The DIO2 locus in humans contains several putative CCCTC-binding factor (CTCF) binding sites, including one that is overlapping with the rs225014 location.
The new helix forms many complimentary interactions with the rest of the protein and re-models the original electrophilic substrate-binding site towards one that is more enclosed, albeit flexible.
If a program is known to give satisfactory results for protein binding sites similar to the one that is targeted, it may be used alone, but if no such information is available, the performance of the programs would be unpredictable.
Together, these results indicate that PABPC1 has two binding sites for GW182 proteins: one that is contributed by the RRM1 domain and another by the MLLE domain.
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With CH58, a network of structural changes involving such mutations acted to configure the conformation of LCDR3 from one that would only tolerate antigen binding to one that was optimal for it.
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It is intriguing that the hydrophobic core residues for which we observe the repacking upon ligand binding include the ones that were previously identified to be part of the hydrophobic cluster that constitutes the allosteric network in KIX.
This is again emphasized through Figs. 3c and 4c which marks only residues that are part of the binding site, and among these, the ones that are predicted to be involved in functional divergence are marked in red, suggesting that quite a few residues that are forming the cavity can be statistically predicted to be contributing to functional divergence.
P-values for two SNPs, both from the same locus (AY108077, in IBM2 Bin 6.04, with similarity to a calmodulin-binding heat-shock protein), were the only ones that were significant using a Bonferroni-corrected critical value of 0.05/847 = 0.000059.
