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| Xavier Daura, University of Barcelona |
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| Xavier Daura studied Biological Sciences at the Universitat Autònoma de Barcelona (UAB). In 1996, he obtained a Doctor degree in Biological Sciences by the same university for work performed on the simulation and modelling of metallo-carboxypeptidases and their peptide inhibitors, under the supervision of Profs. F. Xavier Avilés and Enrique Querol. He then moved to the Laboratorium für Physikalische Chemie of ETH Zürich, where he joined the group for Informatikgestützte Chemie led by Prof. Wilfred F. van Gunsteren. During his 6-year postdoctoral stay at ETH he worked, primarily, on the study of peptide folding by molecular-dynamics simulation. In 2002 he was appointed Research Professor by the Catalan Institution for Research and Advanced Studies (ICREA) and took this position to the Institute of Biotechnology and Biomedicine (IBB) of the UAB, where he currently leads a group on Computational Biology. Current research interests of his group include the study of peptide folding and aggregation by molecular-dynamics simulation and the modelling of protein-peptide interactions and protein segments. Since December 2004 he is vice-director of the IBB.
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Aspects of beta-peptide folding from molecular-dynamics simulation
Xavier Daura, Catalan Institution for Research and Advanced Studies(ICREA) and Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona, E-08193 Bellaterra (Barcelona), Spain
Due mostly to work from the groups of D. Seebach at ETH Zürich and S.H. Gellman at University of Wisconsin, there is now considerable knowledge on the chemistry and "biology" - the possible biomedical and biotechnological applications - of beta-peptides. Since 1997, stimulated by D. Seebach and co-workers, we have been working on several aspects of beta-peptide structure and dynamics, including folding thermodynamics and kinetics. My presentation will be centred around two such aspects, which we have been recently investigating. The first one refers to the accessible conformational spaces of two beta-peptides in methanol at different temperatures, which we have analysed in terms of network theory. Here, the populated conformational states are determined by clustering peptide structures sampled at regular time intervals during the simulation. Each conformational state represents, thereafter, a node in the graph -network-. Links between nodes correspond to bidirectional transitions between conformational states -clusters- sampled during the simulation. Comparison of the resulting graphs to theoretical models gives us information on the properties of the conformational free-enthalpy landscape of the peptides. The second one refers to the energetics of one of these two peptides, which we have analysed using classical-thermodynamics formulae that relate free-enthalpy and entropy differences over a temperature range to enthalpies and heat capacities at constant pressure. Two of the conclusions from this work were unexpected.
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