SAXSMoW 3.0: New advances in the determination of the molecular weight of proteins in dilute solutions from SAXS intensity data on a relative scale.

SAXSMoW (SAXS Molecular Weight) is an online platform widely used over the past few years for determination of molecular weights of proteins in dilute solutions. The scattering intensity retrieved from small-angle X-ray scattering (SAXS) raw data is the sole input to SAXSMoW for determination of molecular weights of proteins in liquid. The current updated SAXSMoW version 3.

Synchrotron Radiation Applied to Real-Time Studies of the Kinetics of Growth of Aluminum Nitride Thin Multilayers.

This article reports the design, construction, and first use of an experimental device consisting of a specially designed vacuum chamber equipped with a reactive sputtering magnetron (RSM) to be used for controlled deposition of thin films on a Si(100) flat substrate. The setup was designed to allow for in situ and real-time recordings of X-ray diffraction patterns during the growth of the deposited films and was installed in the X-ray diffraction and spectroscopy beamline emerging from a superconducting wiggler source at the Brazilian Synchrotron Light Laboratory. The first use of the RSM setup was an in situ and real-time X-ray diffraction study of processes of growth of multilayered aluminum nitride thin films, whereas the operation parameters of the reactor were sequentially changed.

SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale.

Knowledge of molecular weight, oligomeric states, and quaternary arrangements of proteins in solution is fundamental for understanding their molecular functions and activities. We describe here a program SAXSMoW 2.0 for robust and quick determination of molecular weight and oligomeric state of proteins in dilute solution, starting from a single experimental small-angle scattering intensity curve, I(q), measured on a relative scale.

Effect of Nanoclustering and Dipolar Interactions in Heat Generation for Magnetic Hyperthermia.

Biomedical magnetic colloids commonly used in magnetic hyperthermia experiments often display a bidisperse structure, i.e., are composed of stable nanoclusters coexisting with well-dispersed nanoparticles.

Controlled growth of extended arrays of CoSi2 hexagonal nanoplatelets buried in Si(001), Si(011) and Si(111) wafers.

Because of their high electrical conductivity CoSi2 nanostructures are potential candidates for preparing ordered nano-arrays to be used as electrode interconnectors and contacts in microelectronic devices. We here describe a controlled procedure for the endotaxial growth of hexagonal CoSi2 nanoplatelets buried in differently oriented single crystalline Si wafers on which a Co-doped SiO2 thin film was previously deposited. These nanomaterials were obtained by a clean procedure consisting of isothermal annealing at 750 °C under a He atmosphere of Co-doped SiO2 thin films deposited onto the surface of three differently oriented flat Si substrates, namely Si(001), Si(011) and Si(111).

Synthesis of ultra-small cysteine-capped gold nanoparticles by pH switching of the Au(I)-cysteine polymer.

We report a synthetic approach for the production of ultra-small (0.6 nm) gold nanoparticles soluble in water with a precise control of the nanoparticle size. Our synthetic approach utilizes a pH-depending Au-cysteine polymer as a quencher for the AuNPs grown.

X-ray reflectivity analysis of titanium dioxide thin films grown by cathodic arc deposition.

TiO2 thin films deposited by a vacuum arc on a glass substrate were characterized by X-ray reflectivity (XRR), X-ray diffraction (XRD), scanning electron microscopy (SEM) and atomic force microscopy (AFM). Several thin films with different amounts of deposited TiO2 mass and different deposition and annealing temperatures were studied. A qualitative analysis of the XRD patterns indicated the presence of the anatase and/or rutile crystalline phases in most of the studied samples.

Reactive sputter magnetron reactor for preparation of thin films and simultaneous in situ structural study by X-ray diffraction.

The purpose of the designed reactor is (i) to obtain polycrystalline and∕or amorphous thin films by controlled deposition induced by a reactive sputtering magnetron and (ii) to perform a parallel in situ structural study of the deposited thin films by X-ray diffraction, in real time, during the whole growth process. The designed reactor allows for the control and precise variation of the relevant processing parameters, namely, magnetron target-to-sample distance, dc magnetron voltage, and nature of the gas mixture, gas pressure and temperature of the substrate. On the other hand, the chamber can be used in different X-ray diffraction scanning modes, namely, θ-2θ scanning, fixed α-2θ scanning, and also low angle techniques such as grazing incidence small angle X-ray scattering and X-ray reflectivity.

Shape changes of Pt nanoparticles induced by deposition on mesoporous silica.

Polyvinylpyrollidone (PVP)-capped platinum nanoparticles (NPs) are found to change shape from spherical to flat when deposited on mesoporous silica substrates (SBA-15). Transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), and extended X-ray absorption fine structure (EXAFS) analyses are used in these studies. The SAXS results indicate that, after deposition, the 2 nm NPs have an average gyration radius 22% larger than in solution, while the EXAFS measurements indicate a decrease in first neighbor co-ordination number from 9.

Crystallite size-dependent phases in nanocrystalline ZrO(2)-Sc(2)O(3).

ZrO(2)-10, 12 and 14 mol% Sc(2)O(3) nanopowders were prepared by using a nitrate-lysine gel-combustion synthesis. These materials were studied by synchrotron X-ray powder diffraction (SXPD) and Raman spectroscopy after calcination at different temperatures from 650 to 1200 degrees C, which led to samples with different average crystallite sizes, up to about 100 nm. The results from SXPD and Raman analyses indicate that, depending on Sc(2)O(3) content, the metastable t''-form of the tetragonal phase or the cubic phase are fully retained at room temperature in nanocrystalline powders, provided an average crystallite sizes lower than approximately 30 nm.

Interleukin-22 forms dimers that are recognized by two interleukin-22R1 receptor chains.

Interleukin-22 (IL-22) is a class 2 cytokine whose primary structure is similar to that of interleukin 10 (IL-10) and interferon-gamma (IFN-gamma). IL-22 induction during acute phase immune response indicates its involvement in mechanisms of inflammation. Structurally different from IL-10 and a number of other members of IL-10 family, which form intertwined inseparable V-shaped dimers of two identical polypeptide chains, a single polypeptide chain of IL-22 folds on itself in a relatively globular structure.

Low-resolution structures of thyroid hormone receptor dimers and tetramers in solution.

High-resolution X-ray structures of thyroid hormone (TH) receptor (TR) DNA and ligand binding domains (DBD and LBD) have yielded significant insights into TR action. Nevertheless, the TR DBD and LBD act in concert to mediate TH effects upon gene expression, and TRs form multiple oligomers; however, structures of full-length TRs or DBD-LBD constructs that would clarify these influences are not available. Here, we report low-resolution X-ray structures of the TRbeta DBD-LBD construct in solution which define the shape of dimers and tetramers and likely positions of the DBDs and LBDs.

Local structure and near-infrared emission features of neodymium-based amine functionalized organic/inorganic hybrids.

Nd(3+)-based organic/inorganic hybrids have potential application in the field of integrated optics. Attractive sol-gel derived di-urea and di-urethane cross-linked poly(oxyethylene) (POE)/siloxane hybrids (di-ureasils and di-urethanesils, respectively) doped with neodymium triflate (Nd(CF(3)SO(3))(3)) were examined by Fourier transform mid-infrared (FT-IR), Raman (FT-Raman), (29)Si magic-angle spinning (MAS) nuclear magnetic resonance (NMR) and photoluminescence spectroscopies, and small-angle X-ray scattering (SAXS). The goals of this work were to determine which cation coordinating site of the host matrix (ether oxygen atoms or carbonyl oxygen atoms) is active in each of the materials analyzed, its influence on the nanostructure of the samples and its relation with the photoluminescence properties.

Structural rearrangements in the thyroid hormone receptor hinge domain and their putative role in the receptor function.

The thyroid hormone receptor (TR) D-domain links the ligand-binding domain (LBD, EF-domain) to the DNA-binding domain (DBD, C-domain), but its structure, and even its existence as a functional unit, are controversial. The D domain is poorly conserved throughout the nuclear receptor family and was originally proposed to comprise an unfolded hinge that facilitates rotation between the LBD and the DBD. Previous TR LBD structures, however, have indicated that the true unstructured region is three to six amino acid residues long and that the D-domain N terminus folds into a short amphipathic alpha-helix (H0) contiguous with the DBD and that the C terminus of the D-domain comprises H1 and H2 of the LBD.

Set-up and experimental parameters of the protein crystallography beamline at the Brazilian National Synchrotron Laboratory.

The Brazilian National Synchrotron Light Laboratory (LNLS) has a dedicated protein crystallography beamline. The optical elements of the beamline include an elastically bent cylindrical mirror and a triangular bent-crystal monochromator, which focus synchrotron radiation at the position of the sample in the vertical and horizontal planes, respectively. The monochromatic radiation is tunable between 2.

Structural insights into the beta-xylosidase from Trichoderma reesei obtained by synchrotron small-angle X-ray scattering and circular dichroism spectroscopy.

The enzyme beta-xylosidase from Trichoderma reesei, a member of glycosil hydrolase family 3 (GH3), is a glycoside hydrolase which acts at the glycosidic linkages of 1,4-beta-xylooligosaccharides and that also exhibits alpha-l-arabinofuranosidase activity on 4-nitrophenyl alpha-l-arabinofuranoside. In this work, we show that the enzyme forms monomers in solution and derive the low-resolution molecular envelope of the beta-xylosidase from small-angle X-ray scattering (SAXS) data using the ab initio simulated annealing algorithm. The radius of gyration and the maximum dimension of the beta-xylosidase are 30.

Aggregation processes and formation of silico-calco-alkaline gels under high ionic strength.

This paper presents a systematic in situ study of the process of formation of silico-calco-alkaline gels starting from a liquid colloidal solution containing different alkaline ions and different calcium concentration until the final gel state. The combined use of X-ray and neutron small-angle scattering (SAS) and dynamical rheometry techniques lead to a consistent description of the structure of the aggregates and of the mechanisms of aggregation involved in gel formation. SAS results indicate that the aggregates are fractal objects, their structure strongly depending on calcium ion concentration.

Low resolution structural study of two human HSP40 chaperones in solution. DJA1 from subfamily A and DJB4 from subfamily B have different quaternary structures.

Proteins that belong to the heat shock protein (Hsp) 40 family assist Hsp70 in many cellular functions and are important for maintaining cell viability. A knowledge of the structural and functional characteristics of the Hsp40 family is therefore essential for understanding the role of the Hsp70 chaperone system in cells. In this work, we used small angle x-ray scattering and analytical ultracentrifugation to study two representatives of human Hsp40, namely, DjA1 (Hdj2/dj2/HSDJ/Rdj1) from subfamily A and DjB4 (Hlj1/DnaJW) from subfamily B, and to determine their quaternary structure.

Average protein density is a molecular-weight-dependent function.

The mass density of proteins is a relevant basic biophysical quantity. It is also a useful input parameter, for example, for three-dimensional structure determination by protein crystallography and studies of protein oligomers in solution by analytic ultracentrifugation. We have performed a critical analysis of published, theoretical, and experimental investigations about this issue and concluded that the average density of proteins is not a constant as often assumed.

Crystalline structure of dental enamel after Ho:YLF laser irradiation.

Irradiation of teeth with lasers using specific wavelengths and energy densities produces surface melting. This effect has been already applied to different procedures such as caries prevention and hypersensitivity reduction. The aim of this study is to characterize the crystalline structure of bovine enamel after holmium laser irradiation.

Commissioning and operation of the first brazilian synchrotron light source.

The synchrotron light source designed and constructed at the LNLS is composed of a 1.37 GeV electron storage ring and a 120 MeV linac for low-energy injection. The storage ring has been commissioned and has already reached the designed electron-beam energy, current and emittance.

Conformation of the Z19 prolamin by FTIR, NMR, and SAXS.

The alpha zein, the maize storage prolamin, is a mixture of several homologous polypeptides that shows two bands in SDS-PAGE, called Z19 and Z22. The conformation studies carried out by several authors in this mixture are conflicting. To elucidate these inconsistencies, we analyzed the conformation of the Z19 fraction, extracted from BR451 maize variety by Fourier transform infrared spectroscopy, nuclear magnetic resonance, and small-angle X-ray scattering.

Free human mitochondrial GrpE is a symmetric dimer in solution.

The co-chaperone GrpE is essential for the activities of the Hsp70 system, which assists protein folding. GrpE is present in several organisms, and characterization of homologous GrpEs is important for developing structure-function relationships. Cloning, producing, and conformational studies of the recombinant human mitochondrial GrpE are reported here.

Low resolution structures of the retinoid X receptor DNA-binding and ligand-binding domains revealed by synchrotron X-ray solution scattering.

Nuclear receptors are ligand-inducible transcription factors that share structurally related DNA-binding (DBD) and ligand-binding (LBD) domains. Biochemical and structural studies have revealed the modular nature of DBD and LBD. Nevertheless, the domains function in concert in vivo.

Domain motions and quaternary packing of phosphofructokinase-2 from Escherichia coli studied by small angle x-ray scattering and homology modeling.

The binding of MgATP and fructose-6-phosphate to phosphofructokinase-2 from Escherichia coli induces conformational changes that result in significant differences in the x-ray-scattering profiles compared with the unligated form of the enzyme. When fructose- 6-phosphate binds to the active site of the enzyme, the pair distribution function exhibits lower values at higher distances, indicating a more compact structure. Upon binding of MgATP to the allosteric site of the enzyme, the intensity at lower angles increases as a consequence of tetramer formation, but differences along higher angles also suggest changes at the tertiary structure level.