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Bioinformatic analysis of the entire −989/−318 region revealed the existence of four putative binding sites that could be recognized by the ApiAP2 protein PB000252.02.0, based on homology with the P. falciparum protein PF11_0404.
Although earlier studies [24], [25] have shown some specific effects of TNFα on HepG2 cells, our results demonstrate a wholesome analysis of TNFα effect on HepG2 cells that correlates the altered transcriptome profile with identification of conserved transcription factor binding sites that could determine several hepatic pathological states.
Although that study did not attempt to determine the presence of genomic TR binding sites that could potentially regulate the expression of these genes, the results suggest that the pattern of response of GTF3c1 expression in the cerebella of TH-manipulated animals may not be uncommon for TH regulated genes.
Since the underlying cause of this induction is proposed to be linked to a transcriptional mechanism [13] [17], we cloned a proximal sequence of the PGC-1α promoter and analyzed this fragment with stringent computer-assisted analyses to identify candidate transcription factor binding sites that could mediate the AICAR effect.
Only binding sites that could be uniquely mapped both ways were considered for the rest of the analyses.
We collected the information about 46659 protein ligand binding sites, that could overlap between structures of one protein.
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This gives us an idea about the nature of the binding site that could be an important input for 3D pharmacophore design.
The DNA region we refer to as island 4 is positioned next to an estrogen responsive element (ERE) binding site that could be involved in breast cancer.
The significance of this tight clustering is unclear at present, as these aa's have not been associated with known interactions, but this could form a new unidentified binding site that could have a critical role in telomere protection.
Endothelin 2 (EDN2) is another example for a gene with a putative promoter HIF1 binding site that could be involved in the differential expression of genes in the CoCl2 treatment.
Furthermore, in simulations of substrate-free LeuT with bound Na+, and in corresponding EPR studies, the presence of Na+ was observed to increase the accessibility of the binding site that could aid substrate binding, thus suggesting the possible order of binding of ions and substrate.
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binding pockets that could
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binding targets that could
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