1
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Martínez-Fernández L, Ranković ML, Canon F, Nahon L, Giuliani A, Milosavljević AR, Martin-Somer A. Photodissociation of leucine-enkephalin protonated peptide: an experimental and theoretical perspective. RSC Adv 2024; 14:16809-16820. [PMID: 38784408 PMCID: PMC11112675 DOI: 10.1039/d4ra01690d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Understanding the competing processes that govern far ultraviolet photodissociation (FUV-PD) of biopolymers such as proteins is a challenge. Here, we report a combined experimental and theoretical investigation of FUV-PD of protonated leucine-enkephalin pentapeptide ([YGGFL + H]+) in the gas-phase. Time-dependent density functional theory (TD-DFT) calculations in combination with experiments and previous results for amino acids and shorter peptides help in rationalizing the evolution of the excited states. The results confirm that fragmentation of [YGGFL + H]+ results mainly from vibrationally excited species in the ground electronic state, populated after internal conversion. We also propose fragmentation mechanisms for specific photo-fragments such as tyrosine side chain loss (with an extra hydrogen) or hydrogen loss. In general, we observe the same mechanisms as for smaller peptides or protonated Tyr and Phe, that are not quenched by the presence of other amino acids. Nevertheless, we also found some differences, as for H loss, in part due to the fact that the charge is solvated by the peptide chain and not only by the COOH terminal group.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química Física de Materiales, Instituto de Química Física de Materiales, Instituto de Química Física Blas Cabrera, CSIC 28006 Madrid Spain
| | - Miloš Lj Ranković
- Institute of Physics Belgrade, University of Belgrade Pregrevica 118 11080 Belgrade Serbia
| | - Francis Canon
- SOLEIL l'Orme des Merisiers, St Aubin, BP48, F-91192 Gif sur Yvette Cedex France
| | - Laurent Nahon
- SOLEIL l'Orme des Merisiers, St Aubin, BP48, F-91192 Gif sur Yvette Cedex France
| | - Alexandre Giuliani
- SOLEIL l'Orme des Merisiers, St Aubin, BP48, F-91192 Gif sur Yvette Cedex France
- INRAE, Dpet. Transform UAR1008, Rue de la Géraudière, BP 71627 F-44316 Nantes France
| | | | - Ana Martin-Somer
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid Módulo 14 28049 Spain
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2
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Aloui I, Legros V, Giuliani A, Buchmann W. Ultraviolet Photoactivation Using Synchrotron Radiation for Tandem Mass Spectrometry of Polysiloxanes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:901-912. [PMID: 33673733 DOI: 10.1021/jasms.0c00392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gas-phase decompositions of polymer ions play an important role in mass spectrometry to obtain accurate structural information. In this work, UV photoactivation experiments were performed from two poly(dimethylsiloxane)s bearing different end groups (two trimethylsilyl, or α-sec-butyl and ω- trimethylsilyl). Precursor ions, such as [Polysiloxane+Cation]+ produced by an electrospray source, were stored in a linear ion trap and then submitted to synchrotron UV irradiation during different activation times and over a range of wavelengths (52 to 248 nm) from extreme UV (XUV) to deep UV. Upon photoactivation of a precursor ion from poly(dimethylsiloxane) (PDMS; with two trimethylsilyl end groups, [PDMS25+Na]+), important fragmentations were observed, including the loss of a methyl radical followed by various heterolytic cleavages along the polymer backbone, for photon energies typically >9.5-10 eV (ionization threshold of the neutral oligomer). This report focuses on different aspects: (i) the identification of the UV photodissociation (UV-PD) products of PDMS, (ii) the influence of the irradiation time for two photon energies (10 or 20 eV), (iii) the influence of the energy of the photon for two activation times (100 or 5000 ms), (iv) the influence of the nature of the cation, and (v) the influence of the end groups of PDMS. Synchrotron UV irradiation with a tunable wavelength was a great opportunity to study the effect of the photon energy and to probe the original mechanisms of ion decomposition from poly(dimethylsiloxane).
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Affiliation(s)
- Inès Aloui
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Véronique Legros
- Proteomic Platform, Institut Jacques Monod, 75205 CEDEX 13 Paris, France
| | - Alexandre Giuliani
- Disco Beamline, Université Paris-Saclay, Synchrotron Soleil, 91190, Saint-Aubin, France
- UAR1008, Transform, INRAe, Rue de la Géraudière, F-44316 Nantes, France
| | - William Buchmann
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
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3
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Silzel JW, Murphree TA, Paranji RK, Guttman MM, Julian RR. Probing the Stability of Proline Cis/Trans Isomers in the Gas Phase with Ultraviolet Photodissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1974-1980. [PMID: 32808771 DOI: 10.1021/jasms.0c00242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although most peptide bonds in proteins exist in the trans configuration, when cis peptide bonds do occur, they can have major impact on protein structure and function. The rapid identification of cis peptide bonds is therefore an important task. Peptide bonds containing proline are more likely to adopt the cis configuration because the ring connecting the side chain and backbone in proline flattens the energetic landscape relative to amino acids with free side chains. Examples of cis proline isomers have been identified in both solution and in the gas phase by a variety of structure-probing methods. Mass spectrometry is an attractive potential method for identifying cis proline due to its speed and sensitivity; however, the question remains of whether cis/trans proline isomers originating in solution are preserved during ionization and manipulation within a mass spectrometer. Herein, we investigate the gas-phase stability of isolated solution-phase cis and trans proline isomers using a synthetic peptide sequence with a Tyr-Pro-Pro motif. A variety of dissociation methods were explored to evaluate their potential to distinguish cis/trans configuration, including collision-induced dissociation, radical-directed dissociation, and photodissociation. Only photodissociation employed in conjunction with extremely gentle electrospray and charge solvation by 18-crown-6 ether was able to distinguish cis/trans isomers for our model peptide, suggesting that any thermal activation during transfer or while in the gas phase leads to isomer scrambling. Furthermore, the necessity for 18-crown-6 suggests that intramolecular charge solvation taking place during electrospray ionization can override cis/trans isomer homogeneity. Overall, the results suggest that solution-phase cis/trans proline isomers are fragile and easily lost during electrospray, requiring careful selection of instrument parameters and consideration of charge solvation to prevent cis/trans scrambling.
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Affiliation(s)
- Jacob W Silzel
- Department of Chemistry, University of California, 501 Big Springs Road, Riverside, California 92521, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rajan K Paranji
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miklos M Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ryan R Julian
- Department of Chemistry, University of California, 501 Big Springs Road, Riverside, California 92521, United States
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4
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Kaliakin DS, Fedorov DG, Alexeev Y, Varganov SA. Locating Minimum Energy Crossings of Different Spin States Using the Fragment Molecular Orbital Method. J Chem Theory Comput 2019; 15:6074-6084. [DOI: 10.1021/acs.jctc.9b00641] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Danil S. Kaliakin
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
| | - Yuri Alexeev
- Computational Science Division and Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Sergey A. Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
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5
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Morrison LJ, Chai W, Rosenberg JA, Henkelman G, Brodbelt JS. Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry. Phys Chem Chem Phys 2018; 19:20057-20074. [PMID: 28722742 DOI: 10.1039/c7cp04073c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.
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6
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Doan TN, Fujihara A. Enantiomer-Selective Photo-Induced Reaction of Protonated Tryptophan with Disaccharides in the Gas Phase. ORIGINS LIFE EVOL B 2017; 48:123-130. [DOI: 10.1007/s11084-017-9544-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
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7
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DeBlase AF, Harrilal CP, Lawler JT, Burke NL, McLuckey SA, Zwier TS. Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]+ and [YGPAA+H]+ Ions: A Stereochemical “Twist” on the β-Hairpin Turn. J Am Chem Soc 2017; 139:5481-5493. [PMID: 28353347 DOI: 10.1021/jacs.7b01315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew F. DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Christopher P. Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - John T. Lawler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Nicole L. Burke
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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8
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Schöneich C. Novel chemical degradation pathways of proteins mediated by tryptophan oxidation: tryptophan side chain fragmentation. J Pharm Pharmacol 2017; 70:655-665. [DOI: 10.1111/jphp.12688] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/11/2016] [Indexed: 01/04/2023]
Abstract
Abstract
Objectives
This minireview focuses on novel degradation pathways of proteins in solution via intermediary tryptophan (Trp) radical cations, which are generated via photo-induced electron transfer to suitable acceptors such as disulfide bonds.
Methods
Gas-phase mass spectrometry studies had indicated the potential for Trp radical cations to fragment via release of 3-methylene-3H-indol-1-ium from the side chain. HPLC-MS/MS analysis demonstrates that analogous fragmentation reactions occur during the exposure of peptides and proteins to light or accelerated stability testing.
Key findings
The light exposure of selected peptides and monoclonal antibodies leads to the conversion of Trp to glycine (Gly) or glycine hydroperoxide (GlyOOH), where GlyOOH could be reduced to hydroxyglycine, which undergoes subsequent cleavage. Product formation is consistent with Cα–Cβ fragmentation of intermediary Trp radical cations. For the peptide octreotide and specific glycoforms of IgG1 Fc domains, Trp side chain cleavage in aqueous solution is indicated by the formation of 3-methyleneindolenine (3-MEI), which adds to nucleophilic side chains, for example to Lys residues adjacent to the original Trp residues.
Conclusions
Trp side chain cleavage leads to novel reaction products on specific peptide and protein sequences, which may have consequences for potency and immunogenicity.
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Affiliation(s)
- Christian Schöneich
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
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9
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Kumar S, Lucas B, Fayeton J, Scuderi D, Alata I, Broquier M, Barbu-Debus KL, Lepère V, Zehnacker A. Photofragmentation mechanisms in protonated chiral cinchona alkaloids. Phys Chem Chem Phys 2016; 18:22668-77. [DOI: 10.1039/c6cp04041a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Photo-fragmentation of protonated alkaloids results in C8–C9 cleavage accompanied or not by hydrogen migration, with a stereochemistry-dependent branching ratio.
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Affiliation(s)
- Sunil Kumar
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- France
| | - Bruno Lucas
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- France
| | - Jacqueline Fayeton
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- France
| | - Debora Scuderi
- Univ. Paris-Sud
- Laboratoire de Chimie Physique
- UMR8000, and CNRS
- Orsay
- France
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- France
| | - Michel Broquier
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- France
| | - Valeria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- CNRS
- Univ. Paris-Sud
- Université Paris-Saclay
- France
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10
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11
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Alata I, Scuderi D, Lepere V, Steinmetz V, Gobert F, Thiao-Layel L, Le Barbu-Debus K, Zehnacker-Rentien A. Exotic Protonated Species Produced by UV-Induced Photofragmentation of a Protonated Dimer: Metastable Protonated Cinchonidine. J Phys Chem A 2015; 119:10007-15. [DOI: 10.1021/acs.jpca.5b06506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ivan Alata
- Institut des Sciences
Moléculaires d’Orsay (ISMO), CNRS, Univ Paris-Sud, Université Paris Saclay, F-91405 Orsay, France
| | - Debora Scuderi
- Laboratoire de
Chimie Physique (LCP), CNRS, Univ Paris-Sud, Université Paris Saclay, F-91405 Orsay, France
| | - Valeria Lepere
- Institut des Sciences
Moléculaires d’Orsay (ISMO), CNRS, Univ Paris-Sud, Université Paris Saclay, F-91405 Orsay, France
| | - Vincent Steinmetz
- Laboratoire de
Chimie Physique (LCP), CNRS, Univ Paris-Sud, Université Paris Saclay, F-91405 Orsay, France
| | - Fabrice Gobert
- Laboratoire de
Chimie Physique (LCP), CNRS, Univ Paris-Sud, Université Paris Saclay, F-91405 Orsay, France
| | - Loïc Thiao-Layel
- Laboratoire de
Chimie Physique (LCP), CNRS, Univ Paris-Sud, Université Paris Saclay, F-91405 Orsay, France
| | - Katia Le Barbu-Debus
- Institut des Sciences
Moléculaires d’Orsay (ISMO), CNRS, Univ Paris-Sud, Université Paris Saclay, F-91405 Orsay, France
| | - Anne Zehnacker-Rentien
- Institut des Sciences
Moléculaires d’Orsay (ISMO), CNRS, Univ Paris-Sud, Université Paris Saclay, F-91405 Orsay, France
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12
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Soorkia S, Dehon C, S SK, Pérot-Taillandier M, Lucas B, Jouvet C, Barat M, Fayeton JA. Ion-Induced Dipole Interactions and Fragmentation Times: Cα-Cβ Chromophore Bond Dissociation Channel. J Phys Chem Lett 2015; 6:2070-2074. [PMID: 26266504 DOI: 10.1021/acs.jpclett.5b00792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The fragmentation times corresponding to the loss of the chromophore (Cα-Cβ bond dissociation channel) after photoexcitation at 263 nm have been investigated for several small peptides containing tryptophan or tyrosine. For tryptophan-containing peptides, the aromatic chromophore is lost as an ionic fragment (m/z 130), and the fragmentation time increases with the mass of the neutral fragment. In contrast, for tyrosine-containing peptides the aromatic chromophore is always lost as a neutral fragment (mass = 107 amu) and the fragmentation time is found to be fast (<20 ns). These different behaviors are explained by the role of the postfragmentation interaction in the complex formed after the Cα-Cβ bond cleavage.
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Affiliation(s)
- Satchin Soorkia
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Christophe Dehon
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Sunil Kumar S
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Marie Pérot-Taillandier
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Bruno Lucas
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Christophe Jouvet
- ‡Physique des Interactions Ioniques et Moléculaires (PIIM), UMR 7345, CNRS, Aix-Marseille Université, 13397 Marseille Cedex 20, France
| | - Michel Barat
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Jacqueline A Fayeton
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
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13
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Byskov CS, Jensen F, Jørgensen TJD, Nielsen SB. On the photostability of peptides after selective photoexcitation of the backbone: prompt versus slow dissociation. Phys Chem Chem Phys 2015; 16:15831-8. [PMID: 24945849 DOI: 10.1039/c4cp02015d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vulnerability of biomolecules to ultraviolet radiation is intimately linked to deexcitation pathways: photostability requires fast internal conversion to the electronic ground state, but also intramolecular vibrational redistribution and cooling on a time scale faster than dissociation. Here we present a protocol to disentangle slow and non-hazardous statistical dissociation from prompt cleavage of peptide bonds by 210 nm light based on experiments on protonated peptides isolated in vacuo and tagged by 18-crown-6 ether (CE). The weakest link in the system is between the charged site and CE, which is remote from the initial site of excitation. Hence loss of CE serves as direct proof that energy has reached the charge-site end, leaving the backbone intact. Our work demonstrates that excitation of tertiary amide moieties (proline linkages) results in both prompt dissociation and statistical dissociation after energy randomisation over all vibrational degrees of freedom.
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14
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Canon F, Milosavljević AR, Nahon L, Giuliani A. Action spectroscopy of a protonated peptide in the ultraviolet range. Phys Chem Chem Phys 2015; 17:25725-33. [DOI: 10.1039/c4cp04762a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Action spectroscopy of substance P, a model undecapeptide, has been probed from 5.2 eV to 20 eV.
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Affiliation(s)
- Francis Canon
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- UMR1324 Centre des Sciences du Goût et de l'Alimentation
| | | | - Laurent Nahon
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
| | - Alexandre Giuliani
- Synchrotron Soleil
- l'Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- Uar1008
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15
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Giuliani A, Milosavljević AR, Canon F, Nahon L. Contribution of synchrotron radiation to photoactivation studies of biomolecular ions in the gas phase. MASS SPECTROMETRY REVIEWS 2014; 33:424-441. [PMID: 24375654 DOI: 10.1002/mas.21398] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Photon activation of ions in the visible and ultraviolet range attracts a growing interest, partly for its promising applications in tandem mass spectrometry. However, this task is not trivial, as it requires notably high brilliance photon sources. Hence, most of the work in that field has been performed using lasers. Synchrotron radiation is a source continuously tunable over a wide photon energy range and which possesses the necessary characteristics for ion activation. This review focuses on the array of applications of synchrotron radiation in photon activation of ions ranging from near UV to soft X-rays.
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Affiliation(s)
- Alexandre Giuliani
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin, 91192, Gif-sur-Yvette, France; UAR1008 CEPIA, INRA, 44316, Nantes, France
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16
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Zabuga AV, Kamrath MZ, Boyarkin OV, Rizzo TR. Fragmentation mechanism of UV-excited peptides in the gas phase. J Chem Phys 2014; 141:154309. [DOI: 10.1063/1.4897158] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aleksandra V. Zabuga
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Z. Kamrath
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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17
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Kopysov V, Nagornova NS, Boyarkin OV. Identification of Tyrosine-Phosphorylated Peptides Using Cold Ion Spectroscopy. J Am Chem Soc 2014; 136:9288-91. [DOI: 10.1021/ja5053544] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir Kopysov
- Laboratoire
de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Natalia S. Nagornova
- Laboratoire
de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Oleg V. Boyarkin
- Laboratoire
de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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18
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Zehnacker A. Chirality effects in gas-phase spectroscopy and photophysics of molecular and ionic complexes: contribution of low and room temperature studies. INT REV PHYS CHEM 2014. [DOI: 10.1080/0144235x.2014.911548] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Soorkia S, Dehon C, Kumar SS, Pedrazzani M, Frantzen E, Lucas B, Barat M, Fayeton JA, Jouvet C. UV Photofragmentation Dynamics of Protonated Cystine: Disulfide Bond Rupture. J Phys Chem Lett 2014; 5:1110-6. [PMID: 26274457 DOI: 10.1021/jz500158j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Disulfide bonds (S-S) play a central role in stabilizing the native structure of proteins against denaturation. Experimentally, identification of these linkages in peptide and protein structure characterization remains challenging. UV photodissociation (UVPD) can be a valuable tool in identifying disulfide linkages. Here, the S-S bond acts as a UV chromophore and absorption of one UV photon corresponds to a σ-σ* transition. We have investigated the photodissociation dynamics of protonated cystine, which is a dimer of two cysteines linked by a disulfide bridge, at 263 nm (4.7 eV) using a multicoincidence technique in which fragments coming from the same fragmentation event are detected. Two types of bond cleavages are observed corresponding to the disulfide (S-S) and adjacent C-S bond ruptures. We show that the S-S cleavage leads to three different fragment ions via three different fragmentation mechanisms. The UVPD results are compared to collision-induced dissociation (CID) and electron-induced dissociation (EID) studies.
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Affiliation(s)
- Satchin Soorkia
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Christophe Dehon
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - S Sunil Kumar
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Mélanie Pedrazzani
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Emilie Frantzen
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Bruno Lucas
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Michel Barat
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Jacqueline A Fayeton
- †Institut des Sciences Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud, F-91405 Orsay Cedex, France
| | - Christophe Jouvet
- ‡Aix Marseille Université, CNRS, PIIM UMR 7375, 13397 Marseille Cedex 20, France
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Scuderi D, Lepere V, Piani G, Bouchet A, Zehnacker-Rentien A. Structural Characterization of the UV-Induced Fragmentation Products in an Ion Trap by Infrared Multiple Photon Dissociation Spectroscopy. J Phys Chem Lett 2014; 5:56-61. [PMID: 26276181 DOI: 10.1021/jz402348n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protonated cinchona alkaloids and their dimers undergo photochemical reaction in the gas phase, leading to UV-specific photofragments, not observed by collision-induced dissociation. Simultaneous coupling of UV and IR lasers with a Paul ion trap has been achieved for obtaining the vibrational spectrum of the fragments arising from the photodissociation. The structure of the photoproduced radical has been fully characterized by comparing the experimental spectrum to that simulated by DFT calculations.
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Affiliation(s)
- Debora Scuderi
- †Laboratoire de Chimie Physique and ‡Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, CNRS, F-91405 Orsay, France
| | - Valeria Lepere
- †Laboratoire de Chimie Physique and ‡Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, CNRS, F-91405 Orsay, France
| | - Giovanni Piani
- †Laboratoire de Chimie Physique and ‡Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, CNRS, F-91405 Orsay, France
| | - Aude Bouchet
- †Laboratoire de Chimie Physique and ‡Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, CNRS, F-91405 Orsay, France
| | - Anne Zehnacker-Rentien
- †Laboratoire de Chimie Physique and ‡Institut des Sciences Moléculaires d'Orsay, Université Paris-Sud, CNRS, F-91405 Orsay, France
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Duffy MJ, Kelly O, Calvert CR, King RB, Belshaw L, Kelly TJ, Costello JT, Timson DJ, Bryan WA, Kierspel T, Turcu ICE, Cacho CM, Springate E, Williams ID, Greenwood JB. Fragmentation of neutral amino acids and small peptides by intense, femtosecond laser pulses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1366-1375. [PMID: 23817831 DOI: 10.1007/s13361-013-0653-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 06/02/2023]
Abstract
High power femtosecond laser pulses have unique properties that could lead to their application as ionization or activation sources in mass spectrometry. By concentrating many photons into pulse lengths approaching the timescales associated with atomic motion, very strong electric field strengths are generated, which can efficiently ionize and fragment molecules without the need for resonant absorption. However, the complex interaction between these pulses and biomolecular species is not well understood. To address this issue, we have studied the interaction of intense, femtosecond pulses with a number of amino acids and small peptides. Unlike previous studies, we have used neutral forms of these molecular targets, which allowed us to investigate dissociation of radical cations without the spectra being complicated by the action of mobile protons. We found fragmentation was dominated by fast, radical-initiated dissociation close to the charge site generated by the initial ionization or from subsequent ultrafast migration of this charge. Fragments with lower yields, which are useful for structural determinations, were also observed and attributed to radical migration caused by hydrogen atom transfer within the molecule.
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Affiliation(s)
- Martin J Duffy
- Centre for Plasma Physics, School of Mathematics and Physics, Queen's University Belfast, Belfast, UK
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Schafheimer N, King J. Tryptophan cluster protects human γD-crystallin from ultraviolet radiation-induced photoaggregation in vitro. Photochem Photobiol 2013; 89:1106-15. [PMID: 23683003 PMCID: PMC3823069 DOI: 10.1111/php.12096] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 05/12/2013] [Indexed: 11/30/2022]
Abstract
Exposure to ultraviolet radiation (UVR) is a significant risk factor for age-related cataract, a disease of the human lens and the most prevalent cause of blindness in the world. Cataract pathology involves protein misfolding and aggregation of the primary proteins of the lens, the crystallins. Human γD-crystallin (HγD-Crys) is a major γ-crystallin in the nucleus of the human lens. We report here analysis of UVR-induced damage to HγD-Crys in vitro. Irradiation of solutions of recombinant HγD-Crys with UVA/UVB light produced a rise in solution turbidity due to polymerization of the monomeric crystallins into higher molecular weight aggregates. A significant fraction of this polymerized protein was covalently linked. Photoaggregation of HγD-Crys required oxygen and its rate was protein concentration and UVR dose dependent. To investigate the potential roles of individual tryptophan residues in photoaggregation, triple W:F mutants of HγD-Crys were irradiated. Surprisingly, despite reducing UVR absorbing capacity, multiple W:F HγD-Crys mutant proteins photoaggregated more quickly and extensively than wild type. The results reported here are consistent with previous studies that postulated that an energy transfer mechanism between the highly conserved pairs of tryptophan residues in HγD-Crys could be protective against UVR-induced photodamage.
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Dehon C, Soorkia S, Pedrazzani M, Jouvet C, Barat M, Fayeton JA, Lucas B. Photofragmentation at 263 nm of small peptides containing tyrosine: the role of the charge transfer on CO. Phys Chem Chem Phys 2013; 15:8779-88. [DOI: 10.1039/c3cp50720c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Aravind G, Klærke B, Rajput J, Toker Y, Andersen LH, Bochenkova AV, Antoine R, Lemoine J, Racaud A, Dugourd P. Photodissociation pathways and lifetimes of protonated peptides and their dimers. J Chem Phys 2012; 136:014307. [PMID: 22239781 DOI: 10.1063/1.3671943] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Photodissociation lifetimes and fragment channels of gas-phase, protonated YA(n) (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ~200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of ~2 μs. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.
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Affiliation(s)
- G Aravind
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
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Kalcic CL, Reid GE, Lozovoy VV, Dantus M. Mechanism elucidation for nonstochastic femtosecond laser-induced ionization/dissociation: from amino acids to peptides. J Phys Chem A 2012; 116:2764-74. [PMID: 22141398 DOI: 10.1021/jp208421d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Femtosecond laser-induced ionization/dissociation (fs-LID) has been demonstrated as a novel ion activation method for use in tandem mass spectrometry. The technique opens the door to unique structural information about biomolecular samples that is not easily accessed by traditional means. fs-LID is able to cleave strong bonds while keeping weaker bonds intact. This feature has been found to be particularly useful for the mapping of post-translational modifications such as phosphorylation, which is difficult to achieve by conventional proteomic studies. Here we investigate the laser-ion interaction on a fundamental level through the characterization of fs-LID spectra for the protonated amino acids and two series of derivatized samples. The findings are used to better understand the fs-LID spectra of synthetic peptides. This is accomplished by exploring the effects of several single-residue substitutions.
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Affiliation(s)
- Christine L Kalcic
- Departments of Chemistry, Michigan State University East Lansing, Michigan 48824, USA
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Kumar SS, Lucas B, Soorkia S, Barat M, Fayeton JA. Cα–Cβ chromophore bond dissociation in protonated tyrosine-methionine, methionine-tyrosine, tryptophan-methionine, methionine-tryptophan and their sulfoxide analogs. Phys Chem Chem Phys 2012; 14:10225-32. [DOI: 10.1039/c2cp40773f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kumar SS, Pérot-Taillandier M, Lucas B, Soorkia S, Barat M, Fayeton JA. UV photodissociation dynamics of deprotonated 2'-deoxyadenosine 5'-monophosphate [5'-dAMP-H]-. J Phys Chem A 2011; 115:10383-90. [PMID: 21776981 DOI: 10.1021/jp204738q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The UV photodissociation dynamics of deprotonated 2'-deoxyadenosine 5'-monophosphate ([5'-dAMP-H](-)) has been studied using a unique technique based on the coincident detection of the ion and the neutral fragments. The observed fragment ions are m/z 79 (PO(3)(-)), 97 (H(2)PO(4)(-)), 134 ([A-H](-)), 177 ([dAMP-H-A-H(2)O](-)), and 195 ([dAMP-H-A](-)), where "A" refers to a neutral adenine molecule. The relative abundances are comparable to that found in previous studies on [5'-dAMP-H](-) employing different excitation processes, i.e., collisions and UV photons. The fragmentation times of the major channels have been measured, and are all found to be on the microsecond time scale. The fragmentation mechanisms for all channels have been characterized using velocity correlation plots of the ion and neutral fragment(s). The findings show that none of the dissociation channels of [5'-dAMP-H](-) is UV specific and all proceed via statistical fragmentation on the ground state after internal conversion, a result similar to fragmentations induced by collisions.
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Affiliation(s)
- S Sunil Kumar
- Institut des Science Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud 11, F-91405 Orsay Cedex, France
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Antoine R, Dugourd P. Visible and ultraviolet spectroscopy of gas phase protein ions. Phys Chem Chem Phys 2011; 13:16494-509. [PMID: 21811728 DOI: 10.1039/c1cp21531k] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.
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Diedrich JK, Julian RR. Site-selective fragmentation of peptides and proteins at quinone-modified cysteine residues investigated by ESI-MS. Anal Chem 2010; 82:4006-14. [PMID: 20405909 DOI: 10.1021/ac902786q] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Described herein are several unique analytical applications utilizing mass spectrometry and the selective modification of the free thiol form of cysteine in both peptides and proteins by various quinones. This simple modification can be used to quantify the number of free or disulfide bound cysteines in a protein. In addition, quinone modification can also be used to easily probe the solvent accessibility of cysteine residues, which provides information about protein structure or folding state. Furthermore, the chromophoric properties of the quinone moiety can be leveraged for site specific photodissociation of the backbone. The photodissociation reveals both the presence and location of modified cysteine residues. For example, cleavage of the protein backbone of alpha-hemoglobin is observed selectively at a single cysteine out of 140 residues in the whole protein. This selective backbone fragmentation is accompanied by a parent ion mass loss, which is unique to the modifying quinone. When combined, this information can be used to determine both the presence and site of modification generated by naturally occurring molecules, such as dopamine, which can harness quinone chemistry to modify proteins.
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Affiliation(s)
- Jolene K Diedrich
- Department of Chemistry, University of California, Riverside, California 92521, USA
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