to thrombin was correlated quantitatively with partial inhibition of the rate of the thrombin-antithrombin reaction, maximally decreasing the bimolecular rate constants 1.7-and 2.1-fold, respectively. These results support a mechanism in which thrombin and the thrombin-Hir 54 -65 complex can associate with antithrombin and undergo formation of the covalent thrombin-antithrombin complex at modestly different rates, with inactivation of exosite I leading to dissociation of the peptide occurring subsequent to the ratelimiting inactivation of thrombin. This mechanism may function physiologically in localizing the activity of thrombin by allowing inactivation of thrombin that is bound in exosite I-mediated complexes with regulatory proteins, such as thrombomodulin and fibrin, without prior dissociation of these complexes. Concomitant with inactivation of thrombin, the thrombin-antithrombin complex may be irreversibly released due to exosite I inactivation.The activity of the blood clotting enzyme, thrombin, is determined by a balance between proteolytic action on physiological substrates, and irreversible inactivation by the serpin, antithrombin. The substrate specificity of thrombin is regulated by macromolecular effectors which interact with the enzyme at either of two electropositive sites, exosites I and II (1, 2). Exosite I has been defined in crystallographic studies as the site occupied by the extended COOH-terminal sequence of the specific thrombin inhibitor, hirudin (3-5). Exosite II is a distinct site which binds heparin and other ligands (1). Specific binding of COOH-terminal hirudin peptides, particularly N-acetyl-hirudin 53-64 (Hirugen 1 ; Ref. 6), to thrombin has been used to establish an important functional role for exosite I in mediating thrombin interactions. The peptide inhibits thrombin hydrolysis of the substrates, fibrinogen (7), factors V and VIII (8), and activation of the thrombin receptor (9, 10); it dissociates thrombin from regulatory interactions with fibrin I and II (7, 11) and thrombomodulin (12, 13); and it inhibits thrombin inactivation by the serpin, heparin cofactor II (14,15). By contrast to these interactions, the rate of thrombin inactivation by antithrombin is decreased only 1.9-fold by Hirugen (7), contributing to the conclusion that recognition of antithrombin by thrombin does not involve exosite I significantly (7,(15)(16)(17)(18). Binding of regulatory macromolecules to exosite I results in similarly modest effects on the rate of thrombin inactivation by antithrombin. Thrombin binding to fibrin I increases the rate 2. 8-fold (19, 20), while fibrin II reduces the rate 1.6-fold (21). The rate of inactivation of thrombin bound to thrombomodulin is unaffected or decreased ϳ2-fold for thrombomodulin lacking covalently attached chondroitin sulfate (22-25), and increased 2-8-fold for thrombomodulin containing the attached glycosaminoglycan (23)(24)(25)(26)(27).The information available indicates that the catalytic site of thrombin is accessible to antithrombin when the proteinase i...