Barreras naturales para las horquillas de replicación DNA en Schizosaccharomyces pombe

106 p.-35 fig.En la naturaleza, el crecimiento vegetativo de S. pombe es normalmente haploide. Sólo bajo condiciones ambientales adversas, como en condiciones de ayuno de fuentes nitrógeno, dos células de tipos de apareamiento contrarios, P (plus) y M (minus), conjugan y forman un cigoto diploide (Egel, 1989; Dalgaard y Klar, 2001). Para cada tipo de apareamiento, existen células denominadas switchable (s) y células unswitchable (u). Cada célula de S. pombe que acaba de adquirir un tipo de apareamiento concreto, da lugar a otra del tipo de apareamiento contrario tras dos divisiones mitóticas. Cuando una célula u se divide da lugar a dos células del mismo tipo de apareamiento que la célula parental, una de ellas s y la otra u. Cuando se divida, la célula s dará lugar a una célula u de tipo de apareamiento contrario a la parental y a otra célula s del mismo tipo de apareamiento que la parental (Miyata y Miyata, 1981; Egel y Eie, 1987; Klar, 1987, 1990). Aunque el mecanismo molecular responsable del cambio del tipo de apareamiento en S. pombe no se conoce aún en detalle, algunas de las claves han sido ya descifradas (ver Dalgaard y Klar, 2001 y apartado 1.4.2.). Una vez que producida la conjugación, los núcleos se fusionan y el cigoto diploide resultante sufre meiosis inmediatamente. El cigoto se convierte en una estructura de resistencia denominada asca, que contiene cuatro esporas haploides. Este proceso representa un ejemplo de diferenciación celular. Cuando las condiciones ambientales vuelven a ser favorables, las esporas son liberadas y pueden germinar, cerrándose de este modo el ciclo. Las poblaciones naturales de S. pombe, son homotálicas, es decir, están compuestas por células de los dos tipos de apareamiento y entran en diferenciación sexual bajo condiciones de estrés ambiental. En el laboratorio, a menudo se emplean estirpes heterotálicas, las cuales necesitan otra estirpe del tipo de apareamiento contrario para aparear. En el laboratorio se puede promover la entrada de los cigotos a la división mitótica y seleccionarlos usando mutaciones auxotróficas complementarias en el proceso de conjugación, obteniendo así estirpes diploides que, eventualmente, pueden inducirse a entrar en ciclo mitótico colocándolas en unas condiciones de cultivo adecuadas.Financiación del Proyecto SAF2001-1740; de la Beca del CSIC de Postgrado para la Formación y Especialización en Líneas de Investigación para el Sector Industrial con REF.: I3P-BPG2004 y del Proyecto BFU2004-00125/BMC.Peer reviewe

Structural insight into GRIP1-PDZ6 in Alzheimer’s disease: study from protein expression data to molecular dynamics simulations

<p>Protein–protein interaction domain, PDZ, plays a critical role in efficient synaptic transmission in brain. Dysfunction of synaptic transmission is thought to be the underlying basis of many neuropsychiatric and neurodegenerative disorders including Alzheimer’s disease (AD). In this study, Glutamate Receptor Interacting Protein1 (GRIP1) was identified as one of the most important differentially expressed, topologically significant proteins in the protein–protein interaction network. To date, very few studies have analyzed the detailed structural basis of PDZ-mediated protein interaction of GRIP1. In order to gain better understanding of structural and dynamic basis of these interactions, we employed molecular dynamics (MD) simulations of GRIP1-PDZ6 dimer bound with Liprin-alpha and GRIP1-PDZ6 dimer alone each with 100 ns simulations. The analyses of MD simulations of Liprin-alpha bound GRIP1-PDZ6 dimer show considerable conformational differences than that of peptide-free dimer in terms of SASA, hydrogen bonding patterns, and along principal component 1 (PC1). Our study also furnishes insight into the structural attunement of the PDZ6 domains of Liprin-alpha bound GRIP1 that is attributed by significant shift of the Liprin-alpha recognition helix in the simulated peptide-bound dimer compared to the crystal structure and simulated peptide-free dimer. It is evident that PDZ6 domains of peptide-bound dimer show differential movements along PC1 than that of peptide-free dimers. Thus, Liprin-alpha also serves an important role in conferring conformational changes along the dimeric interface of the peptide-bound dimer. Results reported here provide information that may lead to novel therapeutic approaches in AD.</p

Structural insight into <i>Mycobacterium tuberculosis</i> maltosyl transferase inhibitors: pharmacophore-based virtual screening, docking, and molecular dynamics simulations

<div><p>Pharmacophore-based virtual screening, subsequent docking, and molecular dynamics (MD) simulations have been done to identify potential inhibitors of maltosyl transferase of <i>Mycobacterium tuberculosis</i> (mtb GlgE). Ligand and structure-based pharmacophore models representing its primary binding site (pbs) and unique secondary binding site 2 (sbs2), respectively, were constructed based on the three dimensional structure of mtb GlgE. These pharmacophore models were further used for screening of ZINC and antituberculosis compounds database (ATD). Virtually screened molecules satisfying Lipinski’s rule of five were then analyzed using docking studies and have identified 23 molecules with better binding affinity than its natural substrate, maltose. Four top scoring ligands from ZINC and ATD that either binds to pbs or sbs2 have been subjected to 10 ns each MD simulations and binding free energy calculations. Results of these studies have confirmed stable protein ligand binding. Results reported in the article are likely to be helpful in antitubercular therapeutic development research.</p></div

Brief description of previously unreported disease markers in .

<p>*Topologically significant disease markers.</p><p>Brief description of previously unreported disease markers in .</p

Hubs & bottlenecks in .

<p>Hubs & bottlenecks in .</p

Previously unreported disease markers in .

<p>*Topologically significant disease markers.</p>#<p>disease markers associated with dopamine and other neurotransmitters.</p><p>Previously unreported disease markers in .</p

Construction and Analysis of the Protein-Protein Interaction Networks Based on Gene Expression Profiles of Parkinson's Disease

<div><p>Background</p><p>Parkinson's Disease (PD) is one of the most prevailing neurodegenerative diseases. Improving diagnoses and treatments of this disease is essential, as currently there exists no cure for this disease. Microarray and proteomics data have revealed abnormal expression of several genes and proteins responsible for PD. Nevertheless, few studies have been reported involving PD-specific protein-protein interactions.</p><p>Results</p><p>Microarray based gene expression data and protein-protein interaction (PPI) databases were combined to construct the PPI networks of differentially expressed (DE) genes in post mortem brain tissue samples of patients with Parkinson's disease. Samples were collected from the substantia nigra and the frontal cerebral cortex. From the microarray data, two sets of DE genes were selected by 2-tailed <i>t</i>-tests and Significance Analysis of Microarrays (SAM), run separately to construct two Query-Query PPI (QQPPI) networks. Several topological properties of these networks were studied. Nodes with High Connectivity (hubs) and High Betweenness Low Connectivity (bottlenecks) were identified to be the most significant nodes of the networks. Three and four-cliques were identified in the QQPPI networks. These cliques contain most of the topologically significant nodes of the networks which form core functional modules consisting of tightly knitted sub-networks. Hitherto unreported 37 PD disease markers were identified based on their topological significance in the networks. Of these 37 markers, eight were significantly involved in the core functional modules and showed significant change in co-expression levels. Four (ARRB2, STX1A, TFRC and MARCKS) out of the 37 markers were found to be associated with several neurotransmitters including dopamine.</p><p>Conclusion</p><p>This study represents a novel investigation of the PPI networks for PD, a complex disease. 37 proteins identified in our study can be considered as PD network biomarkers. These network biomarkers may provide as potential therapeutic targets for PD applications development.</p></div

Research methodology.

<p>Research methodology.</p

QQPPI network built from the dataset obtained using SAM (FDR 0.19%) (GeneChip A).

<p>Orange coloured square nodes represent hubs (HC nodes). Yellow coloured triangular nodes represent bottlenecks (bottlenecks). The core functional module containing 3,4-cliques are represented using blue coloured edges. Non-hub non-bottleneck nodes are coloured green if they are directly connected to a hub or a bottleneck, and grey otherwise. Inset: Subset of the QQPPI network containing hubs and bottlenecks only.</p

Previously reported PD-associated disease markers in and .

<p>Previously reported PD-associated disease markers in and .</p