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Poly-glutamine (polyQ) protein aggregation is a primary cause of more than 30 human neurodegenerative disorders that are associated with protein misfolding and aggregation. To better understand the process of aggregation, we simulated aggregation of a widely studied mutant of the Huntington's disease protein, the polyQ expansion in exon 1 of the Huntingtin (htt) gene. The purpose of the simulation is to provide a mechanistic understanding of the polyQ mutation, and to identify its protein-protein interactions that initiate protein misfolding and aggregation. In the simulation, we observe the progression of the aggregation process in real-time, which identifies a five-stage growth mechanism for the protein. The simulation shows that the initiation of the aggregation process is triggered by the formation of multimeric interfaces within the protein. The critical interactions are glutamine binding and glutamine cluster formation, which control the stability of the protein. The simulation then proceeds to four distinct aggregation stages: (i) an initial stage with non-nucleated growth, (ii) a second with nucleated growth, (iii) a third with diffuse nucleation, and (iv) a fourth with localized growth. The simulation suggests that the polyQ mutation accelerates the nucleation stage and the growth of nuclei, which suggests that the mutation acts as a nucleating agent. The simulation reveals that the mutation destabilizes the native state and increases the conformational change of the protein.
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