Crystallographic analysis of the pH-dependent binding of iminobiotin by streptavidin

Streptavidin binds 2'-iminobiotin in a pH-dependent fashion-affinity decreases as the pH is lowered. This property makes the purification of compounds conjugated to streptavidin or iminobiotin possible under mild conditions by affinity chromatography. In order to understand the molecular details of this pH-dependent binding, we analyzed the crystal structures of the complex of core streptavidin with 2'-iminobiotin at pH values 4.0 and 7.5. The two structures are very similar to each other even at their binding sites. Although the relative abundance of the protonated species of the ligand is increased more than 3,000-fold on going from pH 7.5 to pH 4.0, both structures contain only the nonprotonated form of the ligand. Streptavidin selects the nonprotonated form, which, at pH 4.0, is one part in 7.9 X 10(7).