Sequence Effects on the Conformational Properties of the Amyloid β(1 -28) Peptide: Testing a Proposed Mechanism for the α → β Transition

Molecular dynamics simulations have been used to successfully reproduce the observed pHdependent conformational properties of the amyloid β(1 - 28) peptide [Kirshenbaum and Daggett (1995) Biochemistry, 34, 7629-7639]. On the basis of these simulations a mechanism was proposed for the unfolding of the N-terminal portion of the peptide at neutral pH when beginning from the helical conformation. It was proposed that interactions between the side chains of Ser 8 and Glu 11 are important in determining the pH dependence of the helix content. Here we further investigate this proposed mechanism and the residues involved in the conformational transition by performing computational “mutagenesis” studies. On the basis of simulations of the mutant peptides, the importance of the Ser 8-Glu 11 interaction is substantiated, and further details of the conformational transition are elucidated.