Each ligand has a specific binding preference with an ErbB subtype; for instance, EGF has high affinity to ErbB1, HB-EGF interacts with ErbB1 and ErbB4, and NRG1 binds to ErbB3 and ErbB4.
The five pro-survival proteins Bcl-xL, Mcl-1, Bcl-2, Bcl-w and Bfl-1 differ in their binding preferences, with Bcl-xL, Bcl-2 and Bcl-w sharing similar interaction profiles for many natural sensitizers and small molecules.
Here we report that the fungal SREBPs diversified their DNA binding preferences concomitantly with an expansion in function.
It is likely, therefore, that the composition of pre-mRNP is the result of competition among proteins with overlapping binding preferences, each with a range of affinities for different sequences (Abdul-Manan and Williams, 1996) and sometimes able to bind cooperatively.
Our results indicate that the ancestral STAT protein had the capacity to bind to 3 n and 4 n sites and that specific STAT binding preferences evolved with the radiation of the vertebrate STAT family.
We further examined the histone binding preferences of UHRF1-GFP with an in vitro histone tail binding assay.
We constructed the binding preference of each TF with a simple heuristic which assesses the binding preference for a TF from a set of known binding sites.
Seven of the factors (CTCF, E2F4, E2F6, GABP, Max, c-Fos, and c-Myc) are Pol II factors with specific DNA binding preferences, one (TAF1) is a basal Pol II factor, four (BDP1, BRF1, BRF2, and TFIIIC-110) are general Pol III factors, and one (RPC155) is a Pol III subunit that is enriched at Pol III transcription start sites and has strongly correlated peak heights between K562 and HeLa-S3 [ 35].
In the TF target gene prediction analysis, the raw DNA duplex destabilization energies were converted into probability values using a Bayesian transformation method, and each TF's binding preference is predicted with a heuristic method (see Section 2 for details).
Therefore, the Unc45bFlag/Hsp90 complex has a binding preference consistent with molecular chaperone activity.
