Effect of urea concentration on aggregation of amyloidogenic hexapeptides (NFGAIL)

We have performed large-scale all-atom molecular dynamics (MD) simulations to study the aggregation behavior of four NFGAIL hexapeptides in the aqueous urea solution, with a urea concentration ranging from 0 to 5 M. We find that urea in general suppresses the peptide aggregation, but suppression slows down in the intermediation concentration regime around 3 M. Two competing mechanisms of urea are determined: urea molecules accumulated near the first solvation shell (FSS) tend to unfold the hexapeptide, which favors aggregation; on the other hand, the tight hydrogen bonds formed between urea and peptide mainchains hinder the association of peptides which disfavors the formation of the β-sheet. Furthermore, the different nonlinear urea concentration dependences of the urea-peptide and peptide-peptide hydrogen bonds lead to a nonmonotonic behavior, with a weak enhancement in the peptide aggregation around 3 M.