Discrete molecular dynamics simulations of peptide aggregation

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 [Formula presented] and an intersheet distance of [Formula presented] which agree with experimental observations. Our model explains these results as follows: hydrogen-bond interactions give rise to the interstrand spacing in [Formula presented] sheets, while [Formula presented] interactions between side chains make [Formula presented] strands parallel to each other and allow [Formula presented] 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.