Low-Resolution Molecular Models Reveal the Oligomeric State of the PPAR and the Conformational Organization of Its Domains in Solution

The peroxisome proliferator-activated receptors (PPARs) regulate genes involved in lipid and carbohydrate metabolism, and are targets of drugs approved for human use. Whereas the crystallographic structure of the complex of full length PPAR gamma and RXR alpha is known, structural alterations induced by heterodimer formation and DNA contacts are not well understood. Herein, we report a small-angle X-ray scattering analysis of the oligomeric state of hPPAR gamma alone and in the presence of retinoid X receptor (RXR). The results reveal that, in contrast with other studied nuclear receptors, which predominantly form dimers in solution, hPPAR gamma remains in the monomeric form by itself but forms heterodimers with hRXR alpha. The low-resolution models of hPPAR gamma/RXR alpha complexes predict significant changes in opening angle between heterodimerization partners (LBD) and extended and asymmetric shape of the dimer (LBD-DBD) as compared with X-ray structure of the full-length receptor bound to DNA. These differences between our SAXS models and the high-resolution crystallographic structure might suggest that there are different conformations of functional heterodimer complex in solution. Accordingly, hydrogen/deuterium exchange experiments reveal that the heterodimer binding to DNA promotes more compact and less solvent-accessible conformation of the receptor complex.

Structure of the haptoglobin-haemoglobin complex

Red cell haemoglobin is the fundamental oxygen-transporting molecule in blood, but also a potentially tissue-damaging compound owing to its highly reactive haem groups. During intravascular haemolysis, such as in malaria and haemoglobinopathies(1), haemoglobin is released into the plasma, where it is captured by the protective acute-phase protein haptoglobin. This leads to formation of the haptoglobin-haemoglobin complex, which represents a virtually irreversible non-covalent protein-protein interaction(2). Here we present the crystal structure of the dimeric porcine haptoglobin-haemoglobin complex determined at 2.9 angstrom resolution. This structure reveals that haptoglobin molecules dimerize through an unexpected beta-strand swap between two complement control protein (CCP) domains, defining a new fusion CCP domain structure. The haptoglobin serine protease domain forms extensive interactions with both the alpha- and beta-subunits of haemoglobin, explaining the tight binding between haptoglobin and haemoglobin. The haemoglobin-interacting region in the alpha beta dimer is highly overlapping with the interface between the two alpha beta dimers that constitute the native haemoglobin tetramer. Several haemoglobin residues prone to oxidative modification after exposure to haem-induced reactive oxygen species are buried in the haptoglobin-haemoglobin interface, thus showing a direct protective role of haptoglobin. The haptoglobin loop previously shown to be essential for binding of haptoglobin-haemoglobin to the macrophage scavenger receptor CD163 (ref. 3) protrudes from the surface of the distal end of the complex, adjacent to the associated haemoglobin alpha-subunit. Small-angle X-ray scattering measurements of human haptoglobin-haemoglobin bound to the ligand-binding fragment of CD163 confirm receptor binding in this area, and show that the rigid dimeric complex can bind two receptors. Such receptor cross-linkage may facilitate scavenging and explain the increased functional affinity of multimeric haptoglobin-haemoglobin for CD163 (ref. 4).

Characterization of Heparin-induced Glyceraldehyde-3-phosphate Dehydrogenase Early Amyloid-like Oligomers and Their Implication in alpha-Synuclein Aggregation

Lewy bodies and Lewy neurites, neuropathological hallmarks of several neurological diseases, are mainly made of filamentous assemblies of alpha-synuclein. However, other macromolecules including Tau, ubiquitin, glyceraldehyde-3-phosphate dehydrogenase, and glycosaminoglycans are routinely found associated with these amyloid deposits. Glyceraldehyde-3-phosphate dehydrogenase is a glycolytic enzyme that can form fibrillar aggregates in the presence of acidic membranes, but its role in Parkinson disease is still unknown. In this work, the ability of heparin to trigger the amyloid aggregation of this protein at physiological conditions of pH and temperature is demonstrated by infrared and fluorescence spectroscopy, dynamic light scattering, small angle x-ray scattering, circular dichroism, and fluorescence microscopy. Aggregation proceeds through the formation of short rod-like oligomers, which elongates in one dimension. Heparan sulfate was also capable of inducing glyceraldehyde-3-phosphate dehydrogenase aggregation, but chondroitin sulfates A, B, and C together with dextran sulfate had a negligible effect. Aided with molecular docking simulations, a putative binding site on the protein is proposed providing a rational explanation for the structural specificity of heparin and heparan sulfate. Finally, it is demonstrated that in vitro the early oligomers present in the glyceraldehyde-3-phosphate dehydrogenase fibrillation pathway promote alpha-synuclein aggregation. Taking into account the toxicity of alpha-synuclein prefibrillar species, the heparin-induced glyceraldehyde-3-phosphate dehydrogenase early oligomers might come in useful as a novel therapeutic strategy in Parkinson disease and other synucleinopathies.

Hofmeister effects on the colloidal stability of poly(ethylene glycol)-decorated nanoparticles

The colloidal stability of poly(ethylene glycol)-decorated poly(methyl methacrylate), PMMA/Tween-20, particles was investigated by means of phase separation measurements, in the presence of sodium fluoride (NaF), sodium chloride, sodium bromide, sodium nitrate, or sodium thiocyanate (NaSCN) at 1.0 mol L-1. Following Hofmeister's series, the dispersions of PMMA/Tween-20 destabilized faster in the presence of NaF than with NaSCN. After the phase separation, the systems were homogenized and except for the dispersions in NaF, re-dispersed particles took longer to destabilize, indicating that anions adsorbed on the particles, creating a new surface. Except for F- ions, the adsorption of anions on the polar outmost shell was evidenced by means of tensiometry and small-angle X-ray scattering measurements. Fluoride ions induced the dehydration of the polar shell, without affecting the polar shell electron density, and the formation of very large aggregates. A model was proposed to explain the colloidal behavior in the presence of Hofmeister ions.

Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+

Abstract Background Ferredoxin-NADP(H) reductases (FNRs) are flavoenzymes that catalyze the electron transfer between NADP(H) and the proteins ferredoxin or flavodoxin. A number of structural features distinguish plant and bacterial FNRs, one of which is the mode of the cofactor FAD binding. Leptospira interrogans is a spirochaete parasitic bacterium capable of infecting humans and mammals in general. Leptospira interrogans FNR (LepFNR) displays low sequence identity with plant (34% with Zea mays) and bacterial (31% with Escherichia coli) FNRs. However, LepFNR contains all consensus sequences that define the plastidic class FNRs. Results The crystal structures of the FAD-containing LepFNR and the complex of the enzyme with NADP+, were solved and compared to known FNRs. The comparison reveals significant structural similarities of the enzyme with the plastidic type FNRs and differences with the bacterial enzymes. Our small angle X-ray scattering experiments show that LepFNR is a monomeric enzyme. Moreover, our biochemical data demonstrate that the LepFNR has an enzymatic activity similar to those reported for the plastidic enzymes and that is significantly different from bacterial flavoenzymes, which display lower turnover rates. Conclusion LepFNR is the first plastidic type FNR found in bacteria and, despite of its low sequence similarity with plastidic FNRs still displays high catalytic turnover rates. The typical structural and biochemical characteristics of plant FNRs unveiled for LepFNR support a notion of a putative lateral gene transfer which presumably offers Leptospira interrogans evolutionary advantages. The wealth of structural information about LepFNR provides a molecular basis for advanced drugs developments against leptospirosis.

The influence of both urea and 2,2,2

The influence of external agents on proteins function and structure is essential to elucidate the unfolding pathways and self-assemble properties. The knowledge of the protein amyloid fibril formation process is important due to the fields that this subjected is related, in particular for the neurodegenerative disorders. In the present work we studied the influence of both urea and 2,2,2-Trifluoroethanol (TFE) and temperature on the structure and proteinprotein interactions of Bovine Serum Albumin (BSA), by means of UV-Vis spectroscopy, static fluorescence and small angle X-ray scattering technique. The experiments were performed in samples composed by 10 and 3 mg/ml of BSA at pH 5.8, near the protein pI. First, Thioflavin-T fluorescence measurements indicated that urea, in the absence of TFE, was able to increase the amyloid fibril formation of BSA at 45oC and increasing the urea concentration the rate of amyloid fibril formation also increases. Concerning the presence of TFE, SAXS data suggest that BSA tridimensional structure is not altered by the presence of TFE 5% and 10% v/v in all studied protein concentrations. Interestingly, the presence of TFE on the urea-containing BSA also increases the rate of amyloid fibril formation, as compared to the TFE-free system, indicating that TFE can catalyze the amyloid-fibril formation. The presence of TFE 20% v/v, however, induces the formation of aggregates, but at this time we were not able to infer if such aggregates are amyloidlike or amorphous. Taking together, the results give support to infer that BSA can for fibrils in the presence of urea at 45oC and TFE can act as a stabilizer or as a denaturant agent for BSA.

Clay-containing block copolymer nanocomposites with aligned morphology prepared by extrusion

Clay-containing nanocomposites of polystyrene-b-poly(ethylene-co-butylene)-b-polystyrene (SEBS) copolymers having cylindrical domains were obtained by melt extrusion using a tape die. One type of sample (SEBS-MA) had maleic anhydride attached to the middle block. Two types of organoclays were added, namely Cloisite 20A and Cloisite 30B. Small angle X-ray scattering and transmission electron microscopy (TEM) analyses showed that the addition of 20A clay to SEBS and SEBS-MA resulted in nanocomposites with intercalated and partially exfoliated structures, respectively. The addition of 30B clay to SEBS and SEBS-MA promoted the formation of composites containing relatively large micron-sized and partially exfoliated clay particles, respectively. Our TEM analysis revealed that clay particles embedded in SEBS are preferably in contact with the polystyrene cylindrical domains, while in SEBS-MA they are in contact with the maleated matrix. The extrusion processing promoted alignment of the axes of the polystyrene cylinders along the extrusion direction in all samples, and the basal planes of the clay particles were mostly parallel to the main external surfaces of the extruded tapes. © 2013 Society of Chemical Industry.

Staphylococcus aureus thiaminase II: oligomerization warrants proteolytic protection against serine proteases

Staphylococcus aureus TenA (SaTenA) is a thiaminase type II enzyme that catalyzes the deamination of aminopyrimidine, as well as the cleavage of thiamine into 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) and 5-(2-hydroxyethyl)-4-methylthiazole (THZ), within thiamine (vitamin B1) metabolism. Further, by analogy with studies of Bacillus subtilis TenA, SaTenA may act as a regulator controlling the secretion of extracellular proteases such as the subtilisin type of enzymes in bacteria. Thiamine biosynthesis has been identified as a potential drug target of the multi-resistant pathogen S. aureus and therefore all enzymes involved in the S. aureus thiamine pathway are presently being investigated in detail. Here, the structure of SaTenA, determined by molecular replacement and refined at 2.7 A ° resolution to an R factor of 21.6% with one homotetramer in the asymmetric unit in the orthorhombic space group P212121, is presented. The tetrameric state of wild-type (WT) SaTenA was postulated to be the functional biological unit and was confirmed by small-angle X-ray scattering (SAXS) experiments in solution. To obtain insights into structural and functional features of the oligomeric SaTenA, comparative kinetic investigations as well as experiments analyzing the structural stability of the WT SaTenA tetramer versus a monomeric SaTenA mutant were performed.

Properties of a new poly-ether-glycol copolymer.

Triblock copolymers are made of monomer segments, being the central part usually hydrophobic and the outer parts hydrophilic. By varying sizes, molecular weights and monomer types of the segments one obtains different final molecules, with different physico-chemical properties, which are directly related to the performance of the final product. Looking for new products to be used, among other possibilities, in biological applications, a new polymer (Figure 1) was synthesized by the Dow Chemical and studied by Size Exclusion Chromatography, Fourier Transformed Infrared Spectrometry, Small-angle X-ray Scattering (SAXS) and its cloud point was determined by measuring light transmittance. The studies showed low molecular polydispersivety, but different polarities in the macromolecules fractions. Due to the low solubility of Diol in water, a mixture of water/butyl diglycol was used as solvent. An extensive analysis by SAXS was performed for concentrations from 50 wt% to 80 wt% of Diol in solution. Small concentrations showed very low signal to noise ratio, making it impossible to be analysed. The scattering intensity including the form factor of polydisperse non-homogeneous spheres, and the structure factor of interacting hard spheres was fitted to the curves. As the polymer concentration is high, the fitting of form factors of direct and reverse micelles were compared. The results for direct micelles were better up to 80 wt%, whereas at 90 wt% and 95 wt% the curves were better fitted by reverse micelles. It might seem odd that direct micelles are present up to such high concentrations, but it might have been caused by the presence of butyl diglycol, which increases the solubility of Diol in water. The inner and outer radius of the micelles, electron density distribution, and interaction radius of the micelles were obtained. The polydispersivety increases with Diol concentration. Besides, the interaction radius increases with solvent concentration, even when reversed micelles are present. In the last case, accompanied by an increase of inner radius (water content), as there are fewer Diol molecules to involve the water nuclei, which become larger, further apart, and in less number.

Morphology and topography analysis of mesoporous titania templated by micrometric latex sphere arrays

In this work, mesoporous titania is prepared by templating latex sphere arrays with four different sphere diameters at the micrometric scale (phi > 1 mu m). The mesoporous titania homogeneously covers the latex spheres and substrate, forming a thin coating characterized by N-2 adsorption isotherm, small angle X-rays scattering, atomic force, field emission and transmission electronic microscopies. Mesoporous titania has been templated into different shapes such as hollow particles and monoliths according to the amount of sol used to fill the voids of the close packed latex spheres. Titania topography strongly depends on the adsorption of polymeric segments over latex spheres surface, which could be decreased by changing the dimensions of latex spheres (phi = 9.5 mu m) generating a lamellar architecture. Thus, micrometric latex sphere arrays can be used to achieve new surface patterns for mesoporous materials via a fast and inexpensive chemical route for construction of functional devices in different technological fields such as energy conversion, inclusion chemistry and biomaterials. (C) 2011 Elsevier Inc. All rights reserved.

Interionic Interactions in Imidazolic Ionic Liquids Probed by Soft X-ray Absorption Spectroscopy

This work investigates pure ionic liquids (ILs) derived from an imidazolium ring with different carbonic chains and halides or bis(trifluoromethanesulfonilimide) (TFSI-) as anions, using X-ray absorption near edge spectroscopy (XANES) at different energies (N, S, O, F, and Cl edges) to probe the interionic interactions. XANES data show that the interaction with the anion is weaker when the cation is an imidazolium than when the salt is formed by smaller cations, as lithium, independently of the length of the carbonic chain attached to the imidazolium cation. The results also show that, for all studied as, it is not observed any influence of the anion on the XANES spectra of the cation, nor the opposite. 1-Methylimidazolium with Cl-, a small and strongly coordinating anion, presents in the N K XANES spectrum a splitting of the band corresponding to nitrogen in the imidazolic ring, indicating two different chemical environments. For this cation with TFSI-, on the contrary, this splitting was not observed, showing that the anion has a weaker interaction with the imidazolic ring, even without a lateral carbonic chain.

Gaussian deconvolution: a useful method for a form-free modeling of scattering data from mono- and multilayered planar systems

A new method for analysis of scattering data from lamellar bilayer systems is presented. The method employs a form-free description of the cross-section structure of the bilayer and the fit is performed directly to the scattering data, introducing also a structure factor when required. The cross-section structure (electron density profile in the case of X-ray scattering) is described by a set of Gaussian functions and the technique is termed Gaussian deconvolution. The coefficients of the Gaussians are optimized using a constrained least-squares routine that induces smoothness of the electron density profile. The optimization is coupled with the point-of-inflection method for determining the optimal weight of the smoothness. With the new approach, it is possible to optimize simultaneously the form factor, structure factor and several other parameters in the model. The applicability of this method is demonstrated by using it in a study of a multilamellar system composed of lecithin bilayers, where the form factor and structure factor are obtained simultaneously, and the obtained results provided new insight into this very well known system.

A NEW METHOD TO QUANTIFY X-RAY SUBSTRUCTURES IN CLUSTERS OF GALAXIES

We present a new method to quantify substructures in clusters of galaxies, based on the analysis of the intensity of structures. This analysis is done in a residual image that is the result of the subtraction of a surface brightness model, obtained by fitting a two-dimensional analytical model (beta-model or Sersic profile) with elliptical symmetry, from the X-ray image. Our method is applied to 34 clusters observed by the Chandra Space Telescope that are in the redshift range z is an element of [0.02, 0.2] and have a signal-to-noise ratio (S/N) greater than 100. We present the calibration of the method and the relations between the substructure level with physical quantities, such as the mass, X-ray luminosity, temperature, and cluster redshift. We use our method to separate the clusters in two sub-samples of high-and low-substructure levels. We conclude, using Monte Carlo simulations, that the method recuperates very well the true amount of substructure for small angular core radii clusters (with respect to the whole image size) and good S/N observations. We find no evidence of correlation between the substructure level and physical properties of the clusters such as gas temperature, X-ray luminosity, and redshift; however, analysis suggest a trend between the substructure level and cluster mass. The scaling relations for the two sub-samples (high-and low-substructure level clusters) are different (they present an offset, i. e., given a fixed mass or temperature, low-substructure clusters tend to be more X-ray luminous), which is an important result for cosmological tests using the mass-luminosity relation to obtain the cluster mass function, since they rely on the assumption that clusters do not present different scaling relations according to their dynamical state.

Synchrotron X-ray diffraction characterization of healthy and fluorotic human dental enamel

With the introduction of fluoride as the main anticaries agent used in preventive dentistry, and perhaps an increase in fluoride in our food chain, dental fluorosis has become an increasing world-wide problem. Visible signs of fluorosis begin to become obvious on the enamel surface as opacities, implying some porosity in the tissue. The mechanisms that conduct the formation of fluorotic enamel are unknown, but should involve modifications in the basic physical-chemistry reactions of demineralization and remineralisation of the enamel of the teeth, which is the same reaction of formation of the enamel's hydroxyapatite (HAp) in the maturation phase. The increase of the amount of fluoride inside of the apatite will result in gradual increase of the lattice parameters. The aim of this work is to characterize the healthy and fluorotic enamel in human tooth using Synchrotron X-ray diffraction. All the scattering profile measurements were carried out at the X-ray diffraction beamline (XRD1) at the Brazilian Synchrotron Light Laboratory-LNLS, Campinas, Brazil. X-ray diffraction experiments were performed both in powder samples and polished surfaces. The powder samples were analyzed to obtain the characterization of a typical healthy enamel pattern. The polished surfaces were analyzed in specific areas that have been identified as fluorotic ones. X-ray diffraction data were obtained for all samples and these data were compared with the control samples and also with the literature data. (c) 2012 Elsevier Ltd. All rights reserved.

The relationship between gamma Cassiopeiae's X-ray emission and its circumstellar environment

gamma Cas is the prototypical classical Be star and is recently best known for its variable hard X-ray emission. To elucidate the reasons for this emission, we mounted a multiwavelength campaign in 2010 centered around four XMM-Newton observations. The observational techniques included long baseline optical interferometry (LBOI) from two instruments at CHARA, photometry carried out by an automated photometric telescope and H alpha observations. Because gamma Cas is also known to be in a binary, we measured radial velocities from the H alpha line and redetermined its period as 203.55 +/- 0.20 days and its eccentricity as near zero. The LBOI observations suggest that the star's decretion disk was axisymmetric in 2010, has an system inclination angle near 45 degrees, and a larger radius than previously reported. In addition, the Be star began an "outburst" at the beginning of our campaign, made visible by a brightening and reddening of the disk during our campaign and beyond. Our analyses of the new high resolution spectra disclosed many attributes also found from spectra obtained in 2001 (Chandra) and 2004 (XMM-Newton). As well as a dominant hot (approximate to 14 keV) thermal component, the familiar attributes included: (i) a fluorescent feature of Fe K even stronger than observed at previous times; (ii) strong lines of N VII and Ne XI lines indicative of overabundances; and (iii) a subsolar Fe abundance from K-shell lines but a solar abundance from L-shell ions. We also found that two absorption columns are required to fit the continuum. While the first one maintained its historical average of 1 x 10(21) cm(-2), the second was very large and doubled to 7.4 x 10(23) cm(-2) during our X-ray observations. Although we found no clear relation between this column density and orbital phase, it correlates well with the disk brightening and reddening both in the 2010 and earlier observations. Thus, the inference from this study is that much (perhaps all?) of the X-ray emission from this source originates behind matter ejected by gamma Cas into our line of sight.