The folding mechanism and key metastable state identification of the PrP127–147 monomer studied by molecular dynamics simulations and Markov state model analysis

transition. Employing extensive replica exchange molecular dynamics (REMD) and conventional MD simulations, we sample a huge number of conformations of PrP127-147. Using the Markov state model (MSM), we identify the metastable conformational states of this fragment and the kinetic network of transitions between the states. The resulting MSM reveals that disordered random-coiled conformations are the dominant structures. A key metastable folded state with typical extended β-sheet structures is identified with Pro137 being located in a turn region, consistent with a previous experimental report. Conformational analysis reveals that intrapeptide hydrophobic interaction and two key residue interactions, including Arg136-His140 and Pro137-His140, contribute a lot to the formation of ordered extended β-sheet states. However, network pathway analysis from the most populated disordered state indicates that the formation of extended β-sheet states is quite slow (at the millisecond level), as large structural rearrangement is needed from disordered states. We speculate that the formation process of the extended β-sheet folded states may represent an important event during the early formation of prion oligomers and the results of our study provide insights into the molecular details of the early stage of prion aggregation.