1
|
Lambeth TR, Julian RR. Efficient Isothiocyanate Modification of Peptides Facilitates Structural Analysis by Radical-Directed Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1338-1345. [PMID: 34670075 DOI: 10.1021/jasms.1c00237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Radical-directed dissociation (RDD) is a powerful technique for structural characterization of peptides in mass spectrometry experiments. Prior to analysis, a radical precursor must typically be appended to facilitate generation of a free radical. To explore the use of a radical precursor that can be easily attached in a single step, we modified peptides using a "click" reaction with iodophenyl isothiocyanate. Coupling with amine functional groups proceeds with high yields, producing stable iodophenylthiourea-modified peptides. Photodissociation yields were recorded at 266 and 213 nm for the 2-, 3-, and 4-iodo isomers of the modifier and found to be highest for the 4-iodo isomer in nearly all cases. Fragmentation of the modified peptides following collisional activation revealed favorable losses of the tag, and electronic structure calculations were used to evaluate a potential mechanism involving hydrogen transfer within the thiourea group. Examination of RDD data revealed that 4-iodobenzoic acid, 4-iodophenylthiourea, and 3-iodotyrosine yield similar fragmentation patterns for a given peptide, although differences in fragment abundance are noted. Iodophenyl isothiocyanate labeling in combination with RDD can be used to differentiate isomeric amino acids within peptides, which should facilitate simplified evaluation of isomers present in complex biological samples.
Collapse
Affiliation(s)
- Tyler R Lambeth
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
| |
Collapse
|
2
|
Edwards HM, Wu HT, Julian RR, Jackson GP. Differentiating aspartic acid isomers and epimers with charge transfer dissociation mass spectrometry (CTD-MS). Analyst 2022; 147:1159-1168. [PMID: 35188507 DOI: 10.1039/d1an02279b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability to understand the function of a protein often relies on knowledge about its detailed structure. Sometimes, seemingly insignificant changes in the primary structure of a protein, like an amino acid substitution, can completely disrupt a protein's function. Long-lived proteins (LLPs), which can be found in critical areas of the human body, like the brain and eye, are especially susceptible to primary sequence alterations in the form of isomerization and epimerization. Because long-lived proteins do not have the corrective regeneration capabilities of most other proteins, points of isomerism and epimerization that accumulate within the proteins can severely hamper their functions and can lead to serious diseases like Alzheimer's disease, cancer and cataracts. Whereas tandem mass spectrometry (MS/MS) in the form of collision-induced dissociation (CID) generally excels at peptide characterization, MS/MS often struggles to pinpoint modifications within LLPs, especially when the differences are only isomeric or epimeric in nature. One of the most prevalent and difficult-to-identify modifications is that of aspartic acid between its four isomeric forms: L-Asp, L-isoAsp, D-Asp, and D-isoAsp. In this study, peptides containing isomers of Asp were analyzed by charge transfer dissociation (CTD) mass spectrometry to identify spectral features that could discriminate between the different isomers. For the four isomers of Asp in three model peptides, CTD produced diagnostic ions of the form cn+57 on the N-terminal side of iso-Asp residues, but not on the N-terminal side of Asp residues. Using CTD, the L- and D forms of Asp and isoAsp could also be differentiated based on the relative abundance of y- and z ions on the C-terminal side of Asp residues. Differentiation was accomplished through a chiral discrimination factor, R, which compares an ion ratio in a spectrum of one epimer or isomer to the same ion ratio in the spectrum of a different epimer or isomer. The R values obtained using CTD are as robust and statistically significant as other fragmentation techniques, like radical directed dissociation (RDD). In summary, the extent of backbone and side-chain fragments produced by CTD enabled the differentiation of isomers and epimers of Asp in a variety of peptides.
Collapse
Affiliation(s)
- Halle M Edwards
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA.
| | - Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Glen P Jackson
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA. .,Department of Forensic and Investigative Science, West Virginia University, Morgantown, WV, USA
| |
Collapse
|
3
|
Narreddula VR, McKinnon BI, Marlton SJP, Marshall DL, Boase NRB, Poad BLJ, Trevitt AJ, Mitchell TW, Blanksby SJ. Next-generation derivatization reagents optimized for enhanced product ion formation in photodissociation-mass spectrometry of fatty acids. Analyst 2021; 146:156-169. [DOI: 10.1039/d0an01840f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Next-generation derivatives for photodissociation-mass spectrometry for fatty acids generating photoproduct yields of up to 97% at 266 nm.
Collapse
Affiliation(s)
- Venkateswara R. Narreddula
- School of Chemistry and Physics
- Science and Engineering Faculty
- Queensland University of Technology
- Brisbane
- Australia
| | - Benjamin I. McKinnon
- Molecular Horizons and School of Chemistry and Molecular Bioscience
- University of Wollongong
- Wollongong
- Australia
| | - Samuel J. P. Marlton
- Molecular Horizons and School of Chemistry and Molecular Bioscience
- University of Wollongong
- Wollongong
- Australia
| | - David L. Marshall
- Central Analytical Research Facility
- Institute for Future Environments
- Queensland University of Technology
- Brisbane
- Australia
| | - Nathan R. B. Boase
- School of Chemistry and Physics
- Science and Engineering Faculty
- Queensland University of Technology
- Brisbane
- Australia
| | - Berwyck L. J. Poad
- Central Analytical Research Facility
- Institute for Future Environments
- Queensland University of Technology
- Brisbane
- Australia
| | - Adam J. Trevitt
- Molecular Horizons and School of Chemistry and Molecular Bioscience
- University of Wollongong
- Wollongong
- Australia
| | - Todd W. Mitchell
- School of Medicine
- University of Wollongong
- Wollongong
- Australia
- Illawarra Health and Medical Research Institute
| | - Stephen J. Blanksby
- School of Chemistry and Physics
- Science and Engineering Faculty
- Queensland University of Technology
- Brisbane
- Australia
| |
Collapse
|
4
|
Van Orman BL, Wu HT, Julian RR. Differentiation of peptide isomers by excited-state photodissociation and ion-molecule interactions. Phys Chem Chem Phys 2020; 22:23678-23685. [PMID: 33052992 DOI: 10.1039/d0cp04111d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Solvochromatic effects are most frequently associated with solution-phase phenomena. However, in the gas phase, the absence of solvent leads to intramolecular solvation that can be driven by strong forces including hydrogen bonds and ion-dipole interactions. Here we examine whether isomerization of a single residue in a peptide results in structural changes sufficient to shift the absorption of light by an appended chromophore. By carrying out the experiments inside a mass spectrometer, we can easily monitor photodissociation yield as a readout for chromophore excitation. A series of peptides of different lengths, charge states, and position and identity of the isomerized residue were examined by excitation with both 266 and 213 nm light. The results reveal that differences in intramolecular solvation do lead to solvochromatic shifts in many cases. In addition, the primary product following photoexcitation is a radical. Ion-molecule reactions with this radical and adventitious oxygen were monitored and also found to vary as a function of isomeric state. In this case, differences in intramolecular solvation alter the availability of the reactive radical. Overall, the results reveal that small changes in a single amino acid can influence the overall structural ensemble sufficient to alter the efficiency of multiple gas-phase reactions.
Collapse
Affiliation(s)
- Brielle L Van Orman
- Department of Chemistry, University of California, Riverside, California 92521, USA.
| | - Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, California 92521, USA.
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, California 92521, USA.
| |
Collapse
|
5
|
Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
Collapse
Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
6
|
Talbert LE, Zhang X, Hendricks N, Alizadeh A, Julian RR. Synthesis of New S-S and C-C Bonds by Photoinitiated Radical Recombination Reactions in the Gas Phase. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 441:25-31. [PMID: 31607789 PMCID: PMC6788626 DOI: 10.1016/j.ijms.2019.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Photoinitiated radical chemistry has proven to be useful for breaking covalent bonds within many biomolecules in the gas phase. Herein, we demonstrate that radical chemistry is useful for bond synthesis in the gas phase. Single peptides containing two cysteine residues capped with propylmercaptan (PM) often form disulfide bonds following ultraviolet excitation at 266 nm and loss of both PM groups. Similarly, noncovalently bound peptide pairs where each peptide contains a single cysteine residue can be induced to form disulfide bonds. Comparison with disulfide bound species sampled directly from solution yields identical collisional activation spectra, suggesting that native disulfide bonds have been recapitulated in the gas phase syntheses. Another approach utilizing radical chemistry for covalent bond synthesis involves creation of a reactive diradical that can first abstract hydrogen from a target peptide, creating a new radical site, and then recombine the second radical with the new radical to form a covalent bond. This chemistry is illustrated with 2-(hydroxymethyl-3,5-diiodobenzoate)-18-crown-6 ether, which attaches noncovalently to protonated primary amines in peptides and proteins. Following photoactivation and crosslinking, the site of noncovalent adduct attachment can frequently be determined. The ramifications of these observations on peptide structure and noncovalent attachment of 18-crown-6-based molecules is discussed.
Collapse
|
7
|
Marlton SJP, McKinnon BI, Ucur B, Maccarone AT, Donald WA, Blanksby SJ, Trevitt AJ. Selecting and identifying gas-phase protonation isomers of nicotineH+ using combined laser, ion mobility and mass spectrometry techniques. Faraday Discuss 2019; 217:453-475. [DOI: 10.1039/c8fd00212f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protonation isomers of gas-phase nicotineH+ are separated and assigned using a combination of FAIMS and UV photodissociation action spectroscopy.
Collapse
Affiliation(s)
| | | | - Boris Ucur
- School of Chemistry
- University of Wollongong
- Wollongong
- Australia
| | | | | | - Stephen J. Blanksby
- Central Analytical Research Facility
- Institute for Future Environments
- Queensland University of Technology
- Brisbane
- Australia
| | - Adam J. Trevitt
- School of Chemistry
- University of Wollongong
- Wollongong
- Australia
| |
Collapse
|
8
|
Differentiation of peptide isomers and epimers by radical-directed dissociation. Methods Enzymol 2019; 626:67-87. [DOI: 10.1016/bs.mie.2019.06.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
9
|
Riggs DL, Hofmann J, Hahm HS, Seeberger PH, Pagel K, Julian RR. Glycan Isomer Identification Using Ultraviolet Photodissociation Initiated Radical Chemistry. Anal Chem 2018; 90:11581-11588. [PMID: 30179447 PMCID: PMC11216535 DOI: 10.1021/acs.analchem.8b02958] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glycans are fundamental biological macromolecules, yet despite their prevalence and recognized importance, a number of unique challenges hinder routine characterization. The multiplicity of OH groups in glycan monomers easily afford branched structures and alternate linkage sites, which can result in isomeric structures that differ by minute details. Herein, radical chemistry is employed in conjunction with mass spectrometry to enable rapid, accurate, and high throughput identification of a challenging series of closely related glycan isomers. The results are compared with analysis by collision-induced dissociation, higher-energy collisional dissociation, and ultraviolet photodissociation (UVPD) at 213 nm. In general, collision-based activation struggles to produce characteristic fragmentation patterns, while UVPD and radical-directed dissociation (RDD) can distinguish all isomers. In the case of RDD, structural differentiation derives from radical mobility and subsequent fragmentation. For glycans, the energetic landscape for radical migration is flat, increasing the importance of the three-dimensional structure. RDD is therefore a powerful and straightforward method for characterizing glycan isomers.
Collapse
Affiliation(s)
- Dylan L. Riggs
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA 92521, USA
| | - Johanna Hofmann
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6, 14195 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Heung S. Hahm
- Department for Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter H. Seeberger
- Department for Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Institute for Chemistry and Biochemistry, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Kevin Pagel
- Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society Faradayweg 4-6, 14195 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie Universitaet Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA 92521, USA
| |
Collapse
|
10
|
Williams PE, Marshall DL, Poad BLJ, Narreddula VR, Kirk BB, Trevitt AJ, Blanksby SJ. Comparing Positively and Negatively Charged Distonic Radical Ions in Phenylperoxyl Forming Reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1848-1860. [PMID: 29869328 DOI: 10.1007/s13361-018-1988-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
In the gas phase, arylperoxyl forming reactions play a significant role in low-temperature combustion and atmospheric processing of volatile organic compounds. We have previously demonstrated the application of charge-tagged phenyl radicals to explore the outcomes of these reactions using ion trap mass spectrometry. Here, we present a side-by-side comparison of rates and product distributions from the reaction of positively and negatively charge tagged phenyl radicals with dioxygen. The negatively charged distonic radical ions are found to react with significantly greater efficiency than their positively charged analogues. The product distributions of the anion reactions favor products of phenylperoxyl radical decomposition (e.g., phenoxyl radicals and cyclopentadienone), while the comparable fixed-charge cations yield the stabilized phenylperoxyl radical. Electronic structure calculations rationalize these differences as arising from the influence of the charged moiety on the energetics of rate-determining transition states and reaction intermediates within the phenylperoxyl reaction manifold and predict that this influence could extend to intra-molecular charge-radical separations of up to 14.5 Å. Experimental observations of reactions of the novel 4-(1-carboxylatoadamantyl)phenyl radical anion confirm that the influence of the charge on both rate and product distribution can be modulated by increasing the rigidly imposed separation between charge and radical sites. These findings provide a generalizable framework for predicting the influence of charged groups on polarizable radicals in gas phase distonic radical ions. Graphical Abstract.
Collapse
Affiliation(s)
- Peggy E Williams
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
- Failure and Materials Analysis Branch, Flight Systems Division, Naval Surface Warfare Center Crane, Crane, IN, USA
| | - David L Marshall
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Berwyck L J Poad
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Venkateswara R Narreddula
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Benjamin B Kirk
- School of Chemistry, University of Wollongong, Wollongong, NSW, Australia
| | - Adam J Trevitt
- School of Chemistry, University of Wollongong, Wollongong, NSW, Australia
| | - Stephen J Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia.
| |
Collapse
|
11
|
Lyon YA, Sabbah GM, Julian RR. Differences in α-Crystallin isomerization reveal the activity of protein isoaspartyl methyltransferase (PIMT) in the nucleus and cortex of human lenses. Exp Eye Res 2018; 171:131-141. [PMID: 29571628 DOI: 10.1016/j.exer.2018.03.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/16/2018] [Accepted: 03/19/2018] [Indexed: 01/12/2023]
Abstract
Although it is well-known that protein turnover essentially stops in mature lens fiber cells, mapping out the ensuing protein degradation and its effects on lens function over time remains challenging. In particular, isomerization is a common, spontaneous post-translational modification that occurs over long timescales and generates products invisible to most analytical methods. Nevertheless, isomerization can significantly impact protein structure, function, and solubility, which are all necessary to maintain clarity and proper refractive index within the lens. Herein, we examine the degree of isomerization occurring in crystallin proteins in the human eye lens as a function of both age and location within the lens. A novel mass spectrometric technique leveraging radical chemistry enables detailed characterization of proteins extracted from the cortex and nucleus of the lens. It is observed that the degree of isomerization increases significantly between the cortex and nucleus and between water-soluble and water-insoluble fractions. Interestingly, the abundance of L-isoAsp is low in the water-soluble cortex despite being the dominant product generated by isomerization of Asp in vitro, suggesting that Protein L-isoaspartyl methyltransferase (PIMT) is active in the cortex and suppresses the accumulation of L-isoAsp. The abundance of L-isoAsp increases dramatically in the nucleus, revealing that PIMT activity decreases over time in the center of the lens. In addition, the growth of L-isoAsp in the nuclear fraction suggests protein isomerization continues within the nucleus, despite the fact that most of the protein within the nucleus has become insoluble. Additionally, it is demonstrated that sequential Asp residues lead to isomerization hotspots in human crystallin proteins and that the isomerization profiles for αA and αB crystallin are notably different. Although αA is more prone to isomerization, αB loses solubility more rapidly upon modification. These differences are likely related to the distribution of Asp residues within αA and αB, which are in turn connected to refractive index. The high Asp content of αA is a hazard in terms of isomerization and aging, but it serves to enhance the refractive index of αA relative to αB, and may explain why αA is only found in the eye.
Collapse
Affiliation(s)
- Yana A Lyon
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA 92521, USA
| | - Georgette M Sabbah
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA 92521, USA.
| |
Collapse
|
12
|
Riggs DL, Gomez SV, Julian RR. Sequence and Solution Effects on the Prevalence of d-Isomers Produced by Deamidation. ACS Chem Biol 2017; 12:2875-2882. [PMID: 28984444 PMCID: PMC5696650 DOI: 10.1021/acschembio.7b00686] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Deamidation of asparagine is a spontaneous and irreversible post-translational modification associated with a growing list of human diseases. While pervasive, deamidation is often overlooked because it represents a relatively minor chemical change. Structural and functional characterization of this modification is complicated because deamidation of asparagine yields four isomeric forms of Asp. Herein, radical directed dissociation (RDD), in conjunction with mass spectrometry, is used to identify and quantify all four isomers in a series of model peptides that were subjected to various deamidation conditions. Although primary sequence significantly influences the rate of deamidation, it has little impact on the relative proportions of the product isomers. Furthermore, the addition of ammonia can be used to increase the rate of deamidation without significantly perturbing isomer populations. Conversely, external factors such as buffer conditions and temperature alter product distributions but exhibit less dramatic effects on the deamidation rate. Strikingly, the common laboratory and biologically significant bicarbonate buffer is found to strongly promote racemization, yielding increased amounts of d-Asp and d-isoAsp. These outcomes following deamidation have broad implications in human aging and should be considered during the development of protein-based therapeutics.
Collapse
Affiliation(s)
- Dylan L. Riggs
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Sonia V. Gomez
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
| |
Collapse
|
13
|
Bonner J, Lyon YA, Nellessen C, Julian RR. Photoelectron Transfer Dissociation Reveals Surprising Favorability of Zwitterionic States in Large Gaseous Peptides and Proteins. J Am Chem Soc 2017; 139:10286-10293. [PMID: 28678494 PMCID: PMC5543396 DOI: 10.1021/jacs.7b02428] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Structural
characterization of proteins in the gas phase is becoming
increasingly popular, highlighting the need for a greater understanding
of how proteins behave in the absence of solvent. It is clear that
charged residues exert significant influence over structures in the
gas phase due to strong Coulombic and hydrogen-bonding interactions.
The net charge for a gaseous ion is easily identified by mass spectrometry,
but the presence of zwitterionic pairs or salt bridges has previously
been more difficult to detect. We show that these sites can be revealed
by photoinduced electron transfer dissociation, which produces characteristic
c and z ions only if zwitterionic species are present. Although previous
work on small molecules has shown that zwitterionic pairs are rarely
stable in the gas phase, we now demonstrate that charge-separated
states are favored in larger molecules. Indeed, we have detected zwitterionic
pairs in peptides and proteins where the net charge equals the number
of basic sites, requiring additional protonation at nonbasic residues.
For example, the small protein ubiquitin can sustain a zwitterionic
conformer for all charge states up to 14+, despite having only 13
basic sites. Virtually all of the peptides/proteins examined herein
contain zwitterionic sites if both acidic and basic residues are present
and the overall charge density is low. This bias in favor of charge-separated
states has important consequences for efforts to model gaseous proteins
via computational analysis, which should consider not only charge
state isomers that include salt bridges but also protonation at nonbasic
residues.
Collapse
Affiliation(s)
- James Bonner
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Yana A Lyon
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Christopher Nellessen
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Ryan R Julian
- Department of Chemistry, University of California , Riverside, California 92521, United States
| |
Collapse
|
14
|
Lyon YA, Beran G, Julian RR. Leveraging Electron Transfer Dissociation for Site Selective Radical Generation: Applications for Peptide Epimer Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1365-1373. [PMID: 28374314 PMCID: PMC5497491 DOI: 10.1007/s13361-017-1627-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 06/07/2023]
Abstract
Traditional electron-transfer dissociation (ETD) experiments operate through a complex combination of hydrogen abundant and hydrogen deficient fragmentation pathways, yielding c and z ions, side-chain losses, and disulfide bond scission. Herein, a novel dissociation pathway is reported, yielding homolytic cleavage of carbon-iodine bonds via electronic excitation. This observation is very similar to photodissociation experiments where homolytic cleavage of carbon-iodine bonds has been utilized previously, but ETD activation can be performed without addition of a laser to the mass spectrometer. Both loss of iodine and loss of hydrogen iodide are observed, with the abundance of the latter product being greatly enhanced for some peptides after additional collisional activation. These observations suggest a novel ETD fragmentation pathway involving temporary storage of the electron in a charge-reduced arginine side chain. Subsequent collisional activation of the peptide radical produced by loss of HI yields spectra dominated by radical-directed dissociation, which can be usefully employed for identification of peptide isomers, including epimers. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Yana A Lyon
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Gregory Beran
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California-Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
| |
Collapse
|
15
|
Hamdy OM, Alizadeh A, Julian RR. The innate capacity of proteins to protect against reactive radical species. Analyst 2016; 140:5023-8. [PMID: 26051477 DOI: 10.1039/c5an00798d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Maintaining redox homeostasis, or the balance of oxidant and antioxidant forces, is essential for proper cellular functioning in biology. Although the antioxidant nature of many small molecules such as vitamin c and glutathione have been thoroughly investigated, contributions to redox homeostasis from larger biomolecules have received less attention. Evidence has shown that some proteins are antioxidant (in a non-catalytic sense), but large scale examination of this property for a diverse set of proteins has proven difficult. Herein, radical-directed dissociation mass spectrometry (RDD-MS) is used to examine the antioxidant capacity of a series of proteins with diverse biological roles, persistence intervals, and localizations. Digestion of these proteins reveals that all contain antioxidant peptide regions. Examination of the amino acid content of the antioxidant peptides does not reveal significant differences relative to normal peptides, suggesting that sequence may be more important than residue content. Sequence homology analysis across organisms reveals that antioxidant regions are frequently conserved, although many of these regions are also known to have other functions which may have influenced evolutionary pressure. Regardless of the origin, it is clear that many proteins may play secondary roles as sacrificial antioxidants within the cellular milieu.
Collapse
Affiliation(s)
- Omar M Hamdy
- Department of Chemistry, University of California, Riverside, California 92521, USA.
| | | | | |
Collapse
|
16
|
Pham HT, Julian RR. Characterization of glycosphingolipid epimers by radical-directed dissociation mass spectrometry. Analyst 2016; 141:1273-8. [DOI: 10.1039/c5an02383a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Radical chemistry can efficiently distinguish isomers varying in position at a single alcohol.
Collapse
|
17
|
Hendricks NG, Julian RR. Leveraging ultraviolet photodissociation and spectroscopy to investigate peptide and protein three-dimensional structure with mass spectrometry. Analyst 2016; 141:4534-40. [DOI: 10.1039/c6an01020b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent advances in mass spectrometry and lasers have facilitated the development of novel experiments combining the benefits of both technologies.
Collapse
Affiliation(s)
| | - Ryan R. Julian
- Department of Chemistry
- University of California
- Riverside
- USA
| |
Collapse
|
18
|
Lyon YA, Julian RR. Photolytic determination of charge state for large proteins and fragments in an ion trap mass spectrometer. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:322-326. [PMID: 26406343 DOI: 10.1002/rcm.7109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/06/2014] [Accepted: 11/29/2014] [Indexed: 06/05/2023]
Abstract
RATIONALE One of the major shortcomings of linear ion trap mass spectrometers is poor resolution. Failure to resolve isotopic peaks makes charge state determination for large proteins very difficult, hindering the ability to perform top-down proteomics. METHODS Peptides, proteins and corresponding fragments modified with para-iodobenzoate were trapped and irradiated with 266 nm light from an Nd:YAG laser. Loss of iodine due to photodissociation was then used to assign charge states by measuring the corresponding m/z shifts. RESULTS Initial experiments on small peptides illustrate the feasibility of the method. Further studies performed on larger proteins in higher charge states yielded similar results, revealing that fragment ions over a significant mass range either remain in or are quickly cooled to the laser overlap region of the ion trap. CONCLUSIONS Rapid charge state assignment for both whole molecules and collision-induced dissociation (CID) fragments can be obtained by photoactivation of chromophores with labile carbon-iodine bonds.
Collapse
Affiliation(s)
- Yana A Lyon
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| |
Collapse
|
19
|
Gilbert JD, Fisher CM, Bu J, Prentice BM, Redwine JG, McLuckey SA. Strategies for generating peptide radical cations via ion/ion reactions. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:418-26. [PMID: 25800024 PMCID: PMC4372815 DOI: 10.1002/jms.3548] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 11/14/2014] [Accepted: 11/16/2014] [Indexed: 05/25/2023]
Abstract
Several approaches for the generation of peptide radical cations using ion/ion reactions coupled with either collision induced dissociation (CID) or ultraviolet photo dissociation (UVPD) are described here. Ion/ion reactions are used to generate electrostatic or covalent complexes comprised of a peptide and a radical reagent. The radical site of the reagent can be generated multiple ways. Reagents containing a carbon-iodine (C-I) bond are subjected to UVPD with 266-nm photons, which selectively cleaves the C-I bond homolytically. Alternatively, reagents containing azo functionalities are collisionally activated to yield radical sites on either side of the azo group. Both of these methods generate an initial radical site on the reagent, which then abstracts a hydrogen from the peptide while the peptide and reagent are held together by either electrostatic interactions or a covalent linkage. These methods are demonstrated via ion/ion reactions between the model peptide RARARAA (doubly protonated) and various distonic anionic radical reagents. The radical site abstracts a hydrogen atom from the peptide, while the charge site abstracts a proton. The net result is the conversion of a doubly protonated peptide to a peptide radical cation. The peptide radical cations have been fragmented via CID and the resulting product ion mass spectra are compared to the control CID spectrum of the singly protonated, even-electron species. This work is then extended to bradykinin, a more broadly studied peptide, for comparison with other radical peptide generation methods. The work presented here provides novel methods for generating peptide radical cations in the gas phase through ion/ion reaction complexes that do not require modification of the peptide in solution or generation of non-covalent complexes in the electrospray process.
Collapse
Affiliation(s)
| | | | | | | | | | - Scott A. McLuckey
- Address reprint requests to: Dr. S. A. McLuckey 560 Oval Drive Department of Chemistry Purdue University West Lafayette, IN 47907-2084, USA Phone: (765) 494-5270 Fax: (765) 494-0239
| |
Collapse
|
20
|
Tao Y, Julian RR. Identification of amino acid epimerization and isomerization in crystallin proteins by tandem LC-MS. Anal Chem 2014; 86:9733-41. [PMID: 25188914 PMCID: PMC4188265 DOI: 10.1021/ac502296c] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Post-translational modifications that do not result in a change in mass are particularly difficult to detect by mass spectrometry. For example, isomerization of aspartic acid or epimerization of any chiral residue within a peptide do not lead to mass shifts but can be identified by examination of independently acquired tandem mass spectra or by combination with another technique. For analysis of a biological sample, this means that liquid chromatography or some other type of separation must be used to first separate the isomers from one another. Furthermore, each specific m/z of interest must be sampled repeatedly to allow for comparison of the tandem mass spectra from each separated isomer, which contrasts with the traditional approach in proteomics where the goal is typically to avoid resampling the same m/z. We illustrate that isomerization and epimerization of peptides can be identified in this fashion by examination of long-lived crystallin proteins extracted from a sheep eye lens. Tandem mass spectrometry relying on a combination of radical directed dissociation (RDD) and collision induced dissociation (CID) following separation by liquid chromatography was used to identify modified peptides. Numerous sites of isomerization and epimerization, including several that have not been previously identified, were determined with peptide specificity. It is demonstrated that the specific sites of amino acid isomerization within each peptide can be identified by comparison with synthetic peptides. For α-crystallin proteins, the sites that undergo the greatest degree of isomerization correspond to disordered regions, which may have important implications on chaperone functionality within the context of aging.
Collapse
Affiliation(s)
- Yuanqi Tao
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | | |
Collapse
|
21
|
Zhang X, Julian RR. Radical additions to aromatic residues in peptides facilitate unexpected side chain and backbone losses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:626-635. [PMID: 24488753 DOI: 10.1007/s13361-013-0810-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/06/2013] [Accepted: 12/08/2013] [Indexed: 06/03/2023]
Abstract
Accurate identification of fragments in tandem mass spectrometry experiments is aided by knowledge of relevant fragmentation mechanisms. Herein, novel radical addition reactions that direct unexpected side-chain dissociations at tryptophan and tyrosine residues are reported. Various mechanisms that can account for the observed dissociation channels are investigated by experiment and theory. The propensity for radical addition at a particular site is found to be primarily under kinetic control, which is largely dictated by molecular structure. In certain peptides, intramolecular radical addition reactions are favored, which leads to the observation of numerous unexpected fragments. In one pathway, radical addition leads to migration of an aromatic side chain to another residue. Alternatively, radical addition followed by hydrogen atom loss leads to cyclization of the peptide and increased observation of internal sequence fragments. Radical addition reactions should be considered when assigning fragmentation spectra obtained from activation of hydrogen deficient peptides.
Collapse
Affiliation(s)
- Xing Zhang
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | | |
Collapse
|
22
|
Hamdy OM, Lam S, Julian RR. Identification of inherently antioxidant regions in proteins with radical-directed dissociation mass spectrometry. Anal Chem 2014; 86:3653-8. [PMID: 24621190 DOI: 10.1021/ac500425f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Antioxidant peptides such as glutathione play critically important roles within cells by opposing the action of oxidative species. Similarly all proteins may, as a secondary function, potentially contribute to the antioxidant capacity of the cellular milieu, though this possibility has not been thoroughly explored previously. Herein it is demonstrated that, in addition to radical quenching solution-phase behavior, antioxidant peptides display an astonishing ability to sequester radicals in the gas phase. Compared to other peptides of similar sequence and size, radical antioxidant peptides exhibit very little radical-directed dissociation when subjected to collisional activation in the gas phase. Importantly, this property can be leveraged in highly sensitive and rapid mass spectrometry based experiments to identify antioxidant peptides. Examination of peptides derived from human serum albumin (HSA), which is a protein known to behave as an antioxidant, revealed three previously unknown peptide regions that exhibit antioxidant capacity. One of these peptides, VAHRFK, shows antioxidant capacity comparable to that of glutathione. It is likely that these peptide regions contribute to the overall antioxidant capacity of HSA. In comparison with previous methods, the present technique is significantly more sensitive and less time-consuming, which should enable more wide-scale examination of antioxidant peptides that are relevant to redox homeostasis, food chemistry, and disease.
Collapse
Affiliation(s)
- Omar M Hamdy
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | | | | |
Collapse
|
23
|
Pham HT, Julian RR. Mass Shifting and Radical Delivery with Crown Ether Attachment for Separation and Analysis of Phosphatidylethanolamine Lipids. Anal Chem 2014; 86:3020-7. [DOI: 10.1021/ac403754j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Huong T. Pham
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| |
Collapse
|
24
|
Marshall DL, Hansen CS, Trevitt AJ, Oh HB, Blanksby SJ. Photodissociation of TEMPO-modified peptides: new approaches to radical-directed dissociation of biomolecules. Phys Chem Chem Phys 2014; 16:4871-9. [DOI: 10.1039/c3cp54825b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
25
|
Hansen CS, Kirk BB, Blanksby SJ, O'Hair RAJ, Trevitt AJ. UV photodissociation action spectroscopy of haloanilinium ions in a linear quadrupole ion trap mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:932-940. [PMID: 23609184 DOI: 10.1007/s13361-013-0615-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 03/05/2013] [Accepted: 03/10/2013] [Indexed: 06/02/2023]
Abstract
UV-vis photodissociation action spectroscopy is becoming increasingly prevalent because of advances in, and commercial availability of, ion trapping technologies and tunable laser sources. This study outlines in detail an instrumental arrangement, combining a commercial ion-trap mass spectrometer and tunable nanosecond pulsed laser source, for performing fully automated photodissociation action spectroscopy on gas-phase ions. The components of the instrumentation are outlined, including the optical and electronic interfacing, in addition to the control software for automating the experiment and performing online analysis of the spectra. To demonstrate the utility of this ensemble, the photodissociation action spectra of 4-chloroanilinium, 4-bromoanilinium, and 4-iodoanilinium cations are presented and discussed. Multiple photoproducts are detected in each case and the photoproduct yields are followed as a function of laser wavelength. It is shown that the wavelength-dependent partitioning of the halide loss, H loss, and NH3 loss channels can be broadly rationalized in terms of the relative carbon-halide bond dissociation energies and processes of energy redistribution. The photodissociation action spectrum of (phenyl)Ag2 (+) is compared with a literature spectrum as a further benchmark.
Collapse
|
26
|
Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195-1700, United States
| | | |
Collapse
|
27
|
Osburn S, Berden G, Oomens J, Gulyuz K, Polfer NC, O'Hair RAJ, Ryzhov V. Structure and Reactivity of the Glutathione Radical Cation: Radical Rearrangement from the Cysteine Sulfur to the Glutamic Acid α-Carbon Atom. Chempluschem 2013; 78:970-978. [DOI: 10.1002/cplu.201300057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Indexed: 12/19/2022]
|
28
|
Zhang X, Julian RR. Exploring radical migration pathways in peptides with positional isomers, deuterium labeling, and molecular dynamics simulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:524-533. [PMID: 23361370 DOI: 10.1007/s13361-012-0540-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 11/08/2012] [Accepted: 11/09/2012] [Indexed: 06/01/2023]
Abstract
One of the keys for understanding radical directed dissociation in peptides is a detailed knowledge of the factors that mediate radical migration. Peptide radicals can be created by a variety of means; however, in most circumstances, the originally created radicals must migrate to alternate locations in order to facilitate fragmentation such as backbone cleavage or side chain loss. The kinetics of radical migration are examined herein by comparing results from ortho-, meta-, and para-benzoyl radical positional isomers for several peptides. Isomers of a constrained cyclic peptide generated by several orthogonal radical initiators are also probed as a function of charge state. Cumulatively, the results suggest that small changes in radical position can significantly impact radical migration, and overall structural flexibility of the peptide is also an important controlling factor. A particularly interesting pathway for the peptide RGYALG that is sensitive to ortho versus meta or para substitution was fully mapped out by a suite of deuterium labeled peptides. This data was then used to optimize parameters in molecular dynamics-based simulations, which were subsequently used to obtain further insight into the structural underpinnings that most strongly influence the kinetics of radical migration.
Collapse
Affiliation(s)
- Xing Zhang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | | |
Collapse
|
29
|
Tao Y, Quebbemann NR, Julian RR. Discriminating d-Amino Acid-Containing Peptide Epimers by Radical-Directed Dissociation Mass Spectrometry. Anal Chem 2012; 84:6814-20. [PMID: 22812429 DOI: 10.1021/ac3013434] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuanqi Tao
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Neil R. Quebbemann
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| |
Collapse
|
30
|
Zhang X, Julian RR. Photoinitiated intramolecular diradical cross-linking of polyproline peptides in the gas phase. Phys Chem Chem Phys 2012; 14:16243-9. [PMID: 23111659 DOI: 10.1039/c2cp42242e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xing Zhang
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | | |
Collapse
|
31
|
Moore BN, Julian RR. Dissociation energies of X–H bonds in amino acids. Phys Chem Chem Phys 2012; 14:3148-54. [DOI: 10.1039/c2cp23443b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|