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Discrete molecular dynamics simulations of peptide aggregation

S. Peng·F. Ding·B. Urbanc·S. V. Buldyrev·L. Cruz·H. E. Stanley·N. V. Dokholyan
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Abstract

We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet structure. This structure has an inter-strand distance of 0.48 nm and an inter-sheet distance of 1.0 nm, which agree with experimental observations. In this model, the hydrogen bond interactions give rise to the inter-strand spacing in beta-sheets, while the Go interactions among side chains make beta-strands parallel to each other and allow beta-sheets to pack into layers. The aggregates also contain free edges which may allow for further aggregation of model peptides to form elongated fibrils.

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S. Peng, F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz, H. E. Stanley, N. V. Dokholyan. 2003-12-30. Discrete molecular dynamics simulations of peptide aggregation. https://doi.org/10.1103/physreve.69.041908

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