32791 20171130135647.0 doi 10.1371/journal.pcbi.1003835 sideral 89224 ART-2014-89224 eng (orcid)0000-0001-5072-0645 Tapia-Rojo, R. Universidad de Zaragoza Mesoscopic Model and Free Energy Landscape for Protein-DNA Binding Sites: Analysis of Cyanobacterial Promoters 2014 Access copy available to the general public Unrestricted The identification of protein binding sites in promoter sequences is a key problem to understand and control regulation in biochemistry and biotechnological processes. We use a computational method to analyze promoters from a given genome. Our approach is based on a physical model at the mesoscopic level of protein-DNA interaction based on the influence of DNA local conformation on the dynamics of a general particle along the chain. Following the proposed model, the joined dynamics of the protein particle and the DNA portion of interest, only characterized by its base pair sequence, is simulated. The simulation output is analyzed by generating and analyzing the Free Energy Landscape of the system. In order to prove the capacity of prediction of our computational method we have analyzed nine promoters of Anabaena PCC 7120. We are able to identify the transcription starting site of each of the promoters as the most populated macrostate in the dynamics. The developed procedure allows also to characterize promoter macrostates in terms of thermo-statistical magnitudes (free energy and entropy), with valuable biological implications. Our results agree with independent previous experimental results. Thus, our methods appear as a powerful complementary tool for identifying protein binding sites in promoter sequences. info:eu-repo/grantAgreement/ES/MINECO/FIS2011-25167 info:eu-repo/grantAgreement/ES/MINECO/BFU2012-31458 info:eu-repo/grantAgreement/ES/MICINN/BFU2009-07424 info:eu-repo/grantAgreement/ES/DGA/E19 info:eu-repo/grantAgreement/ES/DGA/B18 info:eu-repo/semantics/openAccess by http://creativecommons.org/licenses/by/3.0/es/ 4.62 2014 MATHEMATICAL & COMPUTATIONAL BIOLOGY 4 / 57 = 0.07 2014 Q1 T1 BIOCHEMICAL RESEARCH METHODS 11 / 79 = 0.139 2014 Q1 T1 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion (orcid)0000-0003-0698-6555 Mazo, J.J. Universidad de Zaragoza Hernández, J.Á. (orcid)0000-0002-2742-3711 Peleato, M.L. Universidad de Zaragoza (orcid)0000-0001-8644-4574 Fillat, M.F. Universidad de Zaragoza (orcid)0000-0002-9551-624X Falo, F. Universidad de Zaragoza 2003 395 Universidad de Zaragoza Departamento de Física de la Materia Condensada Física de la Materia Condensada 1002 060 Universidad de Zaragoza Departamento de Bioquímica y Biología Molecular y Celular Bioquímica y Biología Molecular 1002 412 Universidad de Zaragoza Departamento de Bioquímica y Biología Molecular y Celular Fisiología Vegetal 10, 10 (2014), e100383 [10 p.] PLoS Comput. Biol. PLoS Computational Biology 1553-734X 2003825 http://zaguan.unizar.es/record/32791/files/texto_completo.pdf Versión publicada 118923 http://zaguan.unizar.es/record/32791/files/texto_completo.jpg?subformat=icon icon Versión publicada oai:zaguan.unizar.es:32791 articulos driver 2017-11-30-13:53:35 ARTICLE