1,720,965 research outputs found
On the interplay between the trans and cis interactions in classical cadherins : a mutagenesis and crystallographic study
No full textLAUREA MAGISTRALELe caderine classiche, i cui membri prototipici sono la E- e P-caderina, sono proteine trasmembrana calcio dipendenti la cui funzione è quella di mediare l’adesione cellulare formando la giunzione aderente attraverso la loro dimerizzazione omotipica. Esse esercitano un ruolo centrale nel mantenimento dell’integrità tissutale e, attraverso i loro segnali intracellulari, influiscono sull’attività di molti signaling pathways che influenzano la sopravvivenza, motilità, crescita, differenziazione e organizzazione di molti tessuti biologici. Per la loro importanza nella regolazione dei segnali cellulari, rappresentano un nodo centrale nelle reti biologiche e la loro deregolazione è osservata in patologie come il cancro. In questi anni, la crescente conoscenza molecolare sulla loro funzione ha messo in evidenza come possano anche essere considerati importanti target farmaceutici. Tuttavia, il targeting delle caderine è complicato poiché esse sono estremamente flessibili e sono caratterizzate da molti stati conformazionali; inoltre, il loro processo di dimerizzazione non è ancora pienamente compreso.
Questo lavoro di tesi si concentra sull’analisi della relazione tra l’interazione trans, cioè il meccanismo di domain swapping che permette la dimerizzazione di caderine che protrudono da cellule adese, e l’interazione cis, che permette il clustering laterale nella giunzione aderente tra caderine che protrudono dalla stessa cellula. Totale cooperatività tra queste due interazioni è sempre stata presunta in letteratura ma mai dimostrata sperimentalmente.
Il sistema utilizzato per questo studio è la P-caderina, poiché, se opportunamente mutata, essa può essere forzata ad assumere tutti gli stadi conformazionali che ne caratterizzano la traiettoria di dimerizzazione.
Le tecniche e la teoria descritte in questo lavoro comprendono tutti gli aspetti legati all’ingegnerizzazione dei mutanti, alla loro produzione ricombinante, isolamento, purificazione, cristallizzazione e caratterizzazione strutturale.
In conclusione, alcuni risultati preliminari per l’ottenimento di strutture cristallografiche della E-caderina in complesso con molecole peptidomimetiche sono mostrati e discussi.Cadherins are calcium-dependent transmembrane glycoproteins whose main function is to mediate adherens junction formation via their homotypic dimerization. Classical cadherins play a pivotal role in the maintenance of tissue integrity and, through their downstream signaling, they influence the activity of many key signaling pathways that affect survival, motility, growth, cell differentiation and tissue organization. Because of their importance in the regulation of the inside-out signaling they represent a signaling hub in the biological network and their dysregulation is often observed in pathological conditions, such as cancer. Over the years, our growing knowledge on the function and the molecular mechanism of cadherins has supported the notion that they can be viewed also as potential pharmaceutical targets. However, targeting cadherins is a complicated task since they are extremely flexible and therefore their dimerization process, which is not yet fully understood, is characterized by many different conformational states.
This thesis work concentrates on the analysis of the interplay between the trans interaction, i.e. the domain swapping mechanism that allows the dimerization of cadherins protruding from two adhering cells, and the cis interaction, that allows lateral clustering of cadherins protruding from the same cell within the adherens junction. An extreme cooperativity between these two interactions has been always assumed in the literature but never experimentally demonstrated.
The system we used to study this relationship is human P-cadherin. In fact, by mutating key residues in their natural sequence, this member of the classical cadherin family can likely be tuned to adopt all the different conformational states that characterize their dimerization trajectory.
The techniques and theory described in this work comprise all the molecular biology needed for the engineering of protein mutants, their recombinant production, isolation, purification and crystallization.
Finally, some preliminary results on the first attempts to obtain the crystal structures of E-cadherin in complex with peptidomimetic drugs are also shown and discussed
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
E-cadherin and Choline Kinase: two challenging drug discovery targets
Full text linkThe data presented in this thesis was generated using molecular biology, protein chemistry and X-ray
crystallography techniques. However, while the methodologies employed are essentially the same,
the research work presented here refers to two different proteins, which are part of different research
projects in the laboratory. For this reason, the content of this thesis is divided in two independent
parts, each provided with an introduction and a general overview of the research topic and state-ofthe-
art, a materials and methods section discussing the techniques used and the protocols followed,
and a section where the results are presented and discussed in detail.
The first half of the thesis deals with the structural characterization of the complex between human
E-cadherin and three different small molecule potential inhibitors identified via a fragment-based
drug discovery (FBDD) screening campaign that was conducted using a library of commercially
available small fluorinated chemical fragments. For this screening phase, we used 19F-NMR as
readout. The NMR experiments were done by our collaborator Dr. Marina Veronesi at the D3
PharmaChemistry division of the Italian Institute of Technology (IIT) in Genova (Italy). Functional
cell adhesion assays to validate the inhibitory effects of the fragments thus identified were carried out
in collaboration with Prof. Frédéric André at the University of Marseille (France).
The second half of the thesis describes the structural characterization of Plasmodium falciparum
Choline Kinase (PfChoK), an important pharmaceutical target in the fight against malaria, as well as
the biochemical characterization of a library of potential inhibitors of PfChoK. These inhibitors were
synthetized in the group of Prof. Luisa Carlota López-Cara at the Department of Pharmaceutical and
Organic Chemistry of the University of Granada (Spain) in the framework of an ongoing
collaboration between the two groups
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
Design, synthesis, biological evaluation and structural characterization of novel GEBR library PDE4D inhibitors
No full textMemory and cognitive functions depend on the cerebral levels of cyclic adenosine monophosphate (cAMP), which are regulated by the phosphodiesterase 4 (PDE4) family of enzymes. Selected rolipram-related PDE4 inhibitors, members of the GEBR library, have been shown to increase hippocampal cAMP levels, providing pro-cognitive benefits with a safe pharmacological profile. In a recent SAR investigation involving a subset of GEBR library compounds, we have demonstrated that, depending on length and flexibility, ligands can either adopt a twisted, an extended or a protruding conformation, the latter allowing the ligand to form stabilizing contacts with the regulatory domain of the enzyme. Here, based on those findings, we describe further chemical modifications of the protruding subset of GEBR library inhibitors and their effects on ligand conformation and potency. In particular, we demonstrate that the insertion of a methyl group in the flexible linker region connecting the catechol portion and the basic end of the molecules enhances the ability of the ligand to interact with both the catalytic and the regulatory domains of the enzyme. (C) 2021 Elsevier Masson SAS. All rights reserved
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