraction. The surface morphological evolution of thin film with irradiation was studied using Atomic Force Microscopy. Power spectral density analysis was used to correlate the roughness variation with structural modifications investigated using X-ray diffraction. Magnetic measurements were carried out using vibrating sample magnetometry and the observed variation in coercivity of the irradiated films is explained on the basis of stress relaxation. Magnetic force microscopy images are subjected to analysis using the scanning probe image processor software. These results are in agreement with the results obtained using vibrating sample magnetometry. The magnetic and structural properties are correlated

Enzymatic and structural characterization of new PLA2 isoform isolated from white venom of Crotalus durissus ruruima

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

Modifications in the correlation function in poly(vinyl alcohol)/silica hybrid wet gels

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

Influence of Ca concentration on the electric, morphological, and structural properties of (Pb,Ca)TiO3 thin films

Pb1-xCaxTiO3 (0.10less than or equal toxless than or equal to0.40) thin films on Pt/Ti/SiO2/Si(100) substrates were prepared by the soft solution process and their characteristics were investigated as a function of the calcium content (x). The structural modifications in the films were studied using x-ray diffraction and micro-Raman scattering techniques. Lattice parameters calculated from x-ray data indicate a decrease in lattice tetragonality with the increasing content of calcium in these films. Raman spectra exhibited characteristic features of pure PbTiO3 thin films. Variations in the phonon mode wave numbers, especially those of lower wave numbers, of Pb1-xCaxTiO3 thin films as a function of the composition corroborate the decrease in tetragonality caused by the calcium doping. As the Ca content (x) increases from 0.10 to 0.40, the dielectric constant at room temperature abnormally increased at 1 kHz from 148 to 430. Also calcium substitution decreased the remanent polarization and coercive field from 28.0 to 5.3 muC/cm(2) and 124 to 58 kV/cm, respectively. These properties can be explained in terms of variations of phase transition (ferroelectric-paraelectric), resulting from the substitution the lead site of PbTiO(3)for the nonvolatile calcium. (C) 2002 American Institute of Physics.

The role of Bi2O3 on the thermal, structural, and optical properties of tungsten-phosphate glasses

Glasses in the ternary system (70 - x)NaPO3-30WO 3-xBi2O3, with x = 0-30 mol %, were prepared by the conventional melt-quenching technique. X-ray diffraction (XRD) measurements were performed to confirm the noncrystalline nature of the samples. The influence of the Bi2O3 on the thermal, structural, and optical properties was investigated. Differential scanning calorimetry analysis showed that the glass transition temperature, Tg, increases from 405 to 440 C for 0 ≤ x ≤ 15 mol % and decreases to 417 C for x = 30 mol %. The thermal stability against devitrification decreases from 156 to 67 C with the increase of the Bi2O3 content. The structural modifications were studied by Raman scattering, showing a bismuth insertion into the phosphate chains by Bi-O-P linkage. Furthermore, up to 15 mol % of Bi 2O3 formation of BiO6 clusters is observed, associated with Bi-O-Bi linkage, resulting in a progressive break of the linear phosphate chains that leads to orthophosphate Q0 units. The linear refractive index, n0, was measured using the prism-coupler technique at 532, 633, and 1550 nm, whereas the nonlinear (NL) refractive index, n 2 was measured at 1064 nm using the Z-scan technique. Values of 1.58 ≤ n0 ≤ 1.88, n2 ≥ 10-15 cm 2/W and NL absorption coefficient, α2 ≤ 0.01 cm/GW, were determined. The linear and NL refractive indices increase with the increase of the Bi2O3 concentration. The large values of n0 and n2, as well as the very small α2, indicate that these materials have large potential for all-optical switching applications in the near-infrared. © 2012 American Chemical Society.