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The flu virus mutations known to resist antiviral drugs appear to occur in an altogether different binding site than the one Dadon and his colleagues discovered.
Competition binding assays with b12 also showed that b121a/2a sera contained significantly higher amounts of antibodies directed toward the CD4 binding site than the gp120 sera.
A reasonable interpretation of this result is that the TMAO stabilizes a conformational ensemble that more closely approximates that of the wild-type enzyme, providing a more substrate-accommodating binding site than the structure with an unfolded LD.
Although such a change could mean that the mutant is more solvated in the pterin binding site than the wild type, it could also be taken as an indication that more ordered water molecules have been expelled from the local environment of the Glu side chain to accommodate BH4 binding.
Interestingly, one of the putative binding site (TAC) is more similar to the consensus binding site than the other (TTT) and increasing evidence indicates that individual Nkx factors are critical regulators of whole organ development [ 40], suggesting a putative role of these regions in development.
The EMSA assay was also inconclusive: one out of the three functional sites determined by luciferase assay showed no evidence of binding of a nuclear protein, which may be due to a the protein requiring a longer binding site than the probe provided, or non-physiological binding conditions.
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Bio-Rad™ AG2-X8, anion-exchangenge resin with weaker binding sites than the AG1-X8 resis, is better suited for polythionate extraction.
Another difference is that the zebrafish promoter had more putative ER binding sites than the human one, while it only had one NF-κB located in the −2321 pb position versus two in the human promoter.
The 3′ UTRs have more binding sites than the 5′ UTRs across all four species.
However, the distantly related species contained significant fewer binding sites than the sensu strictu Saccharomyces species (35% vs. 56%, P < 0.001, Mann–Whitney U test).
In particular, the optimal bandwidth of 100 bp was more accurate in locating constitutive binding sites than the optimal bin width of 400 bp.
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