1,721,040 research outputs found
Investigation of The Role of Aromatic-Backbone Amide Interactions in Peptide and Protein Structure
No full textThe delicate balance of noncovalent interactions determines the three dimensional structure of peptides and proteins. These interactions include hydrogen bonds, salt bridges, weakly polar interactions and the hydrophobic effect. Weakly polar interaction can be between aromatic side chains of amino acids and amides of the polypeptide backbone (Ar-HN). Although, it is known that Ar-HN interactions can be responsible for the formation of local structures in polypeptides, the detailed understanding of their role and significance in peptide and protein structure remains unclear.
In the present study Ar-HN interactions in model peptides and proteins are investigated. Protein database survey of Ar-HN interactions found that Ar(i)-HN(i+l, i+2 and i+3) interactions are more common (7.10%, 2.08% and 0.54%, respectively) than are Ar(i)-HN(i-l, i-2 and i-3) interactions (0.66%, <0.1% and 0.18%, respectively). Ar- HN interactions constrain the x' torsion angle of the aromatic residue. Analyses of the secondary structures of the protein fragments containing Ar-HN interactions showed that Ar-HN interactions were in all types of secondary structures. Search results suggest that Ar-HN interactions have a stabilizing effect on all types of secondary structures.
Interactions between the side chain aromatic rings and hydrogens of backbone amides and CHn of aliphatic groups (tt-CH) were found to constrain individual conformations of the Pro-Xaa (where Xaa is either Phe, Tyr or Trp) and Xaa-Pro fragments. These local structures were found to be independent of the secondary structure of the polypeptide chains in which the fragments were located. This suggests,that weakly polar interactions, like Ar-HN and rr-CH, are weak separately, but in combination, they can have significant influence on the stability of polypeptide structure.
The interaction between the aromatic side chain of the z'th residue and the backbone amide group of the i+2 residue was studied in the tripeptide acetyl-Phe-Gly- Gly-N-methyl amide. It is an ideal model peptide to study such interactions, since side chains in positions i+1 and i+2 do not interfere with the formation of Ar-HN interaction. Simulated annealing studies with and without implicit solvation model using three different force fields (Amber 5.0, CHARMM22 and OPLSAA) found that lowest energy structures of the model peptide contained Ar-HN interaction. Molecular dynamics (MD) simulations revealed, that Ar(i)-HN(i+l) interactions were four times more frequent than were Ar(i)-HN(i+2) interactions in acetyl-Phe-Gly-Gly-N-methyl amide, and that half of the conformations with Ar(i)-HN(i+2) interactions also contained an Ar(i)-HN(i+l) interaction. The solvent access surface area of the Phel side-chain and of the amide groups of Phel, Gly2 and Gly3 involved in Ar-HN interactions was significantly smaller than in residues not involved in such interactions. The number of hydrogen bonds between the solvent and Phel, Gly2 and Gly3 amide groups was also lower in conformations with Ar-HN interactions. Thus, the attractive force between the backbone amide and the side chain aromatic ring is strong enough to outweigh any free energy losses due to solvation of the backbone and entropic costs of backbone and side chain stabilization.
The interaction between the aromatic side chain of Tyr and the a-helical backbone was investigated by studying a-helix stability in Ala based model peptides, with Tyr replacement in the N-terminal and inner helical positions, using circular dichroism, ’H-NMR and molecular dynamics simulations (MD). Interaction between the aromatic ring and the backbone highly depended on the orientation of the aromatic ring to the helical backbone since aromatic-backbone amide, -carbonyl and -aCH interactions were observed in MD. Solvent screening by the aromatic side chain decreased the solvent accessible surface area of some polar backbone groups by more than 80%. The fractional helical content, determined by NMR, suggested that Tyr in inner helical positions destabilized the helix in the peptides, while in N-terminal positions Tyr had the same helix stabilizing effect as had Ala.ProQuest Traditional Publishing Optionxvii, 540 leave
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
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
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
- …
