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Collision-induced dissociation of lys-lys intramolecular crosslinked peptides

  • Amadeu H. Iglesias
  • Luiz F. A. Santos
  • Fabio C. Gozzo
Articles

Abstract

The use of chemical crosslinking is an attractive tool that presents many advantages in the application of mass spectrometry to structural biology. The correct assignment of crosslinked peptides, however, is still a challenge because of the lack of detailed fragmentation studies on resultant species. In this work, the fragmentation patterns of intramolecular crosslinked peptides with disuccinimidyl suberate (DSS) has been devised by using a set of versatile, model peptides that resemble species found in crosslinking experiments with proteins. These peptides contain an acetylated N-terminus followed by a random sequence of residues containing two lysine residues separated by an arginine. After the crosslinking reaction, controlled trypsin digestion yields both intra- and intermolecular crosslinked peptides. In the present study we analyzed the fragmentation of matrix-assisted laser desorption/ionization-generated peptides crosslinked with DSS in which both lysines are found in the same peptide. Fragmentation starts in the linear moiety of the peptide, yielding regular b and y ions. Once it reaches the cyclic portion of the molecule, fragmentation was observed to occur either at the following peptide bond or at the peptide crosslinker amide bond. If the peptide crosslinker bond is cleaved, it fragments as a regular modified peptide, in which the DSS backbone remains attached to the first lysine. This fragmentation pattern resembles the fragmentation of modified peptides and may be identified by common automated search engines using DSS as a modification. If, on the other hand, fragmentation happens at the peptide bond itself, rearrangement of the last crosslinked lysine is observed and a product ion containing the crosslinker backbone and lysine (m/z 222) is formed. The detailed identification of fragment ions can help the development of softwares devoted to the MS/MS data analysis of crosslinked peptides.

Keywords

Peptide Modify Peptide Peptide Crosslinker Suberate Sine Residue 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Supplementary material

13361_2011_200400557_MOESM1_ESM.pdf (97 kb)
Supplementary material, approximately 99 KB.

References

  1. 1.
    Sinz, A. Chemical Cross-Linking and Mass Spectrometry to Map Three-Dimensional Protein Structures and Protein-Protein Interactions. Mass Spectrom. Rev. 2005, 25, 663–682.CrossRefGoogle Scholar
  2. 2.
    Huang, B. X.; Kim, H. Y.; Dass, C. Probing Three-Dimensional Structure of Bovine Serum Albumin by Chemical Cross-Linking and Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2004, 15, 1237–1247.CrossRefGoogle Scholar
  3. 3.
    Young, M. M.; Tang, N.; Hempel, J. C.; Oshiro, C. M.; Taylor, E. W.; Kuntz, I. D.; Gibson, B. W.; Dollinger, G. High Throughput Protein Fold Identification by Using Experimental Constraints Derived from Intramolecular Cross-Links and Mass Spectrometry. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 5802–5806.CrossRefGoogle Scholar
  4. 4.
    Dihazi, G. H.; Sinz, A. Mapping Low-Resolution Three-Dimensional Protein Structures Using Chemical Cross-Linking and Fourier Transform Ion-Cyclotron Resonance Mass Spectrometry. Rapid Commun. Mass Spectrom. 2003, 17, 2005–2014.CrossRefGoogle Scholar
  5. 5.
    Lee, Y. J.; Lackner, L. L.; Nunnari, J. M.; Phinney, B. S. Shotgun Cross-Linking Analysis for Studying Quaternary and Tertiary Protein Structures. J. Proteome Res. 2007, 6, 3908–3917.CrossRefGoogle Scholar
  6. 6.
    Nielsen, T.; Thaysen-Andersen, M.; Larsen, N.; Jorgensen, F. S.; Houen, G.; Hojrup, P. Determination of Protein Conformation by Isotopically Labeled Cross-Linking and Dedicated Software: Application to the Chaperone, Calreticulin. Int. J. Mass Spectrom. 2007, 268, 217–226.CrossRefGoogle Scholar
  7. 7.
    Rappsilber, J.; Siniossoglou, S.; Hurt, E. C.; Mann, M. A Generic Strategy to Analyze the Spatial Organization of Multi-Protein Complexes by Cross-Linking and Mass Spectrometry. Anal. Chem. 2000, 72, 267–275.CrossRefGoogle Scholar
  8. 8.
    El-Shafey, A.; Tolic, N.; Young, M. M.; Sale, K.; Smith, R. D.; Kery, V. “Zero-Length” Cross-Linking in Solid State as an Approach for Analysis of Protein-Protein Interactions. Protein Sci. 2006, 15, 429–440.CrossRefGoogle Scholar
  9. 9.
    Kitatsuji, C.; Kurogochi, M.; Nishimura, S. I.; Ishimori, K.; Wakasugi, K. Molecular Basis of Guanine Nucleotide Dissociation Inhibitor Activity of Human Neuroglobin by Chemical Cross-Linking and Mass Spectrometry. J. Mol. Biol. 2007, 368, 150–160.CrossRefGoogle Scholar
  10. 10.
    Carven, G. J.; Stern, L. J. Probing the Ligand-Induced Conformational Change in HLA-DR1 by Selective Chemical Modification and Mass Spectrometry Mapping. Biochemistry 2005, 44, 13625–13637.CrossRefGoogle Scholar
  11. 11.
    Bhat, S.; Sorci-Thomas, M. G.; Alexander, E. T.; Samuel, M. P.; Thomas, M. J. Intermolecular Contact Between Globular N-terminal Fold and C-terminal Domain of ApoA-I Stabilizes Its Lipid-Bound Conformation. J. Biol. Chem. 2005, 280, 33015–33025.CrossRefGoogle Scholar
  12. 12.
    Huang, B. X.; Kim, H. Y. Interdomain Conformational Changes in Akt Activation Revealed by Chemical Cross-Linking and Tandem Mass Spectrometry. Mol. Cell. Proteomics 2006, 5, 1045–1053.CrossRefGoogle Scholar
  13. 13.
    Gertz, M.; Seelert, H.; Dencher, N. A.; Poetsch, A. Interactions of Rotor Subunits in the Chloroplast ATP Synthase Modulated by Nucleotides and by Mg2+. Biochim. Biophys. Acta 2007, 1774, 566–574.CrossRefGoogle Scholar
  14. 14.
    Suchaneck, M.; Radzikowska, A.; Thiele, C. Photo-Leucine and Photo-Methionine Allow Identification of Protein-Protein Interactions in Living Cells. Nat. Methods 2005, 2, 261–268.CrossRefGoogle Scholar
  15. 15.
    Taverner, T.; Hall, N. E.; O’Hair, R. A. J.; Simpson, R. J. Characterization of an Antagonist Interleukin-6 Dimer by Stable Isotope Labelling, Cross-Linking and Mass Spectrometry. J. Biol. Chem. 2002, 277, 46487–46492.CrossRefGoogle Scholar
  16. 16.
    Chang, Z.; Kuchar, J.; Hausinger, R. P. Chemical Cross-Linking and Mass Spectrometric Identification of Sites of Interaction for UreD, EreF, and Urease. J. Biol. Chem. 2004, 279, 15305–15313.CrossRefGoogle Scholar
  17. 17.
    Back, J. W.; Sanz, M. A.; Jong, L.; Koning, L. J.; Nijtmans, L. G. J.; Koster, C. G.; Grivell, L. A.; Spek, H.; Muijsers, A. O. A Structure for the Yeast Prohibitin Complex: Structure Prediction and Evidence from Chemical Crosslinking and Mass Spectrometry. Protein Sci. 2002, 11, 2471–2478.CrossRefGoogle Scholar
  18. 18.
    Maiolica, A.; Cittaro, D.; Borsotti, D.; Sennels, L.; Ciferri, C.; Tarricone, C.; Musacchio, A.; Rappsilber, J. Structural Analysis of Multiprotein Complexes by Cross-Linking, Mass Spectrometry, and Database Searching. Mol. Cell. Proteomics 2007, 6, 2200–2211.CrossRefGoogle Scholar
  19. 19.
    Ahrman, E.; Lambert, W.; Aquilina, J. A.; Robinson, C. V.; Emanuelsson, C. S. Chemical Cross-Linking of the Chloroplast Localized Small Heat-Shock Protein, Hsp21, and the Model Substrate Citrate Synthase. Protein Sci. 2007, 16, 1464–1478.CrossRefGoogle Scholar
  20. 20.
    Azim-Zadeh, O.; Hillebrecht, A.; Linne, U.; Marahiel, M. A.; Klebe, G.; Lingelbach, K.; Nyalwidhe, J. Use of Biotin Derivatives to Probe Conformational Changes in Proteins. J. Biol. Chem. 2007, 282, 21609–21617.CrossRefGoogle Scholar
  21. 21.
    Pimenova, T.; Nazabal, A.; Roschitzki, B.; Seebacher, J.; Rinner, O.; Zenobi, R. Epitope Mapping on Bovine Prion Protein Using Chemical Cross-Linking and Mass Spectrometry. J. Mass Spectrom. 2008, 43, 185–195.CrossRefGoogle Scholar
  22. 22.
    Gabant, G.; Augier, J.; Armengaud, J. Assessment of Solvent Residues Accessibility Using Three Sulfo-NHS-Biotin Reagents in Parallel: Application to Footprint Changes of a Methyltransferase Upon Binding its Substrate. J. Mass Spectrom. 2008, 43, 360–370.CrossRefGoogle Scholar
  23. 23.
    Baker, D. L.; Seyfried, N. T.; Li, H.; Orlando, R.; Terns, R. M.; Terns, M. P. Determination of Protein-RNA Interaction Sites in the Cbf5-H/ACA Guide RNA Complex by Mass Spectrometry Protein Footprinting. Biochemistry 2008, 47, 1500–1510.CrossRefGoogle Scholar
  24. 24.
    Back, J. W.; Hartog, A. F.; Dekker, H. L.; Muijsers, A. O.; Koning, L. J.; Jong, L. A New Crosslinker for Mass Spectrometric Analysis of the Quaternary Structure of Protein Complexes. J. Am. Soc. Mass Spectrom. 2001, 12, 222–227.CrossRefGoogle Scholar
  25. 25.
    Back, J. W.; Jong, L.; Muijsers, A. O.; Koster, C. G. Chemical Cross-Linking and Mass Spectrometry for Protein Structural Modelling. J. Mol. Biol. 2003, 331, 303–313.CrossRefGoogle Scholar
  26. 26.
    Back, J. W.; Notenboom, V.; Koning, L. J.; Muijsers, A. O.; Sixma, T. K.; Koster, C. G.; Jong, L. Identification of Cross-Linked Peptides for Protein Interaction Studies Using Mass Spectrometry and 18O Labeling. Anal. Chem. 2002, 74, 4417–4422.CrossRefGoogle Scholar
  27. 27.
    Tang, X.; Munske, G. R.; Siems, W. F.; Bruce, J. E. Mass Spectrometry Identifiable Cross-Linking Strategy for Studying Protein—Protein Interactions. Anal. Chem. 2005, 77, 311–318.CrossRefGoogle Scholar
  28. 28.
    Chu, F.; Mahrus, S.; Craik, C. S.; Burlingame, A. L. Isotope-Coded and Affinity-Tagged Cross-Linking (ICATXL): An Efficient Strategy to Probe Protein Interaction Surfaces. J. Am. Chem. Soc. 2006, 128, 10362–10363.CrossRefGoogle Scholar
  29. 29.
    Lamos, S. M.; Krusemark, C. J.; McGee, C. J.; Scalf, M.; Smith, L. M.; Belshaw, P. J. Mixed Isotope Photoaffinity Reagents for Identification of Small-Molecule Targets by Mass Spectrometry. Angew. Chem. Int. Ed. 2006, 45, 4329–4333.CrossRefGoogle Scholar
  30. 30.
    Sinz, A. Isotope-Labeled Photoaffinity Reagents and Mass Spectrometry to Identify Protein-Ligand Interactions. Angew. Chem. Int. Ed. 2007, 46, 660–662.CrossRefGoogle Scholar
  31. 31.
    Seebacher, J.; Mallick, P.; Zhang, N.; Eddes, J. S.; Aebersold, R.; Gelb, M. H. Protein Cross-Linking Analysis Using Mass Spectrometry, Isotope-Coded Cross-Linkers, and Integrated Computational Data Processing. J. Proteome Res. 2006, 5, 2270–2282.CrossRefGoogle Scholar
  32. 32.
    Müller, D. R.; Schindler, P.; Towbin, H.; Wirth, U.; Voshol, H.; Hoving, S.; Steinmertz, M. O. Isotope-Tagged Cross-Linking Reagents: A New Tool in Mass Spectrometric Protein Interaction Analysis. Anal. Chem. 2001, 73, 1927–1934.CrossRefGoogle Scholar
  33. 33.
    Petrotchenko, E. V.; Olkhovik, V. K.; Borchers, C. H. Isotopically Coded Cleavable Cross-Linker for Studying Protein-Protein Interactions and Protein Complexes. Mol. Cell. Proteomics 2005, 4, 1167–1179.CrossRefGoogle Scholar
  34. 34.
    Gardsvoll, H.; Gilquin, B.; Du, M. H. L.; Ménèz, A.; Jorgensen, T. J. D.; Ploug, M. Characterization of the Functional Epitope on the Urokinase Receptor. J. Biol. Chem. 2006, 281, 19260–19272.CrossRefGoogle Scholar
  35. 35.
    Gao, Q.; Doneanu, C. E.; Shaffer, S. A.; Adman, E. T.; Goodlett, D. R.; Nelson, S. D. Identification of the Interactions Between Cytochrome P450 2E1 and Cytochrome b5 by Mass Spectrometry and Site-Directed Mutagenesis. J. Biol. Chem. 2006, 281, 20404–20417.CrossRefGoogle Scholar
  36. 36.
    Hurst, G. B.; Lankford, T. K.; Kennel, S. J. Mass Spectrometric Detection of Affinity Purified Crosslinked Peptides. J. Am. Soc. Mass Spectrom. 2004, 15, 832–839.CrossRefGoogle Scholar
  37. 37.
    Sinz, A.; Kalkhof, S.; Ihling, C. Mapping Protein Interfaces by a Trifunctional Cross-Linker Combined with MALDI-TOF and ESI-FTICR Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2005, 16, 1921–1931.CrossRefGoogle Scholar
  38. 38.
    Liu, B.; Archer, C. T.; Burdine, L.; Gillette, T. G.; Kodadek, T. Label Transfer Chemistry for the Characterization of Protein-Protein Interactions. J. Am. Chem. Soc. 2007, 129, 12348–12349.CrossRefGoogle Scholar
  39. 39.
    Davidson, W. S.; Hilliard, G. M. The Spatial Organization of Apolipoprotein A-I on the Edge of Discoidal High Density Lipoprotein Particles. J. Biol. Chem. 2003, 278, 27199–27207.CrossRefGoogle Scholar
  40. 40.
    Kasper, P. T.; Back, J. W.; Vitale, M.; Hartog, A. F.; Roseboom, W.; Koning, L. J.; Maarseveen, J. H.; Muijsers, A. O.; Koster, C. G.; Jong, L. An Aptly Positioned Azido Group in the Spacer of a Protein Cross-Linker for Facile Mapping of Lysines in Close Proximity. ChemBioChem 2007, 8, 1281–1292.CrossRefGoogle Scholar
  41. 41.
    Pearson, K. M.; Pannell, L. K.; Fales, H. M. Intramolecular Cross-Linking Experiments on Cytochrome c and Ribonuclease A Using an Isotope Multiplet Method. Rapid Comm. Mass Spectrom. 2002, 16, 149–159.CrossRefGoogle Scholar
  42. 42.
    Jacobsen, R. B.; Sale, K. L.; Ayson, M. J.; Novak, P.; Hong, J.; Lane, P.; Wood, N. L.; Kruppa, G. H.; Young, M. M.; Schoeniger, J. S. Identification of Novel Quaternary Domain Interactions in the Hsp90 Chaperone, GRP94. Protein Sci. 2006, 15, 1303–1317.CrossRefGoogle Scholar
  43. 43.
    Chu, F.; Maynard, J. C.; Chiosis, G.; Nicchitta, C. V.; Burlingame, A. L. Structure and Dynamics of Dark-State Bovine Rhodopsin Revealed by Chemical Cross-Linking and High-Resolution Mass Spectrometry. Protein Sci. 2006, 15, 1260–1269.CrossRefGoogle Scholar
  44. 44.
    Schilling, B.; Row, R. H.; Gibson, B. W.; Guo, X.; Young, M. M. MS2Assign, Automated Assignment and Nomenclature of Tandem Mass Spectra of Chemically Crosslinked Peptides. J. Am. Soc. Mass Spectrom. 2003, 14, 834–850.CrossRefGoogle Scholar
  45. 45.
    Gaucher, S. P.; Hadi, M. Z.; Young, M. M. Influence of Crosslinker Identity an Position on Gas-Phase Dissociation of Lys-Lys Crosslinked Peptides. J. Am. Soc. Mass Spectrom. 2006, 17, 395–405.CrossRefGoogle Scholar
  46. 46.
    Roepstorff, P.; Fohlman, J. Proposal for a Common Nomenclature for Sequence Ions in Mass Spectra of Peptides. Biomed. Mass Spectrom. 1984, 11, 601.CrossRefGoogle Scholar
  47. 47.
    Biemann, K. Nomenclature for Peptide Fragment Ions. Methods Enzymol. 1990, 193, 886–887.CrossRefGoogle Scholar
  48. 48.
    Paizs, B.; Suhai, S. Fragmentation Pathways of Protonated Peptides. Mass Spectrom. Rev. 2005, 24, 508–548.CrossRefGoogle Scholar
  49. 49.
    Gardner, M. W.; Brodbelt, J. S. Impact of Proline and Aspartic Acid on the Dissociation of Intermolecularly Crosslinked Peptides. J. Am. Soc. Mass. Spectrom. 2008, 19, 344–357.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2009

Authors and Affiliations

  • Amadeu H. Iglesias
    • 1
    • 2
  • Luiz F. A. Santos
    • 1
    • 2
  • Fabio C. Gozzo
    • 1
    • 2
  1. 1.Center for Structural and Molecular BiologyBrazilian Synchrotron Light SourceCampinasBrazil
  2. 2.Institute of ChemistryState University of Campinas-UNICAMP, CP 6154Campinas, SPBrazil

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