Thrombin specificity

Abstract

A model of thrombin interaction with distinct substrates or ligands has been derived from the crystallographic studies of thrombin-inhibitors complexes, and buttressed by functional studies with mutant thrombins, thrombin proteolytic derivatives or antibodies against thrombin. The unique specificity of thrombin for its substrates and ligands may be ascribed to multiple interactions with both the active site cleft and exosite(s) distinct from the active site. Two prominent insertion loops around Trp 50 and Trp 148 project over the active site cleft and play an important role in the substrates selection. Several substrates (fibrinogen, thrombin receptor, heparin cofactor II) or ligands (thrombomodulin, glycoprotein Ib) interact with a large exosite located on the surface of the loop segment 65-76, mainly constituted of basic amino acids, designated anion binding exosite 1. Interaction with these various macromolecules appears to involve a limited number of residues within the large exosite 1. It is conceivable that exosite 1 contains distinct subsites, although most of them may overlap. A second basic exosite (anion binding exosite 2) is located close to the carboxy-terminal B chain helix. Exosite 2 interacts with heparin, the chondroitin sulfate moiety of thrombomodulin and prothrombin activation fragment 2. Interaction of ligands with either exosite 1 or exosite 2 leads to conformational changes of the thrombin molecule, that may be important determinants of thrombin specificity. Whether exosite 2 cooperates with exosite 1 for thrombin interaction with fibrin(ogen) or the thrombin receptor remains to be determined.