Structure and Physicochemical Properties of the Aβ42 Tetramer: Multiscale Molecular Dynamics Simulations

Despite years of intensive research, little is known about oligomeric structures present during Alzheimer's disease (AD). Excess of amyloid beta (Aβ) peptides and their aggregation are the basis of the amyloid cascade hypothesis, which attempts to explain the causes of AD. Because of the intrinsically disordered nature of Aβ monomers and the high aggregation rate of oligomers, their structures are almost impossible to resolve using experimental methods. For this reason, we used a physics-based coarse-grained force field to extensively search for the conformational space of the Aβ42 tetramer, which is believed to be the smallest stable Aβ oligomer and the most toxic one. The resulting structures were subsequently optimized, tested for stability, and compared with the proposed experimental fibril models, using molecular dynamics simulations in two popular all-atom force fields. Our results show that the Aβ42 tetramer can form polymorphic stable structures, which may explain different pathways of Aβ aggregation. The models obtained comprise the outer and core chains and, therefore, are significantly different from the structure of mature fibrils. We found that interaction with water is the reason why the tetramer is more compact and less dry inside than fibrils. Physicochemical properties of the proposed all-atom structures are consistent with the available experimental observations and theoretical expectations. Therefore, we provide possible models for further study and design of higher order oligomers.