Refinement of the thrombin‐bound structure of a hirudin peptide by a restrained electrostatically driven Monte Carlo method

Energy refinement of the structure of a linear peptide, hirudin56–65, bound to thrombin was carried out using a conformational search method in combination with restrained minimization. Five conformations originated from nmr data and distance geometry calculations having a similar global folding pattern but quite different backbone conformations were used as the starting structures. As a result of this approach, a series of low‐energy conformations compatible with a set of upper and lower bounds of interproton distances determined from transferred nuclear Overhauser effects were found. A comparison among the lowest energy conformations of each run showed that the combination of energy refinement plus distance constraints led to a very well‐defined structure for both the backbone and the side chains of the last 7 residues of the polypeptide. Furthermore, the low‐energy conformations generated with this technique contain a segment of 3 10 ‐helix involving the last 5 residues at the COOH terminal end.