Revealing hidden helix propensity in Aβ peptides by molecular dynamics simulations

Using all-atom explicit solvent model and exhaustive replica exchange molecular dynamics simulations we studied the conformational ensembles of several amino-truncated Aβ peptides. In our simulations we specifically monitored the formation of helix structure in the C-terminals of various Aβ fragments. We show that the equilibrium distributions of structures adopted by Aβ23-40 and Aβ10-40 are similar, but sharply distinct from the conformational ensemble of Aβ29-40. The latter features a stable helical structure not present in longer fragments. Because the λ-expansion method applied to Aβ23-40 identified Lys28 as the residue producing the strongest impact on the C-terminal helix structure, we hypothesized that addition of a single Lys28 to Aβ29-40 would change the peptide's conformational ensemble. REMD simulations of Aβ28-40 confirmed this expectation by showing that in this peptide the helix conformation is destabilized and it adopts structures similar to those of Aβ23-40 and Aβ10-40. Therefore, a major conformational switch in the Aβ C-terminal occurs by truncating Aβ peptide after the position Lys28. By comparing our findings with previous studies we argue that Aβ C-terminal harbors helical propensity, which can be revealed by various factors, including environment, ligand binding, or sequence truncation.