Figure 1.
Figure 1. The heparin-dependent mechanism by which antithrombin inhibits coagulation proteases. Native antithrombin (ribbon diagram) circulates in a low activity state (panel A) until it encounters a specific sequence on heparin or heparan sulfate (ball-and-stick), which induces an activating conformational change (panel B). Heparin binding results in extensions (yellow) to helix D (cyan), and the expulsion of the reactive center loop (RCL, yellow coil) from β-sheet A (red). The release of the RCL reorients the reactive center P1 Arg side chain (red ball-and-stick) from contacts with the body of antithrombin for better recognition by proteases. The conformational change also increases the affinity of antithrombin for heparin by approximately 1000-fold through an induced-fit mechanism. Thrombin (cyan, top) interacts with heparin (panel B) and translates until it encounters the prebound antithrombin (panel C). This encounter, or Michaelis complex, then proceeds into the chemistry of proteolysis, resulting in either the translocation of thrombin to the opposite pole of antithrombin to form the inhibited complex (panel D) or the dissociation of the active protease from the cleaved serpin (panel E). The factor that determines the fate of the Michaelis complex is the ratio of the rate of incorporation of the cleaved RCL to the rate of deacylation of the protease acyl intermediate. In either case, the insertion of the RCL into β-sheet A reverses the induced fit mechanism causing the release of heparin. The mutation described in this work is in the part of the RCL, which inserts first the P10 residue of the hinge region and is shown as a green ball (also indicated by arrows). Due to the internal positioning of P10 in the RCL-inserted forms, the strand is transparent in panels D and E. This figure is based on the crystallographic structures of native antithrombin (1e05), pentasaccharide-activated antithrombin (1e03), cleaved bovine antithrombin (1att), the structure of thrombin in complex with heparin cofactor II (1jmo) and the final serpin-protease complex (1ezx). Other details are modeled.

The heparin-dependent mechanism by which antithrombin inhibits coagulation proteases. Native antithrombin (ribbon diagram) circulates in a low activity state (panel A) until it encounters a specific sequence on heparin or heparan sulfate (ball-and-stick), which induces an activating conformational change (panel B). Heparin binding results in extensions (yellow) to helix D (cyan), and the expulsion of the reactive center loop (RCL, yellow coil) from β-sheet A (red). The release of the RCL reorients the reactive center P1 Arg side chain (red ball-and-stick) from contacts with the body of antithrombin for better recognition by proteases. The conformational change also increases the affinity of antithrombin for heparin by approximately 1000-fold through an induced-fit mechanism. Thrombin (cyan, top) interacts with heparin (panel B) and translates until it encounters the prebound antithrombin (panel C). This encounter, or Michaelis complex, then proceeds into the chemistry of proteolysis, resulting in either the translocation of thrombin to the opposite pole of antithrombin to form the inhibited complex (panel D) or the dissociation of the active protease from the cleaved serpin (panel E). The factor that determines the fate of the Michaelis complex is the ratio of the rate of incorporation of the cleaved RCL to the rate of deacylation of the protease acyl intermediate. In either case, the insertion of the RCL into β-sheet A reverses the induced fit mechanism causing the release of heparin. The mutation described in this work is in the part of the RCL, which inserts first the P10 residue of the hinge region and is shown as a green ball (also indicated by arrows). Due to the internal positioning of P10 in the RCL-inserted forms, the strand is transparent in panels D and E. This figure is based on the crystallographic structures of native antithrombin (1e05), pentasaccharide-activated antithrombin (1e03), cleaved bovine antithrombin (1att), the structure of thrombin in complex with heparin cofactor II (1jmo) and the final serpin-protease complex (1ezx). Other details are modeled.

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