title: Molecular dynamics simulation and computational two-dimensional infrared spectroscopic study of model amyloid β-peptide oligomers.
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.
authors: State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China.
authors: Jun
authors: J
authors: Xu
authors: John Z H
authors: JZ
authors: Zhang
authors: Yun
authors: Y
authors: Xiang
mesh_terms: D000595:Amino Acid Sequence; D016229:Amyloid beta-Peptides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry*; D055503:Protein Multimerization; D055550:Protein Stability; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D013055:Spectrophotometry, Infrared; D013696:Temperature; D014867:Water / Q000737:chemistry
chemical_list: D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; D012997:Solvents; C078592:amyloid beta-protein (1-40); D014867:Water