Gas-phase fragmentation of oligoproline peptide ions lacking easily mobilizable protons.
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ABSTRACT:
SUBMITTER: Rudowska M
PROVIDER: S-EPMC3650240 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:RationaleSchiff base modification of peptides has been shown to facilitate their primary structural characterization via tandem mass spectrometry. However, we have discovered a novel rearrangement reaction via ion trap collisional activation involving the imine of the Schiff base and one of several functional groups, particularly the side chains of the basic residues lysine, arginine, and histidine, in the peptide.MethodsGas-phase ion/ion reactions involving an aldehyde-containing reagent were used to generate Schiff-base-modified model peptides in a hybrid triple quadrupole/linear ion trap tandem mass spectrometer. Subsequent ion trap collisional activation was used to study the rearrangement reaction.ResultsSchiff-base-modified peptide ions were found to undergo a rearrangement reaction that was observed to be either a major or minor contributor to the product ion spectrum, depending upon a variety of factors that include, for example, ion polarity, identity of the nucleophile in the peptide (e.g., side chains of lysine, histidine, and arginine), and the position of the nucleophile relative to the imine.ConclusionsRelatively low-energy rearrangement reactions can occur in Schiff-base-modified peptide ions that involve the imine of the Schiff base and a nucleophile present in the polypeptide. While this rearrangement process does not appear to compromise the structural information that can be generated via collisional activation of Schiff-base-modified peptide ions, it can siphon away signal from the structurally diagnostic processes in some instances.
| S-EPMC6657513 | biostudies-literature
Project description:The fragmentation characteristics of b7 ions produced from proline-containing heptapeptides have been studied in detail. The study has utilized the following C-terminally amidated model peptides: PA6, APA5, A2PA4, A3PA3, A4PA2, A5PA, A6P, PYAGFLV, PAGFLVY, PGFLVYA, PFLVYAG, PLVYAGF, PVYAGFL, YPAGFLV, YAPGFLV, YAGPFLV, YAGFPLV, YAGFLPV, YAGFLVP, PYAFLVG, PVLFYAG, A2PXA3, and A2XPA3 (where X = C, D, F, G, L, V, and Y, respectively). The results have shown that b7 ions undergo head-to-tail cyclization and form a macrocyclic structure. Under the collision-induced dissociation (CID) condition, it generates nondirect sequence ions regardless of the position of the proline and the neighboring amino acid residues. This study highlights the unusual and unique fragmentation behavior of proline-containing heptapeptides. Following the head-to-tail cyclization, the ring opens up and places the proline residue in the N-terminal position while forming a regular oxazolone form of b2 ions for all peptide series. Then, the fragmentation reaction pathway is followed by the elimination of proline with its C-terminal neighbor residue as an oxazolone (e.g., PXoxa) for all proline-containing peptide series.
| S-EPMC10401712 | biostudies-literature
Project description:The effect of infrared (IR) irradiation on the electron capture dissociation (ECD) fragmentation pattern of peptide ions was investigated. IR heating increases the internal energy of the precursor ion, which often amplifies secondary fragmentation, resulting in the formation of w-type ions as well as other secondary fragments. Improved sequence coverage was observed with IR irradiation before ECD, likely due to the increased conformational heterogeneity upon IR heating, rather than faster breakdown of the initially formed product ion complex, as IR heating after ECD did not have similar effect. Although the ECD fragment ion yield of peptide ions does not typically increase with IR heating, in double resonance (DR) ECD experiments, fragment ion yield may be reduced by fast resonant ejection of the charge reduced molecular species, and becomes dependent on the folding state of the precursor ion. In this work, the fragment ion yield was monitored as a function of the delay between IR irradiation and the DR-ECD event to study the gas-phase folding kinetics of the peptide ions. Furthermore, the degree of intracomplex hydrogen transfer of the ECD fragment ion pair was used to probe the folding state of the precursor ion. Both methods gave similar refolding time constants of approximately 1.5 s(-1), revealing that gaseous peptide ions often refold in less than a second, much faster than their protein counterparts. It was also found from the IR-DR-ECD study that the intramolecular H. transfer rate can be an order of magnitude higher than that of the separation of the long-lived c/z product ion complexes, explaining the common observation of c. and z type ions in ECD experiments.
| S-EPMC3117249 | biostudies-literature
Project description:Electrospray ionization of methanolic solutions of p-hydroxyphenacyl derivatives HO-C(6)H(4)-C(O)-CH(2)-X (X = leaving group) provides abundant signals for the deprotonated species which are assigned to the corresponding phenolate anions (-)O-C(6)H(4)-C(O)-CH(2)-X. Upon collisional activation in the gas phase, these anions inter alia undergo loss of a neutral "C(8)H(6)O(2)" species concomitant with formation of the corresponding anions X(-). The energies required for the loss of the neutral roughly correlate with the gas phase acidities of the conjugate acids (HX). Extensive theoretical studies performed for X = CF(3)COO in order to reveal the energetically most favorable pathway for the formation of neutral "C(8)H(6)O(2)" suggest three different routes of similar energy demands, involving a spirocyclopropanone, epoxide formation, and a diradical, respectively.
| S-EPMC3065380 | biostudies-literature
Project description:Nitro-fatty acids are electrophilic signaling mediators formed in increased amounts during inflammation by nitric oxide and nitrite-dependent redox reactions. A more rigorous characterization of endogenously-generated species requires additional understanding of their gas-phase induced fragmentation. Thus, collision induced dissociation (CID) of nitroalkane and nitroalkene groups in fatty acids were studied in the negative ion mode to provide mass spectrometric tools for their structural characterization. Fragmentation of nitroalkanes occurred mainly through loss of the NO(2)(-) anion or neutral loss of HNO(2). The CID of nitroalkenes proceeds via a more complex cyclization, followed by fragmentation to nitrile and aldehyde products. Gas-phase fragmentation of nitroalkene functional groups with additional γ or δ unsaturation occurred through a multiple step cyclization reaction process, leading to 5 and 6 member ring heterocyclic products and carbon chain fragmentation. Cyclization products were not obtained during nitroalkane fragmentation, highlighting the role of double bond π electrons during NO(2)(-) rearrangements, stabilization and heterocycle formation. The proposed structures, mechanisms and products of fragmentation are supported by analysis of (13)C and (15)N labeled parent molecules, 6 different nitroalkene positional isomers, 6 nitroalkane positional isomers, accurate mass determinations at high resolution and quantum mechanics calculations. Multiple key diagnostic ion fragments were obtained through this analysis, allowing for the precise placement of double bonds and sites of fatty acid nitration, thus supporting an ability to predict nitro positions in biological samples.
| S-EPMC3286133 | biostudies-literature
Project description:Intra-molecular and inter-molecular cross-linking of protonated polypeptide ions in the gas phase via ion/ion reactions have been demonstrated using N-hydroxysulfosuccinimide (sulfo-NHS)- based reagent anions. The initial step in the ion/ion reaction involves the formation of a long-lived complex between the peptide and reagent, which is a prerequisite for the covalent bioconjugation chemistry. The sulfonate groups on the NHS rings of the homo-bifunctional cross-linking reagents have high affinity for the protonated sites in the peptide and, therefore, facilitate the long-lived complex formation. In addition to the formation of a long-lived chemical complex, intra-molecular cross-linking also requires two unprotonated primary amine sites within a molecule where the covalent modification takes place. Alternatively, inter-molecular cross-linking demands the availability of one neutral primary amine site in each of the two peptides that are being cross-linked. Nucleophilic displacement of two sulfo-NHS groups by the amine functionalities in the peptide is a signature of the covalent cross-linking chemistry in the gas phase. Upon removal of the two sulfo-NHS groups, two amide bonds are formed between an unprotonated, primary amine group of a lysine side chain in the peptide and the carboxyl group in the reagent.
| S-EPMC3241442 | biostudies-literature
Project description:Integral membrane proteins (IMPs) are of great biophysical and clinical interest because of the key role they play in many cellular processes. Here, a comprehensive top down study of 152 IMPs and 277 soluble proteins from human H1299 cells including 11?087 fragments obtained from collisionally activated dissociation (CAD), 6452 from higher-energy collisional dissociation (HCD), and 2981 from electron transfer dissociation (ETD) shows their great utility and complementarity for the identification and characterization of IMPs. A central finding is that ETD is ?2-fold more likely to cleave in soluble regions than threshold fragmentation methods, whereas the reverse is observed in transmembrane domains with an observed ?4-fold bias toward CAD and HCD. The location of charges just prior to dissociation is consistent with this directed fragmentation: protons remain localized on basic residues during ETD but easily mobilize along the backbone during collisional activation. The fragmentation driven by these protons, which is most often observed in transmembrane domains, both is of higher yield and occurs over a greater number of backbone cleavage sites. Further, while threshold dissociation events in transmembrane domains are on average 10.1 (CAD) and 9.2 (HCD) residues distant from the nearest charge site (R, K, H, N-terminus), fragmentation is strongly influenced by the N- or C-terminal position relative to that site: the ratio of observed b- to y-fragments is ?1:3 if the cleavage occurs >7 residues N-terminal and ?3:1 if it occurs >7 residues C-terminal to the nearest basic site. Threshold dissociation products driven by a mobilized proton appear to be strongly dependent on not only relative position of a charge site but also N- or C-terminal directionality of proton movement.
| S-EPMC4018139 | biostudies-literature
Project description:Ab initio molecular dynamics (AIMD) with density functional theory (DFT) was applied to explore conformational motions and collision cross sections (Ω) of folded (2) and extended (7) conformers of doubly charged peptide ions, (Ala-Ala-Leu-Arg + 2H)(2+), in the gas phase at 300 and 473 K. The experimental Ω of (Ala-Ala-Leu-Arg +2H)(2+) was measured as 149 ± 1.2 Å(2) at 298 K. Thermally distributed mean values of Ω for 2 and 7 at 300 and 473 K were only 0.8-1.1% larger than for the equilibrium 0 K structures. Long (>10 ps) trajectory calculations indicated entropy-driven conformational change of 2 to 7 that occurred at random within a ∼ 4 ps time window. The experimental Ω was found to fit the calculated population averaged values for 2 and 7, indicating a rapid conformer interconversion. Overall, thermal breathing had only a minor effect on the peptide ion collision cross sections.
| S-EPMC5032842 | biostudies-literature
Project description:Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.
| S-EPMC7116074 | biostudies-literature
Project description:Protonated tryptic peptides, somatostatin-14, and oxytocin have been subjected to reactions with doubly deprotonated 4-formyl-1,3-benzenedisulfonic acid (FBDSA) in the gas phase. The major product is a negatively-charged complex comprised of the peptide and the reagent. Upon dehydration of the complex, all peptides show evidence for Schiff base formation involving a primary amine of the peptide. Some peptides also show evidence for the formation of a relatively strong electrostatic interaction without Schiff base formation (i.e., a mixture of isomeric precursor ions is generated upon dehydration of the complex). Ion trap collision-induced dissociation of the dehydration products from all peptides examined gave distinct product ion spectra relative to the deprotonated and protonated forms of the peptides. The distinct behavior of the modified ions is attributed to the highly stable charge carrying sulfonate group, which tends to inhibit intramolecular proton transfer in negatively charged species. Modified anions of the peptides with an intramolecular disulfide linkage show evidence for cleavage of both the disulfide linkage and an amide bond in the loop defined by the disulfide bond. Modification of protonated peptides via charge inversion with FBDSA is a useful means for generating novel and distinct ion-types that can provide complementary structural information upon subsequent activation to that obtained from dissociation of protonated or deprotonated forms of the peptide.
| S-EPMC3297198 | biostudies-literature