were done to characterize their individual contribution to HCII activity. Only Y73K rHCII and D75K rHCII have significantly increased heparin cofactor activity compared with wt-rHCII; however, all of the individual rHCII mutants required substantially less glycosaminoglycan at maximal inhibition than did wt-rHCII. Inhibition of either ␣-thrombin/hirugen or ␥ T -thrombin (both with an altered anion-binding exosite-1) by the AR2 rHCII mutants was similar to wt-rHCII. D72N/Y73F/D75N rHCII and D75K rHCII were significantly more active than wt-rHCII in a plasma-based thrombin inhibition assay with glycosaminoglycans. These results indicate that improved thrombin inhibition in the AR2 HCII mutants is mediated by enhanced interactions between the acidic domain and anion-binding exosite-1 of thrombin and that AR2 may be a "molecular rheostat" to promote thrombin inhibition in the presence of glycosaminoglycans.The serine protease thrombin is a critical component in coagulation, inflammation, and wound healing (1-9). Thrombin activity must be carefully regulated to maintain an appropriate balance within the vasculature. One mechanism of thrombin regulation is by serine protease inhibitors (serpins) 1 such as antithrombin (ATIII) and heparin cofactor II (HCII) (10 -14). Heparin cofactor II and ATIII belong to a sub-class of serpins whose activity is greatly enhanced upon binding to glycosaminoglycans like heparin and heparan sulfate (HCII and ATIII) and dermatan sulfate (HCII) (15-18). These glycosaminoglycans are found in vivo on cell surfaces and in extracellular matrix to support these inhibition reactions (19 -23).Heparin cofactor II has several features for thrombin inhibition and specificity that render it novel among heparin-binding serpins (24 -26). Heparin cofactor II has an atypical Leu 444 reactive center residue, whereas the more typical Arg is found in thrombin inhibitors like ATIII or protein C inhibitor (10, 12, 13). The inhibition of thrombin by HCII is enhanced by both heparin and dermatan sulfate, and the glycosaminoglycan binding site is primarily contained within the D-helix region of HCII (15,(27)(28)(29)(30)(31)(32)(33)(34). Although HCII is ϳ30% identical in sequence to antithrombin and other serpins, it has a unique N-terminal extension of ϳ80 residues that contains a tandem repeat of negatively charged acidic residues (9 Asp, 5 Glu, and 2 Tyrsulfate) (25,26). Interestingly, the acidic domain of HCII is homologous to the C terminus of the leech anticoagulant protein hirudin, which is a potent thrombin inhibitor. Within the acidic domain of HCII, the two regions are designated acidic region 1 (AR1) from residues 49 -62 ( 49 DWIPEGEEDD-DYLD 62 ) and acidic region 2 (AR2) from residues 63-75 ( 63 LE-KIFSEDDDYID 75 ). There is substantial evidence that the acidic domain of HCII is involved in facilitating thrombin inhibition, especially in the presence of glycosaminoglycans (27,29,30). Ragg et al. (29,30) initially examined the role of the acidic domain in HCII by either deleting or neutralizing variou...