Development and validation of transferable amide I vibrational frequency maps for peptides

Abstract

Infrared (IR) spectroscopy of the amide I band has been widely utilized for the analysis of peptides and proteins. Theoretical modeling of IR spectra of proteins requires an accurate and efficient description of the amide I frequencies. In this paper, amide I frequency maps for protein backbone and side chain groups are developed from experimental spectra and vibrational lifetimes of N-methylacetamide and acetamide in different solvents. The frequency maps, along with established nearest-neighbor frequency shift and coupling schemes, are then applied to a variety of peptides in aqueous solution and reproduce experimental spectra well. The frequency maps are designed to be transferable to different environments; therefore, they can be used for heterogeneous systems, such as membrane proteins.

Figure 1

Molecular structures of (a) NMAD, (b) ACED, (c) AAO, and (d) AGO.

Figure 2

Simulated and experimental absorption spectra of (a) NMAD and (b) ACED in different solvents. The experimental spectrum of NMAD in D₂O is from DeCamp et al. The experimental spectrum of ACED in CHCl₃ has two peaks and is not shown in the figure.

Figure 3

Theoretical and experimental IR absorption spectra of AAO and AGO in aqueous D₂O solutions.

Figure 4

Sequences of peptides in this study: the AKA peptide, Trpzip2, rIAPP, and hIAPP. Different residues between rIAPP and hIAPP are shown in red in the rIAPP sequence. In both IAPP proteins, Cys2 and Cys7 are connected with disulfide bonds.

Figure 5

Representative snapshots of (a) AKA and (b) Trpzip2.

Figure 6

Theoretical and experimental IR absorption spectra of (a) unlabeled and (b) [12] labeled AKA peptide.

Figure 7

¹³C=¹⁸O labeled peak frequencies as a function of residue number for the AKA peptide. The theoretical isotope shift is taken to be −70 cm⁻¹. Experimental isotope-labeled peak frequencies are shown for residues 12–15.

Figure 8

Theoretical and experimental IR absorption spectra of (a) unlabeled, and (b) T3*– T10* labeled Trpzip2 in D₂O.

Figure 9

¹³C-labeled peak frequencies as a function of residue number for Trpzip2. Residue 13 is the side chain chromophore on Asn6. The theoretical isotope shift is taken to be −43 cm⁻¹. Also shown are experimental^, isotope-labeled peak frequencies at residues 2, 3, 7, and 10.

Figure 10

Representative snapshots of rIAPP monomer in (a) folded, and (b) random coil conformation..

Figure 11

Theoretical (weighted average) and experimental IR line shapes in the amide I stretch region of rIAPP in D₂O. Also shown are line shapes for the folded and random coil states, weighted by their relative probabilities.

Figure 12

Representative snapshots of hIAPP monomer in (a) α-helical, (b) β-hairpin, and (c) random coil conformation.

Figure 13

Theoretical (weighted average) and experimental IR line shapes in the amide I stretch region of hIAPP in D₂O. Also shown are line shapes for the α-helical, β-hairpin, and random coil states, weighted by their relative probabilities.