The unpaired probabilities, the probabilities of not forming pairs, are significantly higher than negative controls and the flanking sequence surrounding the binding site, indicating that SRSF1 proteins tend to bind on single-stranded RNA.
However, this region does not form a part of known antibody binding site indicating that in solution, this region may acquire some conformation that is accessible only to peptide antibodies.
RAB34 contained the putative miR-9 binding site, indicating that it might be one of the targets regulated by miR-9.
Additionally, overexpression of p65 induced activity of the wild-type MMP-9 promoter, but not the promoter reporter with a mutated NF-kappa B binding site, indicating that p65 also plays a role in regulating MMP-9 expression.
Unrestrained docking of the hits discovered here into the 6PG binding site indicated that alternative interactions of the carboxylate group with the area in which the carboxylate group of the substrate binds could also be possible.
Importantly, the essential ERα coactivators AIB1 (also known as SRC3) and p300 were also present at this specific binding site, indicating that ERα is likely to be functional here [ 24].
The largest fluctuation is observed from 425 to 450 residues, because these regions are far away from the binding site, indicating that the flexible amino acids do not affect protein-ligand interaction during MD simulation.
This analysis uncoupled "insulation" (blue) from "preferential contacts" (red) and revealed that preferential contacts are made on one side of the oriented CTCF binding site, indicating that the orientation of the motif likely contributes to directionality of CTCFs long-range interactions.
The widespread distribution of intronic AREs and their particular association with HuR and HuR binding sites indicates that more than half of human genes can be regulated post-transcriptionally by AREs.
