Structures of a peptide fragment of β2‐microglobulin studied by replica‐exchange molecular dynamics simulations – Towards the understanding of the mechanism of amyloid formation

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Abstract
We investigate in detail the structural properties of the monomeric peptide fragment that corresponds to residues 21–31 of β2‐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.