Conformational Transitions of Amyloid-β: A Langevin and Generalized Langevin Dynamics Simulation Study.

Abstract

The dynamics of conformational transitions of the disordered protein, amyloid-β, is studied via Langevin and generalized Langevin dynamics simulations. The transmission coefficient for the unfold–misfold transition of amyloid-β is calculated from multiple independent trajectories that originate at the transition state with different initial velocities and are directly correlated to Kramers and Grote–Hynes theories. For lower values of the frictional coefficient, a well-defined rate constant is obtained, whereas, for higher values, the transmission coefficient decays with time, indicating a breakdown of the Kramers and Grote–Hynes theories and the emergence of a dynamic disorder, which demonstrates the presence of multiple local minima in the misfolding potential energy surface. The calculated free energy profile describes a two-state transition of amyloid-β in the energy landscape. The transition path time distribution computed from these simulations is compared with the related experimental and theoretical results for the unfold–misfold transition of amyloid-β. The high free energy barrier for this transition confirms the misfolding of amyloid-β. These findings offer an insight into the dynamics of the unfold–misfold transition of this protein.