The PACAP specific binding sites which were not shared VIP were termed type I, while the binding sites shared with both PACAP and VIP were termed Type II.
The sequence of this binding site does not resemble any known ATP binding sites, which have much higher binding affinities.
Among many other binding sites lost in the –673 construct were an E-box, a STAT binding site which forms a sequence model (Genomatix modelInspector) together with an ets binding site, and a Myc associated zinc finger binding site (MAZF).
Any binding site which had a p < 0.01 was annotated as a potential miRNA binding site.
When binding to DNA, LysR protein forms a homodimer and targets two specific binding sites, a regulatory binding site, which has the conserved T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAA T-N11-A/TTA-N7/8-GAAig. 2b).
This implies the existence of an optimum binding strength providing maximum flow [5], [10], [11], which depends on particle concentration, width and location, e.g. asymmetry, of the binding site [5], [12].
Furthermore, a 400 bp fragment overlapping with the CTDSP2 5′-UTR, istronglyly activated by expression of FOXO3.A3, which depends on the presence of the two binding sites.
We then use our theoretical model of PMM score distributions to compute the equivalent (theoretical) values Q T (s, b) and C T (s, b), each of which depends on an assumed number of true binding sites, b.
The binding site can accommodate two Mg2+ ions (20, 23, 24), the final coordination of which depends on the bound nucleotide.
Converting to the concentration of free VEGF requires the fraction of free:total VEGF, which depends of the isoform secretion ratio as well as the density of ECM binding sites and the number of VEGF cell surface receptors.
