Aggregation mechanism investigation of the GIFQINS cross-β amyloid fibril

Abstract

Amyloid-like fibrils are found in many fatal diseases, such as Alzheimer's disease, type II diabetes mellitus, and the transmissible spongiform encephalopathies, and prion diseases. The kinetics of fibril formation is still debated and becomes a hotspot. In this study, we intend to utilize room temperature simulation to study the stability of the modeling structure for GIFQINS. The results suggest that the hexamer of GIFQINS is highly stable and consistent with the prediction of Eisenberg. Furthermore, high-temperature molecular dynamics simulation in explicit water is used to study its aggregation mechanisms. The important findings from this work are (a) dimer is not thermodynamically stable state, (b) dissolution of the fibrils is more difficult than aggregation, (c) tetramer (2-2) is the intermediate state and (d) two transition states are corresponding to trimer (2-1) and pentamer (3-2). This is the first time to suggest the tetramer (2-2) as intermediate state with kinetics analysis and can shed light on possible mechanisms of aggregation.