Factors that influence helical preferences for singly charged gas-phase peptide ions: the effects of multiple potential charge-carrying sites

Abstract

Ion mobility-mass spectrometry is used to investigate the structure(s) of a series of model peptide [M + H](+) ions to better understand how intrinsic properties affect structure in low dielectric environments. The influence of peptide length, amino acid sequence, and composition on gas-phase structure is examined for a series of model peptides that have been previously studied in solution. Collision cross sections for the [M + H](+) ions of Ac-(AAKAA)(n)Y-NH(2) (n = 3-6) and Ac-Y(AEAAKA)(n)F-NH(2) (n = 2-5) are reported and correlated with candidate structures generated using molecular modeling techniques. The [M + H](+) ions of the AAKAA peptide series each exhibit a single, dominant ion mobility arrival time distribution (ATD) which correlates to partial helical structures, whereas the [M + H](+) ions of the AEAAKA ion series are composed of ATDs which correlate to charge-solvated globules (i.e., the charge is coordinated or solvated by polar peptide functional groups). These data raise numerous questions concerning intrinsic properties (amino acid sequence and composition as well as charge location) that dictate gas-phase peptide ion structure, which may reflect trends for peptide ion structure in low dielectric environments, such as transmembrane segments.

Figure 1

Ion mobility arrival time distribution (ATD, t_d, upper x-axis) and collision cross-section (Ω, lower x-axis) profiles for [M + H]⁺ ions of (A) Ac-(AAKAA)_nY-NH₂ (n = 3, 4, 5, and 6) and (B) Ac-Y(AEAAKA)_nF-NH₂ (n = 2, 3, 4, and 5). The dashed vertical lines represent the predicted collision cross-sections for globular peptide mobility-mass correlation (a best-fit to a dataset of collision cross-sections (see text)) and the solid vertical lines represent the α-helical ion mobility-mass correlation (calculated collision cross-sections for α-helices of the same amino acid sequence). The shaded profiles are simulated IM profiles for a single collision cross-section, assuming peak broadening is solely due to longitudinal diffusion.

Figure 2

The lowest energy structures generated using molecular dynamics simulations for [M + H]⁺ ions of (A) for Ac-(AAKAA)_nY-NH₂ (n = 3, 4, 5, and 6) and (B) Ac-Y(AEAAKA)_nF-NH₂ (n = 2, 3, 4, and 5). (C) Enlarged view of two charge solvation networks within the modeled structures of (i) AAKAA n = 3 and (ii) AEAAKA n = 3. “N” and “C” indicate the N- and C-termini, respectively. The protonated lysine side chains and all atoms H-bonded to the proton are shown in cylinder representation and dashed green lines represent H-bonds.

Figure 3

Plot of gas- (Eq. 2, [—]) and solution-phase (---) helical content versus number of basic amino acid residues for the AAKAA (■) and AEAAKA (▲). Error bars represent ±1σ for 10 measurements. Solution-phase data taken from Scholtz et al. and adapted from Rohl et al. using AGADIR.,,

Figure 4

Arrival time distributions plotted in terms of collision cross-section for [M + H]⁺ ions of (A) unmodified, (B) methylester-derivatized, (C) acetylated, and (D) sodium-coordinated AEAAKA, n = 2. Panel A contains peak fitting data with peak widths constrained by peak broadening owing solely to longitudinal diffusion (shaded). The solid line is the measured ATD (parent profile). The theoretical subpopulations are filled under the parent profile and the dotted line is the composite fit (in most cases beneath the solid line). The residuals from the deconvolution analysis (not shown) were R² > 0.99. Inset in B, C and D is a predicted peak profile for the indicated collision cross-section broadened only by longitudinal diffusion (shaded). The dashed vertical line represent the globular mobility-mass correlation and the solid vertical line represent thehelical mobility-mass correlation as described in Figure 1.

Figure 5

Arrival time distributions for [M + H]+ ions of (A) Ac-(AAKAA)₃Y-NH₂, (B) Ac-(AAKAA)₆Y-NH₂, (C) Ac-Y(AEAAKA)₃F-NH₂ and (D) Ac-Y(AEAAKA)₄F-NH₂ are shown for 0, 50, and 100 V lab frame ion injection energies. The dashed vertical lines represent the globular mobility-mass correlation and the solid vertical lines represent the helical mobility-mass correlation as described in Figure 1.

Figure 6

Peak deconvolution analysis constrained using peak widths derived from Monte Carlo simulations for AAKAA n = 6 [M + H]⁺ ion (1700V, 100V injection potential). The solid line is the measured IM profile (parent profile). The theoretical subpopulations are shown under the parent profile and the dotted line is the composite fit. The residuals from the deconvolution analysis are shown in the bottom panel (R² > 0.99).