Identification of the functional states of human vitamin K epoxide reductase from molecular dynamics simulations

Abstract

In mammalians, the enzymatic activity of vitamin K epoxide reductase (VKORC1) requires a protein conformational reorganisation that includes several transient enzymatic states involving a dynamic electron transfer. Regarding the structurally non-characterised human enzyme (hVKORC1), this process remains poorly explained and the different redox states of the enzyme generated by its biochemical transformation are unknown. Here, we report a 3D model of the fully reduced hVKORC1 at the atomistic level. By exploring this model through molecular dynamics (MD) simulations, we established the most probable intermediate states of the enzyme which were used for generation of the putative functionally-related enzymatic states. Enzymatic functionality of each state was assigned by probing their recognition properties with respect to vitamin K in its quinone and hydroxyquinone forms. Two states were identified as contributing to the two-step vitamin K transformation. The state highly selective for native vitamin K was further validated through analyses of its free energy of binding with vitamin K agonists (VKAs) that showed a high correlation with the experimental inhibiting constants.