Gly43Asp Mutation effect on the catalytic activity of the coagulation factor X: Molecular Dynamics and Metadynamics simulation studies

Factor X (FX) is a vitamin K-dependent serine protease, which is one of the major players in the blood coagulation cascade. Upon activation to FXa, it converts prothrombin to thrombin, which in turn converts fibrinogen into fibrin (blood clots). More than two million people die each year of arterial or venous thrombosis in USA only. Also FXa deficiency causes blood bleeding (hemostasis) like intracranial bleeding, hemathrosis and gastrointestinal blood loss. Therefore FXa is an interesting target for anti-coagulant and anti-blood bleeding drugs. Experimental in vitro studies showed that the naturally occurring Gly43Asp mutant, identified in patients suffering from severe bleeding episodes, markedly impaired the catalytic activity of FXa. Molecular dynamics simulations were performed for 0.48 microseconds followed by free energy calculations on the wild and mutated FXa enzymes in order to figure out the experimental effect of the Gly43Asp mutation at the atomic level. It was found that the wild type enzyme is more flexible than Gly43Asp mutant which allows the WT to be bind the substrate more efficiently. The selectivity of the conformation sampling is controlled by the hydrogen bond network established within and near the active site. Indeed replacing Gly43 by Asp favors the formation of new hydrogen bonds and rupture of wild type established ones. Our results contribute to the understanding of the FXa structure-function relationship, eventually helping in designing more potent drugs targeting the thrombosis and hemostasis diseases