Additional studies will be required to demonstrate that OST1 can phosphorylate suboptimal sites in vivo.
These results indicate that while OST1 preferentially phosphorylates LXRXX(S/T) motifs in ABF3 in vitro, it is also able to phosphorylate suboptimal sites.
First, MeCP2 favors certain binding sites in vitro [32], but changing the ratio of protein, probe, and non-specific competitor can easily reveal binding to suboptimal sites; placing multiple CpGs on a probe also easily overrides the sequence specificity.
FASTH uses a fast heuristic (i.e. not dynamic programming) for the database search, with search time scaling sub-linearly with database size; it can return a user-specified number (hundreds or thousands) of suboptimal sites, and process multiple databases with rigorous minimum free-energy calculations, in a single search.
Phosphorylation of suboptimal sites by a kinase presented with a substrate bound through a secondary binding site is reminiscent of phosphorylation in trans of non-consensus sites within activation segments (Oliver et al, 2007; Wu et al, 2008).
There are several mechanisms that could explain this, including PPARγ binding to suboptimal sites with the help of C/EBPα, indirect binding by tethering to C/EBPα, and indirect binding via long range chromosomal loops [ 34, 35].
We conclude that H-NS-stimulated pausing on bridged filaments increases the kinetic window for Rho action (Jin et al., 1992), and the apparent preferential effect of Rho on backtrack pauses may allow Rho to terminate at otherwise suboptimal sites.
Besides targeting immunologically suboptimal sites, conventional needle-based approaches potentially lead to needle-stick injuries as well as intentional reuse, which is responsible for transmission of blood-borne diseases, such as hepatitis and HIV [36].
This discrepancy in the gel shift assays is explained by the use of the very high concentrations of pure PTB and the high protein:RNA ratio used to measure stoichiometry by gel shifts, under which conditions and in the absence of competing or accessory nuclear proteins the protein may bind to suboptimal sites.
In conclusion, animal experiments show that gonadotrophin stimulation of a recipient or donor initiated at a reasonable time before and continued to suboptimal sites after grafting could have a positive effect on the viable growth follicle rate, but the impact on the long-term ovarian function and fertility of such treatment must be further investigated.
