Subsequent studies established a descriptor of STAT1 binding preferences with an improved specificity by defining a position-specific weight matrix (PWM) derived from the in vitro binding of STAT1 to synthetic oligonucleotides [14].
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.
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.
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.
With the assumption that the binding preference of a TF is the same to all its binding sites, we estimated the binding preference of each TF with the following heuristic.
In vitro site selection and electrophoretic mobility shift assays (EMSAs) showed that Drosophila Stat has a binding preference for sites with 3 n spacing (Yan et al, 1996).
Instead, it showed a strong binding preference for sialic acids with α2,6 linkages, with minimal binding to sialic acids with α2,3 linkages.
