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 obtained 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.

Conformation of Polyalanine and Polyglycine Dications in the Gas Phase: Insight from Ion Mobility Spectrometry and Replica-Exchange Molecular Dynamics

“…29 Following such lines, the relation between sequence and conformation has been addressed, for example through the substitution of alanine by other residues at different locations, and by incorporating charged residues in the middle of the sequence. 8,30,31 The present work builds upon this effort by systematically investigating how each natural amino acid affects the secondary structure of alanine-and glycine-based peptides. In this purpose ion mobility experiments have been performed together with replica-exchange molecular dynamics simulations.…”

The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions

“…Ruotolo et al showed that gas-phase [M ϩ H] ϩ ions of LLGNVLVVVLAR (derived from bovine hemoglobin) prefer extended (helical) structure(s) resulting in a larger collision cross-section than random coil structures having the same or similar m/z values [12,13], while some post-translationally modified (PTM) peptide ions (phosphopeptides) tend to pack more tightly than the unmodified protonated peptide ions owing to intra-molecular charge-solvation and/or formation of salt-bridged type structures [16,17]. In addition, we have used chemical derivatization via acetylation of the N-terminus and internal basic lysine residues and methylation of the acidic glutamic residues to show that the helical propensity of a given peptide can be increased by reducing the number of 'salt-bridge' intramolecular interactions [18].…”

Effects of charge states, charge sites and side chain interactions on conformational preferences of a series of model peptide ions

“…That is, the dielectric environment of the cell membranes ( = 2) is similar to that of a vacuum ( = 1), but it differs greatly from that of an aqueous solution ( = 80) 53 . Therefore, studies 45 , their counterparts carrying multiple charges in the gas phase have not been examined using ion mobility. Figure 3 shows To interpret the experimental data in an extended conformation, and alternatively more charged lysines also collapse helical structure by breaking backbone H-bonds to form charge-solvated structures.…”

“…In prior IM-MS studies of the singlycharged ions for the two peptides, it was found that gas phase ions of AKn (n = 3-6) have higher helical content (ca. 60% helical) than AEKn, and helical propensity is the highest when charge is aligned with the helix macrodipole, i.e., the charge is located on or near the C-termini 45 . Despite extensive studies of the AKn and AEKn series, the following questions still remain unanswered: (i) how do charge sites and charge states affect conformer preferences; (ii) how do intramolecular interactions involving the polar side chains affect conformer preferences; and (iii) is there any relationship between solution phase and gas phase conformations?…”

“…The model peptides used in this study have been used previously by several groups to probe helical propensities of alanine-containing peptides in solution 43,44 and in low dielectric gas phase (solvent-free) environments 45 . Previous CD studies show that in solution, the helical content of both AKn and AEKn increases as n increases 43,44,46 , and the helical content of AEKn is higher than that of AKn for peptides of comparable length owing to the stabilization afforded by salt bridges.…”