For the simplicity of computation, the tag density at the position d nt (d < L) from the binding site can be approximated by: Given the modeled tag density profile from a binding site, we adopt a least-squares fitting technique to identify TF binding sites.
To identify DNA sequence motifs of OmpR binding sites, we first used the MEME software tool28 with the genomic sequences of binding sites.
This solvent effect analysis follows the assumption that, e.g. a polar compound in a relatively hydrophobic protein binding site may adopt a collapsed bioactive conformer (self-folded, stabilized by intramolecular interactions), which would be probably more similar to conformers optimized using the octanol or chloroform as solvent.
Molecular modeling and dynamics simulations revealed that the ligand binds in an energetically more stable pose in the FDH binding site, as it adopts a more twisty conformation, compared to the natural coenzyme.
It could be also that: the antigenic peptide presents the ability of eliciting a number of conformationally different antibodies each of them recognizing a particular antigenic conformation; or, a single antibody binding site adopts several conformations, each of them capturing a complementary antigen conformation, among a family of preexisting antigen conformations.
Crystal structures of TcTS indicate active site flexibility, in particular that Tyr119 of the acceptor binding site adopts two different orientations: an orientation of Tyr119 that allows it to stack with the acceptor ligand, described by a χ1 value of approximately −60°, and a downward-pointing orientation of Tyr119, essentially blocking the sialic acid binding site, with a χ1 value of 180°.
An unexpected but in retrospect plausible consequence of the mutagenesis was, that the helix αD region, which is in the direct neighbourhood of the ATP-binding site, has adopted a conformation that is more similar to CAPK and less favourable for binding of GTP.
Moreover, we found that the G-rich HIV-1 sequence with three Sp1 binding sites can adopt alternative configuration G-quadruplexes with different interacting sets of G runs and that antibodies specific to the c-kit2 G-quadruplex recognize two of these forms.
For these regulated genes, we investigated if within the respective promoter regions where putative indirect OCT4 binding activity could be confirmed, one could also detect an enrichment of known transcription factor binding sites by adopting a de novo motif discovery approach.
