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Peptide-based foldamers for applications in self-recognition, supramolecular propagation, and photo-induced folding.
Full text linkAbstract
Self-recognition and propagation
Two appropriately functionalized nucleobases, thymine and adenine, have been covalently linked at the N- and C-termini of α-aminoisobutyric acid-rich helical peptide foldamers, at a set of selected chromophores and at fully adenine-capped gold nanoparticles, aiming at driving self-assembly through complementary recognition. These systems were studied in terms of their self-recognition abilities to generate ordered nano-architectures. A crystal-state analysis (by X-ray diffraction) shows that adenine···thymine base pairing, through Watson–Crick intermolecular H-bonding, does take place between either end of each peptide molecule. Evidence for time-dependent foldamer···foldamer associations in solution is provided by circular dichroism measurements. The self-assembly of foldamers, through living supramolecular polymerization, eventually leads to the formation of twisted fibers. It was found that adenine···thymine binding allowed the formation of precisely assembled nano-systems that depend powerfully on their morphologies from the nature of the chromophores utilized. These well-organized supramolecular architectures are able to undergo morphologically self-shaping processes under illumination by visible light, through the activation of the plasmon resonance of gold nanoparticles.
Moreover, three building blocks have been designed to chemically link to a gold surface and vertically self-assemble through thymine–adenine hydrogen bonds. Starting from these building blocks, two different films were engineered on gold surface. These films were characterized by electrochemical and spectroscopic techniques, and were very stable over time and when in contact with solution. Under illumination, they generate current with higher efficiency than similar previously described systems.
Self-recognition and polymerization
A set of four organogelators, from an α-amino acid derivative to a tetrapeptide, covalently linked to an acetylenic moiety, was studied in terms of polymerization efficiencies to afford peptide polyacetylenes (PAs) and polydiacetylenes (PdAs). Peptides were designed to improve the organogelator behavior via formation of intermolecular H-bonding-mediated β-sheet networks as a function of their main chain length. The polymerization experiments were run under appropriate conditions for the various monomers with the aim at elucidating how the monomer self-assembly process might influence polymer formation. Starting compounds and their corresponding polymers were characterized by a variety of spectroscopic and microscopic techniques.
A symmetrical dipeptide-based diacetylene system (DAs) was found to be able to self-assemble in dichloromethane and to form a compact fiber network which resulted in a stable organogel. As a consequence of the organogel formation, we explored the possibility to run a light-induced topochemical polymerization. Evidence for the generation of peptide-based polydiacetylenes is provided by Raman, UV-Vis, and CD spectroscopies and a set of microscopic techniques. Finally, we succeeded in processing a polymeric composite by use of the electrospinning technique, starting from a mixture of a dipeptide-based diacetylene and polymethyl methacrylate.
Photo-induced supramolecular folding
Peptides are well known to play a fundamental therapeutic role and to represent building blocks for numerous useful biomaterials. Stabilizing their active 3D-structure by appropriate modifications remains, however, a challenge. We have expanded the available literature information on the conformational propensities of a promising backbone change of a terminally blocked δ-amino acid residue, a dipeptide mimic, by replacing its central amide moiety with an (E) Cγ=Cβ alkene unit. By DFT calculations, X-ray diffraction in the crystalline state, and FT-IR and NMR spectroscopies in solution we examined the extended vs. folded preferences of analogs of this prototype system. The theoretical and experimental results obtained clearly point to the conclusion that increasing the number of adequately positioned methylations will enhance the preference of the original sequence to fold, thus opening interesting perspectives in the design of conformationally constrained peptidomimetics.
Systems in which an external stimulus elicits a response through some sort of modification at the molecular or supramolecular level bear potential for the development of smart materials and devices. A simple, unsaturated, E–Z photoisomerizable β-amino acid, (Z)-3-aminoprop-2-enoic acid, has been introduced into peptide foldamers through a one-pot chemical coupling, based on Pd/Cu-catalyzed olefin oxidative amidation, between two peptide segments carrying, respectively, a -Gly-NH2 residue at the C-terminus and an acryloyl group at the N-terminus. Reversible conversion between the Z and E configurations of the 3-aminoprop-2-enoic linkage was achieved photochemically. A crystallographic analysis on two model compounds shed light on the consequences, in terms of 3D structure and self-association properties, brought about by the different configuration of the unsaturated linkage. As a proof of concept, E–Z photoisomerization of a 3-aminoprop-2-enoic acid residue, inserted as the junction between two conformationally distinct peptide domains (one helical while the other β-sheet promoter), allowed supramolecular self-association to be reversibly turned on/off.
Finally, we developed a versatile synthetic approach suitable for the stepwise incorporation of multiple, even consecutive, units of the simplest Cα,β-unsaturated β-amino acid, [(E/Z)-3-aminoprop-2-enoic acid] in peptide-based foldamers.
Intrinsically Photoswitchable α/β Peptides toward Two-State Foldamers
No full textA simple, unsaturated, E–Z photoisomerizable β‐amino acid, (Z)‐3‐aminoprop‐2‐enoic acid, has been introduced into peptide foldamers through a one‐pot chemical coupling, based on Pd/Cu‐catalyzed olefin oxidative amidation, between two peptide segments carrying, respectively, a ‐Gly‐NH2 residue at the C‐terminus and an acryloyl group at the N‐terminus. Reversible conversion between the Z and E configurations of the 3‐aminoprop‐2‐enoic linkage was achieved photochemically. A crystallographic analysis on two model compounds shed light on the consequences, in terms of 3D structure and self‐association properties, brought about by the different configuration of the unsaturated linkage. As a proof of concept, E–Z photoisomerization of a 3‐aminoprop‐2‐enoic acid residue, inserted as the junction between two conformationally distinct peptide domains (one helical while the other β‐sheet promoter), allowed supramolecular self‐association to be reversibly turned on/off
Shaping bioinspired photo-responsive microstructures by the light-driven modulation of selective interactions
Full text linkA set of thymine-functionalized chromophores such as tetraphenylporphyrin, azobenzene and carbon quantum dots were synthesized and studied in terms of their self-recognition abilities to generate ordered nano-architectures. Additionally, fully adenine-capped, water soluble, gold nanoparticles were synthesized and properly characterized. In particular, we observed a strong self-recognition between thymine–thymine systems, the fully functionalized adenine-capped nanoparticles act as a “breaking” molecular binder thus to allow complementary recognition with the thymine-functionalized chromophores and the consequent molecular reorganization. It was found that adenine–thymine binding, occurring between these complementary self-organized complex systems, allowed the formation of precisely assembled nano-systems that depend powerfully on their morphologies from the nature of the chromophores utilized. These well-organized supramolecular architectures are able to undergo morphologically self-shaping processes under illumination by visible light, through the activation of the plasmon resonance of gold nanoparticles, which are affected selectively and precisely rearranged by the binding modes of the self-assembled microstructures at the nanoscale level. Finally, these studies were extended to selective molecular recognition at the surface, confirming the high binding affinity of these complex systems even at this level
Light-driven topochemical polymerization under organogel conditions of a symmetrical dipeptide-diacetylene system
No full text
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
Tuning morphological architectures generated through living supramolecular assembly of a helical foldamer end-capped with two complementary nucleobases
Full text linkTwo appropriately functionalized nucleobases, thymine and adenine, have been covalently linked at the N- and C-termini, respectively, of two α-aminoisobutyric acid-rich helical peptide foldamers, aiming at driving self-assembly through complementary recognition. A crystal-state analysis (by X-ray diffraction) on the shorter, achiral foldamer 1 unambiguously shows that adenine⋯thymine base pairing, through Watson–Crick intermolecular H-bonding, does take place between either end of each peptide molecule. In the crystals, π-stacking between base pairs is also observed. Evidence for time-dependent foldamer⋯oldamer associations for the longer, chiral foldamer 2 in solution is provided by circular dichroism measurements. The self-assembly of foldamer 2, through living supramolecular polymerization, eventually leads to the formation of twisted fibers. Such a supramolecular organization can be affected by addition of either pristine adenine or thymine, that acts as a “terminator” by selectively matching a pairing nucleobase at one end of the foldamer. The co-assembly of foldamer 2 with a porphyrin-derivatized thymine, under appropriate experimental conditions, leads to the formation of vesicles which, in turn, can be converted to the fiber morphology by changing the environmental polarity. Conversely, dendrimeric, star polymer-like microstructures are generated when the supramolecular assembly of foldamer 2 is seeded by adenine-capped gold nanoparticles
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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