The structure of gas-phase bradykinin fragment 1–5 (RPPGF) ions: An ion mobility spectrometry and H/D exchange ion-molecule reaction chemistry study

Abstract

Ion mobility-mass spectrometry (IM-MS) data is interpreted as evidence that gas-phase bradykinin fragment 1-5 (BK1-5, RPPGF) [M ϩ H] ϩ ions exist as three distinct structural forms, and the relative abundances of the structural forms depend on the solvent used to prepare the matrix-assisted laser desorption ionization (MALDI) samples. Samples prepared from organic rich solvents (90% methanol/10% water) yield ions having an ion mobility arrival-time distribution (ATD) that is dominated by a single peak; conversely, samples prepared using mostly aqueous solvents (10% methanol/90% water) yield an ATD composed of three distinct peaks. The BK1-5 [M ϩ H] ϩ ions were also studied by gas-phase hydrogen/deuterium (H/D) exchange ion-molecule reactions and this data supports our interpretation of the IM-MS data. Plausible structures for BK1-5 ions were generated by molecular dynamics (MD). Candidate MD-generated structures correlated to measured cross-sections suggest a compact conformer containing a ␤-turn whereas a more extended, open form does not contain such an interaction. This study illustrates the importance of intra-molecular interactions in the stabilization of the gas-phase ions, and these results clearly illustrate that solution-phase parameters (i.e., MALDI sample preparation) greatly influence the structures of gas-phase ions. tudies of peptide and protein structure play a major role in modern molecular biophysics and drive development of new, more specific and sensitive techniques. Gas-phase techniques for sequencing peptides and proteins are well established, and significant progress has been made in developing similar techniques for characterization of secondary (2°) and tertiary (3°) structures of gas-phase peptides/proteins [1][2][3][4][5]. Such studies increase our understanding of intra-molecular interactions and drive development of sequencing algorithms, but the relevance of gas-phase structure, structure in the absence of solvent [6], to solution-phase structure is still an open issue. The most important role of solvent is charge stabilization, and in the gas phase, charge stabilization occurs by intramolecular interactions [7]. Rapid progress is being made in the development of techniques that allow selective solvation (in terms of number of solvent molecules) of gas-phase peptide/protein ions [8], and these studies may serve to further our understanding of how solvent affects structure and function. In addition, gas-phase studies could enhance our understanding of intra-molecular interactions (i.e., hydrogen bonding, van der Waals interactions and hydrophobic forces), as well as how such interactions influence conformations in the solution phase or low dielectric environments (i.e., gas phase, membranes, and/or multimeric complexes).Bradykinin (amino acid sequence RPPGFSPR) has been extensively studied using both experimental and computational techniques. Bradykinin is an excellent model peptide for structural studies because the presence of arginine (R) at both the N-and C-terminus can potent...

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

“…We assumed that protonation occurred on the guanidine group owing to the high proton affinity (PA ϭ 251.2 kcal/mol) for arginine [23], but we also considered whether the most stable structure of the [M ϩ H] ϩ ion is a charge-solvated species, as suggested by Simon et al [31], or zwitterionic species, as suggested by Strittmatter and Williams [28]. To address this question, we used a combination of collision cross-sections obtained by using ion mobility spectrometry (IMS) [45] [46]. Note also that the collision cross-section for [GR ϩ H] ϩ is larger than that for [RG ϩ H] ϩ , and the methyl esters exhibit the same ordering.…”

Fragmentation of doubly-protonated peptide ion populations labeled by H/D exchange with CD3OD

“…The ion mobility and H/D exchange of the nonapeptide bradykinin and related analogues have been extensively studied [10,12,[15][16][17][18][19][20][21][22][23][24][25][26][27][28]. Ion mobility measurements have shown that the singly-and doubly-protonated ions of bradykinin have a similar cross-section, while the triplyprotonated ion has a cross-section that is approximately 15% larger, providing evidence for a much less compact structure [15][16][17].…”

Detection of oligonucleotide gas-phase conformers: H/D exchange and ion mobility as complementary techniques

“…Gas-phase hydrogen/deuterium exchange of small oligonucleotides (dTG, dC 6 and C 6 ) with CD 3 0D was performed in the second hexapole of a Fourier transform ion-cyclotron resonance (FTICR) mass spectrometer. Ion activation experiments were conducted by accelerating the ions at the entrance of the H/D exchange cell under conditions promoting exclusively collisional isomerization.…”

“…The rate of gasphase H/D exchange has been shown to be a function of the reagent used for exchange (nature and concentration), the charge state of the biomolecule, the gasphase basicity/acidity of exchangeable sites, and the internal structure of the biomolecular ions [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18]. Probing the number of exchanged hydrogens and the H/D exchange kinetics makes it possible to distinguish ion populations and to elucidate their structural and thermochemical features.…”

“…Studies combining these two techniques have illustrated the difficulty to compare results from H/D exchange with ion mobility results because these two methods probe different physical properties of an ion [5,6]. In the present work, ion mobility measurements are used to investigate oligonucleotide structures independently of the H/D exchange experiments.…”