Structure and Aggregation Mechanism of β2-Microglobulin (83–99) Peptides Studied by Molecular Dynamics Simulations

Many human neurodegenerative diseases are associated with amyloid fibril formation. The human 99-residue β2-microglobulin (β2m) is one of the most intensively studied amyloid-forming proteins. Recent studies show that the C-terminal fragments 72–99, 83–89, and 91–96 form by themselves amyloid fibrils in vitro and play a significant role in fibrillization of the full-length β2m protein under acidic pH conditions. In this work, we have studied the equilibrium structures of the 17-residue fragment 83–99 in solution, and investigated its dimerization process by multiple molecular dynamics simulations. We find that an intertwined dimer, with the positions of the β-strands consistent with the results for the monomer, is a possible structure for two β2m(83–89) peptides. Based on our molecular-dynamics-generated dimeric structure, a protofibril model is proposed for the full-length β2m protein.