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Raimondi F.,Dulbecco Telethon Institute | Orozco M.,Barcelona Institute for Research in Biomedicine | Orozco M.,Barcelona Supercomputing Center | Orozco M.,National Institute of Bioinformatics | Fanelli F.,Dulbecco Telethon Institute
Structure | Year: 2010

The evolutionary and physical deformability patterns of members of the Ras GTPase superfamily were investigated by Principal Component and Elastic Network-Normal Mode analyses. The study helped to decipher the dynamics information encrypted into the conserved core and to separate the trans-family intrinsic flexibility associated with a common function from the protein motions related to functional specialization of selected families or family members. The conserved core is dynamically divided into two lobes. The deformation modes, which allow the Ras GTPases to accomplish their switching function, are conserved along evolution and are localized in lobe 1 portions close to the nucleotide. These modes lead to functional specialization when associated with evolution-driven deformations of protein portions essentially located in lobe 2, distal from the nucleotide, and involved in peculiar interactions with membrane, guanine nucleotide exchange factors, or effectors. Overall, a complete picture of the functional and evolutionary dynamics of the Ras superfamily emerges. © 2010 Elsevier Ltd. All rights reserved. Source

Marabini R.,Autonomous University of Madrid | MacIas J.R.,CSIC - National Center for Biotechnology | Vargas J.,CSIC - National Center for Biotechnology | Quintana A.,CSIC - National Center for Biotechnology | And 4 more authors.
Acta Crystallographica Section D: Biological Crystallography | Year: 2013

Electron microscopy is a valuable tool for elucidating the three-dimensional structures of macromolecular complexes. As the field matures and the number of solved structures increases, the existence of infrastructures that keep this information organized and accessible is crucial. At the same time, standards and clearly described conventions facilitate software maintenance, benefit interoperability with other packages and allow data interchange. This work describes three developments promoting integrative biology, standardization and workflow processing, namely PeppeR, the EMX initiative and Scipion. © 2013 International Union of Crystallography Printed in Singapore - all rights reserved. Source

Drsata T.,Czech Institute of Organic Chemistry And Biochemistry | Drsata T.,Academy of Sciences of the Czech Republic | Perez A.,State University of New York at Stony Brook | Orozco M.,Barcelona Supercomputing Center | And 6 more authors.
Journal of Chemical Theory and Computation | Year: 2013

The Dickerson-Drew dodecamer (DD) d[CGCGAATTCGCG]2 is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-μs-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback-Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA. © 2012 American Chemical Society. Source

Emperador A.,Barcelona Institute for Research in Biomedicine | Emperador A.,Barcelona Supercomputing Center | Meyer T.,Barcelona Institute for Research in Biomedicine | Meyer T.,Barcelona Supercomputing Center | And 4 more authors.
Proteins: Structure, Function and Bioinformatics | Year: 2010

We have applied all atoms discrete molecular dynamics (DMD) based on a quasiphysical potential to study the flexibility of an extended set of proteins for which atomistic MD simulations are available. The method uses pure physical potentials supplemented by information on secondary structure and despite its simplicity is able to reproduce with good accuracy the dynamics of proteins in solution. The method presents a clear improvement with respect to coarse-grained methods based on structure potentials and opens the possibility to explore dynamics of proteins out from the equilibrium and to trace conformational changes induced by interaction of proteins with both small and macromolecular ligands. © 2009 Wiley-Liss, Inc. Source

Gonzalez S.,Joint IRB BSC program on Computational Biology | Montserrat-sentis B.,Joint IRB BSC program on Computational Biology | Sanchez F.,Polytechnic University of Catalonia | Puiggros M.,Joint IRB BSC program on Computational Biology | And 5 more authors.
Bioinformatics | Year: 2012

Motivation: The prediction and annotation of the genomic regions involved in gene expression has been largely explored. Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding sites (TFBSs) largely unexplored and with important quantitative and qualitative methodological gaps. Results: We have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith-Waterman algorithm that allows local searches of conserved TFBS clusters and the detection of regulatory regions proximal to genes and enhancer regions. ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively. © The Author(s) 2012. Published by Oxford University Press. Source

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