1,720,969 research outputs found
Crystal packing of the c(6)-type cytochrome OmcF from Geobacter sulfurreducens is mediated by an N-terminal Strep-tag II
No full textThe putative outer membrane c-type cytochrome OmcF from Geobacter sulfurreducens contains a single haem group and shows homology to soluble cytochromes c(6), a class of electron-transfer proteins that are typically found in cyanobacterial photosynthetic electron-transfer chains. OmcF was overexpressed heterologously in Escherichia coli as an N-terminal Strep-tag II fusion protein and isolated using streptactin-affinity chromatography followed by size-exclusion chromatography. The structure was solved by Fe SAD using data collected to a resolution of 1.86 A on a rotating copper-anode X-ray generator. In the crystal, packing interactions in one dimension were exclusively mediated through the Strep-tag II sequence. The tag and linker regions were in contact with three further monomers of OmcF, leading to a well defined electron-density map for this engineered and secondary-structure-free region of the molecule
Binding and Reduction of Sulfite by Cytochrome c Nitrite Reductase
No full textPentaheme cytochrome c nitrite reductase (ccNiR) catalyzes the six-electron reduction of nitrite to ammonia as the final step in the dissimilatory pathway of nitrate ammonification. It has also been shown to reduce sulfite to sulfide, thus forming the only known link between the biogeochemical cycles of nitrogen and of sulfur. We have found the sulfite reductase activity of ccNiR from Wolinella succinogenes to be significantly smaller than its nitrite reductase activity but still several times higher than the one described for dissimilatory, siroheme-containing sulfite reductases. To compare the sulfite reductase activity of ccNiR with our previous data on nitrite reduction, we determined the binding mode of sulfite to the catalytic heme center of ccNiR from W. succinogenes at a resolution of 1.7 A. Sulfite and nitrite both provide a pair of electrons to form the coordinative bond to the Fe(III) active site of the enzyme, and the oxygen atoms of sulfite are found to interact with the three active site protein residues conserved within the enzyme family. Furthermore, we have characterized the active site variant Y218F of ccNiR that exhibited an almost complete loss of nitrite reductase activity, while sulfite reduction remained unaffected. These data provide a first direct insight into the role of the first sphere of protein ligands at the active site in ccNiR catalysis
Strukturelle Studien an der Eisen(II)/[alpha]-Ketoglutarat-abhängigen Dioxygenase PlaO1 aus Streptomyces sp. Tü6071
No full textPhenalinolactones are highly modified Terpenes, produced by Streptomyces sp. Tü6071. Their complex synthesis is not only of biosynthetic interest, they also show moderate antibiotic activity, what makes them a subject of ongoing research. A striking feature of the phenalinolactones is their highly oxidized γ-butyrolactone moiety, which is most likely the active part of these molecules. The Fe(II)/α-ketoglutarate dependent dioxygenase PlaO1 has been assigned to carry out this reaction. This enzyme is of particular interest, as the formation of the γ-butyrolactone ring has to involve an oxidative cyclization and a rearrangement reaction.
In the course of this thesis, PlaO1 has been overexpressed heterologously, purified in high amounts and crystallized using microseeding-techniques. The crystal structures of PlaO1 in complex with iron, iron and α-ketoglutarate and succinate have been determined. In addition, substrate docking simulations have been carried out for the PlaO1 structure with a model of the mostly insoluble main substrate.
It could be shown that the structure of PlaO1 highly resembles the two known crystal structures of Fe(II)/α-ketoglutarate dependent enzymes of the TauD/TdfA family, although the substrate and reaction of PlaO1 differs significantly from the substrates and reactions of these related enzymes. Analysis of the docking results allowed identification of certain residues as putative binding partners for the substrate and to draw conclusions on possible binding-modes for the substrate, which could be compared to hypotheses for the reaction mechanism of PlaO1.
Phenalinolactone sind hochgradig modifizierte Terpene und werden von Streptomyces sp. Tü6071 produziert. Da deren komplexe Synthese nicht nur biosynthetisch interessant ist, sondern sie auch moderate antibiotische Aktivität aufweisen sind sie Gegenstand aktueller Forschung. Ein herausragendes Merkmal der Phenalinolactone ist der hochgradig oxidierte γ-Butyrolacton-Rest, welcher vermutlich den aktiven Teil dieser Moleküle darstellt.
Als verantwortlich für die Synthese dieses Restes wurde die Fe(II)/α-ketoglutaratabhängige Dioxygenase PlaO1 identifiziert. Dieses Enzym ist insofern interessant, als die Bildung des γ-Butyrolactons eine oxidative Zyklisierung und eine Umlagerungsreaktion umfassen muss.
Im Verlauf dieser Arbeit konnte PlaO1 in großen Mengen heterolog überexprimiert und aufgereinigt werden und mit Hilfe von Microseeding-Techniken kristallisiert werden. Die Kristallstrukturen für PlaO1 im Komplex mit Eisen, mit Eisen und α-Ketoglutarat sowie mit Succinat konnten bestimmt werden. Des Weiteren wurden für die PlaO1-Struktur Docking-Simulationen mit einem Modell des schwer löslichen Hauptsubstrates durchgeführt.
Es konnte gezeigt werden, dass die Kristallstruktur von PlaO1 große Ähnlichkeit mit den beiden bekannten Strukturen von Fe(II)/α-ketoglutaratabhängigen Dioxygenasen aus der TauD/TdfA-Familie aufweist, obwohl sich das Substrat von PlaO1 und die katalysierte Reaktion deutlich von den Substraten und Reaktionen der verwandten Enzyme unterscheiden. Durch die Auswertung der Docking-Ergebnisse konnten bestimmte Aminosäuren als mögliche Bindungspartner für das Substrat identifiziert werden und Rückschlüsse auf die Substratbindung gezogen und mit Hypothesen für die PlaO1-Reaktion verglichen werden
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe 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
Get PDF“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
Get PDFWe 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
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
- …
