Heparin cofactor II (HCII) is a plasma serine protease inhibitor whose ability to inhibit ␣-thrombin is accelerated by a variety of sulfated polysaccharides in addition to heparin and dermatan sulfate. Previous investigations have indicated that calcium spirulan (Ca-SP), a novel sulfated polysaccharide, enhanced the rate of inhibition of ␣-thrombin by HCII. In this study, we investigated the mechanism of the activation of HCII by Ca-SP. Interestingly, in the presence of Ca-SP, an N-terminal deletion mutant of HCII (rHCII-⌬74) inhibited ␣-thrombin, as native recombinant HCII (native rH-CII) did. The second-order rate constant for the inhibition of ␣-thrombin by rHCII-⌬74 was 2.0 ؋ 10 8 M ؊1 min ؊1 in the presence of 50 g/ml Ca-SP and 10,000-fold higher than in the absence of Ca-SP. The rates of native rHCII and rHCII-⌬74 for the inhibition of ␥-thrombin were increased only 80-and 120-fold, respectively. Our results suggested that the anion-binding exosite I of ␣-thrombin was essential for the rapid inhibition reaction by HCII in the presence of Ca-SP and that the N-terminal acidic domain of HCII was not required. Therefore, we proposed a mechanism by which HCII was activated allosterically by Ca-SP and could interact with the anionbinding exosite I of thrombin not through the N-terminal acidic domain of HCII. The Arg 103 3 Leu mutant bound to Ca-SP-Toyopearl with normal affinity and inhibited ␣-thrombin in a manner similar to native rHCII. These results indicate that Arg 103 in HCII molecule is not critical for the interaction with Ca-SP.Thrombin is considered to be the pivotal enzyme in the coagulation pathway (1). Besides its critical role in hemostasis, thrombin elicits cellular responses through the thrombin receptor that may contribute to inflammation, wound healing, and atherosclerosis (2). Heparin cofactor II (HCII) 1 is an important plasma protein that selectively inhibits thrombin (3). A number of sulfated polysaccharides in addition to heparin and dermatan sulfate catalyze HCII to accelerate markedly the reaction of HCII with thrombin (4 -6). Marine algae are a rich source of sulfated polysaccharides with novel structures (7).Calcium spirulan (Ca-SP) is a novel sulfated polysaccharide isolated from a blue-green alga Spirulina platensis by Hayashi et al. (8,9). They reported an inhibitory effect of Ca-SP on the replication of enveloped viruses. We have recently showed that Ca-SP enhances the rate of inhibition of thrombin by HCII and that the molecular conformation maintained by calcium ions is essential to exhibit antithrombin activity (10). However, the mechanism of activation of HCII by Ca-SP has not been clarified. Current evidence suggests that binding of either heparin or dermatan sulfate to HCII displaces the N-terminal acidic domain of the inhibitor, which normally occupies the glycosaminoglycan-binding site. The N-terminal acidic domain then binds to the anion-binding exosite I of thrombin, facilitating proteolytic attack on the reactive site peptide bond of HCII (11). Deletions within the N-te...