Mesoscopic Model and Free Energy Landscape for Protein-DNA Binding Sites: Analysis of Cyanobacterial Promoters

doi:10.1371/journal.pcbi.1003835

Mesoscopic Model and Free Energy Landscape for Protein-DNA Binding Sites: Analysis of Cyanobacterial Promoters

Figure 3

DNA opening versus protein position.

Base pair mean opening (upper panels) and particle histogram (lower panels) calculated for each of the nine studied promoters. The horizontal axis represent the base pair positions counted from the coding starting point ATG (). We use this criterion to label the binding sites of the simulated promoters. The experimentally identified TSSs are shaded and their exact location marked with solid bars. In every case a peak appears close to each TSS, meaning this region is “softer” and thus likely to form bubbles, supporting their key role in regulatory processes. The total A-T content of Anabaena PCC7120 genome is around [18]. The A-T content of each analyzed sequence is: alr0750 (61%); argC (64%); nifB (68%); conR (57%); furA (66%); furB (65%); petH (62%); petF (63%); ntcA (65%).

doi: https://doi.org/10.1371/journal.pcbi.1003835.g003