Dermatan sulfate and heparin can be fractionated by affinity for heparin cofactor II.

Commercial preparations of dermatan sulfate and heparin were applied to a concanavalin A-agarose to which heparin cofactor II had been noncovalently bound. Small amounts of both mucopolysaccharides bound to the column with relatively high affinity. Heparin and dermatan sulfate which were eluted from the affinity column catalyzed the inhibition of thrombin by heparin cofactor II to a greater degree than did the respective unfractionated mucopolysaccharides. Dermatan sulfate did not catalyze thrombin inhibition by antithrombin III. The results suggest that heparin cofactor II differs from antithrombin III with respect to the mucopolysaccharide binding site.