1,720,959 research outputs found
Solvent Accessibility in the Distal Heme Pocket of the Nitrosyl d1-Heme Complex of Pseudomonas Stutzeri cd1 Nitrite Reductase.
No full textIn nitrite reductase (cd1 NIR) the c-heme mediates electron transfer to the catalytic d1-heme where nitrite (NO2-) is reduced to nitric oxide (NO). An interesting feature of this enzyme is the relative lability of the reaction product NO bound to the d1-heme. Marked differences in the c- to d1-heme electron-transfer rates were reported for cd1 NIRs from different sources, e.g. Pseudomonas stutzeri (P. stutzeri) and Pseudomonas aeruginosa (P. aeruginosa). While the three dimensional structure of the P. aeruginosa enzyme has been determined, that of the P. stutzeri enzyme is still unknown. The difference in electron transfer rates prompted us to compare the structural properties of the d1-heme pocket of P. stutzeri cd1 NIR with those of the P. aeruginosa wild type enzyme (WT) and its Y10F using their nitrosyl d1-heme complexes. We applied high field pulse Electron Paramagnetic Resonance (EPR) techniques that detect nuclear spins in the close environment of the spin bearing Fe(II)-NO entity. We observed no significant differences in the rhombic g-tensor and detected a proximal histidine ligand with 14N hyperfine and quadrupole interactions similar to those of P. aeruginosa WT and Y10F mutant complexes. We did observe significant differences in the H-bond network involving the NO ligand and a larger solvent accessibility in P. stutzeri attributed to the lack of tyrosine residue in its N-terminus. In P. aeruginosa cd1 NIR Tyr10 is H-bonded to the NO, afforded by domain swapping. These findings support an earlier suggestion that the large difference in the c- to d1-heme electron transfer rates in the two enzymes is associated with the open conformation of the d1-heme pocket
High field pulse EPR and DFT calculations of nitrosyl d-(1) heme complex of cd(1) nitrite reductase: From resolved ligand nuclear frequencies to structure and function
No full textHeme d1 Nitrosyl Complex of cd1 Nitrite Reductase Studied by High-Field-Pulse Electron Paramagnetic Resonance Spectroscopy
No full textW-band (95 GHz) HYSCORE and pulse ENDOR are used to characterize the nitrosyl d(1) heme complex (d(1)NO) of cd(1) nitrite reductase from Pseudomonas aeruginosa in the wild type and the Y10F mutant. The spectra and the derived (14)N hyperfine and quadrupole interactions were found to be the same for wt and Y10F. This suggests that Tyr10 does not influence the NO ligand orientation in the reduced state in solution. This study is the first application of HYSCORE at high fields and shows its potential for characterizing low gamma nuclei with large hyperfine couplings
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
Dynamic hydrogen bonding network in the distal pocket of the nitrosyl complex of Pseudomonas aeruginosa cd1 nitrite reductase
No full textcd(1) nitrite reductase (NIR) is a key enzyme in the denitrification process that
reduces nitrite to nitric oxide (NO). It contains a specialized d(1)-heme
cofactor, found only in this class of enzymes, where the substrate, nitrite,
binds and is converted to NO. For a long time, it was believed that NO must be
released from the ferric d(1)-heme to avoid enzyme inhibition by the formation of
ferrous-nitroso complex, which was considered as a dead-end product. However,
recently an enhanced rate of NO dissociation from the ferrous form, not observed
in standard b-type hemes, has been reported and attributed to the unique
d(1)-heme structure (Rinaldo, S.; Arcovito, A.; Brunori, M.; Cutruzzolà, F. J.
Biol. Chem. 2007, 282, 14761-14767). Here, we report on a detailed study of the
spatial and electronic structure of the ferrous d(1)-heme NO complex from
Pseudomonas aeruginosa cd(1) NIR and two mutants Y10F and H369A/H327A in
solution, searching for the unique properties that are responsible for the
relatively fast release. There are three residues at the "distal" side of the
heme (Tyr(10), His(327), and His(369)), and in this work we focus on the
identification and characterization of possible H-bonds they can form with the
NO, thereby affecting the stability of the complex. For this purpose, we have
used high field pulse electron-nuclear double resonance (ENDOR) combined with
density functional theory (DFT) calculations. The DFT calculations were essential
for assigning and interpreting the ENDOR spectra in terms of geometric structure.
We have shown that the NO in the nitrosyl d(1)-heme complex of cd(1) NIR forms
H-bonds with Tyr(10) and His(369), whereas the second conserved histidine,
His(327), appears to be less involved in NO H-bonding. This is in contrast to the
crystal structure that shows that Tyr(10) is removed from the NO. We have also
observed a larger solvent accessibility to the distal pocket in the mutants as
compared to the wild-type. Moreover, it was shown that the H-bonding network
within the active site is dynamic and that a change in the protonation state of
one of the residues does affect the strength and position of the H-bonds formed
by the others. In the Y10F mutant, His(369) is closer to the NO, whereas mutation
of both distal histidines displaces Tyr(10), removing its H-bond. The
implications of the H-bonding network found in terms of the complex stability and
catalysis 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
- …
