Structures of a peptide fragment of β 2-microglobulin studied by replica-exchange molecular dynamics simulations – Towards the understanding of the mechanism of amyloid formation

Abstract

We investigate in detail the structural properties of the monomeric peptide fragment that corresponds to residues 21–31 of β 2-microglobulin. As a first step towards the understanding of the mechanism of the amyloid formation, we have performed a replica-exchange molecular dynamics simulation of this peptide with explicit water molecules. We analyze various structural properties as functions of temperature. Although the corresponding part of the native protein is a fully extended β-strand, our results show that β-hairpin structures are formed with high frequency around 310 K. We conjecture that this β-hairpin formation is closely related to the amyloid fibrillogenesis.