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

ABSTRACT: 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 nin

SUBMITTER: Tapia-Rojo R 

PROVIDER: S-EPMC4183373 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature