1
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Zima V, Vlk M, Wan J, Cvačka J, Tureček F. Tracking Isomerizations of High-Energy Adenine Cation Radicals by UV-Vis Action Spectroscopy and Cyclic Ion Mobility Mass Spectrometry. J Phys Chem A 2023. [PMID: 37433135 DOI: 10.1021/acs.jpca.3c03179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
We report experimental and computational studies of protonated adenine C-8 σ-radicals that are presumed yet elusive reactive intermediates of oxidative damage to nucleic acids. The radicals were generated in the gas phase by the collision-induced dissociation of C-8-Br and C-8-I bonds in protonated 8-bromo- and 8-iodoadenine as well as by 8-bromo- and 8-iodo-9-methyladenine. Protonation by electrospray of 8-bromo- and 8-iodoadenine was shown by cyclic-ion mobility mass spectrometry (c-IMS) to form the N-1-H, N-9-H and N-3-H, N-7-H protomers in 85:15 and 81:19 ratios, respectively, in accordance with the equilibrium populations of these protomers in water-solvated ions that were calculated by density functional theory (DFT). Protonation of 8-halogenated 9-methyladenines yielded single N-1-H protomers, which was consistent with their thermodynamic stability. The radicals produced from the 8-bromo and 8-iodo adenine cations were characterized by UV-vis photodissociation action spectroscopy (UVPD) and c-IMS. UVPD revealed the formation of C-8 σ-radicals along with N-3-H, N-7-H-adenine π-radicals that arose as secondary products by hydrogen atom migrations. The isomers were identified by matching their action spectra against the calculated vibronic absorption spectra. Deuterium isotope effects were found to slow the isomerization and increase the population of C-8 σ-radicals. The adenine cation radicals were separated by c-IMS and identified by their collision cross sections, which were measured relative to the canonical N-9-H adenine cation radical that was cogenerated in situ as an internal standard. Ab initio CCSD(T)/CBS calculations of isomer energies showed that the adenine C-8 σ-radicals were local energy minima with relative energies at 76-79 kJ mol-1 above that of the canonical adenine cation radical. Rice-Ramsperger-Kassel-Marcus calculations of unimolecular rate constants for hydrogen and deuterium migrations resulting in exergonic isomerizations showed kinetic shifts of 10-17 kJ mol-1, stabilizing the C-8 σ-radicals. C-8 σ-radicals derived from N-1-protonated 9-methyladenine were also thermodynamically unstable and readily isomerized upon formation.
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Affiliation(s)
- Václav Zima
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Mikuláš Vlk
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Jiahao Wan
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
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2
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Wan J, Brož B, Liu Y, Huang SR, Marek A, Tureček F. Resolution of Identity in Gas-Phase Dissociations of Mono- and Diprotonated DNA Trinucleotide Codons by 15N-Labeling and Computational Structure Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1936-1950. [PMID: 36040435 DOI: 10.1021/jasms.2c00194] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dissociations of DNA trinucleotide codons as gas-phase singly and doubly protonated ions were studied by tandem mass spectrometry using 15N-labeling to resolve identity in the nucleobase loss and backbone cleavages. The monocations showed different distributions of nucleobase loss from the 5'-, middle, and 3'-positions depending on the nucleobase, favoring cytosine over guanine, adenine, and thymine in an ensemble-averaged 62:27:11:<1 ratio. The distribution for the loss of the 5'-, middle, and 3'-nucleobase was 49:18:33, favoring the 5'-nucleobase, but also depending on its nature. The formation of sequence w2+ ions was unambiguously established for all codon mono- and dications. Structures of low-Gibbs-energy protomers and conformers of dAAA+, dGGG+, dCCC+, dTTT+, dACA+, and dATC+ were established by Born-Oppenheimer molecular dynamics and density functional theory calculations. Monocations containing guanine favored classical structures protonated at guanine N7. Structures containing adenine and cytosine produced classical nucleobase-protonated isomers as well as zwitterions in which two protonated bases were combined with a phosphate anion. Protonation at thymine was disfavored. Low threshold energies for nucleobase loss allowed extensive proton migration to occur prior to dissociation. Loss of the nucleobase from monocations was assisted by neighboring group participation in nucleophilic addition or proton abstraction, as well as allosteric proton migrations remote from the reaction center. The optimized structures of diprotonated isomers for dAAA2+ and dACA2+ revealed combinations of classical and zwitterionic structures. The threshold and transition-state energies for nucleobase-ion loss from dications were low, resulting in facile dissociations involving cytosine, guanine, and adenine.
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Affiliation(s)
- Jiahao Wan
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Břetislav Brož
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Yue Liu
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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3
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Liu Y, Ma C, Nováková G, Marek A, Tureček F. Charge-Tagged Nucleosides in the Gas Phase: UV-Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals. J Phys Chem A 2021; 125:6096-6108. [PMID: 34240862 DOI: 10.1021/acs.jpca.1c03477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cytidine ribonucleosides were furnished at O5' with fixed-charge 6-trimethylammoniumhexan-1-aminecarbonyl tags and studied by UV-vis photodissociation action spectroscopy in the gas phase to probe isolated nucleobase chromophores in their neutral, protonated, and hydrogen-adduct radical forms. The action spectrum of the doubly charged cytidine conjugate showed bands at 310 and 270 nm that were assigned to the N3- and O2-protonated cytosine tautomers formed by electrospray, respectively. In contrast, cytidine conjugates coordinated to dibenzo-18-crown-6-ether (DBCE) in a noncovalent complex were found to strongly favor protonation at N3, forming a single-ion tautomer. This allowed us to form cytidine N3-H radicals by electron transfer dissociation of the complex and study their action spectra. Cytidine radicals showed only very weak absorption in the visible region of the spectrum for dipole-disallowed transitions to the low (A and B) excited states. The main bands were observed at 360, 300, and 250 nm that were assigned with the help of theoretical vibronic spectra obtained by time-dependent density functional theory calculations of multiple (>300) radical vibrational configurations. Collision-induced dissociations of cytidine radicals proceeded by major cleavage of the N1-C1' glycosidic bond leading to loss of cytosine and competitive loss of N3-hydrogen atom. These dissociations were characterized by calculations of transition-state structures and energies using combined Born-Oppenheimer molecular dynamics and DFT calculations. Overall, cytidine radicals were found to be kinetically and thermodynamically more stable than previously reported analogous adenosine and guanosine radicals.
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Affiliation(s)
- Yue Liu
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Congcong Ma
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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Huang SR, Tureček F. Cation Radicals of Hachimoji Nucleobases P and Z: Generation in the Gas Phase and Characterization by UV-Vis Photodissociation Action Spectroscopy and Theory. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:373-386. [PMID: 33206519 DOI: 10.1021/jasms.0c00381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report the generation of gas-phase cation radicals of unusual nucleobases 5-aza-7-deazaguanine (P) and 6-amino-5-nitro-(1H)pyrid-2-one (Z) that have been used as building blocks of base-expanded (hachimoji) DNA. The cation radicals were generated by collision-induced intramolecular electron transfer and dissociation of ternary copper-terpyridine complexes. The cation radicals were characterized by deuterium labeling and tandem mass spectrometry including MS3 collision-induced dissociation, UV-vis photodissociation, and action spectroscopy. Vibronic absorption UV-vis spectra were calculated by time-dependent density functional theory (TD-DFT) and compared with the action spectra to unequivocally assign the most closely matching structures for the gas-phase cation radicals. Ab initio calculations up to the coupled clusters-complete basis set (CCSD(T)/CBS) level of theory were used to rank by energy the P and Z neutral molecules and cation-radical isomers and provided transition-state and dissociation energies. The 5-aza-7-deazaguanine cation radicals were determined to have the canonical N-1-H, 6-oxo structure (P1+•) that was the global energy minimum within this group of isomers. The Z cation radicals were found to have the 1H-pyrid-2-one structure (Z1+•). The formation of P1+• and Z1+• was shown to be controlled by the solution thermodynamics of the Cu-terpyridine complexes and the kinetics of their dissociations. We also report and compare CCSD(T)/CBS-calculated adiabatic recombination energies of cation radicals for the entire hachimoji set of eight nucleobases, P+• (7.92 eV), Z+• (8.51 eV), S+• (8.51 eV), B+• (7.76 eV), T+• (8.98 eV), C+• (8.62 eV), A+• (8.32 eV), and G+• (7.97 eV), to assess the thermodynamics of base-to-base electron transfer following random ionization.
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Affiliation(s)
- Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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5
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Huang SR, Nováková G, Marek A, Tureček F. The Elusive Noncanonical Isomers of Ionized 9-Methyladenine and 2′-Deoxyadenosine. J Phys Chem A 2020; 125:338-348. [DOI: 10.1021/acs.jpca.0c10293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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6
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Huang SR, Tureček F. Cation Radicals of Hachimoji Nucleobases. Canonical Purine and Noncanonical Pyrimidine Forms Generated in the Gas Phase and Characterized by UV–Vis Photodissociation Action Spectroscopy. J Phys Chem A 2020; 124:7101-7112. [DOI: 10.1021/acs.jpca.0c06227] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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7
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Zhang K, Ma L, Zhou M, Shi Y, Li S, Wang Y, Kong X. Wavelength-Dependent Ultraviolet Photodissociation of Protonated Tryptamine. J Phys Chem A 2020; 124:5280-5287. [PMID: 32536155 DOI: 10.1021/acs.jpca.0c02528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Ultraviolet photodissociation (UVPD) experiments of protonated tryptamine ([Tryp+H]+) have been implemented by a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer combined with a wavelength-tunable optical parametric oscillator (OPO) laser. UVPD mass spectra under different laser wavelengths have been obtained, in which the dependence of the yield of fragment ions on the laser wavelength was observed. The UVPD spectrum of [Tryp+H]+ has been obtained in the range of 210-310 nm. Besides the previously reported two competitive channels of H loss and NH3 loss, two important channels of losing CH2NH and CH2NH2 units were observed and further studied by UV-UV tandem mass spectrometry and theoretical calculations. Interestingly, results show that the pair of competitive channels of CH2NH loss and CH2NH2 loss are both from the McLafferty-type rearrangement caused by ππ* electronic excited states. After the excitation, the two different dissociation pathways produce two different ion-neutral complexes, respectively. The wavelength-dependent dissociation and the existing competitive channels shown in this study reflect the diversity of UVPD processes of such organic molecules.
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Affiliation(s)
- Kailin Zhang
- School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, China.,State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Lifu Ma
- School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Min Zhou
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China.,Department of Physics, Anhui Normal University, Wuhu 241000, China
| | - Yingying Shi
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Shuqi Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Yan Wang
- School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Xianglei Kong
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China.,Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
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8
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Huang SR, Liu Y, Tureček F. UV–vis Photodissociation Action Spectroscopy Reveals Cytosine–Guanine Hydrogen Transfer in DNA Tetranucleotide Cation Radicals upon One-Electron Reduction. J Phys Chem B 2020; 124:3505-3517. [DOI: 10.1021/acs.jpcb.0c01693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shu R. Huang
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Yue Liu
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle, Washington 98195-1700, United States
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9
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Liu Y, Huang SR, Tureček F. Guanine–adenine interactions in DNA tetranucleotide cation radicals revealed by UV/vis photodissociation action spectroscopy and theory. Phys Chem Chem Phys 2020; 22:16831-16842. [DOI: 10.1039/d0cp02362k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Hydrogen-rich cation radicals (GATT + 2H)+˙ and (AGTT + 2H)+˙ represent oligonucleotide models of charged hydrogen atom adducts to DNA.
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Affiliation(s)
- Yue Liu
- Department of Chemistry
- University of Washington
- Seattle
- USA
| | - Shu R. Huang
- Department of Chemistry
- University of Washington
- Seattle
- USA
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10
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Asakawa D, Takahashi H, Iwamoto S, Tanaka K. Hydrogen atom attachment to histidine and tryptophan containing peptides in the gas phase. Phys Chem Chem Phys 2019; 21:11633-11641. [DOI: 10.1039/c9cp00083f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this study, we focus on the gas-phase fragmentation induced by the attachment of hydrogen atoms to the histidine and tryptophan residue side-chains in the peptide that provides the fragment ions due to Cα–Cβ bond cleavage.
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Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST)
- National Metrology Institute of Japan (NMIJ)
- Tsukuba
- Japan
| | - Hidenori Takahashi
- Koichi Tanaka Mass Spectrometry Research Laboratory
- Shimadzu Corporation
- Kyoto 604-8511
- Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory
- Shimadzu Corporation
- Kyoto 604-8511
- Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory
- Shimadzu Corporation
- Kyoto 604-8511
- Japan
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11
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Mu X, Song T, Siu CK, Chu IK. Tautomerization and Dissociation of Molecular Peptide Radical Cations. CHEM REC 2017. [DOI: 10.1002/tcr.201700013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiaoyan Mu
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
| | - Tao Song
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
| | - Chi-Kit Siu
- Department of Biology and Chemistry; City University of Hong Kong; 83 Tat Chee Avenue Kowloon Tong, Hong Kong SAR P. R. China
| | - Ivan K. Chu
- Department of Chemistry; University of Hong Kong; Pokfulam, Hong Kong SAR P. R. China
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12
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Cao X, Wang Y, Mo Y, Wu L, Mo W. Friedel-Crafts dealkylation reaction mediated by a stereoselective proton transfer in the fragmentation of protonated cyclic indolyl α-amino esters. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1454-1460. [PMID: 27321832 DOI: 10.1002/rcm.7579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/01/2016] [Accepted: 04/02/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Chiral cyclic indolyl α-amino esters are valuable substructures of peptides and peptidomimetics. Systematically exploring the fragmentation behavior of the protonated cyclic indolyl α-amino esters by a combination of high-resolution high-energy collisional dissociation mass spectrometry, hydrogen-deuterium exchange experiments and density functional theory (DFT) calculations is useful for further understanding their intrinsic properties and the fragmentation mechanisms of peptidomimetics constructed with them. METHODS All high-resolution high-energy collisional dissociation tandem mass spectrometry experiments were carried out using electrospray ionization hybrid Quadrupole-Orbitrap mass spectrometry in positive ion mode. Only the labile hydrogens were exchanged with deuterium in hydrogen-deuterium exchange experiments. Theoretical calculations were carried out by the DFT method at the B3LYP level with the 6-311G(d,p) basis set in the Gaussian 03 package of programs. RESULTS In the fragmentation of protonated cyclic indolyl α-amino esters, when the two labile hydrogens on the N(8) position are successively transferred to the C(3) and C(4) positions, a Friedel-Crafts dealkylation reaction takes place spontaneously, with concomitant formation of an ion-neutral complex of [cyclic N-sulfonyl ketimino esters/protonated indoles]. Direct separation of this complex formed the protonated indoles, while a stereoselective proton transfer between the two components in the complex gave rise to protonated cyclic N-sulfonyl ketimino esters, which coincided with the hydrogen-deuterium experiments. CONCLUSIONS Using H/D exchange experiments combined with theoretical calculations, a Friedel-Crafts dealkylation reaction mediated by a stereoselective proton transfer in the [cyclic N-sulfonyl ketimino esters/protonated indoles] complex was proposed for the fragmentation of protonated cyclic indolyl α-amino esters in high-energy collisional dissociation tandem mass spectrometry for the first time. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Xiaoji Cao
- Research Center of Analysis and Measurement, Zhejiang University of Technology, 18 Chaowang Rd, Hangzhou, Zhejiang, 310014, P.R., China
| | - Ye Wang
- College of Chemical Engineering, Zhejiang University of Technologys, 18 Chaowang Rd, Hangzhou, Zhejiang, 310014, P.R., China
| | - Yawen Mo
- College of Chemical Engineering, Zhejiang University of Technologys, 18 Chaowang Rd, Hangzhou, Zhejiang, 310014, P.R., China
| | - Liang Wu
- College of Chemical Engineering, Zhejiang University of Technologys, 18 Chaowang Rd, Hangzhou, Zhejiang, 310014, P.R., China
| | - Weimin Mo
- Research Center of Analysis and Measurement, Zhejiang University of Technology, 18 Chaowang Rd, Hangzhou, Zhejiang, 310014, P.R., China
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13
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Fujihara A, Matsuo S, Tajiri M, Wada Y, Hayakawa S. Hypervalent radical formation probed by electron transfer dissociation of zwitterionic tryptophan and tryptophan-containing dipeptides complexed with Ca2+ and 18-crown-6 in the gas phase. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:1124-1129. [PMID: 26456780 DOI: 10.1002/jms.3628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/08/2015] [Accepted: 06/08/2015] [Indexed: 06/05/2023]
Abstract
The relationship between peptide structure and electron transfer dissociation (ETD) is important for structural analysis by mass spectrometry. In the present study, the formation, structure and reactivity of the reaction intermediate in the ETD process were examined using a quadrupole ion trap mass spectrometer equipped with an electrospray ionization source. ETD product ions of zwitterionic tryptophan (Trp) and Trp-containing dipeptides (Trp-Gly and Gly-Trp) were detected without reionization using non-covalent analyte complexes with Ca(2+) and 18-crown-6 (18C6). In the collision-induced dissociation, NH3 loss was the main dissociation pathway, and loss related to the dissociation of the carboxyl group was not observed. This indicated that Trp and its dipeptides on Ca(2+) (18C6) adopted a zwitterionic structure with an NH3 (+) group and bonded to Ca(2+) (18C6) through the COO(-) group. Hydrogen atom loss observed in the ETD spectra indicated that intermolecular electron transfer from a molecular anion to the NH3 (+) group formed a hypervalent ammonium radical, R-NH3 , as a reaction intermediate, which was unstable and dissociated rapidly through N-H bond cleavage. In addition, N-Cα bond cleavage forming the z1 ion was observed in the ETD spectra of Trp-GlyCa(2+) (18C6) and Gly-TrpCa(2+) (18C6). This dissociation was induced by transfer of a hydrogen atom in the cluster formed via an N-H bond cleavage of the hypervalent ammonium radical and was in competition with the hydrogen atom loss. The results showed that a hypervalent radical intermediate, forming a delocalized hydrogen atom, contributes to the backbone cleavages of peptides in ETD.
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Affiliation(s)
- Akimasa Fujihara
- Department of Chemistry, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Sou Matsuo
- Department of Chemistry, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Michiko Tajiri
- Department of Molecular Medicine, Osaka Medical Center and Research Institute for Maternal and Child Health, Sakai, Osaka, 594-1101, Japan
| | - Yoshinao Wada
- Department of Molecular Medicine, Osaka Medical Center and Research Institute for Maternal and Child Health, Sakai, Osaka, 594-1101, Japan
| | - Shigeo Hayakawa
- Department of Chemistry, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
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14
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Piatkivskyi A, Happ M, Lau JKC, Siu KWM, Hopkinson AC, Ryzhov V. Investigation of Fragmentation of Tryptophan Nitrogen Radical Cation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1388-1393. [PMID: 25962366 DOI: 10.1007/s13361-015-1134-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/10/2015] [Indexed: 06/04/2023]
Abstract
This work describes investigation of the fragmentation mechanism of tryptophan N-indolyl radical cation, H3N(+)-TrpN(•) (m/z 204) studied via DFT calculations and several gas-phase experimental techniques. The main fragment ion at m/z 131, shown to be a mixture of up to four isomers including 3-methylindole (3MI) π-radical cation, was found to undergo further loss of an H atom to yield one of the two isomeric m/z 130 ions. 3-Methylindole radical cation generated independently (via CID of [Cu(II)(terpy)3MI](•2+)) displayed gas-phase reactivity partially similar to that of the m/z 131 fragment, further confirming our proposed mechanism. CID of deuterated tryptophan N-indolyl radical cation (m/z 208) suggested that up to six H atoms are involved in the pathway to formation of the m/z 131 ion, consistent with hydrogen atom scrambling during CID of protonated Trp.
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Affiliation(s)
- Andrii Piatkivskyi
- Department of Chemistry and Biochemistry, and Center for Biochemical and Biophysical Studies, Northern Illinois University, DeKalb, IL, 60115, USA
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15
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Purushotham U, Sastry GN. A comprehensive conformational analysis of tryptophan, its ionic and dimeric forms. J Comput Chem 2013; 35:595-610. [DOI: 10.1002/jcc.23482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/08/2013] [Accepted: 10/13/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Uppula Purushotham
- Center for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad 500607 Andhra Pradesh India
| | - G. Narahari Sastry
- Center for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka, Hyderabad 500607 Andhra Pradesh India
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Ledvina AR, Chung TW, Hui R, Coon JJ, Tureček F. Cascade dissociations of peptide cation-radicals. Part 2. Infrared multiphoton dissociation and mechanistic studies of z-ions from pentapeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1351-1363. [PMID: 22669762 PMCID: PMC3619414 DOI: 10.1007/s13361-012-0409-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/07/2012] [Accepted: 05/08/2012] [Indexed: 05/28/2023]
Abstract
Dissociations of z(4) ions from pentapeptides AAXAR where X=H, Y, F, W, and V produce dominant z(2) ions that account for >50 % of the fragment ion intensity. The dissociation has been studied in detail by experiment and theory and found to involve several isomerization and bond-breaking steps. Isomerizations in z(4) ions proceed by amide trans→cis rotations followed by radical-induced transfer of a β-hydrogen atom from the side chain, forming stable C(β) radical intermediates. These undergo rate-determining cleavage of the C(α)-CO bond at the X residue followed by loss of the neutral AX fragment, forming x(2) intermediates. The latter were detected by energy-resolved resonant excitation collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) experiments. The x(2) intermediates undergo facile loss of HNCO to form z(2) fragment ions, as also confirmed by energy-resolved CID and IRMPD MS(4) experiments. The loss of HNCO from the x(2) ion from AAHWR is kinetically hampered by the Trp residue that traps the OCNH radical group in a cyclic intermediate.
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Affiliation(s)
- Aaron R Ledvina
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
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Chung TW, Hui R, Ledvina A, Coon JJ, Tureček F. Cascade dissociations of peptide cation-radicals. Part 1. Scope and effects of amino acid residues in penta-, nona-, and decapeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1336-50. [PMID: 22669761 PMCID: PMC3619428 DOI: 10.1007/s13361-012-0408-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/05/2012] [Accepted: 05/08/2012] [Indexed: 05/16/2023]
Abstract
Amino acid residue-specific backbone and side-chain dissociations of peptide z ions in MS(3) spectra were elucidated for over 40 pentapeptides with arginine C-terminated sequences of the AAXAR and AAHXR type, nonapeptides of the AAHAAXX"AR and AAHAXAX"AR type, and AAHAAXX"AAR decapeptides. Peptide z(n) ions containing amino acid residues with readily transferrable benzylic or tertiary β-hydrogen atoms (Phe, Tyr, His, Trp, Val) underwent facile backbone cleavages to form dominant z(n-2) or z(n-3) ions. These backbone cleavages are thought to be triggered by a side-chain β-hydrogen atom transfer to the z ion C(α) radical site followed by homolytic dissociation of the adjacent C(α)-CO bond, forming x(n-2) cation-radicals that spontaneously dissociate by loss of HNCO. Amino acid residues that do not have readily transferrable β-hydrogen atoms (Gly, Ala) do not undergo the z(n) → z(n-2) dissociations. The backbone cleavages compete with side-chain dissociations in z ions containing Asp and Asn residues. Side-chain dissociations are thought to be triggered by α-hydrogen atom transfers that activate the C(β)-C(γ) or C(β)-heteroatom bonds for dissociations that dominate the MS(3) spectra of z ions from peptides containing Leu, Cys, Lys, Met, Ser, Arg, Glu, and Gln residues. The Lys, Arg, Gln, and Glu residues also participate in γ-hydrogen atom transfers that trigger other side-chain dissociations.
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Affiliation(s)
- Thomas W Chung
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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