The thrombus formation process is a composite mechanism with great capacity for intrinsic amplification. The amplification will ensure a fast enzymatic route that will prevent excessive blood loss in the event of vessel injury. However, for such a powerful pro-thrombotic system there is also a need for regulatory functions, to stop thrombus growth from spreading too far away from the site of injury. Protein C is activated by thrombin to activated protein C (APC), the mechanism dependent on the association of thrombin and protein C with the endothelial cell membrane protein, thrombomodulin. APC, together with its cofactor protein S, functions as an inhibitor of coagulation by inhibiting the cofactors factor Va and factor VIIIa through enzymatic cleavage [54]. It has been found that thrombin is an allosteric enzyme that shows two different conformations depending on Na+ binding. The thrombin conformation where Na+ is bound yields a higher efficiency towards activation of fibrinogen and the PAR receptor while the conformation without Na+ is slower. The thrombin activation rate of the coagulation inhibitor protein C is however not affected and is the same for both conformations [55]. Another inhibitor of the coagulation system is the tissue factor pathway inhibitor (TFPI), which is able to inhibit both factor Xa and the TF-factor VIIa complex [56]. Antithrombin (AT) is a protein that can trap thrombin and thus inhibit thrombin’s enzymatic capabilities. Heparin binding enhances the activity of AT mediated inactivation of thrombin profoundly by colocalization of the two proteins [57]. Several of the inhibitors that are involved in the coagulation  process belong to the serpin protein superfamily (reviewed in [58]), that inhibit their target protease by forming a covalent bond to its catalytic site [59].