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On the other hand, care has to be taken for large binding sites in which different parts can be occupied by ligands.
The proteins often had binding sites in which multiple interactions can be formed with target molecules by high specific affinities or catalysis activities.
We note that the involvement of miR-15 miRNAs in the elastin feedback loop was not predicted in previous studies [35], [52], and indeed could not have been anticipated based on predictions of miRNA binding sites in which only the 3' UTR is considered.
Or, we may have failed to identify additional binding sites, in which case the sites we mutated may be functional but not essential, due to the presence of other, redundant sites for the same TFs.
The worst scenario will occur when weak binding sites have completely opposite supporting data distribution compared to that of strong binding sites, in which case the fitted regression model will predict against the weak binding sites.
A QuikChange II mutagenesis kit (Agilent Technologies, Santa Clara, CA) was used to produce the mutant with altered binding sites, in which both NRF-2 binding sites have a mutation of CCGGAA to CCTTAA (Virbasius et al., 1993).
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The second region is the PPant binding site, in which the backbone N-H groups of Ala145 and Gly184 in monomer B form hydrogen bonds to the carbonyl oxygen atom of the β-alanine component of PPant.
Instead we have postulated that in the primary repertoire, all or most antigen receptors have a bipartite binding site, in which diverse CDR3 loops act as a highly antigen specific 'core' whereas other CDRs bind in a largely opportunistic fashion.
Here, we demonstrate that the insulin-induced inhibition of GSK3 and its unique substrate specificity are explained by the existence of a phosphate binding site in which Arg-96 is critical.
This conclusion might explain the functionality of several ABC transporters with one degenerate nucleotide binding site, in which the ATP binding capability of both sites is preserved but hydrolytic activity is present in only one of the sites.
In the neuronal culture experiments, we actually used a milder mutant for the third binding site, in which only two of the hydrophobic residues in repeats 11 and 12 were changed to Gln (LF to Q).
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