The mutation of Gly12 to Val12 in the A alpha chains of human fibrinogen Rouen is associated with a delayed proteolytic release of fibrinopeptide A (FpA or A alpha 1 to 16 of fibrinogen) by thrombin, leading to a bleeding disorder. Analogs of FpA and FpA Rouen have been designed that include a Pro15 to replace Val15 in natural FpA and to mimic the frequent occurrences of a proline residue at equivalent positions of other protein substrates of thrombin. The Pro15 analogs of FpA and FpA Rouen bind specifically to the active site of thrombin as shown by thrombin-induced differential line broadening and transferred nuclear Overhauser effects (transferred NOEs). Pro15 is well tolerated by the thrombin-bound structures of both FpA and FpA Rouen in solution, resulting in enhanced conformational stabilities of the thrombin-FpA complexes. The Val12 mutation in FpA Rouen causes backbone conformational changes in residues Val12 and Gly13 accompanied by an expansion of the hydrophobic cluster of FpA to accommodate the bulky side-chain of Val12. The single turn of helical structure between residues Asp7 and Glu11 is stabilized by hydrogen bonds from the side-chain carboxylate of Asp7 to the exposed backbone NH groups of Ala10 and/or Leu9 (N-capping), and by hydrogen bonds between the exposed backbone carbonyl groups of residues Phe8 and Leu9, and the backbone NH groups of Gly12/Val12 and Gly13 (C-capping). The bound structure of FpA Rouen may be further stabilized by a non-polar (i,i + 4) interaction between the aromatic side-chain of Phe8 and the aliphatic side-chain of Val12. Despite these optimized intrapeptide interactions, the thrombin-peptide interactions are highly dynamic as indicated by the fast rate of dissociation (koff > 100 s-1) of the peptide ligands from the thrombin complexes. Sequence comparison between mammalian fibrinopeptides A and B suggests that the specificity of thrombin is dictated by a four-residue consensus motif, Phe(P4)-Xxx(P3)-Pro(P2)-Arg(P1) or FXPR, when Xxx at P3 can be a charged or a neutral polar residue capable of specific interactions with residues near the active site of thrombin.