Fragmentation of the deprotonated ions of peptides containing cysteine, cysteine sulfinic acid, cysteine sulfonic acid, aspartic acid, and glutamic acid

Synthesis and conformational preferences of peptides and proteins with cysteine sulfonic acid

Cysteine sulfonic acid (Cys-SO₃H; cysteic acid) is an oxidative post-translational modification of cysteine, resulting from further oxidation from cysteine sulfinic acid (Cys-SO₂H). Cysteine sulfonic acid is considered an irreversible post-translational modification, which serves as a biomarker of oxidative stress that has resulted in oxidative damage to proteins. Cysteine sulfonic acid is anionic, as a sulfonate (Cys-SO₃^-; cysteate), in the ionization state that is almost exclusively present at physiological pH (pK_a ∼ -2). In order to understand protein structural changes that can occur upon oxidation to cysteine sulfonic acid, we analyzed its conformational preferences, using experimental methods, bioinformatics, and DFT-based computational analysis. Cysteine sulfonic acid was incorporated into model peptides for α-helix and polyproline II helix (PPII). Within peptides, oxidation of cysteine to the sulfonic acid proceeds rapidly and efficiently at room temperature in solution with methyltrioxorhenium (MeReO₃) and H₂O₂. Peptides containing cysteine sulfonic acid were also generated on solid phase using trityl-protected cysteine and oxidation with MeReO₃ and H₂O₂. Using methoxybenzyl (Mob)-protected cysteine, solid-phase oxidation with MeReO₃ and H₂O₂ generated the Mob sulfone precursor to Cys-SO₂^- within fully synthesized peptides. These two solid-phase methods allow the synthesis of peptides containing either Cys-SO₃^- or Cys-SO₂^- in a practical manner, with no solution-phase synthesis required. Cys-SO₃^- had low PPII propensity for PPII propagation, despite promoting a relatively compact conformation in ϕ. In contrast, in a PPII initiation model system, Cys-SO₃^- promoted PPII relative to neutral Cys, with PPII initiation similar to Cys thiolate but less than Cys-SO₂^- or Ala. In an α-helix model system, Cys-SO₃^- promoted α-helix near the N-terminus, due to favorable helix dipole interactions and favorable α-helix capping via a sulfonate-amide side chain-main chain hydrogen bond. Across all peptides, the sulfonate side chain was significantly less ordered than that of the sulfinate. Analysis of Cys-SO₃^- in the PDB revealed a very strong propensity for local (i/i or i/i + 1) side chain-main chain sulfonate-amide hydrogen bonds for Cys-SO₃^-, with >80% of Cys-SO₃^- residues exhibiting these interactions. DFT calculations conducted to explore these conformational preferences indicated that side chain-main chain hydrogen bonds of the sulfonate with the intraresidue amide and/or with the i + 1 amide were favorable. However, hydrogen bonds to water or to amides, as well as interactions with oxophilic metals, were weaker for the sulfonate than the sulfinate, due to lower charge density on the oxygens in the sulfonate.

Gas-Phase Dissociation Chemistry of Deprotonated RGD

We investigate the structure and dissociation pathways of the deprotonated amphoteric peptide arginylglycylasparic acid, [RGD-H]^-. We model the pertinent gas-phase structures and fragmentation chemistry of the precursor anions and predominant sequence-informative bond cleavages (b₂+H₂O, c₂, and z₁ peaks) and compare these predictions to our tandem mass spectra and infrared spectroscopy experiments. Formation of the b₂+H₂O anions requires rate-limiting intramolecular back biting to cleave the second amide bond and generate an anhydride structure. Facile cleavage of the newly formed ester bond with concerted expulsion of a cyclic anhydride neutral generates the product structure. IR spectroscopy supports this b₂+H₂O anion having structures that are essentially identical to C-terminally deprotonated arginylglycine, [RG-H]^-. Formation of the c₂ anion is predicted to require concerted expulsion of CO₂ from the aspartyl side chain carboxylate and cleavage of the N-C_alpha bond to produce a proton-bound dimer of arginylglycinamide and acrylate. Proton transfers within the dimer then enable predominant detection of a c₂ anion with the negative charge nominally on the central, glycine nitrogen (amidate structure) as the proton affinity of this structure is predicted to be lower than acrylate by ∼27 kJ mol^-1. Alternate means of cleaving the same N-C_alpha bond produce deprotonated cis-1,4-dibut-2-enoic acid z₁ anion structures. These lowest energy processes involve C-H proton mobilization from the aspartyl side chain prior to N-C_alpha bond cleavage consistent with proposals from the literature.

An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides

Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

The specific cleavage of lactone linkage to open-loop in cyclic lipopeptide during negative ESI tandem mass spectrometry: the hydrogen bond interaction effect of 4-ethyl guaiacol

Mass spectrometry is a valuable tool for the analysis and identification of chemical compounds, particularly proteins and peptides. Lichenysins G, the major cyclic lipopeptide of lichenysin, and the non-covalent complex of lichenysins G and 4-ethylguaiacol were investigated with negative ion ESI tandem mass spectrometry. The different fragmentation mechanisms for these compounds were investigated. Our study shows the 4-ethylguaiacol hydrogen bond with the carbonyl oxygen of the ester group in the loop of lichenysins G. With the help of this hydrogen bond interaction, the ring structure preferentially opens in lactone linkage rather than O-C bond of the ester-group to produce alcohol and ketene. Isothermal titration 1H-NMR analysis verified the hydrogen bond and determined the proportion of subject and ligand in the non-covalent complex to be 1∶1. Theoretical calculations also suggest that the addition of the ligand can affect the energy of the transition structures (TS) during loop opening.

Ion mobility spectrometry, infrared dissociation spectroscopy, and ab initio computations toward structural characterization of the deprotonated leucine-enkephalin peptide anion in the gas phase

Although the sequencing of protonated proteins and peptides with tandem mass spectrometry has blossomed into a powerful means of characterizing the proteome, much less effort has been directed at their deprotonated analogues, which can offer complementary sequence information. We present a unified approach to characterize the structure and intermolecular interactions present in the gas-phase pentapeptide leucine-enkephalin anion by several vibrational spectroscopy schemes as well as by ion-mobility spectrometry, all of which are analyzed with the help of quantum-chemical computations. The picture emerging from this study is that deprotonation takes place at the C terminus. In this configuration, the excess charge is stabilized by strong intramolecular hydrogen bonds to two backbone amide groups and thus provides a detailed picture of a potentially common charge accommodation motif in peptide anions.

Fragmentation characteristics of deprotonated N-linked glycopeptides: influences of amino acid composition and sequence

Glycopeptide structural analysis using tandem mass spectrometry is becoming a common approach for elucidating site-specific N-glycosylation. The analysis is generally performed in positive-ion mode. Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. The CID spectra of glycopeptides having a short peptide sequence were dominated by type (i) glycan fragments (e.g., (2,4)AR, (2,4)AR-1, D, and E ions). These fragments define detailed structural features of the glycan moiety such as branching. For glycopeptides with medium or long peptide sequences, the major fragments were type (ii) ions (e.g., [peptide + (0,2)X0-H](-) and [peptide-NH3-H](-)). The appearance of type (iii) ions strongly depended on the peptide sequence, and especially on the presence of Asp, Asn, and Glu. When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36](-), was abundantly formed. Observed fragments are reasonably explained by a combination of existing fragmentation rules suggested for N-glycans and peptides.

Mass spectrometric characterization of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine N-oxidized metabolites bound at Cys34 of human serum albumin

2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a heterocyclic aromatic amine that is formed during the cooking of meats and poultry. PhIP is a carcinogen in rodents and a potential human carcinogen. Several short-term biomarkers of PhIP have been established for human biomonitoring, but validated long-term biomarkers of the biologically effective dose of PhIP remain to be developed. Metabolites of PhIP have been reported to covalently bind to human serum albumin (SA), which is the most abundant protein in plasma; however, the chemical structures of PhIP-SA adducts are unknown. Cysteine(34) is one of 35 conserved Cys residues in SA across species. Thirty-four of these Cys are involved in 17 disulfide bonds. The single unpaired Cys(34) residue in SA is well-known to react with carcinogenic metabolites and toxic electrophiles. 2-Nitro-1-methyl-6-phenylimidazo[4,5-b]pyridine (NO(2)-PhIP), 2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]pyridine (HONH-PhIP), and 2-nitroso-1-methyl-6-phenylimidazo[4,5-b]pyridine (NO-PhIP), three genotoxic metabolites of PhIP, were reacted with purified human SA or human plasma, and the SA adduction products, following enzymatic digestion, were separated by ultra performance liquid chromatography and characterized with a linear quadrupole ion trap mass spectrometer. The major adduct of NO(2)-PhIP was formed at the Cys(34) of SA with bond formation occurring between the sulfhydryl group of Cys and the C-2 imidazole atom of PhIP. The major adducts formed between SA and HNOH-PhIP or NO-PhIP were identified as acid-labile sulfinamide linkages at Cys(34). These PhIP-SA adducts represent a measure of bioactivation of PhIP and may serve as long-term biomarkers of the biologically effective dose of PhIP.

Negative ion fragmentation of cysteic acid containing peptides: cysteic acid as a fixed negative charge

We present here a study of the collision induced dissociation (CID) of deprotonated cysteic acid containing peptides produced by MALDI. The effect of cysteic acid (C(ox)) position is interrogated by considering the positional isomers, C(ox)LVINVLSQG, LVINVLSQGC(ox), and LVINVC(ox)LSQG. Although considerable variation between the CID spectra is observed, the mechanistic picture that emerges involves charge retention at the deprotonated cysteic acid side chain. Fragmentation occurs in the proximity of the cysteic acid group by charge directed mechanisms as well as remote from this group to form ions, which may be rationalized by charge remote mechanisms. Additionally, the formation of the SO(3)(-•) ion is observed in all cases. Fragmentation of C(ox)LVINVLSQC(ox) provides both N- and C-terminal, y and b ions, respectively indicating that the negative charge may be retained at either of the cysteic acids; however, there is some evidence that charge retention at the C-terminal cysteic acid may be preferred. Fragmentation of tryptic type peptides containing a C-terminal arginine or lysine residue is considered through comparison of three peptides C(ox)LVINKLSQG, C(ox)LVINVLSQK, and C(ox)LVINVLSQR. Lastly, we rationalize the formation of b(n-1)+ H(2)O and a(n-1) ions through a mechanism involving rearrangement of the C-terminal residue to form a mixed anhydride intermediate.

Effect of cysteic acid position on the negative ion fragmentation of proteolytic derived peptides

A study on the effect of cysteic acid position on the types of fragment ions formed by collision-induced dissociation (CID) of [M - H](-) ions is presented. Of particular note is the observation of d-type fragment ions for peptides that contain an N-terminal cysteic acid (fixed negative charge) and cleavable amino acid side chains possessing a β-γ carbon-carbon bond. For example, the CID mass spectrum of oxidized cys-kemptide (C(ox)LRRASLG) [M - H + O(3)](-) ions contains abundant series of d-type fragment ions, and similar results are observed for oxidized cysteine-containing ribonuclease A proteolytic peptides. The d(i) fragment ions are assumed to arise by a charge-remote and/or charge-assisted fragmentation mechanism, which both occur at high collision energies and involve consecutive reactions (i.e., the formation of a(i) ions followed by the elimination of the side chain to form d(i) ions).

Amino acid influence on copper binding to peptides: cysteine versus arginine

Matrix assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) and theoretical calculations [density functional theory (DFT)] were utilized to investigate the influence of cysteine side chain on Cu(+) binding to peptides and how Cu(+) ions competitively interact with cysteine (-SH/SO(3)H) versus arginine. Results from theoretical and experimental (fragmentation reactions) studies on [M + Cu](+) and [M + 2Cu - H](+) ions suggest that cysteine side chains (-SH) and cysteic acid (-SO(3)H) are important Cu(+) ligands. For example, we show that Cu(+) ions are competitively coordinated to the -SH or SO(3)H groups; however, we also present evidence that the proton of the SH/SO(3)H group is mobile and can be transferred to the arginine guanidine group. For [M + 2Cu - H](+) ions, deprotonation of the -SH/SO(3)H group is energetically more favorable than that of the carboxyl group, and the resulting thiolate/sulfonate group plays an important role in the coordination structure of [M + 2Cu - H](+) ions, as well as the fragmentation patterns.

Expanding the functional diversity of proteins through cysteine oxidation

The polarizable sulfur atom in cysteine is subject to numerous post-translational oxidative modifications in the cellular milieu, which regulates a wide variety of biological phenomena such as catalysis, metal binding, protein turnover, and signal transduction. The application of chemical rationale to describe the features of different cysteine oxoforms affords a unique perspective on this rapidly expanding field. Moreover, a chemical framework broadens our understanding of the functional roles that specific cysteine oxidation states can play and facilitates the development of mechanistic proposals, which can be tested in both biochemical and cellular studies.