Journal of Physical Chemistry B, Vol.114, No.39, 12701-12707, 2010
Model Amyloid Peptide B18 Monomer and Dimer Studied by Replica Exchange Molecular Dynamics Simulations
Peptide misfolding and aggregation are the early steps during the formation of amyloid fibrils. Understanding these processes in detail is crucial for the development of therapeutic strategies against amyloid diseases. Here I present temperature replica exchange molecular dynamics (TREMD) simulations of the model amyloid peptide B18 in the mono- and dimeric states in explicit aqueous solution. Both the monomer and the dimer involve beta-sheets consisting of different residues in different registers with comparable statistical weight. The dimer forms Mira- as well as intermolecular beta-sheets. The average beta-sheet content is in agreement with previous estimates from circular dichroism (CD) spectra for monomers and is lower for dimers. The tendency of 13 18 to form beta-sheets likely contributes to its fibrillogenic property. For both the monomer and the dimer, individual peptides form U-shaped or other partially collapsed conformations. Combined with data from electron microscopy, this suggests that for higher aggregates during fibrillization B18 undergoes a transition from U-shaped to outstretched conformations. The tendency of B 18 to form U-shaped conformations, intramolecular beta-sheets, and intermolecular beta-sheets with different register will contribute to the lag phase for fibril formation.