Similarly to the PDZbase data, we found extensive binding overlap between the PDZs in terms of raw numbers although with a distribution that was mildly shifted towards even more binding overlap between PDZs (Fig. S5).
Indeed, TF co-associations were identified based on ChIP-seq peak-binding overlaps in C. elegans modENCODE studies (Araya et al., 2014), but the underlying sequence recognition mechanisms were not apparent.
More recently, co-crystal structures of EGFR have been solved with three different Nbs, of which two block the movement of EGFR and the third interferes with ligand binding due to an overlap in the binding site [ 48].
These crystal structures clearly show an overlap in the binding of ATP and the aminocoumarin, specifically the binding site of the noviose sugar and the adenine ring of ATP overlap (Fig. 3b).
Docking CTP on CoaE reveals that the there is an overlap in the binding pocket utilized by CTP and DCoA which renders an explanation for the inhibition shown by CTP.
Although there was some overlap in the binding pattern, it was interesting to note that some proteins interacted specifically with the wild-type catalytically suppressed form of MK-STYX, but not the catalytically competent mutant form of the protein.
Similarly, while there is an overlap in the binding partners of EBP50 and NHERF2 in epithelial cells like NHE3, there are also evidences indicating their unique specificity for protein partners and cellular functions [ 14, 35].
On the other hand, the OCT binding sites showed top scores in the BOYER_NANOG data set (blue in Additional file 1, Figure S1A) and conversely, NANOG showed top scores in the BOYER_OCT4 data set (blue in Additional file 1, Figure S1B), indicating, as expected, a significant overlap in the binding sites for these two transcription factors.
Sidney et al. recently reported an extensive overlap in the peptide binding specificity of DP alleles, but peptide binding by Asp84 (DP 1) alleles could clearly be distinguished from Gly84 (DP 2) alleles by a preference for positively charged side-chain residues, notably arginine and lysine.
These binding overlaps are close in size to the binding overlaps expected across biological replicates of genome-wide-binding experiments (>50%) (Bardet et al., 2012).
