Accelerated Molecular Dynamics Simulations of Thrombin-Thrombomodulin Reveal Potential for Entropic Allostery

The specificity of the serine protease thrombin is altered from procoagulative cleavage of fibrinogen to anticoagulative cleavage of protein C upon distal binding of cofactor thrombomodulin (TM). The fourth EGF-like domain of TM (TM4) is necessary to elicit this response, though it makes no direct contact with thrombin. While this effect can be described as allosteric, crystal structures of apo and TM bound thrombin do not reveal a significant structural change, making a significant enthalpic contribution to allostery unlikely. We hypothesize that allostery in thrombin may instead occur through a primarily entropic mechanism.To investigate the potential for entropic allostery in thrombin a series of accelerated molecular dynamics (AMD) simulations were performed. AMD applies a bias energy to the underlying potential of a classic MD system to model longer timescales on which allosteric events are more likely to occur. Residue by residue cross-correlation analysis and community network models constructed from the resulting trajectories are indicative of an allosteric pathway between the thrombin active site and TM4. In addition, order parameters back-calculated from trajectories of apo and TM bound thrombin, show differential dynamics near the thrombin active site and TM binding site. Together these results show that TM binding alters thrombin dynamics in a manner that could reasonably contribute to the observed change in specificity through entropic allostery.