Dimerization Process of Amyloid-β(29-42) Studied by the Hamiltonian Replica-Permutation Molecular Dynamics Simulations

The amyloid-beta peptides fom amyloid fibrils which are associated with Alzheimers's disease. Amyloid-beta(29-42) is it C-terminal fragment and a critical determinant of the amyloid formation rate. This fragment forms the amyloid fibril by itself. However, the fragment conformation in the fibril has yet to be determined. The oligomerization process including the dimerization process is also still unknown. The dimerization process corresponds to an early process of the amyloidogenesis. In order to investigate the dimerization process and conformations we applied the Hamiltonian replica permutation method which is a better alternative to the Hamiltonian replica-exchange method to two amyloid-beta(29-42) molecules in explicit water solvent. At the first step of the dimerization process two amyloid-beta(29-42) molecules came close to each other and had intermolecular side chain contacts. When two molecules had the intermolecules side chain contacts, the amyloid-beta(29-42) tended to have intramolecular secondary structures espically. beta-hairpin structures The two molecules had intermolecular beta-bridge structures by coming much closer at the sencond step of the dimerization process. Formation of these intermolecular beta-bridge structures was induced by the beta-hairpin structures. The intermolecular beta-sheet structures elongated at the final step. Structures of the amyloid-beta(29-42) in the monomer and dimer states are also shown with the free energy landscapes, which were obatined by performing efficient sampling in the conformational space in our simulations.