Epitope region identification challenges of intrinsically disordered proteins in neurodegenerative diseases: Secondary structure dependence of α-synuclein on simulation techniques and force field parameters.

Due to fast aggregation processes of many disordered proteins in neurodegenerative diseases, it is difficult to study their epitope regions at the monomeric and oligomeric levels. Computer simulations complement experiments and have been used to identify the epitope regions of proteins. Residues that adopt β-sheet conformation play a central role in the oligomerization and aggregation mechanisms of such proteins, including α-synuclein, which is at the center of Parkinson's and Alzheimer's diseases.