Thrombin activation of the factor XI dimer is a multi-staged process for each subunit

Factor XI (FXI), a protein in the intrinsic coagulation pathway, can be activated by two enzymes. In hemostasis, FXI is activated by thrombin, while FXIIa-mediated activation is prothrombotic. The interactions between FXI and its activating enzymes are poorly understood due to their transient nature. Here, we applied structural proteomics, molecular dynamics simulations and binding assays to investigate the interface between thrombin and FXI including the dynamics underlying FXI activation. We demonstrate that activation of FXI is a multi-staged process, where thrombin first binds to Pro520 on FXI, after which it migrates towards the activation site by engaging the apple 1 domain and finally Arg378. We validated with known mutation sites and additionally found that Pro520 is conserved in prekallikrein (PK). This enables binding of thrombin even though it cannot activate PK. Understanding the exact binding of thrombin to FXI points a way for future interventions for bleeding or thrombosis.