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A binding pocket for phenolic substrates in laccases
No full textFungal laccases, belonging to the multicopper oxidases, can catalyze the oxidation of a large number of aromatic (especially phenolic), inorganic and xenobiotic compounds. In multicopper oxidases, the T1 Cu site accepts electrons from the substrate and transfers them to a T2/T3 trinuclear Cu cluster, which binds and activates O2 for reduction to H2O. The first X-ray structure available for a laccase, from Coprinus Cinereus, reveals a molecular architecture consisting of three b-barrel cupredoxin-like domains.1 In order to assess the structural features helping the phenolic substrates recognition, we have performed a comparative structural study on three fungal laccases: the one from Coprinus Cinereus, and two (POXC and POXA1b) from Pleurotus Ostreatus. Homology models are employed for POXC and POXA1b. First, a channel providing access to the T1 copper site, about 7 Å deep, is located at the interface between the structural domains 2 and 3. The T1-copper coordinating His457, analogous to the coordinating histidines involved in the electron transfer to other copper-proteins, is solvent exposed at the channel bottom. Docking calculations are then performed in such a cleft for two phenolic compounds: 2,6-di-methoxyphenol (DMP) and 2,6-di-t-butylphenol (DTBP), respectively a good and a bad substrate2 for laccases. The hydroxyl reducing group of DMP is shown to be at catalytic distance from His457. A possible role in assisting the catalytic oxidation is also suggested for Asp205, which forms an H-bond with the phenolic hydroxyl group and is conserved among fungal laccases. On the contrary, DTBP is shown not to match the cleft. A structure based sequence alignment between fungal laccases and the homologous ascorbate oxidase (AO)3 is also presented, which allows to outline a significant correspondence between their predicted substrate pockets.
References
1. Ducros V. et al. (1998) Nature Struct. Biol. 5, 310. 2. Xu F. (1996) Biochemistry 35, 323. 3. Messerschmidt A. et al. (1992) J. Mol. Biol. 224, 179
BICYCLIC PEPTIDES AS MODELS OF CALCIUM BINDING SITES. SYNTHESIS AND CONFORMATION OF A HOMODETIC UNDECAPEPTIDE.
No full text
CD CONFORMATIONAL STUDIES ON SYNTHETIC PEPTIDES ENCOMPASSING THE PROCESSING DOMAIN OF THE OCYTOCIN-NEUROPHYSIN PRECURSOR
No full textBICYCLIC PEPTIDES AS MODELS OF CALCIUM BINDING SITES. SYNTHESIS AND CONFORMATION OF A HOMODETIC UNDECAPEPTIDE.
No full textElucidation of the structure of constrained bicyclopeptides in solution by two-dimensional cross-relaxation spectroscopy: Amatoxin analogues
No full textThe evaluation of peptide structures in solution is made feasible by the combined use of two-dimensional NMR in the laboratory (NOESY) and rotating frames (ROESY), and by the use of molecular dynamics calculations. The present paper describes how both the NMR method and molecular dynamics calculations were applied to very rigid synthetic bicyclic peptides that are analogues of natural amatoxins. The NMR theory, which allows the estimate of interatomic distances between interacting nuclei, is briefly discussed. The experimental data were compared with those of known solid-state structures. Three amatoxin analogues have been examined. Of these, one is biologically active (S-deoxo γ[R] OH-Ile3-amaninamide) and its structure in the solid state has recently been worked out. The second and third analogues (S-deoxo-Ile3-Ala5-amaninamide and S-deoxo-D-Ile3-amaninamide, respectively) are inactive and their solid-state structures are unknown. The data presented confirm the authors' previous hypothesis that lack of biological activity of S-deoxo-Ile3-Ala5-amaninamide is due to the masking of the tryptophan ring by the methyl group of L-Ala and not to massive conformational changes of the analogue
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
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