208 research outputs found

    Thymulin (facteur thymique sérique) and zinc contents of the thymus glands of malnourished children

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    Protein-energy malnutrition (PEM) leads to an immune deficiency, which is now well documented. Some investigators have suggested that the associated zinc deficiency is important in thymic involution and changes in cellular immunity. To evaluate the respective roles of nutritional deficiency, infection, and zinc in the alteration of thymic function, we measured the amounts of thymulin (facteur thymique sérique, or FTS) and of Zn in the thymus glands of 58 Senegalese children who died in various stages of malnutrition. In the severe forms (marasmus, kwashiorkor, and marasmic kwashiorkor) the thymus was tiny and contained very little thymulin. The Zn content of the thymus was high whatever the nutritional state of the subject and was related significantly only to the presence of infections. In Senegalese children thymic atrophy and depleted thymulin content are associated with severe PEM but not systemic infection or depleted thymic Zn content. (Résumé d'auteur

    Chemical diffusion of fluorine in melts in the system Na2OAl2O3SiO2

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    The volatilization of fluorine from three melts in the system Na2OAl2O3SiO2 has been investigated at 1 atm pressure and 1200–1400°C. The melts chosen have base compositions corresponding to albite, jadeite and a peraluminous melt with 75 mole % SiO2. Melt spheres were suspended from platinum loops in a vertical tube furnace in a flow of oxygen gas, then quenched, sectioned and analysed by electron microprobe. The microprobe scans indicate that transport of fluorine to the melt-vapor interface is by binary, concentration-independent interdiffusion of fluorine and oxygen. FO interdiffusivity increases in the order albite < peraluminous < jadeite. There is no simple reciprocal relationship between FO interdiffusivity and melt viscosity. Comparison with data on high-pressure interdiffusivity of fluorine and oxygen in jadeite melt indicates that FO interdiffusivity increases with pressure from 0.001 to 10 kbar while the activation energy remains unchanged. Fluorine chemical diffusivity in albite melt is substantially lower than H2O chemical diffusivity in obsidian melts suggesting that different diffusive mechanisms are responsible for the transport of F and H2O in igneous melts. Fluorine diffuses in albite melt via an anionic exchange with oxygen whereas water probably diffuses in obsidian melt via an alkali exchange mechanism

    PocketMatch: A new algorithm to compare binding sites in protein structures

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    Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental&#xd;&#xa;requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of&#xd;&#xa;the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.&#xd;&#xa;&#xd;&#xa;Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant&#xd;&#xa;manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless&#xd;&#xa;combined with chemical nature of amino acids.&#xd;&#xa;&#xd;&#xa;Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and&#xd;&#xa;high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along&#xd;&#xa;with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

    Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites

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    A new binding site comparison algorithm using optimal superposition of the continuous pharmacophoric property distributions is reported. The method demonstrates high sensitivity in discovering both, distantly homologous and convergent binding sites. Good quality of superposition is also observed on multiple examples. Using the new approach, a measure of site similarity is derived and applied to clustering of ligand binding pockets in PDB

    MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions

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    Analysis of protein–ligand complexes and recognition of spatially conserved physico-chemical properties is important for the prediction of binding and function. Here, we present two webservers for multiple alignment and recognition of binding patterns shared by a set of protein structures. The first webserver, MultiBind (http://bioinfo3d.cs.tau.ac.il/MultiBind), performs multiple alignment of protein binding sites. It recognizes the common spatial chemical binding patterns even in the absence of similarity of the sequences or the folds of the compared proteins. The input to the MultiBind server is a set of protein-binding sites defined by interactions with small molecules. The output is a detailed list of the shared physico-chemical binding site properties. The second webserver, MAPPIS (http://bioinfo3d.cs.tau.ac.il/MAPPIS), aims to analyze protein–protein interactions. It performs multiple alignment of protein–protein interfaces (PPIs), which are regions of interaction between two protein molecules. MAPPIS recognizes the spatially conserved physico-chemical interactions, which often involve energetically important hot-spot residues that are crucial for protein–protein associations. The input to the MAPPIS server is a set of protein-protein complexes. The output is a detailed list of the shared interaction properties of the interfaces

    Beauty Is in the Eye of the Beholder: Proteins Can Recognize Binding Sites of Homologous Proteins in More than One Way

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    Understanding the mechanisms of protein–protein interaction is a fundamental problem with many practical applications. The fact that different proteins can bind similar partners suggests that convergently evolved binding interfaces are reused in different complexes. A set of protein complexes composed of non-homologous domains interacting with homologous partners at equivalent binding sites was collected in 2006, offering an opportunity to investigate this point. We considered 433 pairs of protein–protein complexes from the ABAC database (AB and AC binary protein complexes sharing a homologous partner A) and analyzed the extent of physico-chemical similarity at the atomic and residue level at the protein–protein interface. Homologous partners of the complexes were superimposed using Multiprot, and similar atoms at the interface were quantified using a five class grouping scheme and a distance cut-off. We found that the number of interfacial atoms with similar properties is systematically lower in the non-homologous proteins than in the homologous ones. We assessed the significance of the similarity by bootstrapping the atomic properties at the interfaces. We found that the similarity of binding sites is very significant between homologous proteins, as expected, but generally insignificant between the non-homologous proteins that bind to homologous partners. Furthermore, evolutionarily conserved residues are not colocalized within the binding sites of non-homologous proteins. We could only identify a limited number of cases of structural mimicry at the interface, suggesting that this property is less generic than previously thought. Our results support the hypothesis that different proteins can interact with similar partners using alternate strategies, but do not support convergent evolution
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