Molecular modeling of the complex formed between thrombin and a model oligopeptide corresponding to the Gln32-Gln42 sequence of FXIII-A.

The oligopeptide contains the thrombin cleavage site (Arg37-Gly38) and the Val34Leu mutation site. (A, B) Orientation of model oligopeptides representing the wild-type Val34 (A) and the mutant Leu34 (B) FXIII-A on the surface of thrombin. Hydrophobic domains are shown in green. Blue and red represent basic and acidic regions, respectively. Val34 and Leu34 are shown in pink. (C, D) Optimized geometry of complex formed by thrombin and Val34 (C) or Leu34 (D) model oligopeptides. Val34 (C) and Leu34 (D) residues are shown in yellow. Thrombin residue numbers Pro64, Trp65, and Trp163 were obtained from the macromodel data file and correspond to Pro412, Trp413, and Trp511, respectively, in the prothrombin sequence. For the oligopeptide the Corey-Pauling-Kultun rendering was applied. For the demonstration of thrombin residues the liquorice rendering was used.