1,720,987 research outputs found
Probing the Determinants of Porosity in Protein Frameworks: Co-crystals of Cytochrome c and an Octa-anionic Calix[4]arene
No full textSulfonato-calix[n]arenes (sclxn) are promising tools to generate crystalline protein frameworks. Two crystal structures of an octa-ionic calix[4]arene (sclx4mc) in complex with yeast or horse heart cytochrome c (cytc) are reported. Highly porous honeycomb or tubular assemblies were obtained with yeast or horse cytc, respectively. Related frameworks were obtained previously with sclx8 and sclx6 but not with sclx4, suggesting that the ligand charge is a contributing factor
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
Complex Formation between Cytochrome c and a Tetra-alanino-calix[4]arene
No full textOwing to their remarkable features, calix[n]arenes are being exploited to study different aspects of molecular recognition, including protein complexation. Different complexation modes have been described, depending on the moieties that complement the aromatic cavity, allowing for function regulation and/or controlled assembly of the protein target. Here, a rigid cone calix[4]arene, bearing four anionic alanine units at the upper rim, was tested as a ligand for cytochrome c. Cocrystallization attempts were unfruitful, preventing a solid-state study of the system. Next, the complex was studied using NMR spectroscopy, which revealed the presence of two binding sites at lysine residues with dissociation constants (K(d)) in the millimolar range
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
CHAPTER 4. Protein Modulation by Cucurbiturils
No full textCucurbiturils are a class of macrocycles that feature highly interesting molecular characteristics that enable interfacing with proteins. These macrocycles, of different ring sizes, can act as host molecules to form stable inclusion complexes with various protein elements as guests. This combination of diverse macrocycle ring sizes with the large variety of protein elements, ranging from individual amino acids to protein segments, has provided a wealth of opportunities to bring cucurbiturils to applications in protein modulation. Cucurbit[6]uril, cucurbit[7]uril, and cucurbit[8]uril are the most prominent examples with applications in protein binding, as their chemical characteristics appear to be ideally suited to recognize different protein epitopes with high affinity. This interplay has allowed these cucurbiturils to be used for protein binding with concomitant functional modulation, which includes the study and modulation of protein activity and protein assembly. This chapter will provide an overview of the amino acid, peptide and protein recognition as well as protein modulatory activities of cucurbit[6]uril, cucurbit[7]uril, and cucurbit[8]uril. Specific examples will illustrate the broader potential for molecular recognition of proteins by cucurbiturils.</p
Supramolecular approaches for protein framework modulation
No full textProteins are the building block of choice in nature to make complex, functional frameworks. The choice of 20 amino acids provides a rich diversity of sequence possibilities, allowing for the evolution of a wide range of structures that carry out unique functions. There is great interest in manufacturing highly ordered (supramolecular) protein architectures with a view to equal or exceed the structural properties demonstrated by nature’s examples. However, the structural diversity and complexity of proteins pose a challenge to controlled protein assembly. This thesis describes the use of macrocycles, macrocycle-metal complexes, mutagenesis, seeding, and crystallization to overcome this challenge, specifically exploiting supramolecular interactions between synthetic macrocyclic hosts and macromolecular guests. NMR spectroscopy and X-ray crystallography were used to observe host-guest interactions in solution and in the solid state. The model protein cytochrome c was cocrystallized with a complex of sulfonatothiacalix[4]arene (tsclx4) and zinc to yield two distinct crystal forms depending on the concentration of zinc. Further investigation was conducted with a histidine mutant of the trimeric protein RSL, yielding a dinuclear tsclx4/Zn complex, suggesting that the macrocycle-metal complex is an adaptable protein binder.1 Modulation of a previously described cubic assembly2 of sulfonato-calix[8]arene (sclx8) and RSL was carried out by surface charge modification and cross-seeding. Three mutants of RSL were generated to investigate the effect of replacing aspartic acid with asparagine. The goal was to alleviate charge repulsion with the acidic macrocycle and therefore enable cocrystallization at higher pH. Two cocrystal forms were obtained with one of the mutants, both requiring the same pH as the original structure. Control over which crystal form grew was enabled via seeding. The remaining mutants and wild type RSL were unaffected by cross-seeding in these conditions, suggesting replacement of the acidic side chain with an amide at this site is necessary for framework modulation. When this mutant was crystallized in the same conditions as native RSL,2 , an essentially identical assembly was observed. However, cocrystallization of a histidine mutant under these conditions resulted in an altered framework. The results reveal an attractive method for engineering protein frameworks.3 Complexation of sclx8 and Pent, a designed pentameric β-propeller lectin (developed by the Tawfik laboratory) was evaluated by using NMR spectroscopy and X-ray crystallography. Two crystal forms of the Pent – sclx8 complex were obtained, depending apparently on the ionic strength of the crystallization conditions. In conditions containing PEG as the sole precipitant, a 1:1 complex was obtained, where the calixarene forms multivalent interactions with the cationic protein surface. When the ionic strength is increased, a dimer of proteins sandwiches the calixarene. In this case the protein may be considered the host and the calixarene the guest. Strong binding to the concave, cationic pocket on Pent was observed in NMR, confirmed by a slow exchange process on the NMR time scale. This data,indicative of ~µM affinity, was consistent with the large protein – calixarene interface observed in the crystal structures. The calixarene scaffold, with its large surface area (~1500 Å2 for the pleated loop), is a versatile multivalent protein binder.4 The Pent – sclx8 system was further investigated with different crystallization conditions, yielding an icosahedral assembly of pentamers. This icosahedral assembly was confirmed using SAXS under similar conditions. The high porosity (∼70% solvent content) may have resulted in the lowresolution X-ray data of the crystals. However, Pent – sclx6 cocrystals provided evidence that sclx6 bound to the lysine-containing vertex of the pentamer. These data suggested that sclx8 may bind in a similar fashion, resulting in the formation of an icosahedron.5 Though this subject is still relatively new, much work has been done to understand protein – calixarene interactions. The results described in this thesis highlight the potential for macrocyclemediated protein assembly towards the fabrication of functional materials. Further work expanding on the concept of supramolecular synthons in protein – macrocycle frameworks may lead to precise framework fabrication across a range of different systems
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
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