The specific cleavage of fibrinogen by the serine proteinase thrombin (EC 3.4.21.5) initiates the polymer ization of fibrin monomers, a primary event in blood clot formation. 1 Fibrinogen (M r 340,000) is a covalently linked dimer of three peptide chains, with stoichiometry (Aα,Bβ,γ) 2 . 2 The cleavage releases two peptides, fibrinopeptides A (FPA) and B (FPB) from the amino-termini of chains Act and Bβ, respectively, thereby revealing recognition sites for aggregation with the 7 chain.Thrombin exhibits primarily a trypsin-like specific ity, that is, a preference for arginyl P1 residues 3 (see Bode and Stubbs in this issue of Seminars for nomencla ture). The cleavage of fibrinogen by thrombin represents a very specific reaction, however. Of the 376 Arg/LysXaa bonds in the fibrinogen molecule, thrombin cleaves in the native state only four, releasing the fibrinopeptides. 3 Residues of fibrinogen contributing to this excep tional specificity have been localized to the first 51 amino acids of the Aα-chain. 4,5 This region has been further dissected to explore subsites, assigning roles (in order of importance) to fragments F1-F23, F33-F44, and F45-F51 6 (fibrinogen residues are prefixed by the letter "F", D-phenylalanyl-L-prolyl-L-arginine chloromethyl-ketone (PPACK) residues by "I", and hirudin residues by "H"). Two separate sites in thrombin outside S1 have been proposed as conferring this additional specificityone apolar, in the unprimed region, 7 ' 8 and one basic postcleavage site (the fibrinogen recognition exosite). [9][10][11] This recognition exosite appears to be in volved in the binding of other proteins, including fibrin itself, thrombomodulin (a cell surface protein that allows thrombin activation of protein C, which in turn shuts down thrombin production) and hirudin (the potent anti coagulant from the saliva of the leech Hirudo medicinalis). 12-14 Hirugen, a sulfated dodecapeptide correspond ing to the hirudin C-terminus, and the nonsulfated C-terminal peptide hirudin (45-65) are competitive inhib itors of fibrinogen cleavage by thrombin, while allowing peptidase activity on small synthetic substrates. 15,16 These sites have recently been identified in a series of crystallographic studies 17-23 (see Bode and Stubbs in this issue). The ternary complex of human α-thrombin with peptides derived from FPA and hirudin 22 (FPA-Hthrombin) allows a structural explanation for the extreme specificity of the fibrinogen-thrombin interaction; a spec ificity whose disruption can lead to severe clotting disor ders. 24 The covalently bound (N-acetylated) decapeptide chloromethylketone (Ac-AspF7-PheF8-LeuF9-AlaF10-GluFll-GlyF12-GlyF13-GlyF14-ValF15-ArgF16-CMK) exhibits little in the way of regular secondary structure (Fig. 1). The acetylated amino-terminal points away from the enzyme, whereby the preceding six residues could extend freely into solution. Asp F7 begins a short stretch (F8-F10) of α-helical conformation with a hydro gen bond from its carboxylate O δ1 to the amide nitrogen of Ala F10. This irregularly hydr...