title: Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?
abstract: We report density functional theory (DFT) calculations of the Raman spectra for hexapeptides of glutamic acid and lysine in three different conformations (alpha, beta and PPII). The wave numbers of amide I, amide II and amide III bands of all three conformations predicted at B3LYP/6-31G and B3LYP/6-31G* are in good agreement with previously reported experimental values of polyglutamic acid and polylysine. Agreement with experiment improves when polarization functions are included in the basis set. Explicit water molecules, H-bonded to the backbone amide groups were found to be absolutely necessary to obtain this agreement. Our results indicate that DFT is a promising tool for assignment of the spectral data on kinetics of conformational changes for peptides during amyloid formation.
authors.affiliation: NanoScience Technology Center and Department of Chemistry, University of Central Florida, Orlando, FL 32826, USA.
authors.forename: Workalemahu Mikre
authors.initials: WM
authors.lastname: Berhanu
authors.forename: Ivan A
authors.initials: IA
authors.lastname: Mikhailov
authors.forename: Artëm E
authors.initials: AE
authors.lastname: Masunov
mesh_terms: D000682:Amyloid / Q000737:chemistry*; D018698:Glutamic Acid / Q000737:chemistry; D006860:Hydrogen Bonding; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D009842:Oligopeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013059:Spectrum Analysis, Raman / Q000379:methods*; D014867:Water / Q000737:chemistry
chemical_list: D000682:Amyloid; D009842:Oligopeptides; D010455:Peptides; D014867:Water; C011083:polyproline; D018698:Glutamic Acid; D008239:Lysine