Nanostructure and giant Hall effect in TMx(SiO2)(1-x) (TM=Co,Fe,Ni) granular system

Granular TMx(SiO2)(1-x) (TM=Co,Fe,Ni) thin films were thermally treated at different temperatures and their magnetotransport and structural properties were studied. Hall resistivity decreases with thermal annealing. Structure was analyzed based on small angle x-ray scattering results. A model of polydisperse system of hard spheres was used for obtaining structural parameters. Analysis reveals that a volume fraction of transition-metal atoms (less than 29%) are forming nanospheres. Changes in giant Hall effect upon annealing can depend on a particular combination of nanoparticle diameter, interparticle distance, and size distribution. (C) 2006 American Institute of Physics.99

Two new sealed sample cells for small angle x-ray scattering from macromolecules in solution and complex fluids using synchrotron radiation

Two different vacuum tight sample cells for in situ temperature dependent small angle scattering from liquids are presented in this article. In the first one, the sample fills a 1 mm thickness gap sealed on both sides by two thin parallel mica windows (volume 300 mul). In the second one, the liquid is injected into a 1 mm cylindrical capillary tube (volume 130 mul). The cells are lodged into temperature controlled chambers directly connected to the beamline vacuum path. Several important improvements with respect to similar instrumentation previously reported are: (1) versatile application of the mica cell, that can be used for all types of samples (gels, liquid crystals, and dispersions in organic solvents) and (2) the design of the chamber for the capillary cell allows registration of wider angle data and a convenient replacement of the capillary tube after each experiment. Signal to background ratio and data reproducibility were tested using protein solutions. We give a brief report of scattering experiments performed with different protein samples and two-dimensional data collection. (C) 2004 American Institute of Physics.75114541454

A New Euler's Formula for DNA Polyhedra

DNA polyhedra are cage-like architectures based on interlocked and interlinked DNA strands. We propose a formula which unites the basic features of these entangled structures. It is based on the transformation of the DNA polyhedral links into Seifert surfaces, which removes all knots. The numbers of components , of crossings , and of Seifert circles are related by a simple and elegant formula: . This formula connects the topological aspects of the DNA cage to the Euler characteristic of the underlying polyhedron. It implies that Seifert circles can be used as effective topological indices to describe polyhedral links. Our study demonstrates that, the new Euler's formula provides a theoretical framework for the stereo-chemistry of DNA polyhedra, which can characterize enzymatic transformations of DNA and be used to characterize and design novel cages with higher genus

The Pyrococcus exosome complex - Structural and functional characterization

The exosome is a conserved eukaryotic enzymatic complex that plays an essential role in many pathways of RNA processing and degradation. Here, we describe the structural characterization of the predicted archaeal exosome in solution using small angle x-ray scattering. The structure model calculated from the small angle x-ray scattering pattern provides an indication of the existence of a disk-shaped structure, corresponding to the "RNases PH ring" complex formed by the proteins aRrp41 and aRrp42. The RNases PH ring complex corresponds to the core of the exosome, binds RNA, and has phosphorolytic and polymerization activities. Three additional molecules of the RNA-binding protein aRrp4 are attached to the core as extended and flexible arms that may direct the substrates to the active sites of the exosome. In the presence of aRrp4, the activity of the core complex is enhanced, suggesting a regulatory role for this protein. The results shown here also indicate the participation of the exosome in RNA metabolism in Archaea, as was established in Eukarya.281106751675

Calorimetric and structural investigation of the interaction of lysozyme and bovine serum albumin with poly(ethylene oxide) and its copolymers

This work reports investigations aiming at verifying the occurrence of specific interactions between lysozyme or bovine serum albumin (BSA) and poly(ethylene oxide) and its copolymers with poly(propylene oxide). Thermal stability of these proteins, followed by means of high sensitivity DSC, was found to be mostly unaffected by the presence of these polymers. Chromatographic experiments (reverse-phase HPLC and size exclusion chromatrography) did not reveal any sign of specific interaction for these mixtures, either. Isothermal titration calorimetry revealed an increase in enthalpy for the mixtures, represented by a positive enthalpy of transfer for these proteins from buffer to polymer solutions. Moreover, SAXS analyses confirmed that at ambient temperatures these polymers do not affect lysozyme structure. In summary, no evidence is found to support earlier suggestions that some kind of complex could be formed between these proteins and poly(ethylene oxide) or its copolymers, but the present results suggest the occurrence of entropically driven hydrophobic effects. (C) 2004 Elsevier B.V. All rights reserved.3841671677

Conserved Central Domains Control the Quaternary Structure of Type I and Type II Hsp40 Molecular Chaperones

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Heat shock protein (Hsp)40s play an essential role in protein metabolism by regulating the polypeptide binding and release cycle of Hsp70. The Hsp4o family is large, and specialized family members direct Hsp70 to perform highly specific tasks. Type I and Type II Hsp40s, such as yeast Ydj1 and Sis1, are homodimers that dictate functions of cytosolic Hsp70, but how they do so is unclear. Type 1 Hsp40s contain a conserved, centrally located cysteine-rich domain that is replaced by a glycine- and methionine-rich region in Type 11 Hsp40s, but the mechanism by which these unique domains influence Hsp40 structure and function is unknown. This is the case because high-resolution structures of full-length forms of these Hsp40s have not been solved. To fill this void, we built low-resolution models of the quaternary structure of Ydj1 and Sis1 with information obtained from biophysical measurements of protein shape, small-angle X-ray scattering, and ab initio protein modeling. Low-resolution models were also calculated for the chimeric Hsp40s YSY and SYS, in which the central domains of Ydj1. and Sis1 were exchanged. Similar to their human homologs, Ydj1 and Sis1 each has a unique shape with major structural differences apparently being the orientation of the J domains relative to the long axis of the dimers. Central domain swapping in YSY and SYS correlates with the switched ability of YSY and SYS to perform unique functions of Sis1 and Ydj1, respectively. Models for the mechanism by which the conserved cysteine-rich domain and glycine- and methionine-rich region confer structural and functional specificity to Type I and Type 11 Hsp40s are discussed. (C) 2008 Elsevier Ltd. All rights reserved.3831155166Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Ministerio da Ciencia e TecnologiaConselho Nacional de Pesquisa e DesenvolvimentoNIH [R03TW007437]Fogarty International CenterNational Institutes of HealthFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)NIH [R03TW007437

Solution studies and structural model of the extracellular domain of the human amyloid precursor protein

The amyloid precursor protein (APP) is the precursor of the beta-amyloid peptide (Abeta), which is centrally related to the genesis of Alzheimer's disease (AD). In addition, APP has been suggested to mediate and/or participate in events that lead to neuronal degeneration in AD. Despite the fact that various aspects of the cell biology of APP have been investigated, little information on the structure of this protein is available. In this work, the solution structure of the soluble extracellular domain of APP (sAPP, composing 89% of the amino acid residues of the whole protein) has been investigated through a combination of size-exclusion chromatography, circular dichroism, and synchrotron radiation small-angle x-ray scattering (SAXS) studies. sAPP is monomeric in solution (65 kDa obtained from SAXS measurements) and exhibits an anisometric molecular shape, with a Stokes radius of 39 or 51 Angstrom calculated from SAXS or chromatographic data, respectively. The radius of gyration and the maximum molecular length obtained by SAXS were 38 Angstrom and 130 Angstrom, respectively. Analysis of SAXS data further allowed building a structural model for sAPP in solution. Circular dichroism data and secondary structure predictions based on the amino acid sequence of APP suggested that a significant fraction of APP (30% of the amino acid residues) is not involved in standard secondary structure elements, which may explain the elongated shape of the molecule recovered in our structural model. Possible implications of the structure of APP in ligand binding and molecular recognition events involved in the biological functions of this protein are discussed.8363513352