Hydrogen Bonding Constrains Free Radical Reaction Dynamics at Serine and Threonine Residues in Peptides

Transient Conformations Leading to Peptide Fragment Ion [c + 2H]+ via Intramolecular Hydrogen Bonding Using MALDI In-source Decay Mass Spectrometry of Serine-, Threonine-, and/or Cysteine-Containing Peptides

The formation of a peptide fragment ion [c + 2H]+ was examined using ultraviolet matrix-assisted laser desorption/ionization in-source decay mass spectrometry (UV/MALDI-ISD MS). Unusually, an ISD experiment with a hydrogen-abstracting oxidative matrix 4-nitro-1-naphthol (4,1-NNL) resulted in a [c + 2H]+ ion when the analyte peptides contained serine (Ser), threonine (Thr), and/or cysteine (Cys) residues, although the ISD with 4,1-NNL merely resulted in [a]+ and [d]+ ions. The [c + 2H]+ ion observed could be rationalized through intramolecular hydrogen atom transfer (HAT), like a Type-II reaction via a seven-membered conformation involving intramolecular hydrogen bonding (HB) between the active hydrogens (-OH and -SH) of the Ser/Thr/Cys residues and the backbone carbonyl oxygen at the adjacent amino (N)-terminal side residue. The ISD of the Cys-containing peptide resulted in the [c + 2H]+ ions, which originated from cleavage at the backbone N-Cα bonds far from the Cys residue, suggesting that the peptide molecule formed 16- and 22-membered transient conformations in the gas phase. The time-dependent density functional theory (TDDFT) calculations of the model structures of the Ser and Cys residues indicated that the Cys residue did not show a constructive bond interaction between the donor thiol (-SH) and carbonyl oxygen (=CO), while the Ser residue formed a distinct intramolecular HB.

Free Radical-Based Sequencing for Native Top-Down Mass Spectrometry

Native top-down proteomics allows for both proteoform identification and high-order structure characterization for cellular protein complexes. Unfortunately, tandem MS-based fragmentation efficiencies for such targets are low due to an increase in analyte ion mass and the low ion charge states that characterize native MS data. Multiple fragmentation methods can be integrated in order to increase protein complex sequence coverage, but this typically requires use of specialized hardware and software. Free-radical-initiated peptide sequencing (FRIPS) enables access to charge-remote and electron-based fragmentation channels within the context of conventional CID experiments. Here, we optimize FRIPS labeling for native top-down sequencing experiments. Our labeling approach is able to access intact complexes with TEMPO-based FRIPS reagents without significant protein denaturation or assembly disruption. By combining CID and FRIPS datasets, we observed sequence coverage improvements as large as 50% for protein complexes ranging from 36 to 106 kDa. Fragment ion production in these experiments was increased by as much as 102%. In general, our results indicate that TEMPO-based FRIPS reagents have the potential to dramatically increase sequence coverage obtained in native top-down experiments.

CADMA-Chem: A Computational Protocol Based on Chemical Properties Aimed to Design Multifunctional Antioxidants

A computational protocol aimed to design new antioxidants with versatile behavior is presented. It is called Computer-Assisted Design of Multifunctional Antioxidants and is based on chemical properties (CADMA-Chem). The desired multi-functionality consists of in different methods of antioxidant protection combined with neuroprotection, although the protocol can also be used to pursue other health benefits. The dM38 melatonin derivative is used as a study case to illustrate the protocol in detail. This was found to be a highly promising candidate for the treatment of neurodegeneration, in particular Parkinson's and Alzheimer's diseases. This also has the desired properties of an oral-drug, which is significantly better than Trolox for scavenging free radicals, and has chelates redox metals, prevents the ●OH production, via Fenton-like reactions, repairs oxidative damage in biomolecules (lipids, proteins, and DNA), and acts as a polygenic neuroprotector by inhibiting catechol-O-methyl transferase (COMT), acetylcholinesterase (AChE) and monoamine oxidase B (MAOB). To the best of our best knowledge, CADMA-Chem is currently the only protocol that simultaneously involves the analyses of drug-like behavior, toxicity, manufacturability, versatile antioxidant protection, and receptor-ligand binding affinities. It is expected to provide a starting point that helps to accelerate the discovery of oral drugs with the potential to prevent, or slow down, multifactorial human health disorders.

New free radical-initiated peptide sequencing (FRIPS) mass spectrometry reagent with high conjugation efficiency enabling single-step peptide sequencing

A newly designed TEMPO-FRIPS reagent, 4-(2,2,6,6-tetramethylpiperidine-1-oxyl) methyl benzyl succinic acid N-hydroxysuccinimide ester or p-TEMPO–Bn–Sc–NHS, was synthesized to achieve single-step free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) for a number of model peptides, including phosphopeptides. The p-TEMPO–Bn–Sc–NHS reagent was conjugated to target peptides, and the resulting peptides were subjected to collisional activation. The peptide backbone dissociation behaviors of the MS/MS and MS³ experiments were monitored in positive ion mode. Fragment ions were observed even at the single-step thermal activation of the p-TEMPO–Bn–Sc–peptides, showing mainly a-/x- and c-/z-type fragments and neutral loss ions. This confirms that radical-driven peptide backbone dissociations occurred with the p-TEMPO–Bn–Sc–peptides. Compared to the previous version of the TEMPO reagent, i.e., o-TEMPO–Bz–C(O)–NHS, the newly designed p-TEMPO–Bn–Sc–NHS has better conjugation efficiency for the target peptides owing to its improved structural flexibility and solubility in the experimental reagents. An energetic interpretation using the survival fraction as a function of applied normalized collision energy (NCE) ascertained the difference in the thermal activation between p-TEMPO–Bn–Sc– and o-TEMPO–Bz–C(O)– radical initiators. This study clearly demonstrates that the application of the p-TEMPO–Bn–Sc– radical initiator can improve the duty cycle, and this FRIPS MS approach has the potential to be implemented in proteomics studies, including phosphoproteomics.

Free-Radical-Mediated Glycan Isomer Differentiation

The inherent structural complexity and diversity of glycans pose a major analytical challenge to their structural analysis. Radical chemistry has gained considerable momentum in the field of mass spectrometric biomolecule analysis, including proteomics, glycomics, and lipidomics. Herein, seven isomeric disaccharides and two isomeric tetrasaccharides with subtle structural differences are distinguished rapidly and accurately via one-step radical-induced dissociation. The free-radical-activated glycan-sequencing reagent (FRAGS) selectively conjugates to the unique reducing terminus of glycans in which a localized nascent free radical is generated upon collisional activation and simultaneously induces glycan fragmentation. Higher-energy collisional dissociation (HCD) and collision-induced dissociation (CID) are employed to provide complementary structural information for the identification and discrimination of glycan isomers by providing different fragmentation pathways to generate informative, structurally significant product ions. Furthermore, multiple-stage tandem mass spectrometry (MS³ CID) provides supplementary and valuable structural information through the generation of characteristic parent-structure-dependent fragment ions.

Development of Novel Free Radical Initiated Peptide Sequencing Reagent: Application to Identification and Characterization of Peptides by Mass Spectrometry

By incorporating a high proton affinity moiety to the charge localized free radical-initiated peptide sequencing (CL-FRIPS) reagent, FRIPS-MS technique has extended the applicability to hydrophobic peptides and peptides without basic amino acid residues (lysine, arginine, and histidine). Herein, the CL-FRIPS reagent has three moieties: (1) pyridine acting as the basic site to locate the proton, (2) 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO, a stable free radical) acting as the free radical precursor to generate the nascent free radical in the gas phase, and (3) N-hydroxysuccinimide (NHS) activated carboxylic acid acting as the coupling site to derivatize the N-terminus of peptides. The CL-FRIPS reagent allows for the characterization of peptides by generating sequencing ions, enzymatic cleavage-like radical-induced side chain losses, and the loss of TEMPO simultaneously via one-step collisional activation. Further collisional activation of enzymatic cleavage-like radical-induced side chain loss ions provides more information for the structure determination of peptides. The application of CL-FRIPS reagent to characterize peptides is proved by employing bovine insulin as the model peptide. Both scaffold structure of bovine insulin and sequencing information of each chain are achieved. Graphical Abstract.

Free Radical-Initiated Peptide Sequencing Mass Spectrometry for Phosphopeptide Post-translational Modification Analysis

Free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) was employed to analyze a number of representative singly or doubly protonated phosphopeptides (phosphoserine and phosphotyrosine peptides) in positive ion mode. In contrast to collision-activated dissociation (CAD) results, a loss of a phosphate group occurred to a limited degree for both phosphoserine and phosphotyrosine peptides, and thus, localization of a phosphorylated site was readily achieved. Considering that FRIPS MS supplies a substantial amount of collisional energy to peptides, this result was quite unexpected because a labile phosphate group was conserved. Analysis of the resulting peptide fragments revealed the extensive production of a-, c-, x-, and z-type fragments (with some minor b- and y-type fragments), suggesting that radical-driven peptide fragmentation was the primary mechanism involved in the FRIPS MS of phosphopeptides. Results of this study clearly indicate that FRIPS MS is a promising tool for the characterization of post-translational modifications such as phosphorylation. Graphical Abstract.

Free radical-initiated peptide sequencing (FRIPS)-based cross-linkers for improved peptide and protein structure analysis

Free radical-initiated peptide sequencing (FRIPS) has recently been introduced as an analytical strategy to create peptide radical ions in a predictable and effective way by collisional activation of specifically modified peptides ions. FRIPS is based on the unimolecular dissociation of open-shell ions and yields fragments that resemble those obtained by electron capture dissociation (ECD) or electron transfer dissociation (ETD). In this review article, we describe the fundamentals of FRIPS and highlight its fruitful combination with chemical cross-linking/mass spectrometry (MS) as a highly promising option to derive complementary structural information of peptides and proteins. FRIPS does not only yield exhaustive sequence information of cross-linked peptides, but also defines the exact cross-linking sites of the connected peptides. The development of more advanced FRIPS cross-linkers that extend the FRIPS-based cross-linking/MS approach to the study of large protein assemblies and protein interaction networks can be eagerly anticipated.

Detection of Neutral CO Lost During Ionic Dissociation Using Atmospheric Pressure Thermal Dissociation Mass Spectrometry (APTD-MS)

Elucidation of ion dissociation patterns is particularly important to structural analysis by mass spectrometry (MS). However, typically, only the charged fragments from an ion dissociation event are detected in tandem MS experiments; neutrals are not identified. In recent years, we have developed an atmospheric pressure thermal dissociation (APTD) technique that can be applied to dissociate ions at atmosphere pressure and thus provide one way to characterize neutral fragments. In this paper, we focus on the detection of neutral CO resulting from amino acid and peptide ion dissociation. In the first set of experiments, several protonated amino acids (e.g., + 1 ion of phenylalanine) were found to undergo loss of a neutral (s) of total mass 46 Da, a process leading to iminium ion formation. We successfully detected the neutral species CO by using a CO sensor, UV-Vis and MS analysis following selective CO trapping with a rhodium complex. The capture of CO from dissociation of protonated amino acids supports the assignment of the loss of 46 Da to neutral losses of CO and H₂O, rather than loss of formaldehyde or dihydroxycarbene, other possible fragmentation pathways that have been subject of debate for a long time. In a second experiment, we used the APTD method in combination with the CO detection technique, to demonstrate the formation of CO in the conversion of b ions to a ions during peptide ion dissociations. These results showed the potential of APTD in the elucidation of ion dissociation mechanisms, using simple home-built apparatus. Graphical Abstract ᅟ.

Comprehensive Investigation of the Antioxidant and Pro-oxidant Effects of Phenolic Compounds: A Double-Edged Sword in the Context of Oxidative Stress?

Oxidative stress (OS) is a health-threatening process that is involved, at least partially, in the development of several diseases. Although antioxidants can be used as a chemical defense against OS, they might also exhibit pro-oxidant effects, depending on environmental conditions. In this work, such a dual behavior was investigated for phenolic compounds (PhCs) within the framework of the density functional theory and based on kinetic data. Multiple reaction mechanisms were considered in both cases. The presence of redox metals, the pH, and the possibility that PhCs might be transformed into benzoquinones were identified as key aspects in the antioxidant versus pro-oxidant effects of these compounds. The main virtues of PhCs as antioxidants are their radical trapping activity, their regeneration under physiological conditions, and their behavior as OH-inactivating ligands. The main risks of PhCs as pro-oxidants are predicted to be the role of phenolate ions in the reduction of metal ions, which can promote Fenton-like reactions, and the formation of benzoquinones that might cause protein arylation at cysteine sites. Although the benefits seem to overcome the hazards, to properly design chemical strategies against OS using PhCs, it is highly recommended to carefully explore their duality in this context.

Oxidation of Acid, Base, and Amide Side-Chain Amino Acid Derivatives via Hydroxyl Radical

Hydroxyl radical (^•OH) is known to be highly reactive. Herein, we analyze the oxidation of acid (Asp and Glu), base (Arg and Lys), and amide (Asn and Gln) containing amino acid derivatives by the consecutive attack of two ^•OH. In this work, we study the reaction pathway by means of density functional theory. The oxidation mechanism is divided into two steps: (1) the first ^•OH can abstract a H atom or an electron, leading to a radical amino acid derivative, which is the intermediate of the reaction and (2) the second ^•OH can abstract another H atom or add itself to the formed radical, rendering the final oxidized products. The studied second attack of ^•OH is applicable to situations where high concentration of ^•OH is found, e.g., in vitro. Carbonyls are the best known oxidation products for these reactions. This work includes solvent dielectric and confirmation's effects of the reaction, showing that both are negligible. Overall, the most favored intermediates of the oxidation process at the side chain correspond to the secondary radicals stabilized by hyperconjugation. Intermediates show to be more stable in those cases where the spin density of the unpaired electron is lowered. Alcohols formed at the side chains are the most favored products, followed by the double-bond-containing ones. Interestingly, Arg and Lys side-chain scission leads to the most favored carbonyl-containing oxidation products, in line with experimental results.

Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS

We have synthesized a homobifunctional amine-reactive cross-linking reagent, containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) and a benzyl group (Bz), termed TEMPO-Bz-linker, to derive three-dimensional structural information of proteins. The aim for designing this novel cross-linker was to facilitate the mass spectrometric analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). In an initial study, we had investigated the fragmentation behavior of TEMPO-Bz-derivatized peptides upon collision activation in (+)-electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) experiments. In addition to the homolytic NO-C bond cleavage FRIPS pathway delivering the desired odd-electron product ions, an alternative heterolytic NO-C bond cleavage, resulting in even-electron product ions mechanism was found to be relevant. The latter fragmentation route clearly depends on the protonation of the TEMPO-Bz-moiety itself, which motivated us to conduct (-)-ESI-MS, CID-MS/MS, and MS³ experiments of TEMPO-Bz-cross-linked peptides to further clarify the fragmentation behavior of TEMPO-Bz-peptide molecular ions. We show that the TEMPO-Bz-linker is highly beneficial for conducting FRIPS in negative ionization mode as the desired homolytic cleavage of the NO-C bond is the major fragmentation pathway. Based on characteristic fragments, the isomeric amino acids leucine and isoleucine could be discriminated. Interestingly, we observed pronounced amino acid side chain losses in cross-linked peptides if the cross-linked peptides contain a high number of acidic amino acids. Graphical Abstract ᅟ.

Chemical repair of protein carbon-centred radicals: long-distance dynamic factors

The thermodynamic and kinetic study of the repair reactions of three damaged aliphatic amino acids (alanine, valine, and leucine) with dihydrolipoic acid (DHLA) in a polar and a nonpolar solvent is presented in this work. Two simplified protein models were explored in the most common conformations (alpha helix and beta sheet). Calculations are performed at the M06-2X-SMD/6-31++G(d,p) level of theory. DHLA has shown to be an excellent antioxidant repair agent through hydrogen-transfer reaction involving the thiol groups, with rate constants close to diffusion control in most cases. The stability of the initial protein radical is not the most important factor determining the rate of the repair reaction because stabilizing intermolecular interactions involving the protein and the antioxidant can provide additional stability to some transition states accelerating the repair of sites that would otherwise not be so quickly repaired.

Role of Hydrogen Bonding on the Reactivity of Thiyl Radicals: A Mass Spectrometric and Computational Study Using the Distonic Radical Ion Approach

Experimental and computational quantum chemistry investigations of the gas-phase ion-molecule reactions between the distonic ions ⁺H₃N(CH₂)_nS^• (n = 2-4) and the reagents dimethyl disulfide, allyl bromide, and allyl iodide demonstrate that intramolecular hydrogen bonding can modulate the reactivity of thiyl radicals. Thus, the 3-ammonium-1-propanethiyl radical (n = 3) exhibits the lowest reactivity of these distonic ions toward all substrates. Theoretical calculations on this distonic ion highlight that its most stable conformation involves a six-membered ring configuration, and that it has the strongest intramolecular hydrogen bond. In addition, the calculations indicate that the barrier heights for radical abstraction by this hydrogen-bond-stabilized 3-ammonium-1-propanethiyl radical are the highest among the systems examined, consistent with the experimental observations.

Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals

We report a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-rich and hydrogen-deficient types. Stable, long-lived, hydrogen-rich peptide cation radicals, such as [AAAYR + 2H](+●) and several of its sequence and homology variants, were generated by electron transfer dissociation (ETD) of peptide-crown-ether complexes, and their CID-MS(3) dissociations were found to be dramatically different from those upon ETD of the respective peptide dications. All of the hydrogen-rich peptide cation radicals contained major (77%-94%) fractions of species having radical chromophores created by ETD that underwent photodissociation at 355 nm. Analysis of the CID and UVPD spectra pointed to arginine guanidinium radicals as the major components of the hydrogen-rich peptide cation radical population. Hydrogen-deficient peptide cation radicals were generated by intramolecular electron transfer in Cu(II)(2,2':6',2″-terpyridine) complexes and shown to contain chromophores absorbing at 355 nm and undergoing photodissociation. The CID and UVPD spectra showed major differences in fragmentation for [AAAYR](+●) that diminished as the Tyr residue was moved along the peptide chain. UVPD was found to be superior to CID in localizing Cα-radical positions in peptide cation radical intermediates. Graphical Abstract ᅟ.

Eradicating mass spectrometric glycan rearrangement by utilizing free radicals

We designed and synthesized a methylated free radical activated glycan sequencing reagent (Me-FRAGS) for eliminating mass spectrometric glycan rearrangement.

Mass spectrometric glycan rearrangement is problematic because it provides misleading structural information. Here we report on a new reagent, a methylated free radical activated glycan sequencing reagent (Me-FRAGS), which combines a free radical precursor with a methylated pyridine moiety that can be coupled to the reducing terminus of glycans. The collisional activation of Me-FRAGS-derivatized glycans generates a nascent free radical that concurrently induces abundant glycosidic bond and cross-ring cleavage without the need for subsequent activation. The product ions resulting from glycan rearrangement, including internal residue loss and multiple external residue losses, are precluded. Glycan structures can be easily assembled and visualized using a radical driven glycan deconstruction diagram (R-DECON diagram). The presence and location of N-acetylated saccharide units and branch sites can be identified from the characteristic dissociation patterns observed only at these locations. The mechanisms of dissociation are investigated and discussed. This Me-FRAGS based mass spectrometric approach creates a new blueprint for glycan structure analysis.

A computational study of radical initiated protein backbone homolytic dissociation on all natural amino acids

Hydroxyl radical (˙OH) is known to be one of the most reactive species. The attack of this radical onto the backbone of all natural amino acids is investigated.

Theoretical examination of competitive β-radical-induced cleavages of N–Cα and Cα–C bonds of peptides

Selective cleavages of N–Cα and Cα–C bonds of β-radical tautomers of amino acid residues in radical peptides have been examined theoretically by means of the density functional theory at the M06-2X/6-311++G(d,p) level. The majority of the bond cleavages are homolytic via β-scission. Their energy barriers depend largely on the ability of the radical being stabilized in the transition structures and the availability of a mobile proton in the vicinity of the β-radical center. The N–Cα bond is less favorably cleaved than the Cα–C bond (except Ser and Thr) for systems without a mobile proton. It is because, firstly, the homolytic cleavage is less favorable for the more polar N–Cα bond than for the less polar Cα–C bond. Secondly, a less stable σ-radical localized on the amide nitrogen atom of the incipient N-terminal fragment is formed for the former, while a more stable radical delocalized in a π*(CO)-like orbital of the incipient C-terminal fragment is formed for the latter. In the presence of a mobile proton N-terminal to the β-radical center, some degrees of heterolytic cleavage character, as preferred by the polar N–Cα bond, are observed. Consequently, its barrier is reduced. If the mobile proton is located at the C-terminal amide oxygen of the β-radical center, the Cα–C bond cleavage will be significantly suppressed. It is because the radical in the incipient C-terminal fragment becomes more localized as a σ-radical on the carbon atom of its protonated amide group. With basic amino acid residues, the Cα–C bond cleavage can be reactivated. Heterolytic cleavage of the polar N–Cα bond can be largely facilitated if a mobile proton N-terminal to the β-radical center is available and the radical in the incipient C-terminal fragment is sufficiently stabilized, for instance, by the aromatic side chain of Trp and Tyr. Therefore, cleavages of the N–Cα bond induced by the β-radical tautomer of Trp and Tyr are often preferred as compared with cleavages of the Cα–C bond in peptide radical cations containing mobile protons.

Mechanisms and energetics of free radical initiated disulfide bond cleavage in model peptides and insulin by mass spectrometry

We investigate the mechanism of disulfide bond cleavage in gaseous peptide and protein ions initiated by a covalently-attached regiospecific acetyl radical using mass spectrometry (MS). Highly selective S-S bond cleavages with some minor C-S bond cleavages are observed by a single step of collisional activation. We show that even multiple disulfide bonds in intact bovine insulin are fragmented in the MS2 stage, releasing the A- and B-chains with a high yield, which has been challenging to achieve by other ion activation methods. Yet, regardless of the previous reaction mechanism studies, it has remained unclear why (1) disulfide bond cleavage is preferred to peptide backbone fragmentation, and why (2) the S-S bond that requires the higher activation energy conjectured in previously suggested mechanisms is more prone to be cleaved than the C-S bond by hydrogen-deficient radicals. To probe the mechanism of these processes, model peptides possessing deuterated β-carbon(s) at the disulfide bond are employed. It is suggested that the favored pathway of S-S bond cleavage is triggered by direct acetyl radical attack at sulfur with concomitant cleavage of the S-S bond (SH2). The activation energy for this process is substantially lower by ∼9-10 kcal mol-1 than those of peptide backbone cleavage processes determined by density functional quantum chemical calculations. Minor reaction pathways are initiated by hydrogen abstraction from the α-carbon or the β-carbon of a disulfide, followed by β-cleavages yielding C-S or S-S bond scissions. The current mechanistic findings should be generally applicable to other radical-driven disulfide bond cleavages with different radical species such as the benzyl and methyl pyridyl radicals.

Modelling the chemical repair of protein carbon-centered radicals formed via oxidative damage with dihydrolipoic acid

Dihydrolipoic acid repairs carbon-centred radicals at diffusion-controlled rates via HAT mechanism.