Crystal Structures of Apolipoprotein(a) Kringle IV37 Free and Complexed with 6-Aminohexanoic Acid and withp-Aminomethylbenzoic Acid: Existence of Novel and Expected Binding Modes

Abstract

Kringles are protein modules found within a wide variety of fibrinolytic and coagulation-related proteins that show binding affinity for lysine, lysine analogs and for fibrin. We report here the crystal structures of apolipoprotein(a) kringle IV37 (apo(a) K4₃₇) in its free state and in separate complexes with two ω-amino acids, 6-aminohexanoic acid (6AHA) andp-aminomethylbenzoic acid (PAMBA). The structures of the unliganded form and of both complexes have been determined and refined by restrained least-squares methods to about 2.0 Å. The overall kringle architecture is essentially identical with that determined in other kringles but it shows some small significant structural changes in the lysine binding site. There is virtually no difference in conformation between the unliganded and complexed forms, suggesting that apo(a) K4₃₇does not undergo any conformational rearrangement upon binding. The 6AHA molecule binds to apo(a) K4₃₇in a completely different way from that observed with the kringle 4 of plasminogen (PGK4). Its amino group makes an ion pair interaction with the two aspartate residues (Asp55/Asp57) of the anionic center and its carboxylate group faces out into the solvent making water-mediated contacts with the protein. The mode of binding of PAMBA resembles more that described for 6AHA when bound to PGK4. The PAMBA molecule is bound by ion pair interactions with the two aspartate residues (Asp55/Asp57) and with Arg71 from the cationic center and by van der Waals contacts. The relative importance of the cationic center from kringles for binding zwitterionic ligands is discussed.