Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations

Abstract

Mounting spectroscopic evidence indicates that alanine predominantly adopts extended polyproline II (PPII) conformations in short polypeptides. Here we analyze Raman optical activity (ROA) spectra of N-acetylalanine-N'-methylamide (Ala dipeptide) in H2O and D2O using density functional theory on Monte Carlo (MC) sampled geometries to examine the propensity of Ala dipeptide to adopt compact right-handed (alpha(R)) and left-handed (alpha(L)) helical conformations. The computed ROA spectra based on MC-sampled alpha(R) and PPII peptide conformations contain all the key spectral features found in the measured spectra. However, there is no significant similarity between the measured and computed ROA spectra based on the alpha(L)- and beta-conformations sampled by the MC methods. This analysis suggests that Ala dipeptide populates the alpha(R) and PPII conformations but no substantial population of alpha(L)- or beta-structures, despite sampling alpha(L)- and beta-structures in our MC simulations. Thus, ROA spectra combined with the theoretical analysis allow us to determine the dominant populated structures. Including explicit solute-solvent interactions in the theoretical analysis is essential for the success of this approach.

FIGURE 1

(A) Ball and stick model for the N-acetylalanine-N′-methylamide (Ala dipeptide). The peptide backbone structure in Ala dipeptide is defined by φ- and ψ-dihedral angles. (B) Free energy differences of Ala dipeptide conformations in water computed using MC simulations. α_R, α_L, β, and PPII conformational regions are shown on the Ramachandran map. (C) the computed φ- and ψ-distribution (gray) resembles the empirically derived φ, ψ distribution of amino acid residues (black) in neither canonical helix nor sheet secondary structures in protein x-ray crystal structures (61).

FIGURE 2

SCP backscattering ROA (A and C) and Raman (B and D) spectra of H₂O-Ala dipeptide clusters. The computed spectra (black) are averaged over a collection of dipeptide conformations from PPII (A and B) and α_R (C and D) regions of the Ramachandran map (inset in A and C). The experimental spectra (gray; in arbitrary units) are from Deng et al. (48).

FIGURE 3

SCP backscattering ROA (A and C) and Raman (B and D) spectra of D₂O-Ala dipeptide clusters. The computed spectra (black) are averaged over a collection of dipeptide conformations from PPII (A and B) and α_R (C and D) regions of the Ramachandran map (inset in A and C). The experimental spectra (gray; in arbitrary units) are from Deng et al. (48).

FIGURE 4

ROA (A and C) and Raman (B and D) scattering cross section contributions of Ala dipeptide (red), water (blue), and peptide-water interactions (black) to the total ROA and Raman scattering cross sections of Ala dipeptide-water clusters (green). These computed spectra are averaged over a collection of dipeptide conformations from PPII (A and B) and α_R (C and D) regions of the Ramachandran map.

FIGURE 5

SCP backscattering ROA spectra computed (black) for a representative PPII (φ = −68° and ψ = 135°; A and C) and an α_R-conformation of Ala dipeptide (φ = −73° and ψ = −30°; B and D). Experimental spectra (gray; in arbitrary units) in H₂O (A and B) and D₂O (C and D) are from Deng et al. (48).

FIGURE 6

Group coupling matrices for the ROA intensity differences associated with the vibrations in the low wave number range decomposed into contributions from groups of atoms in Ala dipeptide for a PPII (φ = −68° and ψ = 135°; A) and an α_R (φ = −73° and ψ = −30°; B) conformation. The groups of atoms in Ala dipeptide are shown in panel I. Positive and negative ROA intensity differences are shown as black and gray circles, respectively.