Heparin and dermatan sulfate activate heparin cofactor II (HCII) comparably, presumably by liberating the amino terminus of HCII to bind to exosite I of thrombin. To explore this model of activation, we systematically substituted basic residues in the glycosaminoglycanbinding domain of HCII with neutral amino acids and measured the rates of thrombin inactivation by the mutants. Mutant , demonstrated a ϳ130-fold increased rate of thrombin inactivation that was unaffected by the presence of glycosaminoglycans. The increased rate reflects displacement of the amino terminus of mutant D because (a) mutant D inactivates ␥-thrombin at a 65-fold slower rate than ␣-thrombin, (b) hirudin-(54 -65) decreases the rate of thrombin inactivation, and (c) deletion of the amino terminus of mutant D reduces the rate of thrombin inactivation ϳ100-fold. We also examined the contribution of glycosaminoglycan-mediated bridging of thrombin to HCII to the inhibitory process. Whereas activation of HCII by heparin was chain-length dependent, stimulation by dermatan sulfate was not, suggesting that dermatan sulfate does not utilize a template mechanism to accelerate the inhibitory process. Fluorescence spectroscopy revealed that dermatan sulfate evokes greater conformational changes in HCII than heparin, suggesting that dermatan sulfate stimulates HCII by producing more effective displacement of the amino terminus.Heparin cofactor II (HCII), 1 a serpin found in human plasma at a concentration of 1.2 M, selectively inactivates thrombin in a reaction that is accelerated Ͼ1000-fold by glycosaminoglycans (GAGs) such as heparin, dermatan sulfate, and heparan sulfate (1). A second serpin, antithrombin (AT), also inactivates thrombin but differs from HCII in four important ways. First, whereas HCII only inactivates thrombin, AT inactivates other coagulation enzymes including factors Xa and IXa (2). Second, the high affinity interaction of heparin with AT is mediated by a unique pentasaccharide sequence found only in a subpopulation of heparin molecules (3-5). In contrast, heparin does not possess a high affinity sequence for HCII (6). Furthermore, dermatan sulfate (DS), a GAG found in the extracellular matrix of connective tissue (7, 8), activates HCII, but has no effect on AT (1). Third, the uncatalyzed rate of thrombin inactivation by AT is about 10-fold faster than that for HCII, probably reflecting differences in the amino acid residue at their P-1 position, with AT containing an Arg residue and HCII a Leu (9). Fourth, HCII possesses a unique 75-amino acid domain at its amino terminus that binds to thrombin exosite I, an interaction analogous to the binding of the carboxyl terminus of hirudin to exosite I (1).Although the uncatalyzed rate of thrombin inactivation by HCII is slower than that for AT, in the presence of heparin or DS, HCII inactivates thrombin at a rate similar to that at which AT inactivates thrombin when heparin is present (1, 10). The current model to explain GAG-mediated catalysis of HCII inactivation of thrombin suggests ...