Dynamics of Aβ42 Tetramer by REST2-CHARMM36m Simulations

It has long been recognized that one-third of individuals with Alzheimer's disease (AD) have no cognitive deficit, underscoring the limitations of therapeutic strategies based solely on the amyloid cascade hypothesis. This observation does not negate the clinical relevance of targeting amyloid deposition or clearance, but rather emphasizes that amyloid pathology constitutes only one component of a multifactorial disease process. Due to the intrinsic disorder of the Aβ40 and Aβ42 peptides, the early transient oligomers, widely believed to represent the first neurotoxic species, remain inaccessible to atomic-level characterization. In this study, we focus on the Aβ42 tetramer, although the literature remains divided regarding the identity of the earliest dominant detectable oligomeric species. Given the size of the system, it is currently computationally infeasible to capture equilibrium oligomer structures starting from randomly coiled monomers with arbitrary orientations. In a recent study, AlphaFold2, which is not designed for intrinsically disordered proteins (IDP), provided three candidate topologies: (i) a four α-helix bundle in which helices span the C-terminal region and (ii) two conformations with high β-sheet contents. In this study, we initiate our simulations from the helix topology, as the α-helical content is most consistent with circular dichroism and FTIR experimental data. We employ replica exchange with solute tempering (REST2) in combination with the CHARMM36m force field. Our simulations consistently show that the Aβ42 tetramer relaxes to a heterogeneous random-coil ensemble, indicating that oligomers larger than tetramers are required to stabilize structured assemblies and initiate fibril growth.