Modeling interactions of PAR1 with Activated Protein C (APC)
John Griffin, TSRI
The project built structural models of the N-terminus of Protease Activated Receptor 1 (PAR-1) interacting with Activated Protein C (APC) to identify mutations that will favor cleavage of PAR-1 at R46 over R41, as part of research related to blood clot prevention, neural protection in case of stroke, and sepsis protection. AutoDockFR and AutoDock CrankPep were used to dock peptides of various sizes (3 to 8 amino acids) around positions R41 and R46 of PAR-1. Subsequent homology modeling followed by molecular dynamics (MD) simulations were performed to model the interactions between the APC and PAR-1 segments. Based on these models, two mutations of APC were proposed, T254F and A195Q, that were subsequently tested. Additionally, MD simulations explored the structural fluctuation of the C-terminus of the APC light chain and its possible interactions with other segments. Despite these large fluctuations, the C-terminus of the APC light chain stays within the region interacting with Protein S. The conformation most often sampled during the MD simulation shows that K150 and K151 are in close contact with L73, which is also known to alter the binding with Protein S. On the other hand, R143, K146 and R147A are located above the K150 and K151 residues, i.e., further away from the membrane and closer to the protease domain of APC. This suggests that the interface between the APC light chain and Protein S is extended and has a boundary near the APC protease domain.