1,721,177 research outputs found
Retinoids in Mammals: A Crystallographic Perspective
Full text linkRetinoids are involved in several essential processes in mammals, including vision, morphogenesis, spermatogenesis and maintenance of epithelial tissue. Since they are labile compounds, nearly insoluble in water, they are present in body fluids and within the cell bound to specific retinoid-binding proteins. In plasma, a single protein, called retinol-binding protein, delivers the alcoholic form of vitamin A from its store sites to target cells. In the cytoplasm, four different cellular retinol-binding proteins and two retinoic acid-binding proteins have been discovered and structurally characterized to date. Finally, two classes of nuclear receptors for retinoic acid isomers have been characterized. The structure/function relationship for several retinoid-binding proteins is discussed here
Crystal Structure of Liganded and Unliganded Forms of Bovine Plasma Retinol-Binding Protein
No full textThe three-dimensional structures of bovine plasma retinol-binding protein (bRBP) complexed with retinol (space group P2(1)2(1)2(1), a = 46.08, b = 49.12, c = 76. 10 angstrom) and of the unliganded protein prepared in vitro by extracting retinol with ethyl ether (space group P2(1)2(1)2(1), a = 46.55, b = 48.97, c = 76.87 angstrom) have been solved at 1.9 and 1.7 angstrom resolution, respectively. The final crystallographic R factors are 0.190 for holobRBP and 0.196 for the unliganded bRBP.
The model for the bovine holoprotein is quite similar to that of the human protein, with which it exhibits 92% sequence similarity. The root mean square deviation between the alpha-carbons in the two proteins is 0.31 angstrom. The retinol binding site is almost completely preserved. The loops that surround the opening of the beta-barrel are also particularly conserved, in contrast with the presence of several substitutions in parts of the RBP molecule opposite the opening of the calyx that binds retinol.
Despite the fact that unliganded bovine RBP was prepared and crystallized using procedures completely different from those used to obtain the unliganded human RBP, the conformational differences between unliganded and liganded forms of bRBP are almost identical to those found previously between the same forms of human RBP. They mainly involve a few residues in the region extending from amino acid residues 32 to 37. Therefore, similar differences are very likely to exist between holoRBP and the physiologically occurring apoprotein. A not yet identified electron density, different in shape and orientation from retinol, also occupies the central cavity of the beta-barrel in the unliganded bRBP, as found for unliganded human RBP. The functional consequences of the conformational change induced by the removal of retinol on the interaction between RBP and transthyretin, coupled with the conservation of the entrance loops of the beta-barrel in mammalian RBPs, are consistent with their participation in molecular interactions
The Interaction of N-Ethyl Retinamide with Plasma Retinol-Binding Protein (RBP) and the Crystal Structure of the Retinoid-RBP Complex at 1.9 Å Resolution"
No full textThe three-dimensional structure of bovine plasma retinol-binding protein (RBP) complexed with N-ethyl retinamide has been determined at 1.9-angstrom resolution. The crystals of the complex (space group P2(1)2(1)2(1), a = 46.27, b = 49.11, c = 76.41 angstrom) are isomorphous with those of bovine holo and apoRBP. The final crystallographic R factor is 0.172 for 11,261 observed reflections. The model of the retinoid-RBP complex is nearly identical to that of bovine retinol-RBP complex; the root mean square deviations between the alpha-carbons in the two proteins is 0.15 angstrom. The N-ethyl retinamide molecule fits in the beta-barrel in the same position previously occupied by the vitamin. The ethyl group of the retinoid replaces the retinol hydroxyl group and a water molecule hydrogen bonded to it. This substitution has no consequence on the overall conformation of the protein. The modification of the functional end group of retinol does not lead to an apparent loss of affinity of the retinol analog for apoRBP, as established by means of fluorometric titrations with N-ethyl retinamide. However, the binding of the retinoid to RBP abolishes or greatly reduces the affinity of RBP for transthyretin. This behavior further supports the hypothesis that the area of the entrance of the beta-barrel, which includes the ethyl group of the retinoid bound to RBP, is involved in the interaction with transthyretin. Moreover, it indicates a high degree of complementarity of interacting surfaces between RBP and transthyretin. In fact, the replacement of the retinol hydroxyl group and quite small structural changes in the above region of the RBP molecule drastically affect the protein-protein recognition
THE PISCINE PLASMA RETINOL-BINDING PROTEIN. PURIFICATION, PARTIAL AMINO ACID SEQUENCE AND INTERACTION WITH MAMMALIAN TRANSTHYRETIN OF RAINBOW TROUT (ONCORHYNCHUS MYKISS) RETINOL-BINDING PROTEIN
No full text1. Retinol-binding protein (RBP) has been isolated from the pooled plasma or rainbow trouts (Oncorhinchus mykiss) by gel filtration, hydrophobic interaction chromatography and ion-exchange chromatography. By this procedure two forms of the protein, both with a molecular mass (approximately 20 kDa) similar to that of mammalian RBP, were purified to homogeneity. Five amino acid substitutions have been found in the partial (about 60%) sequences of the two forms of trout RBP, which are presumably acetylated at their N terminus. The apparent participation of six conserved cysteines in the formation of disulphide bridges, as in human RBP, and the similarity (about 60%) of the amino acid sequence of trout and mammalian RBPs, indicate the existence of a similar overall structure organization in evolutionary distant RBPs. 2. Although the two forms of trout RBP are not physiologically involved in the formation of any protein--protein complex in plasma, they are capable of interacting with mammalian transthyretin, albeit with a binding affinity (K'd = 15-40 microM) considerably lower than that of mammalian RBP. Our data indicate that the two forms of trout RBP also possess the region that in mammalian RBP has the functional role of binding transthyretin. It is suggested that transthyretin (or a homologous protein) was modified, during phylogenetic development of the non mammalian vertebrates, to acquire a binding site for such a region of the RBP molecule
Structural characterization of HIU-hydrolase and OHCU-decarboxylase, two enzymes involved in the uric acid degradation
No full text
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Ligand Binding and Structural Analysis of a Human Putative Cellular Retinol-binding Protein
Full text linkThree cellular retinol-binding protein (CRBP) types (CRBP I, II, and III) with distinct tissue distributions and retinoid binding properties have been structurally characterized thus far. A human binding protein, whose mRNA is expressed primarily in kidney, heart, and transverse colon, is shown here to be a CRBP family member (human CRBP IV), according to amino acid sequence, phylogenetic analysis, gene structure organization, and x-ray structural analysis. Retinol binding to CRBP IV leads to an absorption spectrum distinct from a typical holo-CRBP spectrum and is characterized by an affinity (K-d = similar to200 nm) lower than those for CRBP I, II, and III, as established in direct and competitive binding assays. As revealed by mutagenic analysis, the presence in CRBP IV of His(108) in place of Gln(108) is not responsible for the unusual holo-CRBP IV spectrum. The 2-Angstrom resolution crystal structure of human apo-CRBP IV is very similar to those of other structurally characterized CRBPs. The side chain of Tyr(60) is present within the binding cavity of the apoprotein and might affect the interaction with the retinol molecule. These results indicate that human CRBP IV belongs to a clearly distinct CRBP subfamily and suggest a relatively different mode of retinol binding for this binding protein
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