1,721,031 research outputs found
1H-NMR and Photo-CIDNP Spectroscopies show a possible Role for Trp23 and Phe31 in Nucleic Acid Binding by P2 Ribonuclease from the archaeon Sulfolobus solfataricus
No full textInvestigations were performed on recombinant ribonuclease P2 from Sulfolobus solfataricus, previously cloned and expressed in Escherichia coli [Fusi, P., Grisa, M., Mombelli, E., Consonni, R., Tortora, P. and Vanoni, M. (1995) Gene 154, 99-103]. NMR and photo-CIDNP spectroscopies showed that the enzyme possesses an aromatic cluster consisting of Phe5, Tyr7, Phe31 and Tyr33 while Trp23 is fully exposed to solvent. Phe31, Tyr33 and Trp23 are located within a triple stranded antiparallel beta-sheet, each one being part of an amino acid stretch matching consensus sequences for RNA binding. Phe31 and Trp23 are exposed to and specifically interact with a flavin dye used as a model ligand, with a topology reminiscent of that found in several eubacterial and eukariotic RNA-binding proteins
“Functional properties of recombinant Azospirillum brasilense glutamate synthase, a complex iron-sulfur flavoprotein”
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A coarse-grain model for cellular growth accounting for ribosome synthesis
Full text linkProtein synthesis in eukaryotes is carried out by ribosomes, large RNA-protein complexes consisting of a small and a large subunit. In this work we present a mathematical model for cellular growth comprising both protein production and ribosome synthesis, properly accounting for both small and large subunits dynamics. The qualitative analysis of the model is carried out according to a simplifying assumption on the proportion of the two ribosomal subunits in stationary growth conditions; such hypothesis is based on a reasonable biological ground. Conditions are given on the model parameters in order to ensure exponential growth and the corresponding growth rate is straightforwardly computed from the model parameters. These results are validated by numerical simulations carried out according to a set of biologically meaningful model parameters. The modified model is better suited to host molecular blow-up of ribosomal synthesis and cell growth within a modular whole-cell model able to act as a scaffold connecting metabolism, growth and cycle
First-principles molecular dynamics investigation of the D-amino acid oxidative half-reaction catalyzed by the flavoenzyme D-amino acid oxidase
No full textLarge-scale Car-Parrinello molecular dynamics simulations Of D-alanine oxidation catalyzed by the flavoenzyme D-ammo acid oxidase have been carried out. A model of the enzyme active site was built by starting from the enzyme X-ray structure, and by testing different subsystems comprising different sets of aminoacyl residues. In this process, the stability of the enzyme-substrate complex was taken as a measure of the accuracy of the model. The activated transfer of the amino acid a-hydrogen from the substrate to the flavin N5 position was then induced by constraining a suitable transfer reaction coordinate, and the free energy profile of the reaction was calculated. The evolution of electronic and structural properties of both enzyme-bound substrate and flavin cofactor along the reaction path is consistent with a hydride-transfer mechanism. The calculated free energy barrier for this process (13 kcal/mol) is in excellent agreement with the activation energy value derived from the experimentally determined rate constant for the corresponding enzyme-catalyzed reaction. The electronic distribution of the reduced flavin shows that the transferred electrons tend to be centered near the C4a position rather than delocalized over the flavin pyrimidine ring. This feature is mechanistically relevant in that such an electronic distribution may promote the subsequent enzyme-catalyzed reduction of molecular oxygen to yield hydrogen peroxide via a postulated flavin 4a-peroxide intermediate. These results also show that a first-principles molecular dynamics approach is suitable to study the mechanism of complex enzymatic processes, provided that a smaller, yet reliable, subsystem of the enzyme can be identified, and special computational techniques are employed to enhance the sampling of the reactive event
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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