Thrombin-bound conformation of a cyclic anticoagulant peptide using transferred nuclear Overhauser effect (NOE), distance geometry, and NOE simulations.

A cyclic hirudin C-terminal fragment, even truncated to eight residues, retains higher activity in binding to thrombin compared with its linear analogue of the same peptide length. In this paper, we report the results of a conformational study of a cyclic hirudin peptide 55-62 ([sequence: see text]) bound to the exosite of thrombin. Based on transferred NOE data and molecular modeling, conformation of the 18-membered ring was well defined with little mobility in the loop region. The backbone conformations of residues Glu (58) to Lys (61) are very similar to those in a native 11-residue linear peptide in the thrombin-bound state [Ni et al. (1990) Biochemistry, vol. 29, pp. 4479-4489; Skrzypczak-Jankun et al. (1991) Journal of Molecular Biology, vol. 221, pp. 1379-1393]. The side chain of Ile (59), the most critical residue, assumes a gauche- conformation, as observed in linear hirudin peptides. The bound conformations of residues Phe(56) and Glu (57) are defined by an iterative procedure involving the matching of computed and experimental transferred NOE intensities. The exosite of thrombin appears to be very specific to both the backbone and the side-chain conformations of the hirudin C-terminal peptides, especially those of residues Phe(56) and Ile(59).