1,720,974 research outputs found
Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL
No full textThe surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible surface of RNA using NMR and the small paramagnetic molecule TEMPOL. We investigated two RNAs with known structures, one that is extremely stable and one that is dynamic. For helical regions, the TEMPOL probing data correlate well with the predicted RNA surface, and the method is able to distinguish subtle variations in atom depths, such as the relative accessibility of pyrimidine versus purine aromatic carbon atoms. Dynamic motions are also detected by TEMPOL probing, and the method accurately reports a previously characterized pH-dependent conformational transition involving formation of a protonated CA pair and base flipping. Some loop regions are observed to exhibit anomalously high accessibility, reflective of motions that are not evident within the ensemble of NMR structures. We conclude that TEMPOL probing can provide valuable insights into the surface accessibility and dynamics of RNA, and can also be used as an independent means of validating RNA structure and dynamics in solution
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
Probing protein surface accessibility with solvent and paramagnetic molecules
No full textThe accessibility of molecular surfaces is a dimension of structural biology that needs to be thoroughly investigated in order to increase the ability to predict a large variety of molecular events which are frequently referred to as allosteric effects. Obtaining convergent results on the surface distribution of cold and hot spots by using different techniques can produce important insight about protein surface dynamics. Site directed spin-labeling, that is the semi-synthetic production of protein or nucleic acid analogues incorporating covalently bound spin labels, is a powerful technique used to prepare NMR and EPR samples in order to map the conformational environment of the inserted paramagnetic moiety. Extensive MD sampling in explicit solvent and docking studies into protein-conformation snapshots extracted from such MD simulations should be performed for the interpretation of PRE data, accounting for all the possible interactions
Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping
No full textThe U6 RNA internal stem-loop (U6 ISL) is a highly conserved domain of the spliceosome that is important for pre-mRNA splicing. The U6 ISL contains an internal loop that is in equilibrium between two conformations controlled by the protonation state of an adenine (pK(a) =6.5). Lower pH favors formation of a protonated C-A(+) wobble pair and base flipping of the adjacent uracil. Higher pH favors stacking of the uracil and allows an essential metal ion to bind at this position. Here, we define the minimal-energy path for this conformational transition. To do this, we solved the U6 ISL structure at higher pH (8.0) in order to eliminate interference from the low-pH conformer. This structure reveals disruption pair and formation of a new C-U pair, which of the protonated C-A explains the preference for a stacked uracil at higher pH. Next, we used nudged elastic band molecular dynamics simulations to calculate the minimum-energy path between the two conformations. Our results indicate that the C-U pair is dynamic, which allows formation of the more stable C-A(+) pair upon adenine protonation. After formation of the C-A(+) pair, the unpaired uracil follows a minor-groove base-flipping pathway. Molecular dynamics simulations suggest that the extrahelical uracil is stabilized by contacts with the adjacent helix. (C) 2009 Elsevier Inc. All rights reserved
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
Sustainable scalable synthesis of sulfide nanocrystals at low cost with an ionic liquid sulfur precursor
No full textIncreasing the sustainability of nanocrystals is crucial to their application and the protection of the environment. Sulfur precursors for their synthesis are commonly obtained through multiple steps from H2S, only to be converted back to H2S during the synthesis of the nanocrystals. This convoluted process requires energy, reduces yields, increases waste and auxiliaries, and complicates recycling. Using H2S directly could drastically improve sustainability, but is prevented by toxicity and handling. We here show that H2S is stabilized by reaction with oleylamine (the most common and versatile ligand in nanoparticle synthesis) to form an ionic liquid precursor that addresses all major principles of green chemistry: it is made in one exothermic step, it leaves the reaction yielding a safer product and allowing the separate recycling of the precursors, and it produces high quality nanocrystals with high yields (sulfur yield > 70%) and concentrations (90 g L−1) in ambient conditions
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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