1
|
Tureček F. Flying DNA Cation Radicals in the Gas Phase: Generation and Action Spectroscopy of Canonical and Noncanonical Nucleobase Forms. J Phys Chem B 2021; 125:7090-7100. [PMID: 34166596 DOI: 10.1021/acs.jpcb.1c03674] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas-phase chemistry of cation radicals related to ionized nucleic acids has enjoyed significant recent progress thanks to the development of new methods for cation radical generation, ion spectroscopy, and reactivity studies. Oxidative methods based on intramolecular electron transfer in transition-metal complexes have been used to generate nucleobase and nucleoside cation radicals. Reductive methods relying on intermolecular electron transfer in gas-phase ion-ion reactions have been utilized to generate a number of di- and tetranucleotide cation radicals, as well as charge-tagged nucleoside radicals. The generated cation radicals have been studied by infrared and UV-visible action spectroscopy and ab initio and density functional theory calculations, providing optimized structures, harmonic frequencies, and excited-state analysis. This has led to the discovery of stable noncanonical nucleobase cation radicals of unusual electronic properties and extremely low ion-electron recombination energies. Intramolecular proton-transfer reactions in cation radical oligonucleotides and Watson-Crick nucleoside pairs have been studied experimentally, and their mechanisms have been elucidated by theory. Whereas the range of applications of the oxidative methods is currently limited to nucleobases and readily oxidizable guanosine, the reductive methods can be scaled up to generate large oligonucleotide cation radicals including double-strand DNA. Challenges in the experimental and computational approach to DNA cation radicals are discussed.
Collapse
Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| |
Collapse
|
2
|
Abdelmouleh M, Lalande M, Nicol E, Frison G, van der Rest G, Poully JC. Chemical Processes Involving 18-Crown-6-Ether in Activated Noncovalent Complexes with Protonated Peptides. Chemphyschem 2021; 22:1243-1250. [PMID: 33881793 DOI: 10.1002/cphc.202100075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Indexed: 11/10/2022]
Abstract
These last decades, it has been widely assumed that 18-crown-6-ether (CE) plays a spectator role during the chemical processes occurring in isolated host-guest complexes between peptides or proteins and CE after activation in mass spectrometers. Our present experimental and theoretical results challenge this hypothesis by showing that CE can abstract a proton or a protonated molecule from protonated peptides after activation by collisions in argon or electron capture/transfer. Furthermore, thanks to comparison between experimental and calculated values of collision cross-sections, we demonstrate that CE can change binding site after electron transfer. We also propose detailed mechanisms for these processes.
Collapse
Affiliation(s)
- Marwa Abdelmouleh
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Mathieu Lalande
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Edith Nicol
- Laboratoire de Chimie Moléculaire, Ecole Polytech, Inst Polytech Paris, CNRS, 91128, Palaiseau, France
| | - Gilles Frison
- Laboratoire de Chimie Moléculaire, Ecole Polytech, Inst Polytech Paris, CNRS, 91128, Palaiseau, France.,Laboratoire de Chimie Théorique, Sorbonne Université and CNRS, 75005, Paris, France
| | - Guillaume van der Rest
- Institut de Chimie Physique, Université Paris Saclay, CNRS, Bâtiment 349, 91405, Orsay, France
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| |
Collapse
|
3
|
Shao P, Chen BL, Ding LP, Luo DB, Lu C, Kuang XY. Prediction of hypervalent molecules: investigation on MnC (M = Li, Na, K, Rb and Cs; n = 1–8) clusters. Phys Chem Chem Phys 2017; 19:25289-25297. [DOI: 10.1039/c7cp03776g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The density of states (DOS) and electron localization function plots of the ground state Li6C cluster.
Collapse
Affiliation(s)
- Peng Shao
- Department of Physics
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Bo-Le Chen
- Department of Physics
- Nanyang Normal University
- Nanyang
- China
- Institute of Atomic and Molecular Physics
| | - Li Ping Ding
- Department of Optoelectronic Science & Technology
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Dao-Bin Luo
- Department of Physics
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Cheng Lu
- Department of Physics
- Nanyang Normal University
- Nanyang
- China
| | - Xiao-Yu Kuang
- Institute of Atomic and Molecular Physics
- Sichuan University
- Chengdu 610065
- China
| |
Collapse
|
4
|
Lermyte F, Łącki MK, Valkenborg D, Gambin A, Sobott F. Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:69-76. [PMID: 27495285 DOI: 10.1007/s13361-016-1444-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/11/2016] [Accepted: 06/26/2016] [Indexed: 06/06/2023]
Abstract
Owing to its versatility, electron transfer dissociation (ETD) has become one of the most commonly utilized fragmentation techniques in both native and non-native top-down mass spectrometry. However, several competing reactions-primarily different forms of charge reduction-occur under ETD conditions, as evidenced by the distorted isotope patterns usually observed. In this work, we analyze these isotope patterns to compare the stability of nondissociative electron transfer (ETnoD) products, specifically noncovalent c/z fragment complexes, across a range of ubiquitin conformational states. Using ion mobility, we find that more extended states are more prone to fragment release. We obtain evidence that for a given charge state, populations of ubiquitin ions formed either directly by electrospray ionization or through collapse of more extended states upon charge reduction, span a similar range of collision cross-sections. Products of gas-phase collapse are, however, less stabilized towards unfolding than the native conformation, indicating that the ions retain a memory of previous conformational states. Furthermore, this collapse of charge-reduced ions is promoted if the ions are 'preheated' using collisional activation, with possible implications for the kinetics of gas-phase compaction. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium
- Center for Proteomics, University of Antwerp, Antwerpen, Belgium
| | | | - Dirk Valkenborg
- Center for Proteomics, University of Antwerp, Antwerpen, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Hasselt, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Antwerp, Belgium
| | - Anna Gambin
- Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerpen, Belgium.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
5
|
Viglino E, Lai CK, Mu X, Chu IK, Tureček F. Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1454-1467. [PMID: 27278824 DOI: 10.1007/s13361-016-1425-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/10/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
We report a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-rich and hydrogen-deficient types. Stable, long-lived, hydrogen-rich peptide cation radicals, such as [AAAYR + 2H](+●) and several of its sequence and homology variants, were generated by electron transfer dissociation (ETD) of peptide-crown-ether complexes, and their CID-MS(3) dissociations were found to be dramatically different from those upon ETD of the respective peptide dications. All of the hydrogen-rich peptide cation radicals contained major (77%-94%) fractions of species having radical chromophores created by ETD that underwent photodissociation at 355 nm. Analysis of the CID and UVPD spectra pointed to arginine guanidinium radicals as the major components of the hydrogen-rich peptide cation radical population. Hydrogen-deficient peptide cation radicals were generated by intramolecular electron transfer in Cu(II)(2,2':6',2″-terpyridine) complexes and shown to contain chromophores absorbing at 355 nm and undergoing photodissociation. The CID and UVPD spectra showed major differences in fragmentation for [AAAYR](+●) that diminished as the Tyr residue was moved along the peptide chain. UVPD was found to be superior to CID in localizing Cα-radical positions in peptide cation radical intermediates. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Emilie Viglino
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, 981915-1700, USA
| | - Cheuk Kuen Lai
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiaoyan Mu
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ivan K Chu
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA, 981915-1700, USA.
| |
Collapse
|
6
|
Pepin R, Laszlo KJ, Peng B, Marek A, Bush MF, Tureček F. Comprehensive Analysis of Gly-Leu-Gly-Gly-Lys Peptide Dication Structures and Cation-Radical Dissociations Following Electron Transfer: From Electron Attachment to Backbone Cleavage, Ion–Molecule Complexes, and Fragment Separation. J Phys Chem A 2013; 118:308-24. [DOI: 10.1021/jp411100c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Robert Pepin
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Kenneth J. Laszlo
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Bo Peng
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Aleš Marek
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- 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
| |
Collapse
|
7
|
Marek A, Pepin R, Peng B, Laszlo KJ, Bush MF, Tureček F. Electron transfer dissociation of photolabeled peptides. Backbone cleavages compete with diazirine ring rearrangements. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1641-1653. [PMID: 23633016 DOI: 10.1007/s13361-013-0630-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/25/2013] [Accepted: 03/25/2013] [Indexed: 06/02/2023]
Abstract
Gas-phase conformations and electron transfer dissociations of pentapeptide ions containing the photo-Leu residue (L*) were studied. Exhaustive conformational search including molecular dynamics force-field, semi-empirical, ab initio, and density functional theory calculations established that the photo-Leu residue did not alter the gas-phase conformations of (GL*GGK + 2H)(2+) and (GL*GGK-NH2 + H)(+) ions, which showed the same conformer energy ranking as the unmodified Leu-containing ions. This finding is significant in that it simplifies conformational analysis of photo-labeled peptide ions. Electron transfer dissociation mass spectra of (GL*GGK + 2H)(2+), (GL*GGK-NH2 + 2H)(2+),(GL*GGKK + 2H)(2+), (GL*GLK + 2H)(2+), and (GL*LGK + 2H)(2+) showed 16 %-21 % fragment ions originating by radical rearrangements and cleavages in the diazirine ring. These side-chain dissociations resulted in eliminations of N2H3, N2H4, [N2H5], and [NH4O] neutral fragments and were particularly abundant in long-lived charge-reduced cation-radicals. Deuterium labeling established that the neutral hydrazine molecules mainly contained two exchangeable and two nonexchangeable hydrogen atoms from the peptide and underwent further H/D exchange in an ion-molecule complex. Electron structure calculations on the charge-reduced ions indicated that the unpaired electron was delocalized between the diazirine and amide π* electronic systems in the low electronic states of the cation-radicals. The diazirine moiety in GL*GGK-NH2was calculated to have an intrinsic electron affinity of 1.5 eV, which was further increased by the Coulomb effect of the peptide positive charge. Mechanisms are proposed for the unusual elimination of hydrazine from the photo-labeled peptide ions.
Collapse
Affiliation(s)
- Aleš Marek
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, WA, USA
| | | | | | | | | | | |
Collapse
|
8
|
Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195-1700, United States
| | | |
Collapse
|
9
|
Zimnicka M, Chung TW, Moss CL, Tureček F. Perturbing Peptide Cation-Radical Electronic States by Thioxoamide Groups: Formation, Dissociations, and Energetics of Thioxopeptide Cation-Radicals. J Phys Chem A 2012; 117:1265-75. [DOI: 10.1021/jp305865q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Magdalena Zimnicka
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle,
Washington 98195-1700,
United States
| | - Thomas W. Chung
- Department of Chemistry, Bagley Hall, Box
351700, University of Washington, Seattle,
Washington 98195-1700,
United States
| | - Christopher L. Moss
- 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
| |
Collapse
|
10
|
Kretschmer R, Schlangen M, Kaupp M, Schwarz H. Neutral Metal Atoms Acting as a Leaving Group in Gas-Phase SN2 Reactions: M(CH3)+ + NH3 → CH3NH3+ + M (M = Zn, Cd, Hg). Organometallics 2012. [DOI: 10.1021/om300116c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Robert Kretschmer
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni
135, 10623 Berlin
| | - Maria Schlangen
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni
135, 10623 Berlin
| | - Martin Kaupp
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni
135, 10623 Berlin
| | - Helmut Schwarz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni
135, 10623 Berlin
- Chemistry Department, Faculty
of Science, King Abdulaziz University,
Jeddah 21589, Saudi Arabia
| |
Collapse
|
11
|
Afonso C, Tabet JC, Giorgi G, Tureček F. Gas-phase doubly charged complexes of cyclic peptides with copper in +1, +2 and +3 formal oxidation states: formation, structures and electron capture dissociation. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:208-220. [PMID: 22359331 DOI: 10.1002/jms.2956] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Copper complexes with a cyclic D-His-β-Ala-L-His-L-Lys and all-L-His-β-Ala-His-Lys peptides were generated by electrospray which were doubly charged ions that had different formal oxidation states of Cu(I), Cu(II) and Cu(III) and different protonation states of the peptide ligands. Electron capture dissociation showed no substantial differences between the D-His and L-His complexes. All complexes underwent peptide cross-ring cleavages upon electron capture. The modes of ring cleavage depended on the formal oxidation state of the Cu ion and peptide protonation. Density functional theory (DFT) calculations, using the B3LYP with an effective core potential at Cu and M06-2X functionals, identified several precursor ion structures in which the Cu ion was threecoordinated to pentacoordinated by the His and Lys side-chain groups and the peptide amide or enolimine groups. The electronic structure of the formally Cu(III) complexes pointed to an effective Cu(I) oxidation state with the other charge residing in the peptide ligand. The relative energies of isomeric complexes of the [Cu(c-HAHK + H)](2+) and [Cu(c-HAHK - H)](2+) type with closed electronic shells followed similar orders when treated by the B3LYP and M06-2X functionals. Large differences between relative energies calculated by these methods were obtained for open-shell complexes of the [Cu(c-HAHK)](2+) type. Charge reduction resulted in lowering the coordination numbers for some Cu complexes that depended on the singlet or triplet spin state being formed. For [Cu(c-HAHK - H)](2+) complexes, solution H/D exchange involved only the N-H protons, resulting in the exchange of up to seven protons, as established by ultra-high mass resolution measurements. Contrasting the experiments, DFT calculations found the lowest energy structures for the gas-phase ions that were deprotonated at the peptide C(α) positions.
Collapse
Affiliation(s)
- Carlos Afonso
- Institut Parisien de Chimie Moléculaire, CNRS-UMR 7201, Université Pierre et Marie Curie-Paris 6, 4 place Jussieu, Paris, France
| | | | | | | |
Collapse
|
12
|
Zhang Y, Zhang H, Cui W, Chen H. Tandem MS analysis of selenamide-derivatized peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1610-1621. [PMID: 21953264 PMCID: PMC3731447 DOI: 10.1007/s13361-011-0170-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/15/2011] [Accepted: 05/15/2011] [Indexed: 05/27/2023]
Abstract
Our previous study showed that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used for selective and rapid derivatization of protein/peptide thiols in high conversion yield. This paper reports the systematic investigation of MS/MS dissociation behaviors of selenamide-derivatized peptide ions upon collision induced dissociation (CID) and electron transfer dissociation (ETD). In the positive ion mode, derivatized peptide ions exhibit tag-dependent CID dissociation pathways. For instance, ebselen-derivatized peptide ions preferentially undergo Se-S bond cleavage upon CID to produce a characteristic fragment ion, the protonated ebselen (m/z 276), which allows selective identification of thiol peptides from protein digest as well as selective detection of thiol proteins from protein mixture using precursor ion scan (PIS). In contrast, NPSP-derivatized peptide ions retain their phenylselenenyl tags during CID, which is useful in sequencing peptides and locating cysteine residues. In the negative ion CID mode, both types of tags are preferentially lost via the Se-S cleavage, analogous to the S-S bond cleavage during CID of disulfide-containing peptide anions. In consideration of the convenience in preparing selenamide-derivatized peptides and the similarity of Se-S of the tag to the S-S bond, we also examined ETD of the derivatized peptide ions to probe the mechanism for electron-based ion dissociation. Interestingly, facile cleavage of Se-S bond occurs to the peptide ions carrying either protons or alkali metal ions, while backbone cleavage to form c/z ions is severely inhibited. These results are in agreement with the Utah-Washington mechanism proposed for depicting electron-based ion dissociation processes.
Collapse
Affiliation(s)
- Yun Zhang
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| |
Collapse
|
13
|
Yamada Y, Ishikawa H, Fuke K. Solvation Structure and Stability of [(CH 3) 2NH] m(NH 3) n–H Hypervalent Clusters: Ionization Potentials and Switching of Hydrogen-Atom Localized Site. J Phys Chem A 2011; 115:8380-91. [DOI: 10.1021/jp204331q] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
14
|
Kretschmer R, Schlangen M, Schwarz H. Effiziente und selektive Monomethylierung kontra N-H-Bindungsaktivierung von Ammoniak: atomares Zink als Abgangsgruppe in einer SN2-Reaktion von “nacktem” Zn(CH3)+ und NH3. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
15
|
Kretschmer R, Schlangen M, Schwarz H. Efficient and selective gas-phase monomethylation versus N-H bond activation of ammonia by "bare" Zn(CH3)+: atomic zinc as a leaving group in an SN2 reaction. Angew Chem Int Ed Engl 2011; 50:5387-91. [PMID: 21538741 DOI: 10.1002/anie.201100096] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/16/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Robert Kretschmer
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | | | | |
Collapse
|
16
|
Moss CL, Chung TW, Wyer JA, Nielsen SB, Hvelplund P, Tureček F. Dipole-guided electron capture causes abnormal dissociations of phosphorylated pentapeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:731-51. [PMID: 21472611 DOI: 10.1007/s13361-011-0083-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/06/2011] [Accepted: 01/08/2011] [Indexed: 05/25/2023]
Abstract
Electron transfer and capture mass spectra of a series of doubly charged ions that were phosphorylated pentapeptides of a tryptic type (pS,A,A,A,R) showed conspicuous differences in dissociations of charge-reduced ions. Electron transfer from both gaseous cesium atoms at 100 keV kinetic energies and fluoranthene anion radicals in an ion trap resulted in the loss of a hydrogen atom, ammonia, and backbone cleavages forming complete series of sequence z ions. Elimination of phosphoric acid was negligible. In contrast, capture of low-energy electrons by doubly charged ions in a Penning ion trap induced loss of a hydrogen atom followed by elimination of phosphoric acid as the dominant dissociation channel. Backbone dissociations of charge-reduced ions also occurred but were accompanied by extensive fragmentation of the primary products. z-Ions that were terminated with a deaminated phosphoserine radical competitively eliminated phosphoric acid and H(2)PO(4) radicals. A mechanism is proposed for this novel dissociation on the basis of a computational analysis of reaction pathways and transition states. Electronic structure theory calculations in combination with extensive molecular dynamics mapping of the potential energy surface provided structures for the precursor phosphopeptide dications. Electron attachment produces a multitude of low lying electronic states in charge-reduced ions that determine their reactivity in backbone dissociations and H- atom loss. The predominant loss of H atoms in ECD is explained by a distortion of the Rydberg orbital space by the strong dipolar field of the peptide dication framework. The dipolar field steers the incoming electron to preferentially attach to the positively charged arginine side chain to form guanidinium radicals and trigger their dissociations.
Collapse
Affiliation(s)
- Christopher L Moss
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA 98195-1700, USA
| | | | | | | | | | | |
Collapse
|
17
|
Chung TW, Moss CL, Zimnicka M, Johnson RS, Moritz RL, Tureček F. Electron-capture and -transfer dissociation of peptides tagged with tunable fixed-charge groups: structures and dissociation energetics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:13-30. [PMID: 21472540 DOI: 10.1007/s13361-010-0012-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 09/26/2010] [Accepted: 10/11/2010] [Indexed: 05/30/2023]
Abstract
Pyridiniummethylcarbonyl moieties that were previously designed on the basis of electronic structure analysis are now utilized as fixed-charge tags with tunable electronic properties to be used for N-terminal peptide derivatization and sequencing by electron-transfer dissociation. Dipeptides AK and KA were derivatized at the peptide N-terminus with 4-dimethylaminopyridinium-N-acetyl (DMAP-ac) and pyridinium-N-acetyl (pyrid-ac) tags of increasing intrinsic recombination energies. Upon the capture of a free electron or electron transfer from fluoranthene anions, (DMAP-ac-AK+H)(2+), (DMAP-ac-KA+H)(2+), (pyrid-ac-AK+H)(2+) and (pyrid-ac-KA+H)(2+) ions, as well as underivatized (AK+2H)(2+), completely dissociated. The fixed-charge tags steered the dissociation upon electron transfer to form abundant backbone N-C(α) bond cleavages, whereas the underivatized peptide mainly underwent H-atom and side-chain losses. Precursor ion structures for the tagged peptides were analyzed by an exhaustive conformational search combined with B3LYP/6-31+G(d,p) geometry optimization and single-point energy calculations in order to select the global energy minima. Structures, relative energies, transition states, ion-molecule complexes, and dissociation products were identified for several charge-reduced species from the tagged peptides. The electronic properties of the charge tags and their interactions with the peptide moieties are discussed. Electrospray ionization and electron-transfer dissociation of larger peptides are illustrated with a DMAP-tagged pentapeptide.
Collapse
Affiliation(s)
- Thomas W Chung
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, WA 98195-1700, USA
| | | | | | | | | | | |
Collapse
|
18
|
Gregersen JA, Tureček F. Mass-spectrometric and computational study of tryptophan radicals (Trp + H)˙ produced by collisional electron transfer to protonated tryptophan in the gas phase. Phys Chem Chem Phys 2010; 12:13434-47. [DOI: 10.1039/c0cp00597e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
19
|
Tureček F, Panja S, Wyer JA, Ehlerding A, Zettergren H, Nielsen SB, Hvelplund P, Bythell B, Paizs B. Carboxyl-Catalyzed Prototropic Rearrangements in Histidine Peptide Radicals upon Electron Transfer: Effects of Peptide Sequence and Conformation. J Am Chem Soc 2009; 131:16472-87. [DOI: 10.1021/ja9050229] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Subhasis Panja
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Jean A. Wyer
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Anneli Ehlerding
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Henning Zettergren
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Steen Brøndsted Nielsen
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Preben Hvelplund
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Benjamin Bythell
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Béla Paizs
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark, and Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| |
Collapse
|
20
|
Sohn CH, Chung CK, Yin S, Ramachandran P, Loo JA, Beauchamp JL. Probing the mechanism of electron capture and electron transfer dissociation using tags with variable electron affinity. J Am Chem Soc 2009; 131:5444-59. [PMID: 19331417 PMCID: PMC2765496 DOI: 10.1021/ja806534r] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Electron capture dissociation (ECD) and electron transfer dissociation (ETD) of doubly protonated electron affinity (EA)-tuned peptides were studied to further illuminate the mechanism of these processes. The model peptide FQpSEEQQQTEDELQDK, containing a phosphoserine residue, was converted to EA-tuned peptides via beta-elimination and Michael addition of various thiol compounds. These include propanyl, benzyl, 4-cyanobenzyl, perfluorobenzyl, 3,5-dicyanobenzyl, 3-nitrobenzyl, and 3,5-dinitrobenzyl structural moieties, having a range of EA from -1.15 to +1.65 eV, excluding the propanyl group. Typical ECD or ETD backbone fragmentations are completely inhibited in peptides with substituent tags having EA over 1.00 eV, which are referred to as electron predators in this work. Nearly identical rates of electron capture by the dications substituted by the benzyl (EA = -1.15 eV) and 3-nitrobenzyl (EA = 1.00 eV) moieties are observed, which indicates the similarity of electron capture cross sections for the two derivatized peptides. This observation leads to the inference that electron capture kinetics are governed by the long-range electron-dication interaction and are not affected by side chain derivatives with positive EA. Once an electron is captured to high-n Rydberg states, however, through-space or through-bond electron transfer to the EA-tuning tags or low-n Rydberg states via potential curve crossing occurs in competition with transfer to the amide pi* orbital. The energetics of these processes are evaluated using time-dependent density functional theory with a series of reduced model systems. The intramolecular electron transfer process is modulated by structure-dependent hydrogen bonds and is heavily affected by the presence and type of electron-withdrawing groups in the EA-tuning tag. The anion radicals formed by electron predators have high proton affinities (approximately 1400 kJ/mol for the 3-nitrobenzyl anion radical) in comparison to other basic sites in the model peptide dication, facilitating exothermic proton transfer from one of the two sites of protonation. This interrupts the normal sequence of events in ECD or ETD, leading to backbone fragmentation by forming a stable radical intermediate. The implications which these results have for previously proposed ECD and ETD mechanisms are discussed.
Collapse
Affiliation(s)
- Chang Ho Sohn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Cheol K. Chung
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Sheng Yin
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Prasanna Ramachandran
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - J. L. Beauchamp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| |
Collapse
|
21
|
Hao C, Turecek F. Host-guest hydrogen atom transfer induced by electron capture. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:639-651. [PMID: 19185509 DOI: 10.1016/j.jasms.2008.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 12/01/2008] [Accepted: 12/01/2008] [Indexed: 05/27/2023]
Abstract
1,n-Alkanediammonium cations in noncovalent complexes with two dibenzo-18-crown-6-ether (DBCE) ligands undergo an unusual intramolecular tandem hydrogen atom and proton transfer to the crown ether ligand upon charge reduction by electron capture. Deuterium labeling established that both migrating hydrogens originated from the ammonium groups. The double hydrogen transfer was found to depend on the length of the alkane chain connecting the ammonium groups. Ab initio calculations provided structures for select alkanediammonium.dibenzo-18-crown-6-ether complexes and dissociation products. This first observation of an intra-complex hydrogen transfer is explained by the unusual electronic properties of the complexes and the substantial hydrogen atom affinity of the aromatic rings in the crown ligand.
Collapse
Affiliation(s)
- Changtong Hao
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | | |
Collapse
|
22
|
Prell JS, O'Brien JT, Holm AIS, Leib RD, Donald WA, Williams ER. Electron capture by a hydrated gaseous peptide: effects of water on fragmentation and molecular survival. J Am Chem Soc 2008; 130:12680-9. [PMID: 18761457 DOI: 10.1021/ja8022434] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of water on electron capture dissociation products, molecular survival, and recombination energy are investigated for diprotonated Lys-Tyr-Lys solvated by between zero and 25 water molecules. For peptide ions with between 12 and 25 water molecules attached, electron capture results in a narrow distribution of product ions corresponding to primarily the loss of 10-12 water molecules from the reduced precursor. From these data, the recombination energy (RE) is determined to be equal to the energy that is lost by evaporating on average 10.7 water molecules, or 4.3 eV. Because water stabilizes ions, this value is a lower limit to the RE of the unsolvated ion, but it indicates that the majority of the available RE is deposited into internal modes of the peptide ion. Plotting the fragment ion abundances for ions formed from precursors with fewer than 11 water molecules as a function of hydration extent results in an energy resolved breakdown curve from which the appearance energies of the b 2 (+), y 2 (+), z 2 (+*), c 2 (+), and (KYK + H) (+) fragment ions formed from this peptide ion can be obtained; these values are 78, 88, 42, 11, and 9 kcal/mol, respectively. The propensity for H atom loss and ammonia loss from the precursor changes dramatically with the extent of hydration, and this change in reactivity can be directly attributed to a "caging" effect by the water molecules. These are the first experimental measurements of the RE and appearance energies of fragment ions due to electron capture dissociation of a multiply charged peptide. This novel ion nanocalorimetry technique can be applied more generally to other exothermic reactions that are not readily accessible to investigation by more conventional thermochemical methods.
Collapse
Affiliation(s)
- James S Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
| | | | | | | | | | | |
Collapse
|
23
|
Chen X, Hao C. Where Does the Electron Go? Electron Distribution and Reactivity of Peptide Cation Radicals Formed by Electron Transfer in the Gas phase. J Am Chem Soc 2008; 130:8818-33. [DOI: 10.1021/ja8019005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaohong Chen
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - Changtong Hao
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700
| |
Collapse
|
24
|
Chung TW, Turecek F. Electronic properties of charge-tagged peptides upon electron capture. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2008; 14:367-378. [PMID: 19136725 DOI: 10.1255/ejms.954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report a computational study of Ala-Lys (AK) and Lys-Ala (KA) dipeptide ions furnished with fixed-charged pyridinium groups that were attached by amide linkers to the N-terminal amino groups. Cation-radicals from one-electron reduction of the doubly charged AK and KA peptide conjugates showed various extents of unpaired electron density being delocalized between the pyridine and peptide moieties. The delocalization depended on the local recombination energies (RE(loc)) of the charged groups. The RE(loc) of the pyridine moieties were modified by introducing electron-donating substituents (CH(3), OCH(3), and N(CH(3))(2)). The RE(loc) of the peptide moieties were found to depend on the peptide conformation and internal solvation of the Lys ammonium groups. Substantial electron delocalization was found for combinations of pyridine substituents and peptide conformers with closely matched RE(loc), such as 4-dimethylamino-pyridine and internally solvated Lys ammonium or unsubstituted pyridine and free (unsolvated) Lys ammonium. The dissociation (DeltaH(diss)) and transition state energies (E(TS)) for the loss of the pyridine ring from the conjugates were found to be DeltaH(diss) = 34-36 kJ mol(-1) and E(TS) = 67-69 kJ mol(-1) for the unsubstituted pyridine moieties, but did not depend much on the peptide sequence.
Collapse
Affiliation(s)
- Thomas W Chung
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, WA 98195-1700, USA
| | | |
Collapse
|
25
|
Chamot-Rooke J, Malosse C, Frison G, Turecek F. Electron capture in charge-tagged peptides. Evidence for the role of excited electronic states. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:2146-2161. [PMID: 17951069 DOI: 10.1016/j.jasms.2007.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Revised: 09/12/2007] [Accepted: 09/13/2007] [Indexed: 05/25/2023]
Abstract
Electron capture dissociation (ECD) was studied with doubly charged dipeptide ions that were tagged with fixed-charge tris-(2,4,6-trimethoxyphenyl)phosphonium-methylenecarboxamido (TMPP-ac) groups. Dipeptides GK, KG, AK, KA, and GR were each selectively tagged with one TMPP-ac group at the N-terminal amino group while the other charge was introduced by protonation at the lysine or arginine side-chain groups to give (TMPP-ac-peptide + H)(2+) ions by electrospray ionization. Doubly tagged peptide derivatives were also prepared from GK, KG, AK, and KA in which the fixed-charge TMPP-ac groups were attached to the N-terminal and lysine side-chain amino groups to give (TMPP-ac-peptide-ac-TMPP)(2+) dications by electrospray. ECD of (TMPP-ac-peptide + H)(2+) resulted in 72% to 84% conversion to singly charged dissociation products while no intact charge-reduced (TMPP-ac-dipeptide + H)(+) ions were detected. The dissociations involved loss of H, formation of (TMPP + H)(+), and N-C(alpha) bond cleavages giving TMPP-CH(2)CONH(2)(+) (c(0)) and c(1) fragments. In contrast, ECD of (TMPP-ac-peptide-ac-TMPP)(2+) resulted in 31% to 40% conversion to dissociation products due to loss of neutral TMPP molecules and 2,4,6-trimethoxyphenyl radicals. No peptide backbone cleavages were observed for the doubly tagged peptide ions. Ab initio and density functional theory calculations for (Ph(3)P-ac-GK + H)(2+) and (H(3)P-ac-GK + H)(2+) analogs indicated that the doubly charged ions contained the lysine side-chain NH(3)(+) group internally solvated by the COOH group. The distance between the charge-carrying phosphonium and ammonium atoms was calculated to be 13.1-13.2 A in the most stable dication conformers. The intrinsic recombination energies of the TMPP(+)-ac and (GK + H)(+) moieties, 2.7 and 3.15 eV, respectively, indicated that upon electron capture the ground electronic states of the (TMPP-ac-peptide + H)(+*) ions retained the charge in the TMPP group. Ground electronic state (TMPP-ac-GK + H)(+*) ions were calculated to spontaneously isomerize by lysine H-atom transfer to the COOH group to form dihydroxycarbinyl radical intermediates with the retention of the charged TMPP group. These can trigger cleavages of the adjacent N-C(alpha) bonds to give rise to the c(1) fragment ions. However, the calculated transition-state energies for GK and GGK models suggested that the ground-state potential energy surface was not favorable for the formation of the abundant c(0) fragment ions. This pointed to the involvement of excited electronic states according to the Utah-Washington mechanism of ECD.
Collapse
Affiliation(s)
- Julia Chamot-Rooke
- Laboratoire des Mécanismes Réactionnels, Department of Chemistry, Ecole Polytechnique, CNRS, Palaiseau, France
| | | | | | | |
Collapse
|
26
|
Chakraborty T, Holm AIS, Hvelplund P, Nielsen SB, Poully JC, Worm ES, Williams ER. On the survival of peptide cations after electron capture: role of internal hydrogen bonding and microsolvation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1675-80. [PMID: 16926097 DOI: 10.1016/j.jasms.2006.07.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 06/20/2006] [Accepted: 07/20/2006] [Indexed: 05/11/2023]
Abstract
Electron capture by both bare and microsolvated small peptide dications was investigated by colliding these ions with sodium vapor in an accelerator mass spectrometer to provide insight into processes that occur on the microsecond time frame. Survival of the intact peptide monocation after electron capture depends strongly on molecular size. For dipeptides, no intact reduced species were observed; the predominant ions correspond to loss of hydrogen and ammonia. In contrast, the intact reduced species was observed for larger peptides. Calculated structures indicate that the diprotonated dipeptide ions form largely extended structures with low probability of internal ionic hydrogen bonding (i.e., charge solvation) whereas internal ionic H-bonding occurs extensively for larger peptide dications. Solvation of the peptide ions with between one to seven methanol molecules reduces the total extent of H loss even for dipeptides where intact reduced species can survive more than a microsecond after electron capture. The yield of ions corresponding to cleavage of NCalpha bonds (c+ and z+* ions) does not depend strongly on peptide size but decreases with the extent of microsolvation for the dipeptide dications. H-bonding appears to play an important role for the survival of the intact reduced ions but less so for the formation of c+ and z+* ions. Our results indicate that electron capture predominantly occurs at the ammonium groups (at least 70 to 80%), and provides important new insights into the electron capture dissociation process.
Collapse
Affiliation(s)
- Tapas Chakraborty
- Department of Chemistry, Indian Institute of Technology, Kanpur, India
| | | | | | | | | | | | | |
Collapse
|
27
|
Belyayev MA, Cournoyer JJ, Lin C, O'Connor PB. The effect of radical trap moieties on electron capture dissociation spectra of substance P. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1429-1436. [PMID: 16875835 DOI: 10.1016/j.jasms.2006.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 06/13/2006] [Accepted: 06/13/2006] [Indexed: 05/11/2023]
Abstract
To further test the hypothesis that electron capture dissociation (ECD) involves long-lived radical intermediates and radical migration occurs within these intermediates before fragmentation, radical trap moieties were attached to peptides with the assumption that they would reduce fragmentation by decreasing the mobility of the radical. Coumarin labels were chosen for the radical traps, and unlabeled, singly-labeled, and doubly-labeled Substance P were analyzed by ECD. The results demonstrated a correlation between the number and position of tags on the peptide and the intensity of side-chain cleavages observed, as well as an inverse correlation between the number of tags on the peptide and the intensity of backbone cleavages. Addition of radical traps to the peptide inhibits backbone cleavages, suggesting that either radical mobility is required for these cleavages, or new noncovalent interactions prevent separation of backbone cleavage fragments. The enhancement of side-chain cleavages and the observation of new side-chain cleavages associated with aromatic groups suggest that the gas-phase conformation of this peptide is substantially distorted from untagged Substance P and involves previously unobserved interactions between the coumarin tags and the phenylalanine residues. Furthermore, the use of a double resonance (DR)-ECD experiment showed that these side-chain losses are all products of long-lived radical intermediate species, which suggests that steric hindrance prevents the coumarin-localized radical from interacting with the backbone while simultaneously increasing the radical rearrangements with the side chains.
Collapse
Affiliation(s)
- Marina A Belyayev
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Jason J Cournoyer
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Cheng Lin
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Peter B O'Connor
- Department of Chemistry, Boston University, Boston, Massachusetts, USA.
| |
Collapse
|
28
|
Lee S, Han SY, Lee TG, Chung G, Lee D, Oh HB. Observation of pronounced b*,y cleavages in the electron capture dissociation mass spectrometry of polyamidoamine (PAMAM) dendrimer ions with amide functionalities. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:536-543. [PMID: 16490359 DOI: 10.1016/j.jasms.2005.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 12/07/2005] [Accepted: 12/08/2005] [Indexed: 05/06/2023]
Abstract
We report the electron capture dissociation (ECD) mass spectrometry of the third generation polyamidoamine (PAMAM) dendrimer that contains amide functionalities. The dendrimer was chosen because it offers a unique opportunity to understand the ECD behavior of the amide functionality in a framework other than peptides/proteins. In this study, PAMAM ECD was found to exhibit a fragmentation pattern strikingly different from that of ordinary peptide/protein ECD. Specifically, ECD of multiply protonated PAMAM ions gave rise to significant b(*),y cleavages as well as S,E dissociations but, unexpectedly, only minor c,z(*) fragmentations are observed. In an effort to account for the unexpectedly different fragmentation pattern, a comparative ECD experiment on the poly(propylene imine) dendrimer in which the amide bond moiety is not available and density functional theory calculations (B3LYP/6-311 + G(d)) investigations on the model system of a charge-solvated single-repeat unit were carried out. On the basis of these results, we discuss here possible implications of intramolecular charge-solvation, energy barriers in dissociation reactions, and macromolecular properties of the dendritic molecule for understanding the reaction pathway of PAMAM ECD.
Collapse
Affiliation(s)
- Sunyoung Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Sinsudong 1, 121-742, Mapogu, Seoul, Republic of Korea
| | - Sang Yun Han
- Division of Chemical Metrology and Materials Evaluation, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Tae Geol Lee
- Division of Chemical Metrology and Materials Evaluation, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Gyusung Chung
- Department of Chemistry, Konyang University, Chungnam, Republic of Korea
| | - Duckhwan Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Sinsudong 1, 121-742, Mapogu, Seoul, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Sinsudong 1, 121-742, Mapogu, Seoul, Republic of Korea.
| |
Collapse
|
29
|
Antoine R, Broyer M, Chamot-Rooke J, Dedonder C, Desfrançois C, Dugourd P, Grégoire G, Jouvet C, Onidas D, Poulain P, Tabarin T, van der Rest G. Comparison of the fragmentation pattern induced by collisions, laser excitation and electron capture. Influence of the initial excitation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:1648-52. [PMID: 16637002 DOI: 10.1002/rcm.2489] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Collision-induced dissociation, laser-induced dissociation and electron-capture dissociation are compared on a singly and doubly protonated pentapeptide. The dissociation spectrum depends on the excitation mechanism and on the charge state of the peptide. The comparison of these results with the conformations obtained from Monte Carlo simulations suggests that the de-excitation mechanism following a laser or an electron-capture excitation is related to the initial geometry of the peptide.
Collapse
Affiliation(s)
- R Antoine
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR 5579 (Université Lyon I et CNRS), 43 Bd du 11 Novembre 1918, 69622 Villeurbanne cedex, France
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Delobel A, Touboul D, Laprévote O. Structural characterization of phosphatidylcholines by atmospheric pressure photoionization mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2005; 11:409-17. [PMID: 16204808 DOI: 10.1255/ejms.760] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The potential of atmospheric pressure photoionization was investigated for the structural analysis of phosphatidylcholine lipids (PCs). [M+H]+ ions of high abundance were obtained, along with several fragment ions. Three of these dissociation products corresponded to quite unusual fragmentation pathways but allowed the determination of both the nature and the position on the glycerol backbone (sn-1 or sn-2) of the fatty acyl chains. The loss of a methyl group from the choline head was also observed. These results suggest a complex ionization mechanism in APPI. However, this method proved to be very powerful for the rapid structural analysis of PC species without using MS/MS experiments.
Collapse
Affiliation(s)
- Arnaud Delobel
- Laboratoire de Spectrométrie de Masse, Institut de Chimie des Substances Naturelles, (ICSN-CNRS), Av. de la Terrasse, F-91198 Gif-Sur-Yvette Cedex, France
| | | | | |
Collapse
|