STRUCTURE-BASED DESIGN TOOLS - STRUCTURAL AND THERMODYNAMIC COMPARISON WITH BIOTIN OF A SMALL-MOLECULE THAT BINDS TO STREPTAVIDIN WITH MICROMOLAR AFFINITY

A small streptavidin-binding ligand was identified which incorporates some of the binding interactions seen in the crystal structures of str eptavidin-biotin, and of streptavidin complexed with cyclo-Ac-[CHPQFC] -NH2, a cyclic peptide ligand with a K-d of 2.3 x 10(-7) M, discovered by phage display. The crystal structure of streptavidin-glycoluril is described and compared with the crystal structures of streptavidin-bi otin and of streptavidin-cyclo-Ac-[CHPQFC]-NH2. The K-d of glycoluril for streptavidin was determined by plasmon resonance measurements to b e 2.5 x 10(-6) M. The differences in the affinities of biotin and glyc oluril for streptavidin were related to the differences in the crystal structures of the complexes and to differences in the determined solu bilities of the ligands. Streptavidin-bound glycoluril has structural characteristics of, and makes interactions common to, both bound bioti n and the bound cyclic peptide ligand. Binding of glycoluril and bioti n is mediated by short, medium strength hydrogen bonds involving the u reido oxygen common to the two ligands. Binding of glycoluril is furth er mediated by a short hydrogen bond involving its unique ureido oxyge n. The structural and physicochemical factors responsible for the weak er binding of glyeoluril compared with biotin an discussed.