The critical and multiple roles of thrombin in blood coagulation are regulated by ligands and cofactors. Zymogen activation imparts proteolytic activity to thrombin and also affects the binding of ligands to its two principal exosites. We have used the activation peptide fragment 1.2 (F12), a ligand for anion-binding exosite 2, to probe the zymogenicity of thrombin by isothermal titration calorimetry. We show that F12 binding is sensitive to subtle aspects of proteinase formation beyond simply reporting on zymogen cleavage. Large thermodynamic differences in F12 binding distinguish between a series of thrombin species poised along the transition of zymogen to proteinase. Thrombin is a pivotal serine proteinase product of the blood coagulation cascade. In addition to catalyzing fibrinogen cleavage and platelet activation to form the blood clot, it also plays essential regulatory roles (1, 2). It catalyzes proteolytic activation steps that amplify flux toward thrombin formation following initiation of the coagulation cascade. Thrombin also functions as a negative regulator by activating protein C in the anticoagulant pathway (3). These opposing roles of thrombin in coagulation derive from its ability to act with specificity on a range of protein substrates, with differing sequences flanking the cleavage sites, in reactions that are regulated by cofactors and two anion-binding exosites (ABE1 and ABE2) 2 found on opposite faces of the proteinase (4, 5). Allosteric control, arising from binding of ligands to different sites, is considered to underlie the regulation of thrombin specificity and its dual role as procoagulant and anticoagulant proteinase (4, 5). Thrombin and the other serine proteinases of blood coagulation contain catalytic domains bearing the chymotrypsin fold (6). In this family, the zymogen precursor is converted to proteinase by cleavage following Arg 15 (7). 3 The nascent N terminus inserts in a sequence-specific manner into an N-terminal binding pocket to form a salt bridge with Asp 194 (7). Salt bridge formation is associated with changes in activation domains, optimization of the primary specificity pocket to facilitate substrate binding, and a flip in the Gly 193 amide bond to form the oxyanion hole (7). These transitions imbue the product with proteolytic activity.Early studies with chymotrypsin suggested the persistence of zymogen-like species at near-neutral pH, related to the partial deprotonation of the new N terminus responsible for salt bridge formation (8). It is nevertheless implicitly assumed that irreversible cleavage at Arg 15 and the concerted transitions that ensue highly favor proteinase formation. This is despite the likely presence of intervening equilibria between substates that lie on the pathway for conversion of zymogen to fully stabilized proteinase. A notable exception is factor VIIa which possesses poor catalytic activity and has been proposed to be zymogenlike when free and stabilized in the proteinase state when bound to tissue factor (9). Na ϩ is considered an essenti...