124,598 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe 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
Semisynthesis of Dimeric Proteins by Expressed Protein Ligation
No full textA one-pot synthesis of homodimeric proteins is described. The synthetic strategy is based on a double expressed protein ligation reaction between thioester peptides and a new bis-cysteinyl linker. The protocol was also applied to the synthesis of heterodimer
Dispelling the Myths Behind First-author Citation Counts
No full textWe 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
Liposome functionalized by Olygobranched Neurotensin peptides to delivery doxorubicin to tumour cells
No full textStructural Analysis of a Helical Peptide Unfolding Pathway
No full textThe analysis of the folding mechanism in peptides adopting welldefined secondary structure is fundamental to understand protein folding. Herein, we describe the thermal unfolding of a 15-mer vascular endothelial growth factor mimicking α-helical peptide (QKL10A) through the combination of spectroscopic and computational analyses. In particular, on the basis of the temperature dependencies of QKL10A Hα chemical shifts we show that the first phase of the thermal helix unfolding, ending at around 320 K, involves mainly the terminal regions. A second phase of the transition, ending at around 333 K, comprises the central helical region of the peptide. The determination of high-resolution QKL10A conformational preferences in water at 313 K allowed us to identify, at atomic resolution, one intermediate of the folding-unfolding pathway. Molecular dynamics simulations corroborate experimental observations detecting a stable central helical turn, which represents the most probable site for the helix nucleation in the folding direction. The data presented herein allows us to draw a folding-unfolding picture for the small peptide QKL10A compatible with the nucleation-propagation model. This study, besides contributing to the basic field of peptide helix folding, is useful to gain an insight into the design of stable helical peptides, which could find applications as molecular scaffolds to target protein-protein interactions. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA
Pragmatic Case Studies as a Source of Unity in Applied Psychology
No full textTo unify or not to unify applied psychology: that is the question. In this article we review pendulum swings in the historical efforts to answer this question—from a comprehensive, positivist, “top-down,” deductive yes between the 1930s and the early 60s, to a postmodern no since then. A rationale and proposal for a limited, “bottom-up,” inductive yes in applied psychology is then presented, employing a case-based paradigm that integrates both positivist and postmodern themes and components. This paradigm is labeled “pragmatic psychology” and, its specific use of case studies, the “Pragmatic Case Study Method” (“PCS Method”). We call for the creation of peer-reviewed journal-databases of pragmatic case studies as a foundational source of unifying applied knowledge in our discipline. As one example, the potential of the PCS Method for unifying different angles of theoretical regard is illustrated in an area of applied psychology, psychotherapy, via the case of Mrs. B. The article then turns to the broader historical and epistemological arguments for the unifying nature of the PCS Method in both applied and basic psychology.Peer reviewe
DESIGN AND CHARACTERIZATION OF MOLECULAR SCAFFOLDS
No full textIn the post-genomic era the study of the interactions between biomolecules and in particular protein-protein interactions is of growing interest, since they are the basis of all the physiological processes mediated by the formation of complexes between biomolecules. Therefore, detailed knowledge of the molecular mechanisms responsible for these interactions is essential to develop molecules capable of modulating the biological activity of the protein target and then its cellular processes.
Currently, the identification of molecules that inhibit or promote protein-protein interactions or protein-nucleic acids is one of the greatest challenges of drug discovery. Unlike the traditional approach based on the design of molecules modeled on specific substrates for enzymatic active sites, the development of compounds able to modulate protein-protein interactions is a more complex process. The interface molecules involved is usually an extended area that includes more non-contiguous regions lacking suitable pockets of binding to small molecules. Moreover, these regions often have elements of secondary structure that once isolated from their context, not having the protein native conformation. So far, several classes of compounds have been used to modulate protein-protein interactions: antibodies, peptides and small organic molecules and rarely miniproteine [1]. The latter, in fact, while constituting the majority of the active ingredients currently on the market are unsuitable to work with very large surface protein. The antibodies show high specificity and are widely used but have high production costs. The peptides are considered, however, good candidates for developing new compounds that interfere with protein-protein recognition [2]. The main approaches currently used to develop compounds of peptidic nature consists in the screening of phage libraries, parallel synthesis of peptides on membrane and rational design.
Latter requires that the structural and biochemical information available on at least one of the two interacting partners and have been identified residues involved in the bond [3]. If the design of peptides that mimic the structural organization of the segments involved in the interaction is expected to introduce first stage of waste in order to stabilize the secondary structure and a second in which you must enter the residues responsible for interaction in the right spatial orientation.
An alternative approach is to use scaffold [4] molecules structurally stable that already have the desired secondary structure, which can be directly introduced into the residues in the correct spatial orientation.
The aim of this PhD project was to design and characterize molecular scaffold, such as peptides and mini-proteins that can modulate the interactions between biomolecules.
This aim was addressed by three different approaches:
• The development of a new synthetic strategy for obtaining polypeptides, functionally active protein expressed by ligation;
• The bio-physical characterization of a helical peptide scaffold;
• The transfer of functional epitopes on a scaffold protein known.
The first strategy consists in developing a procedure for binding by stable covalent bonds the C-terminus of two polypeptide fragments obtained by recombinant expression in bacteria. This strategy allows to obtain peptide model systems [5] and mini-proteins that retain the same functionality of the target protein but whose dimensions are considerably reduced. The synthetic strategy provides for the chemical ligation reaction between two polypeptides activated as the C-terminal thioester and a bifunctional linker is characterized by the presence of two cysteines in position pseudo N-terminal. The linker was synthesized from dall'etilendiammina which they were linked to two cysteine residues via a peptide bond. The mini-protein to the C-terminal thioester was obtained using expression vectors containing inteine [6]. The synthetic procedure was developed using as a model system for the mini-protein, the sequence coding for the cloning site of the vector pTrcHisA. The vector was modified by the insertion dell'inteina MxeGyrA (N198A). The fusion construct was expressed in cells BL21 (DE3) of Escherichia coli and purified by affinity chromatography on chitin resin, the mini-protein thioester was obtained following the dell'inteina splicing in the presence of thiols. Following the mini-protein thioester was used in two separate ligation reactions with the linker, to obtain homodimers and heterodimers. The pure products, characterized by LC-MS, were all obtained with good yields [7]. This synthetic strategy offers the opportunity to unite chemically two protein fragments in a stable manner through the use of a bifunctional linker, which can be suitably modified by varying the length and rigidity of the spacer between the cysteine residues and this has considerable potential for biotechnological applications . This methodology can be used to combine neighboring peptide chains in space but not in sequence, to mimic, for example, discontinuous epitopes, to synthesize scaffolds of small (mini-antibody) as an alternative dimerization domains such as Leucin zipper.
For the second approach has made the chemical and physical characterization of a peptide for its possible use as scaffolds for helical structural reasons.
It was recently described a peptide, QK, able to mimic in vitro and in vivo biological activity of VEGF [8-10] in aqueous solution which assumes a well-defined helical conformation. Analysis of circular dichroism and NMR data indicate that the peptide QK has a thermal stability is unusual for a peptide composed only of natural amino acids. To assess the structural determinants of this stability, the experimental data have been supplemented with molecular dynamics simulations.
Theoretical studies have indicated that the N-terminal region and a hydrophobic contact between the Leu7 and Leu10 are important for the thermal stability of the peptide.
To test these predictions have been synthesized 3 peptides similar QK: QK1-12 that lacks the C-terminal; QK4-15 than the N-terminal and QK10A, in which Leu10 was replaced with un'alanina. The analysis of peptides by circular dichroism and NMR showed that QK1-12, unlike QK4-15, maintains a helical structure and thermal stability similar to QK, QK10A has about half the helical content and does not retain 's unusual thermal stability [11]. Finally, using a combination of experimental techniques such as CD, NMR and MD was possible to characterize at atomic one possible pathway for formation of the peptide helix QK10A and provide information sull'inusuale thermal stability of the peptide QK prerequisite for its use as helical scaffold.
The third approach has included the development of a mini-biologically active protein from a scaffold known. The biological system chosen was that of VEGF and its receptors. An analysis of three-dimensional structure of the complex between VEGF/Flt-1D2 and mutagenesis have identified residues important for binding to VEGF receptors [12], these data demonstrated that the binding region of VEGF receptor includes the helix 17-25.
The scaffold was the chosen Avian Pancreatic Polypeptide (APP), a miniproteina of 36 amino acids, very stable, which owns un'α-helix exposed to solvent and thruster poliprolina type II. Based on the overlap of the propeller of VEGF and the APP scaffold have been designed in which two different molecules have been transferred to the residues responsible for interaction with VEGF receptors and the peptide QK respectively named APP1 and APP_QK. Molecules are designed and the wild type were obtained by recombinant cells BL21 (DE3) of Escherichia coli.
The proteins were purified by affinity chromatography and analyzed by LC-MS. Finally, preliminary in vitro biological assays have shown for the molecule APP_QK a similar activity to that of QK peptide.
In conclusion, this work by providing different approaches contribute significantly to the development of new scaffolds for targeting protein-protein interactions.
BIBLIOGRAFY
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[10] G Santulli, M Ciccarelli, G Palumbo, A Campanile, G Galasso, B Ziaco, GG Altobelli, V Cimini, F Piscione, LD D'Andrea, C Pedone, B Trimarco and G Iaccarino Journal of Translational Medicine 2009, 7:41
[11]D Diana, B Ziaco, G Colombo, G Scarabelli, A Romanelli, C Pedone, R Fattorusso and LD. D’Andrea Chemistry Eur. J. 2008, 14, 4164 – 4166
[12]Wiesmann C., Fuh G., Christinger H.W., Eigenbrot C., Wells J.A., and De Vos A.M., Cell 91: 695-704 (1997
Dr. Edwin Wright Collection: Author Unknown
No full textNotes - The author relates several short stories about his neighbours including Alex McDonell, homesteading and life around Meanook and Athabasca (1 page
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe 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
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