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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.
Favorable positions of functional groups in a binding site can be found and even novel minima, which are not present in the fixed structure.
These regions have been classified by the strength with which water is bound and the nature of the binding site.
As documented above, one is where the short motifs overlap and combine to perform a single binding site.
This is a strong argument for a binding site outside the pore.
The charges are shown arranged nonspecifically to emphasize that such a mechanism is not dependent upon the existence of a specific binding site or pocket.
Residues outside the binding site are represented by surface plot.
A binding site identified by these assays, however, does not necessarily represent a functional target in vivo.
