Structural analyses of experimental 13C edited amide I' IR and VCD for peptide β-sheet aggregates and fibrils using DFT-based spectral simulations.
In the preceding paper, computational models based on density functional theory (DFT) were presented to characterize the sensitivity of vibrational spectroscopic methods (IR, VCD, and Raman) to structural features of β-sheets. Isotopically edited amide I' IR for peptides labeled with (13)C in multiple different sites provides the most structurally distinct signatures of strand alignment, while VCD is sensitive to the sheet twist and intersheet stacking. In this report, we simulate the IR and VCD spectra for models approximating structures of four β-sheet forming peptides previously experimentally studied using these methods with (13)C isotopic editing. Various register alignments are tested. Agreement with experiment is evaluated based on frequency shifts of both the (12)C and (13)C IR amide I' signals, relative intensity patterns, and VCD spectra where available. While for the simulation of IR spectra canonical planar sheets provide a sufficient model system, for VCD simulation twisted, stacked sheets are required in order to reproduce strong couplet-like amide I' VCD. Effects of the solvent (water) and amino acid side chains are also tested by using a simplified, electrostatic solvent model and atomic partial charges for the side chains. Very good agreement with experimental spectra is obtained, particularly for the relative (12)C and (13)C band frequencies. All four peptide models are shown to be antiparallel as had previously been assumed. However, in some cases our simulations are consistent with different register alignment of strands than originally proposed.
Department of Chemistry, University of Wyoming , Laramie, Wyoming 82071, United States.
William R W
WR
Welch
Timothy A
TA
Keiderling
Jan
J
Kubelka
D000577:Amides / Q000737:chemistry*; D016229:Amyloid beta-Peptides / Q000737:chemistry / Q000378:metabolism; D002247:Carbon Isotopes / Q000737:chemistry; D002942:Circular Dichroism; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D013055:Spectrophotometry, Infrared; D055672:Static Electricity
D000577:Amides; D016229:Amyloid beta-Peptides; D002247:Carbon Isotopes; D010446:Peptide Fragments; D010455:Peptides; D012997:Solvents; C417223:amyloid beta-protein (16-22); C551682:amyloid beta-protein (34-42)