Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics
Figure 3
Correlation between Fis binding affinity and the generalized opening profile.
(A) The MCMC average opening profiles (vertical axis in [Å]) of FIS1 and FIS2 as a function of the nucleotide position. The bubble formation region is highlighted in blue while the points-of-contact are highlighted in yellow. (B) Characteristic MCMC opening profile (COP) obtained as the average of the profiles (black squares) of the oligomers with in vitro Fis-DNA binding affinity with KD<1 nM (Table S1). The red line represents a polynomial fit to the data. The bubble formation region is highlighted in blue while the points-of-contact are highlighted in yellow. In panels (A) and (B), the horizontal axes indicate base pair position whereas the vertical axes indicate base pair average displacement (see Materials and Methods). (C) Schematic affinity shape-correlation diagram of the examined in vitro sequences. Each point represents an oligomer with specific direct points-of-contact, correlation with the COP, and measured dissociation constant KD (the data is from Table S1). The Pearson's correlation coefficient (horizontal axis) between the COP and the sequence shape and the KD (vertical logarithmic axis) are the (x, y) coordinates for each oligomer. The red circles depict sequences that violate at least two of the inclusion/exclusion rules while the blue squares correspond to the remaining sequences. The blue ellipse schematically depicts the majority of DNA sequences with good Fis-DNA binding (KD< = 3 nM), and the other two ellipses schematically depict the majority of sequences with low affinity to Fis caused by bad point-of-contacts (pink) or low correlation with COP (green).