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Radical Additions to Aromatic Residues in Peptides Facilitate Unexpected Side Chain and Backbone Losses

Journal of The American Society for Mass Spectrometry

Abstract

Accurate identification of fragments in tandem mass spectrometry experiments is aided by knowledge of relevant fragmentation mechanisms. Herein, novel radical addition reactions that direct unexpected side-chain dissociations at tryptophan and tyrosine residues are reported. Various mechanisms that can account for the observed dissociation channels are investigated by experiment and theory. The propensity for radical addition at a particular site is found to be primarily under kinetic control, which is largely dictated by molecular structure. In certain peptides, intramolecular radical addition reactions are favored, which leads to the observation of numerous unexpected fragments. In one pathway, radical addition leads to migration of an aromatic side chain to another residue. Alternatively, radical addition followed by hydrogen atom loss leads to cyclization of the peptide and increased observation of internal sequence fragments. Radical addition reactions should be considered when assigning fragmentation spectra obtained from activation of hydrogen deficient peptides.

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References

  1. Zhang, X., Julian, R.R.: Photo-initiated intramolecular diradical cross-linking of polyproline peptides in the gas phase. Phys. Chem. Chem. Phys. 14, 16243–16249 (2012)

    Article  CAS  Google Scholar 

  2. Tao, Y.Q., Quebbemann, N.R., Julian, R.R.: 2012. Anal. Chem. 84, 6814–6820 (2012)

    Article  CAS  Google Scholar 

  3. Ly, T., Julian, R.R.: Elucidating the tertiary structure of protein ions in vacuo with site specific photoinitiated radical reactions. J. Am. Chem. Soc. 132, 8602–8609 (2010)

    Article  CAS  Google Scholar 

  4. Zhang, X., Julian, R.R.: Investigating the gas phase structure of KIX with radical directed dissociation and molecular dynamics: Retention retention of the native structure. Int. J. Mass Spectrom. 308, 225–231 (2011)

    Article  CAS  Google Scholar 

  5. Breuker, K., Bruschweiler, S., Tollinger, M.: Electrostatic stabilization of a native protein structure in the gas phase. Angew. Chem. Int. Ed. 50, 873–877 (2011)

    Article  CAS  Google Scholar 

  6. Chu, I.K., Rodriquez, C.F., Lau, T.C., Hopkinson, A.C., Siu, K.W.M.: Molecular radical cations of oligopeptides. J. Phys. Chem. B 104, 3393–3397 (2000)

    Article  CAS  Google Scholar 

  7. Barlow, C.K., McFadyen, W.D., O'Hair, R.A.J.: Formation of cationic peptide radicals by gas-phase redox reactions with trivalent chromium, manganese, iron, and cobalt complexes. J. Am. Chem. Soc. 127, 6109–6115 (2005)

    Article  CAS  Google Scholar 

  8. Laskin, J., Yang, Z.B., Ng, C.M.D., Chu, I.K.: Fragmentation of alpha-radical cations of arginine-containing peptides. J. Am. Soc. Mass Spectrom. 21, 511–521 (2010)

    Article  CAS  Google Scholar 

  9. Headlam, H.A., Mortimer, A., Easton, C.J., Davies, M.J.: Beta-scission of C-3 (beta-carbon) alkoxyl radicals on peptides and proteins: A novel pathway which results in the formation of alpha-carbon radicals and the loss of amino acid side chains. Chem. Res. Toxicol. 13, 1087–1095 (2000)

    Article  CAS  Google Scholar 

  10. Osburn, S., O’Hair, R.A.J.: Unleashing radical sites in noncovalent complexes: the case of the protonated S-nitrosocysteine/18-crown-6 complex. Rapid Commun. Mass Spectrom. 27, 2783–2788 (2013)

    Article  CAS  Google Scholar 

  11. Masterson, D.S., Yin, H.Y., Chacon, A., Hachey, D.L., Norris, J.L., Porter, N.A.: Lysine peroxycarbamates: Free radical-promoted peptide cleavage. J. Am. Chem. Soc. 126, 720–721 (2004)

    Article  CAS  Google Scholar 

  12. Hodyss, R., Cox, H.A., Beauchamp, J.L.: Bioconjugates for tunable peptide fragmentation: Free radical initiated peptide sequencing (FRIPS). J. Am. Chem. Soc. 127, 12436–12437 (2005)

    Article  CAS  Google Scholar 

  13. Hao, G., Gross, S.S.: Electrospray tandem mass spectrometry analysis of S- and N-nitrosopeptides: facile loss of NO and radical-induced fragmentation. J. Am. Soc. Mass Spectrom. 17, 1725–1730 (2006)

    Article  CAS  Google Scholar 

  14. Lee, M., Kang, M., Moon, B., Oh, H.B.: Gas-phase peptide sequencing by TEMPO-mediated radical generation. Analyst 134(8), 1706–1712 (2009)

    Article  CAS  Google Scholar 

  15. Tan, L., Xia, Y.: Gas-phase peptide sulfinyl radical ions: formation and unimolecular dissociation. J. Am. Soc. Mass Spectrom. 23, 2011–2019 (2012)

    Article  CAS  Google Scholar 

  16. Tan, L., Xia, Y.: Gas-phase reactivity of peptide thiyl (RS•), perthiyl (RSS•), and sulfinyl (RSO•) radical ions formed from atmospheric pressure ion/radical reactions. J. Am. Soc. Mass Spectrom. 24, 534–542 (2013)

    Article  CAS  Google Scholar 

  17. Zhang, X., Julian, R.R.: Exploring radical migration pathways in peptides with positional isomers, deuterium labeling, and molecular dynamics simulations. J. Am. Soc. Mass Spectrom. 24, 524–533 (2013)

    Article  CAS  Google Scholar 

  18. Turecek, F., Julian, R.R.: Peptide Radicals and Cation Radicals in the Gas Phase. Mass Spectrom. Chem. Rev. 113, 6691−6733 (2013)

  19. Xu, G.H., Chance, M.R.: Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. Chem. Rev. 107, 3514–3543 (2007)

    Article  CAS  Google Scholar 

  20. Petzold, C.J., Ramirez-Arizmendi, L.E., Heidbrink, J.L., Perez, J., Kenttamaa, H.I.: Gas-phase reactions of charged phenyl radicals with neutral biomolecules evaporated by laser-induced acoustic desorption. J. Am. Soc. Mass Spectrom. 13, 192–194 (2002)

    Article  CAS  Google Scholar 

  21. Huang, Y.Q., Kenttamaa, H.I.: Theoretical and experimental investigations on the reactions of positively charged phenyl radicals with aromatic amino acids. J. Am. Chem. Soc. 127, 7952–7960 (2005)

    Article  CAS  Google Scholar 

  22. Huang, Y.Q., Guler, L., Heidbrink, J., Kenttamaa, H.I.: Reactions of charged phenyl radicals with aliphatic amino acids in the gas phase. J. Am. Chem. Soc. 127, 3973–3978 (2005)

    Article  CAS  Google Scholar 

  23. Pates, G.O., Guler, L., Nash, J.J., Kenttamaa, H.I.: Reactivity and selectivity of charged phenyl radicals toward amino acids in a fourier Fourier transform ion cyclotron resonance mass spectrometer. J. Am. Chem. Soc. 133, 9331–9342 (2011)

    Article  CAS  Google Scholar 

  24. Fu, M.K., Li, S., Archibold, E., Yurkovich, M.J., Nash, J.J., Kenttamaa, H.I.: Reactions of an Aromatic aromatic σsigma,σsigma-Biradical biradical with amino acids and dipeptides in the gas phase. J. Am. Soc. Mass Spectrom. 21, 1737–1752 (2010)

    Article  CAS  Google Scholar 

  25. Li, S., Fu, M.K., Habicht, S.C., Pates, G.O., Nash, J.J., Kenttamaa, H.I.: Phenyl radical-induced damage to dipeptides. J. Org. Chem. 74, 7724–7732 (2009)

    Article  CAS  Google Scholar 

  26. Ly, T., Zhang, X., Sun, Q.Y., Moore, B., Tao, Y.Q., Julian, R.R.: Rapid, quantitative, and site specific synthesis of biomolecular radicals from a simple photocaged precursor. Chem. Commun. 47, 2835–2837 (2011)

    Article  CAS  Google Scholar 

  27. Peng, C.Y., Schlegel, H.B.: Combining synchronous transit and quasi-newton methods to find transition-states. Isr. J. Chem. 33, 449–454 (1993)

    Article  CAS  Google Scholar 

  28. Roepstorff, P., Fohlman, J.: Proposal for a common nomenclature for sequence ions in mass-spectra of peptides. Biomed. Mass Spectrom. 11, 601–601 (1984)

    Article  CAS  Google Scholar 

  29. Julian, R.R., Hodyss, R., Beauchamp, J.L.: Salt bridge stabilization of charged zwitterionic arginine aggregates in the gas phase. J. Am. Chem. Soc. 123, 3577–3583 (2001)

    Article  CAS  Google Scholar 

  30. Song, T., Hao, Q., Law, C.H., Siu, C.K., Chu, I.K.: Novel C-β–C-γ Bond Cleavages of Tryptophan-Containing Peptide Radical Cations. J. Am. Soc. Mass Spectrom. 23, 264–273 (2012)

    Article  CAS  Google Scholar 

  31. Song, T., Ma, C.Y., Chu, I.K., Siu, C.K., Laskin, J.: Mechanistic Examination of C-β–C-γ Bond Cleavages of Tryptophan Residues during Dissociations of Molecular Peptide Radical Cations. J. Phys. Chem. A 117, 1059–1068 (2013)

    Article  CAS  Google Scholar 

  32. Knudsen, E.R., Julian, R.R.: Fragmentation chemistry observed in hydrogen deficient radical peptides generated from N-nitrosotryptophan residues. Int. J. Mass Spectrom. 294, 83–87 (2010)

    Article  CAS  Google Scholar 

  33. Bowman, W.R., Storey, J.M.D.: Synthesis using aromatic homolytic substitution—recent advances. Chem. Soc. Rev. 36, 1803–1822 (2007)

    Article  CAS  Google Scholar 

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Acknowledgments

The authors gratefully acknowledge funding from the National Science Foundation (CHE-074748).

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Correspondence to Ryan R. Julian.

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Zhang, X., Julian, R.R. Radical Additions to Aromatic Residues in Peptides Facilitate Unexpected Side Chain and Backbone Losses. J. Am. Soc. Mass Spectrom. 25, 626–635 (2014). https://doi.org/10.1007/s13361-013-0810-y

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