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Mesoscopic model and free energy landscape for protein-DNA binding sites: Analysis of cyanobacterial promoters

AutorTapia-Rojo, R.; Mazo, J. J.; Hernández, José A.; Peleato, María Luisa; Fillat, María F.; Falo, Fernando
Fecha de publicación2014
EditorPublic Library of Science
CitaciónPLoS Computational Biology 10(10): e1003835 (2014)
ResumenThe 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.
DescripciónThis is an open-access article distributed under the terms of the Creative Commons Attribution License.
Versión del editorhttp://dx.doi.org/10.1371/journal.pcbi.1003835
URIhttp://hdl.handle.net/10261/120588
DOI10.1371/journal.pcbi.1003835
Identificadoresdoi: 10.1371/journal.pcbi.1003835
issn: 1553-734X
e-issn: 1553-7358
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