Thursday, 2nd June, 2011, 11:00-12:00
Simulations of the conformational equilibrium of macromolecules typically reveal a complex network of conformational states and transition rates between the states. In contrast, experimental results, such as dynamical fingerprints of macromolecules, often seem to indicate two- or three state kinetics. Markov state models, which are an efficient method to capture and summarize the information obtained from molecular simulation, can be used to predict these dynamical fingerprints and to reconcile experiment with simulation. In the first part of the lecture, I will given an overview of how to extract metastable states and dominant pathways from a given Markov model. Then, I will use a four-state model of a protein folding equilibrium to illustrate how dynamical fingerprints can be predicted from a given Markov model. From the equations of this method it becomes evident that (i) there might be no process which corresponds to the common notion of folding; (ii) often the experiment will be insensitive to some of the processes present in the system. These effects cause the difference in complexity between experimental and simulation results. Lastly, it is not only possible to predict dynamical fingerprints, but one can also use Markov models to design experiments to selectively measure specific processes. This will be demonstrated for a fluorescence quenching experiment of the MR121-G9-W peptide.
Speaker: Dr. Bettina Keller (Computational Molecular Biology, Freie Universität Berlin, Germany)
Room Seminar Room “Xipre” 173.06 (PRBB – 1st Floor)
Wednesday, 25th May, 2011, 11:00
Speaker: Eduardo Eyras - Computational Genomics, UPF
Room 473.10 PRBB
Monday, 23th May, 2011, 15:30
Speaker: Dr. Jordi Villà i Freixa
Room Sala d’actes, planta baixa, Àrea General HUVH
Monday, 23th May, 2011, 10:00 - 14:00
En el marc de la Plataforma Tecnológica Española de Medicamentos Innovadores, copresidida per Ferran Sanz, director del Programa de Recerca en Informàtica Biomèdica de l'IMIM (Institut de Recerca Hospital del Mar), s'organitza el proper 24 de maig a l'Auditori del Parc de Recerca Biomèdica de Barcelona (PRBB), una Jornada sobre patents en l'àmbit de la biomedicina. Aquesta jornada està dirigida pel professor Pascual Segura, agent de la propietat industrial de la Universitat de Barcelona i director del seu centre de patents. L'objectiu de la Jornada és explicar la importància dels drets de propietat industrial, què es pot patentar i sota quines condicions, entre molts altres temes. La inscripció que és gratuïta podeu realitzar-la clicant aquí.
Speaker: Pascual Segura - Universitat de Barcelona
Room Auditori del PRBB
Thursday, 5th May, 2011, 11:00
We investigated the use of next generation sequencing data, from the 1000 Genomes Pilot Projects, to quantify microsatellite variability in the human population and discover putative new loci involved in trinucleotide repeat expansion diseases.
We analysed microsatellites phylogenetic conservation to learn about the role of selection in shaping microsatellite evolution. The first study concluded that in vertebrate lineages amino acid tandem repeats were more conserved than similar sequences located in non-coding regions. This lead us to the conclusion that evolution was preserving repeats in protein-coding regions. In a second stage we analzed the conservation of microsatellites in different genomic regions, comparing them with the conservation of microsatellite in intergenic region. We concluded that selection was not preserving microsatellites only in exons but also in other genomic regions.
Room room Josep Marull, Dr. Aiguader 80.
Wednesday, 4th May, 2011, 11:00 AM
A revolution is taking place in the study of gene regulation: High-throughput sequencing has become the basis of various techniques, like ChIP-Seq, RNA-Seq, CLIP-Seq, and new techniques evolve constantly. But do we need a new specialized tool to analyze each data type? Not necessarily! We propose Pyicos (http://sourceforge.net/projects/pyicos/), a generic tool that can adapt to various data types, by providing operations that are typically required for their manipulation and analysis. Pyicos is open-source and its input are genomic positions obtained from the mapper of choice. We show the high accuracy of Pyicos by comparing it to methods, specifically designed for the analysis of ChIP-Seq, RNA-Seq or CLIP-Seq data. With its flexibility and suitability for integration, Pyicos provides a convenient basis for the study of gene regulation.
Speaker: Sonja Althammer - Biomedical Informatics, UPF
Room 473.10_Aula
Thursday, 28th April, 2011, 11:00-12:00
Speaker: Prof. Salvador Ventura - Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona
Room Room Xipre 173.06 (PRBB – 1st Floor)
Thursday, 14th April, 2011, 11:00-12:00
A detailed understanding of the biological function of macromolecules requires knowledge of both, their three dimensional structure and their time-dependent fluctuations. Methods to determine the structure of proteins are now well established and the static representations that they provide have contributed much to our understanding of the stability and biological function of proteins (structure-function relationship). In contrast, the characterization of structural fluctuations at atomic resolution is still in its infancy, particularly for motions taking place at biologically relevant time scales (dynamics-function relationship). Such information can be derived from residual dipolar couplings (RDCs) measured by nuclear magnetic resonance (NMR). In this communication we present the determination of native ensembles for globular, multi-domain and disordered proteins that explicitly represent their structural heterogeneity in the sub-millisecond time scale. The detailed descriptions of macromolecular dynamics achieved have allowed us to characterize: i) the transfer of structural information across a surface patch in ubiquitin involved in molecular recognition by the proteins that regulate protein degradation [1], ii) the role of inter-domain motions of T4 Lysozyme in enzymatic catalysis [2], and iii) the native (residual) contacts in chemically denatured ubiquitin that initiate the folding of this protein [3].
Speaker: XAVIER SALVATELLA - Laboratory of Molecular Biophysics, Institute for Research in Biomedicine.
Room Room 473.10 (PRBB - 4th Floor)
Wednesday, 13th April, 2011, Thu, Apr 14, 2011 11:00 AM - Thu, Apr 14, 2011 12:00 PM
Speaker: Larry Stanton - Deputy director of GIS Singapore
Room 473.10 PRBB
Wednesday, 6th April, 2011, Thu, Apr 7, 2011 11:00 AM - Thu, Apr 7, 2011 12:00 PM
Speaker: Sonja Hänzelmann - Functional Genomics. Biomedical Informatics, UPF
Room 473.10 PRBB