The findings are more consistent with a pathway than with a fixed binding site.
The activity of cyclic nucleotide analogs is informative regarding the nature of the binding site and the structural requirements for ligand activity.
We discussed both the classical approach, assuming distributed binding sites in a smeared layer and a one-binding-site model.
Most lipocalins are beta-barrel structures with only one binding site for hydrophobic molecules.
Once assembled, the terminal regions are folded to become the binding site for the next subunits.
The nucleotide binding site is located in a pocket between the two domains.
This analysis should quantitatively reflect the free energy surface sampled by the ligand as it is pulled through the binding site.
More experiments investigating the nucleoside specificity of this binding site is under progression in our laboratory.
