We study the aggregation of peptides using the discrete molecular dynamics simulations. Specifically, at temperatures above the α-helix melting temperature of a single peptide, the model peptides aggregate into a multilayer parallel β-sheet structure. This structure has an interstrand distance of $4.8\AA$ and an intersheet distance of $10\AA ,$ which agree with experimental observations. Our model explains these results as follows: hydrogen-bond interactions give rise to the interstrand spacing in $\beta$ sheets, while $\mathrm{G}ō$ interactions between side chains make $\beta$ strands parallel to each other and allow $\beta$ sheets to pack into layers. An important feature of our results is that the aggregates contain free edges, which may allow for further aggregation of model peptides to form elongated fibrils.

• Received 6 November 2003

DOI:https://doi.org/10.1103/PhysRevE.69.041908