STRUCTURAL INSIGHT INTO THE POLYMORPHISM OF NNQNTF PROTOFIBRIL: IMPORTANCE OF INTERFACIAL WATER, POLAR AND AROMATIC RESIDUES

Polymorphism is widely observed in amyloid fibrils associated with many neurodegenerative diseases. Recent experimental study reported that fibrils formed by the segment NNQNTF of elk prion protein exhibited facial polymorphism with the two β-sheets either in back-to-back (BB) or in face-to-face (FF) packing arrangement. In the BB packing, the side chains of N2, N4 and F6 are interdigitated to form steric zipper, while in the FF packing, the side chains of N1, Q3 and T5 form the interdigitated interface. In this study, we investigate the water-mediated assembly of two preformed β-sheets and the physical interactions that stabilize the two different fibrils using all-atom molecular dynamics (MD) simulations. Multiple MD simulations have been carried out by starting from FF or BB packing of two β-sheets according to the facial polymorphism revealed by X-ray microcrystallography. For both packing patterns, we observe that the assembly of β-sheets is mediated by water molecules in the interface between β-sheets, leading to a long-lived protofibrils with wet interface prior to the formation of dry amyloid fibrils. Detailed structural analysis shows that besides the side chain steric zipper interactions, intra-sheet hydrogen bonding and aromatic stacking interactions play an important role on the stabilization of the protofibril with BB packing, while the intra-sheet and inter-sheet hydrogen bonding interactions are crucial for the formation of BB protofibril. These findings provide insights into the mechanism that lead to the facial polymorphism of NNQNTF fibrils.