Recent work has suggested that the thrombin-bound conformation of fibrinopeptide A exhibits a strand-turn-strand motif, with a beta-turn centered at residues Glu-11 and Gly-12. Our molecular modeling analysis indicates that the published fibrinopeptide conformation cannot bind reasonably to thrombin but that reorientation of two residues by alignment with bovine pancreatic trypsin inhibitor provides a good fit within the deep thrombin cleft and satisfies all of the experimental nuclear Overhauser effect data. Based on this analysis, we have successfully designed and synthesized hybrid peptide mimetic substrates and inhibitors that mimic the proposed beta-turn structure. The results indicate that the turn conformation is an important aspect of thrombin specificity and that our turn mimetic design successfully mimics the thrombin-bound conformation of fibrinopeptide.

Nakanishi, H., Chrusciel, R. A., Shen, R., Bertenshaw, S., Johnson, M. E., Rydel, T. J., Tulinsky, A., & Kahn, M. (1992). Peptide mimetics of the thrombin-bound structure of fibrinopeptide A. Proceedings of the National Academy of Sciences, 89(5), 1705–1709.