Interactions Between The Functional Domains of Antithrombin III

Antithrombin III is the major physiologic inhibitor of the activated serine proteases of the blood coagulation cascade1. Inactivation of the proteases occurs following cleavage of the Arg393-Ser394 peptide bond and formation of a stable complex between this reactive site arginine of antithrombin III and the active site serine of the protease2. Antithrombin III is a member of a superfamily of protease inhibitors3 designated as serine protease inhibitors or “serpins”4. Although all of the members of the serpin family exhibit a high degree of amino acid sequence homology, particularly in the C-terminal portions of the molecules which contain the reactive site residues, the specificities of these inhibitors vary widely5–8. Furthermore, with antithrombin III the relative rates of complex formation with different proteases, for example, thrombin, Factor Xa, Factor IXa, Factor VIIa, are significantly different despite the fact that each of these enzymes displays selectivity for cleavage at arginine side chains. At present, it is not clear what structural features, in addition to the amino acid sequence at the p1 and p1’ positions, determine the kinetics of protease-inhibitor docking and the stability of the resulting complex. However, a variety of approaches, including site-directed mutagenesis, antibody mapping and protein crystallography, are being used to explore these questions.