Incorporation of prothrombin into the prothrombinase complex is essential for rapid thrombin generation at sites of vascular injury. Prothrombin binds directly to anionic phospholipid membrane surfaces where it interacts with the enzyme, factor Xa, and its cofactor, factor Va. We demonstrate that HD1, a thrombin-directed aptamer, binds prothrombin and thrombin with similar affinities (K d values of 86 and 34 nM, respectively) and attenuates prothrombin activation by prothrombinase by over 90% without altering the activation pathway. HD1-mediated inhibition of prothrombin activation by prothrombinase is factor Va-dependent because (a) the inhibitory activity of HD1 is lost if factor Va is omitted from the prothrombinase complex and (b) prothrombin binding to immobilized HD1 is reduced by factor Va. These data suggest that HD1 competes with factor Va for prothrombin binding. Kinetic analyses reveal that HD1 produces a 2-fold reduction in the k cat for prothrombin activation by prothrombinase and a 6-fold increase in the K m , highlighting the contribution of the factor Va-prothrombin interaction to prothrombin activation. As a high affinity, prothrombin exosite 1-directed ligand, HD1 inhibits prothrombin activation more efficiently than Hir 54 -65 (SO 3 ؊ ). These findings suggest that exosite 1 on prothrombin exists as a proexosite only for ligands whose primary target is thrombin rather than prothrombin.Thrombin is the most versatile component of the hemostatic system, mediating procoagulant, anticoagulant, and anti-fibrinolytic pathways (1). The diverse activities of thrombin are regulated, at least in part, by electropositive exosites flanking its active site (2). Exosite 1 binds ligands that interact with the active site of thrombin, including fibrinogen, heparin cofactor II, and protease-activated receptor, the major thrombin receptor on cells (2). In contrast, exosite 2, which binds ligands such as heparin (3, 4) and platelet glycoprotein Ib␣ (5-7), serves to tether thrombin for subsequent interactions with substrates or inhibitors.Prothrombin, the precursor of thrombin, lacks an active site and has immature or inaccessible exosites (8 -10). Because exosite 1 on prothrombin exhibits reduced affinity for certain ligands, it has been designated proexosite 1 (8). This proexosite gains functional activity during prothrombin conversion to thrombin, as evidenced by fluorescent ligand binding studies (11). Thus, Anderson and Bock (11) (SO 3 Ϫ ) that increase with the extent of activation (11, 12). Diminished affinity of other thrombin ligands for proexosite 1 on prothrombin also has been observed (13,14).In contrast to the progressive maturation of proexosite 1, exosite 2 displays more abrupt development. Exosite 2 is not accessible until fragment 2 (F2) is released from prothrombin. Thus, prethrombin 2 (pre2) and thrombin have similar affinities for heparin, whereas meizothrombin (mIIa) and meizothrombin des F1 [mIIa(-F1)], which retain the F2 domain, do not bind heparin (15).Understanding the functional maturat...