Conformational Changes Induced by Methyl Side-Chains in Protonated Tripeptides Containing Glycine and Alanine Residues

Abstract

We present a systematic study of the conformational and isomeric populations in gas-phase protonated tripeptides containing glycine and alanine residues using infrared predissociation spectroscopy of cryogenically cooled ions. Specifically, the protonated forms of Gly-Gly-Gly, Ala-Gly-Gly, Gly-Ala-Gly, Gly-Gly-Ala, Ala-Ala-Gly, Ala-Gly-Ala, Gly-Ala-Ala, and Ala-Ala-Ala allow us to sample all permutations of the methyl side-chain position, providing a comprehensive view of the effects of this simple side-chain on the 3-D structure of the peptide. The individual structural populations for all but one of these peptide species are determined via conformer-specific IR–IR double-resonance spectroscopy and comparison with electronic structure predictions. The observed structures can be classified into three main families defined by the protonation site and the number of internal hydrogen bonds. The relative contribution of each structural family is highly dependent on the exact amino acid sequence of the tripeptide. These observed changes in structural population can be rationalized in terms of the electron-donating effect of the methyl side-chain modulating the local proton affinities of the amine and various carbonyl groups in the tripeptide.

Effects of Methyl Side Chains on the Microsolvation Structure of Protonated Tripeptides

“…Namely, protonation at the amide carbonyl, which represents 65% of the bare Ala 3 H + , disappeared upon the addition of the first water, and the majority (85%) of the population of Ala 3 H + (H 2 O) exist as N w t A . The minor isomer (35%) of bare Ala 3 H + ( N c B ) differs from the minor isomer of Gly 3 H + ( N c A ) by the number of intramolecular H-bonds, which we attributed to the electron-donating effects of the methyl side chains altering the proton affinities of the amine and carbonyl groups . A fraction of this Ala 3 H + N c B structure leads to the formation of N w c H in Ala 3 H + (H 2 O), which is predicted to be 15.9 kJ/mol higher in energy than N w t A by DFT.…”

“…Gaussian widths of 15–60 cm –1 were used for the peaks below 3300 cm –1 corresponding to hydrogen-bonded O–H and N–H groups, and a width of 7 cm –1 was used for all of the other features. The isomer naming scheme used here is similar to what we had previously used (Figure ): ,, the first letter denotes the protonation site ( N for amine, and O for amide carbonyl), the superscript denotes the configuration of the first amide bond ( c for cis and t for trans ), and the last letter denotes the energetic ordering found for the Gly 3 H + and Ala 3 H + species.…”

“…Peptides and large biomolecules can adopt a wide range of three-dimensional (3D) structures due to their highly fluxional nature. The factors that modulate the relative conformational stabilities of peptides include sterics , and intramolecular hydrogen-bond (H-bond) interactions, − both of which depend on the exact amino acid sequence. , Moreover, the presence of a solvent, particularly water, can further alter the conformational landscape through the formation of intermolecular H-bond interactions − that can compete with the intramolecular ones. For long peptides such as proteins, all of these cooperative and competitive interactions combine to define their tertiary structures and therefore dictate their functions.…”

“…However, experimental studies of these structures and interactions with traditional techniques are complicated by the simultaneous presence of multiple conformers and solvation structures, which can severely limit the relevant information that can be extracted. Here, we used conformer-specific infrared spectroscopy ,,− to probe the structures of microsolvated clusters of protonated triglycine and trialanine, revealing the influence of the methyl side chain on the solvent and peptide interactions.…”

Diserinol Isophthalamide: A Novel Reagent for Complexation with Biomolecular Anions in Electrospray Ionization Mass Spectrometry

“…As intermolecular interactions are lost, intramolecular interactions often become the most energetically favored alternative, leading to conformational changes. ,− This phenomenon is especially prominent for charged functional groups, which form stabilizing ionic hydrogen bonds with solvent molecules. ,− Two approaches are typically employed to address any differences between condensed-phase and gas-phase structures. In one approach, model structural motifs such as short peptide sequences, − α-helices, − β-sheets, ,− and β-hairpins ,, are investigated in vacuum to reveal intrinsic structural properties. Characterization of solvent adduct species can then further unravel the contribution of intermolecular interactions. ,,,− Alternatively, native condensed-phase structures are kinetically trapped upon transfer to vacuum by carefully selecting instrument parameters to minimize energy deposition during the electrospray and vacuum transfer processes. ,,,, Experimental and theoretical investigations suggest that, for many model proteins, the condensed-phase structure is largely preserved under the appropriate conditions. ,,, However, in other cases, side chain collapse occurs to accommodate intramolecular hydrogen bonding of desolvated charged moieties, resulting in structural perturbation. ,− …”