Molecular dynamics simulation and computational two-dimensional infrared spectroscopic study of model amyloid β-peptide oligomers

Jun Xu, John Zhang, Yun Xiang

Research output: Contribution to journalArticle

Abstract

Molecular dynamics simulations were carried out to study the structure stability of model amyloid β40 (Aβ40) peptide oligomers, from monomer to hexamer, in aqueous solution at room temperature. The initial oligomer models were built by using the parallel in-register β-sheet fibril structure and then allowed to relax in the simulations. Our simulation results indicated that the stable Aβ40 monomer was a random coil, while the oligomer structures became more fibril-like with the increase of the peptide strands. Linear absorption and two-dimensional infrared spectra of the isotope-labeled oligomers were calculated and analyzed in detail, which revealed the differential secondary structural features characteristic of Aβ40 aggregation. A quantitative relation was established to make connection between the calculated spectra and experimental ensemble measurements.

Original languageEnglish (US)
Pages (from-to)6373-6379
Number of pages7
JournalJournal of Physical Chemistry A
Volume117
Issue number29
DOIs
StatePublished - Jul 25 2013

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oligomers
Oligomers
Amyloid
peptides
Molecular dynamics
molecular dynamics
Infrared radiation
Peptides
Computer simulation
simulation
monomers
Monomers
registers
Isotopes
strands
coils
infrared spectra
Agglomeration
isotopes
aqueous solutions

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Molecular dynamics simulation and computational two-dimensional infrared spectroscopic study of model amyloid β-peptide oligomers. / Xu, Jun; Zhang, John; Xiang, Yun.

In: Journal of Physical Chemistry A, Vol. 117, No. 29, 25.07.2013, p. 6373-6379.

Research output: Contribution to journalArticle

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