pH-dependent conformations of the amyloid β(1-28) peptide fragment explored using molecular dynamics

Kent Kirshenbaum, Valerie Daggett

Research output: Contribution to journalArticle

Abstract

Molecular dynamics simulations were used to successfully reproduce the experimentally observed pH-dependent conformational behavior of a monomeric peptide in aqueous solution. Simulations were conducted at 298 K on a peptide corresponding to residues 1-28 of the amyloid β-peptide [referred to as β(1-28)], which is the primary component of the plaques associated with Alzheimer's disease. β(1-28) was found to be entirely α-helical at low pH. Upon deprotonation of acidic residues at medium pH, helical structure was lost in the N-terminal region. At high pH, some secondary structure was recovered to yield two helices joined by a kink. These results are in good agreement with the NMR solution structure at low pH [Zagorski and Barrow (1992) Biochemistry 31, 5621-5631; Talafous et al. (1994) Biochemistry 33, 7788-7796] and CD and NMR evidence of an α-helix to β-sheet transition at mid-range pH [Barrow et al. (1992) J. Mol. Biol 225, 1075-1093]. Additional simulations were also able to regenerate folded species from partially unfolded conformers. A mechanism for the pH-dependent structural rearrangements is proposed that involves the creation of a hydrogen-bonded pair between Ser 8 and Glu 11. The evidence for the existence of a multiconformational equilibrium of folded and unfolded species of the peptide is discussed.

Original languageEnglish (US)
Pages (from-to)7629-7639
Number of pages11
JournalBiochemistry
Volume34
Issue number23
StatePublished - 1995

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Peptide Fragments
Molecular Dynamics Simulation
Amyloid
Conformations
Molecular dynamics
Peptides
Biochemistry
Nuclear magnetic resonance
Deprotonation
Hydrogen
Computer simulation
Alzheimer Disease

ASJC Scopus subject areas

  • Biochemistry

Cite this

pH-dependent conformations of the amyloid β(1-28) peptide fragment explored using molecular dynamics. / Kirshenbaum, Kent; Daggett, Valerie.

In: Biochemistry, Vol. 34, No. 23, 1995, p. 7629-7639.

Research output: Contribution to journalArticle

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