Taking the middle of ChIP-PET overlap region (i.e., a PET cluster) as the proxy for actual binding site locations, as in [28], we plotted the ratio of the observed distance distribution between binding sites of PPARγ and RXR (Figure 3C) and what would be expected in case of random binding.
Competition for binding will also be expected in cases where the prey is endogenously expressed within the Golgi and capable of competing with the LOC fusion protein for binding to the bait-CAT fusion protein.
Structural independence of binding sites is expected, in particular, for proteins with multiple binding sites located on different protein domains.
More importantly, addition of ATP to the apo-protein results in a decrease in fluorescence emission, as would be expected if nucleotide binding results in an increase in solvent accessibility of the Trp residue in the nucleotide-bound state compared with the apo state.
Deletion mutants that remove residues contributing to the cleft (e.g., Plin2-I) would also be expected to differ in binding interactions and affinity, as was observed with the experimental data demonstrating higher affinity for stearic acid than cholesterol with deletion mutant Plin2-I and decreased affinity for cholesterol when compared to the full-length protein.
Site −13, however, is located in a beta-sheet of the zinc finger domain that plays a significant role in DNA recognition (Dhanasekaran et al. 2006, 2007), and which would be expected to affect binding preferences even in the absence of phylogenic data.
In fact, as might be expected, CTCF-binding divergence generally corresponded with evolutionary distance.
DNA binding was dependent on the size of the DNA fragments used in the assay, suggesting there were multiple sites for binding, as would be expected of a protein binding to DNA in a sequence-independent manner.
In a conformational selection scenario, manipulating the populations of binding-competent states should be expected to affect protein binding.
Such genes would not be expected to contain berenil binding sites in their upstream control regions.
