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In an interesting parallel, however, the hsa-mir-148a has been proposed to bind HLA-C 3′UTR, and a polymorphism in the binding site for this miRNA, which increase the binding strength, has been associated with poor HIV-1 infection control (see the following section).
Enantiomeric 3- 3-hydroxyphenyl pyrrolidine analogues were also prepared in order to test the chirality preference of the orthosteric binding site for this scaffold.
rpL5 forms part of the ribosome binding site for this factor [13].
This increase in NRF-1 correlated with increased expression of genes with a binding site for this transcription factor (Supplemental Figure S3).
A consensus sequence corresponding to a LacI-family operator motif [44] could not be detected in the 5' upstream region of the genes regulated by Lmo2128, so the binding site for this regulator has yet to be identified.
We estimated the importance of each transcription factor by calculating the number of differentially regulated genes within each network that contained a putative binding site for this transcription factor.
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The crystal structure of M. tuberculosis DHFR revealed a glycerol tightly bound close to the binding site for the substrate dihydrofolate; this glycerol-binding motif is absent from the human enzyme.
In complement to these analyses, we also observed that the PDRE consensus was present in 11 out of 14 promoters of regulated genes from three different data sets (Figure S4) and thus highlights the relevance of this binding site for the regulation of these genes.
A recent study focusing on a secondary DNA structure near the gene Hoxb9 revealed that a DNA secondary structure functions as an important binding site for the protein FBXL10 and this structure is conserved between human and mouse [ 30].
Taken together, these results indicate that a functional M6P-binding site in domain 3 is important for the capacity of M6P/IGF2R to decrease anchorage-independent growth of SCC-VII cells, thus providing further evidence for the pivotal importance of this binding site for the cellular activities of the receptor.
It is likely that protein-protein interaction with E2F factors reduces the requirement for the presence of a high-affinity binding site for the recruitment of CUX1 on this class of genes.
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