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Region-specific role of water in collagen unwinding and assembly
Get PDFConformational stability of the collagen triple helix affects its turnover and
determines tissue homeostasis. Although it is known that the presence of imino
acids (prolines or hydroxyprolines) confer stability to the molecule, little is known
regarding the stability of the imino-poor region lacking imino acids, which plays a
key role in collagen cleavage. In particular, there have been continuing debates about
the role of water in collagen stability. We addressed these issues using molecular
dynamics simulations on 30-residue long collagen triple helices, including a structure
that has a biologically relevant 9-residue imino-poor region from type III collagen
(Protein Data Bank ID: 1BKV). We characterized the conformational motion of the
molecule that differs between imino-rich and imino-poor regions using a torsional map
approach. At temperatures of 300 K and above, unwinding initiates at a common
cleavage site, the glycine-isoleucine bond in the imino-poor region. This provides
a linkage between previous observations that unwinding of the imino-poor region
is a requirement for collagenase cleavage, and that isolated collagen molecules are
unstable at body temperature. Unwinding of the imino-poor region is controlled by
dynamic water bridges between backbone atoms with average lifetimes on the order
of a few picoseconds, as the degree of unwinding strongly correlated with the loss
of water bridges, and unwinding could be either prevented or enhanced, respectively
by enforcing or forbidding water bridge formation. While individual water bridges
were short-lived in the imino-poor region, the hydration shell surrounding the entire
molecule was stable even at 330 K. The diameter of the hydrated collagen including the first hydration shell was about 14 ��, in good agreement with the experimentally
measured inter-collagen distances. These results elucidate the general role of water in
collagen turnover: water not only affects collagen cleavage by controlling its torsional
motion, but it also forms a larger-scale lubrication layer mediating collagen self-assembly
A Computational Study of the Role of Hydration in the Assembly of Collagen and Other Bio laments
Get PDFHydration is known to be crucial in biomolecular interactions including ligand binding and self-assembly. In our earlier studies we have shown the key role of water in stabilizing the specific parts of the collagen triple helix depending on the imino acid content. We further showed that the primary hydration shell around collagen could act as a lubricating layer aiding in collagen assembly. But key details on the structure and dynamics of water near protein surfaces and its role in protein-protein interactions remain unclear. In the current study we have developed a novel method to analyze hydration maps around peptides at 1-A resolution around three self-assembling lament systems with known structures, that respectively have hydrated (collagen), dry non-polar and dry polar (amyloid) interfaces. Using computer simulations, we calculate local hydration maps and hydration forces. We find that the primary hydration shells are formed all over the surface, regardless of the types of the underlying amino acids. The weakly oscillating hydration force arises from coalescence and depletion of hydration shells as two laments approach, whereas local water diffusion, orientation, or hydrogen bonding events have no direct effect. Hydration forces between hydrated, polar, and non-polar interfaces differ in the amplitude and phase of the oscillation relative to the equilibrium surface separation. Therefore, water-mediated interactions between these protein surfaces ranging in character from ���hydrophobic��� to ���hydrophilic,��� have a common molecular origin based on the robustly formed hydration shells, which is likely applicable to a broad range of biomolecular assemblies whose interfacial geometry is similar in length scale to those of the present study.
In a related study through simulations we show that the rate of tissue optical clearing by chemical agents correlated with the preferential formation of hydrogen bond bridges between agent and collagen. Hydrogen bond bridge formation disrupts the collagen hydration layer and facilitates replacement by a chemical agent to destabilize the tertiary structure of collagens thereby reducing light scattering. This study suggests that the clearing ability of an alcohol not only depends on its molecular size, but also on the position of hydroxyl groups on its backbone
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
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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