DFT-Level Calculations of IR, VCD and Raman Spectra for 13C-Labeled Beta Sheets

Abstract

With the aid of theoretical models, optical spectroscopy has proven valuable for elucidating secondary structural features in protein systems including β-sheets, which form a large portion of protein assemblies in amyloid systems. For such large systems, computational methods must be both efficient and robust in order to achieve accurate predictions in a timely manner. Quantum chemical methods are in principle the most robust methods available, but suffer from high computational cost that usually makes them impractical for large bimolecular assemblies. In this study optical spectra for β-sheets composed of five strands, ten-amides each, 5x10, were obtained by transferring parameters calculated using DFT for smaller 3x3 sheet segments. Sensitivity of spectra to variations in conformations was examined for parallel, anti-parallel, twisted and flat sheets. Some effects of having strands shifted out of register were also explored. Predicted amide I IR spectra show classic features for parallel and anti-parallel sheets and some new possibilities for discerning between the two are observed, primarily in IR and VCD spectra, while Raman amide I spectra was predicted to be less useful for structural discrimination. Predictions for particular isotopic labeling schemes show clear IR patterns that might be used in elucidating shifts in register for anti-parallel sheets.