Although fibrin-bound thrombin is resistant to inactivation by heparin⅐antithrombin and heparin⅐heparin cofactor II complexes, indirect studies in plasma systems suggest that the dermatan sulfate⅐heparin cofactor II complex can inhibit fibrin-bound thrombin. Herein we demonstrate that fibrin monomer produces a 240-fold decrease in the heparin-catalyzed rate of thrombin inhibition by heparin cofactor II but reduces the dermatan sulfate-catalyzed rate only 3-fold. The protection of fibrinbound thrombin from inhibition by heparin⅐heparin cofactor II reflects heparin-mediated bridging of thrombin to fibrin that results in the formation of a ternary heparin⅐thrombin⅐fibrin complex. This complex, formed as a result of three binary interactions (thrombin⅐fibrin, thrombin⅐heparin, and heparin⅐fibrin), limits accessibility of heparin-catalyzed inhibitors to thrombin and induces conformational changes at the active site of the enzyme. In contrast, dermatan sulfate binds to thrombin but does not bind to fibrin. Although a ternary dermatan sulfate⅐ thrombin⅐fibrin complex forms, without dermatan sulfate-mediated bridging of thrombin to fibrin, only two binary interactions exist (thrombin⅐fibrin and thrombin⅐ dermatan sulfate). Consequently, thrombin remains susceptible to inactivation by heparin cofactor II. This study explains why fibrin-bound thrombin is susceptible to inactivation by heparin cofactor II in the presence of dermatan sulfate but not heparin.Heparin, a sulfated polysaccharide, acts as an anticoagulant by accelerating the inhibition of thrombin and factor Xa by antithrombin (1). Although heparin is widely used for the treatment of acute coronary ischemic syndromes, it has limitations in patients undergoing percutaneous coronary interventions (2) or when used as an adjunct to thrombolytic therapy (3-5). These limitations have been attributed to the inability of the antithrombin⅐heparin complex to inactivate clotting enzymes bound to components of the thrombus, particularly thrombin bound to fibrin (6, 7).Resistance of fibrin-bound thrombin to inactivation by the antithrombin⅐heparin complex reflects the incorporation of thrombin into a ternary heparin⅐thrombin⅐fibrin complex (8-10). To form this complex, heparin interacts with both exosite II on thrombin (11-13) and the D domain of fibrin (14), thereby bridging thrombin to fibrin via exosite II (8). This heightens exosite I-mediated binding of thrombin to fibrin and likely increases the overall affinity of thrombin for fibrin. The formation of the ternary complex, therefore, is a consequence of the presence of two exosites on thrombin, which independently bind fibrin and heparin. Recently, we demonstrated that protection requires ligation of both of thrombin's exosites within the ternary heparin⅐thrombin⅐fibrin complex, a process that impairs access of inhibitor-bound heparin to exosite II on thrombin (15). Thrombin within the ternary complex is protected from inactivation by the heparin⅐heparin cofactor II (HCII) 1 complex to a greater extent than the heparin...