1,720,992 research outputs found
CO escape from myoglobin with metadynamics simulations
No full textThe relatively small size of myoglobin makes it suitable for the investigation of the ligand escape process in respiratory proteins and, in general, an ideal model system for the study of the more general structure-function paradigm. In this work, we use Molecular Dynamics simulations combined with an accelerated algorithm, the metadynamics, to probe the escape of CO from myoglobin. Our approach permits to quantitatively describe the escape process via the reconstruction of the associated free energy surface. Additionally, hints on the involvement of a larger numbers of residues than hitherto assumed in the gating process are extracted from our data
An NMR study on nickel binding sites in Cap43 protein fragments
No full textNMR spectroscopy was used to study the interaction of Ni(II) ions with C-terminal sequence of Cap43 protein where, from Thr341 to Gly 360 residue, a T1R2S3R 4S5H6T7S8E 9G10 ten-amino acid fragment is consecutively repeated three times. The behaviour of ends-blocked Ac-RSRSHTSEG-Am (pept1), Ac-TRSRSHTSEG-Am (pept2), and the three repeats Ac-TRSRSHTSEG-TRSRSHTSEG- TRSRSHTSEG-Am (pept3) peptides towards Ni(II) ions was examined at different pH values and, for pept3, at different ligand-to-metal molar ratios. 1H-1H TOCSY, 1H-13C HSQC, 1H-1H NOESY and 1H-1H ROESY multidimensional NMR techniques were performed to understand the details of metal binding sites and the conformational behaviour of the peptides. The results confirmed that each mono-histidinic sequence of pept3 is able to independently coordinate one, two or three Ni(II) ions for 1:1, 1:2 and 1:3 ligand-to-metal molar ratios, respectively. At higher pH values, the coordination of Ni(II) involves imidazole Nδ of His6 and three preceding deprotonated peptide nitrogens from the backbone, giving a {Nδ, 3N-} chromophore in a square planar geometry. In addition, at lower pH values, the involvement of γ-O of carboxyl group from Glu9 residue with the formation of a macrochelate giving a {Nδ, γ-O -, 4OH2O} chromophore in an octahedral geometry, was evidenced. NMR results allowed us to build a model for the structure of the major complex. Structural changes in the conformation of the peptide with organized Arg4 and Thr7 side chain orientation promoted by nickel coordination, were detected
A new magnetic resonance imaging approach for discriminating Sardinian sheep milk cheese made from heat-treated or raw milk.
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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
NMR studies of zinc binding in a multi-histidinic peptide fragment
No full textA multi-histidinic peptide and its minimal models have been investigated for Zn(II) binding. We have used NMR spectroscopy to probe the binding of zinc to the three repeats (T1R2S3R4S5H6T7S8E9G10)3 and to its mono-histidinic minimal models, the 9- and 10-aminoacid fragment. 1H-1H TOCSY, 1H-13C HSQC, 1H-1H NOESY and 1H-1H ROESY multidimensional NMR techniques were performed to understand the details of metal binding sites and the conformational behaviour of the peptides at different pH values and at different ligand to metal molar ratios. Zinc coordination involves imidazole Nδ of His6 and carboxyl γ-O of Glu9 residues; interaction with peptide oxygens of the His6-Thr7 or Thr7-Ser8 bonds in a tetrahedral arrangement with the minimal model peptides, cannot be excluded. Zinc coordination involves, at physiologic pH, all the three imidazole Nδ donors of His6, His16 and His26 as well as carboxyl γ-O of Glu residues in a tetra, penta or octahedral arrangement with the three repeats, the 30-aminoacid fragment. Zinc complexation induces important structural changes with the C-terminal portion of the ligand, constraining it to leave its disordered conformation. Our results give rise to a model of the induced structure of the peptides when bound to zinc. At high pH, amide deprotonation does not take place and hydroxo or high molecular weight polymeric species may be formed
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
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe 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
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