Identification of potential small molecule binding pockets on Rho family GTPases

Rho GTPases are conformational switches that control a wide variety of signaling pathways critical for eukaryotic cell development and proliferation. They represent attractive targets for drug design as their aberrant function and deregulated activity is associated with many human diseases including cancer. Extensive high-resolution structures (.100) and recent mutagenesis studies have laid the foundation for the design of new structure-based chemotherapeutic strategies. Although the inhibition of Rho signaling with drug-like compounds is an active area of current research, very little attention has been devoted to directly inhibiting Rho by targeting potential allosteric non-nucleotide binding sites. By avoiding the nucleotide binding site, compounds may minimize the potential for undesirable off-target interactions with other ubiquitous GTP and ATP binding proteins. Here we describe the application of molecular dynamics simulations, principal component analysis, sequence conservation analysis, and ensemble small-molecule fragment mapping to provide an extensive mapping of potential small-molecule binding pockets on Rho family members. Characterized sites include novel pockets in the vicinity of the conformationaly responsive switch regions as well as distal sites that appear to be related to the conformations of the nucleotide binding region. Furthermore the use of accelerated molecular dynamics simulation, an advanced sampling method that extends the accessible time-scale of conventional simulations, is found to enhance the characterization of novel binding sites when conformational changes are important for the protein mechanism.

Pedagogia Social Comunitària: un model d’intervenció socioeducativa integral

L’actual situació d’inestabilitat social i econòmica que viu la nostra societat ha evidenciat l’existència de grans bosses de persones que viuen en situació de marginació o exclusió social. Les polítiques socials han donat resposta a situacions concretes, però no han articulat un teixit social fort que permeti incorporar de manera efectiva la persona exclosa, ni prevenir aquests processos. Es presenta en aquest article un model d’intervenció socioeducativa anomenat Pedagogia Social Comunitària que centra la seva acció en dos objectius: la millora de la qualitat de vida i el benestar de les persones, especialment d’aquelles que es troben en situació d’exclusió social; i el foment de la cohesió social. Aquestes finalitats s’operativitzen mitjançant l’increment de la participació, l’empoderament individual i comunitari, la coresponsabilitat i la sensibilització social.

Allosteric conversation in the androgen receptor ligand-binding domain surfaces

Androgen receptor (AR) is a major therapeutic target that plays pivotal roles in prostate cancer (PCa) and androgen insensitivity syndromes. We previously proposed that compounds recruited to ligand-binding domain (LBD) surfaces could regulate AR activity in hormone-refractory PCa and discovered several surface modulators of AR function. Surprisingly, the most effective compounds bound preferentially to a surface of unknown function [binding function 3 (BF-3)] instead of the coactivator-binding site [activation function 2 (AF-2)]. Different BF-3 mutations have been identified in PCa or androgen insensitivity syndrome patients, and they can strongly affect AR activity. Further, comparison of AR x-ray structures with and without bound ligands at BF-3 and AF-2 showed structural coupling between both pockets. Here, we combine experimental evidence and molecular dynamic simulations to investigate whether BF-3 mutations affect AR LBD function and dynamics possibly via allosteric conversation between surface sites. Our data indicate that AF-2 conformation is indeed closely coupled to BF-3 and provide mechanistic proof of their structural interconnection. BF-3 mutations may function as allosteric elicitors, probably shifting the AR LBD conformational ensemble toward conformations that alter AF-2 propensity to reorganize into subpockets that accommodate N-terminal domain and coactivator peptides. The induced conformation may result in either increased or decreased AR activity. Activating BF-3 mutations also favor the formation of another pocket (BF-4) in the vicinity of AF-2 and BF-3, which we also previously identified as a hot spot for a small compound. We discuss the possibility that BF-3 may be a protein-docking site that binds to the N-terminal domain and corepressors. AR surface sites are attractive pharmacological targets to develop allosteric modulators that might be alternative lead compounds for drug design.

The present state of aragonese

How much Aragonese is still spoken remains largely an unknown quantity. Naturally, establishing the number of speakers of any variety begs the question of what speaking a language actually means, and the picture is often clouded by the political interests of particular groups, as is the case in Aragon. The strong claim to the continued widespread use of Aragonese made by such associations as the Consello d"a Fabla in Huesca is counterbalanced by that of the more reactionary, sceptical academics at the University of Saragossa, who maintain that Aragonese varieties, ignoring the Catalan of Aragon spoken right down La Franja, the transition area between Aragon and Catalonia, now only survive in certain pockets of resistance across the north of Huesca. This paper will attempt to provide a summary of the available facts and report on some of the author"s own findings during his more recent trips to Aragon. Keywords Spanish dialectology, Aragonese, standardization of Aragonese, vitality of Aragonese

Descripció geoambiental i paisatgística del sistema platja-duna de cala Borró (cap Ras, Alt Empordà- Costa Brava, Girona)

The geoambiental and landscape description of the beach-dune system of Cala Borró, (Cap Ras), placed in the town of Colera (Alt Empordà), is carried out. The dunar system, developed with orientation and N-S, links three beach pockets following the topographic slopes of the torrential basins. We find coalescence of dunes in the upper zones, which were possibly an object of reafforestation in the 19thC. to avoid erosion

Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7

Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.