Collision-Induced Dissociation of Lys-Lys Intramolecular Crosslinked Peptides

Journal of the American Society for Mass Spectrometry

Volumn 20, Issue 4, 2009, Pages 557-566

  Iglesias, Amadeu H ^a,b   Santos, Luiz F A ^a,b   Gozzo, Fabio C ^a,b  

^a Center for Molecular and Structural Biology   (Brazil)

^b UNIVERSITY OF CAMPINAS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE BONDS; AUTOMATED SEARCHES; CHEMICAL CROSS-LINKING; COLLISION-INDUCED DISSOCIATIONS; CROSS LINKERS; CROSS-LINKING REACTIONS; CROSSLINKED; DATA ANALYSIS; FRAGMENT IONS; FRAGMENTATION PATTERNS; LYSINE RESIDUES; MATRIX-ASSISTED LASER DESORPTION/IONIZATION; MODEL PEPTIDES; PEPTIDE BONDS; RANDOM SEQUENCES; STRUCTURAL BIOLOGIES; TRYPSIN DIGESTIONS;

AMIDES; AMINO ACIDS; CROSSLINKING; DESORPTION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; IONS; MASS SPECTROMETRY; PEPTIDES; SEARCH ENGINES;

AMINES;

CROSS-LINKING REAGENTS; LYSINE; MODELS, MOLECULAR; PEPTIDES; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SUCCINIMIDES; TANDEM MASS SPECTROMETRY;

EID: 62549140539     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2008.11.009     Document Type: Article

References (49)

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