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Deviation in amino acid composition between AChBP and nicotinic receptors, particularly in the complementary face of the binding site, are likely causes for the observed SAR differences.
In addition, the steric and electrostatic properties of the binding site are likely to play a key role in the placement of the thioester moiety in register with the catalytic residues, as required for productive substrate binding, a determinant of turnover rate (kcat).
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Notably, as shown above, "c-Jun bind 1" bound the mtDNA stronger as compared with "c-Jun bind 2" (fig. 3), thus suggesting that the stronger binding site is likely more functionally important than is the weaker site.
This binding site is likely to be an integral membrane protein because (a) it is enriched in the sodium hydroxide-extracted membranes stripped of most of their peripheral membrane proteins, and (b) the binding site is partially extracted by 0.5% Triton X-100.
The predicted ligand binding site is likely to be in the very end of the C-terminal portion.
Considering that the orientation of the lipid within the CD1d binding site is likely to affect the positioning of the head group, these data suggest the surprising possibility that a single type of phospholipid might present two different epitopes for TCR recognition depending on the orientation of binding within the CD1d groove.
Effects of SNPs in the binding site is likely not simple.
The effects of SNPs in the binding site is likely not simple.
Author's Response The role of the putative second NADPH binding site is likely to activate the enzyme.
The ratio of P-values of affinity scores between two alleles can then be used to determine if the TF binding site is likely to be disrupted.
Hence, the S1′ binding site is likely to consist of residues Ser 14, Val 31, and Gly 137 and the catalytic residue Cys 139.
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