Amyloid fibril structure modeling using protein threading and molecular dynamics simulations

Molecular dynamics simulations to investigate the aggregation behaviors of the Abeta(17-42) oligomers

The amyloid beta-peptides (Abetas) are the main protein components of amyloid deposits in Alzheimer's disease (AD). Detailed knowledge of the structure and assembly dynamics of Abeta is important for the development of properly targeted AD therapeutics. So far, the process of the monomeric Abeta assembling into oligomeric fibrils and the mechanism underlying the aggregation process remain unclear. In this study, several molecular dynamics simulations were conducted to investigate the aggregation behaviors of the Abeta(17-42) oligomers associated with various numbers of monomers (dimer, trimer, tetramer, and pentamer). Our results showed that the structural stability of the Abeta(17-42) oligomers increases with increasing the number of monomer. We further demonstrated that the native hydrophobic contacts are positive correlated with the beta-sheet contents, indicating that hydrophobic interaction plays an important role in maintaining the structural stability of the Abeta(17-42) oligomers, particularly for those associated with more monomers. Our results also showed that the stability of the C-terminal hydrophobic segment 2 (residues 30-42) is higher than that of the N-terminal hydrophobic segment 1 (residues 17-21), suggesting that hydrophobic segment 2 may act as the nucleation site for aggregation. We further identified that Met35 residue initiates the hydrophobic interactions and that the intermolecular contact pairs, Gly33-Gly33 and Gly37-Gly37, form a stable "molecular notch", which may mediate the packing of the beta-sheet involving many other hydrophobic residues during the early stage of amyloid-like fibril formation.

Comparison of Alzheimer Abeta(1-40) and Abeta(1-42) amyloid fibrils reveals similar protofilament structures

We performed mass-per-length (MPL) measurements and electron cryomicroscopy (cryo-EM) with 3D reconstruction on an Abeta(1-42) amyloid fibril morphology formed under physiological pH conditions. The data show that the examined Abeta(1-42) fibril morphology has only one protofilament, although two protofilaments were observed with a previously studied Abeta(1-40) fibril. The latter fibril was resolved at 8 A resolution showing pairs of beta-sheets at the cores of the two protofilaments making up a fibril. Detailed comparison of the Abeta(1-42) and Abeta(1-40) fibril structures reveals that they share an axial twofold symmetry and a similar protofilament structure. Furthermore, the MPL data indicate that the protofilaments of the examined Abeta(1-40) and Abeta(1-42) fibrils have the same number of Abeta molecules per cross-beta repeat. Based on this data and the previously studied Abeta(1-40) fibril structure, we describe a model for the arrangement of peptides within the Abeta(1-42) fibril.