메뉴 건너뛰기




Volumn 5, Issue 9, 2006, Pages 2270-2282

Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing

Author keywords

Cross linking; Mass spectrometry; Protein complex; Protein structure; Protein structure prediction; Protein protein interaction; Proteomics

Indexed keywords

BACTERIAL ENZYME; BETA LACTOGLOBULIN; COLICIN; COLICIN E7; CROSS LINKING REAGENT; CYTOCHROME C; DEOXYRIBONUCLEASE; DEUTERIUM; HETERODIMER; LYSOZYME; MYOGLOBIN; PEPTIDE DERIVATIVE; PROTEIN; PROTEIN DERIVATIVE; PROTEIN LM7; RIBONUCLEASE A; SOLVENT; UNCLASSIFIED DRUG; WATER; WATER O 18;

EID: 33748328052     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr060154z     Document Type: Article
Times cited : (106)

References (27)
  • 1
    • 0033648564 scopus 로고    scopus 로고
    • Probing protein surface topology by chemical surface labeling, cross-linking, and mass spectrometry
    • Bennett, K. L.; Matthiesen, T.; Roepstorff, P. Probing protein surface topology by chemical surface labeling, cross-linking, and mass spectrometry. Methods Mol. Biol. 2000, 146, 113-131.
    • (2000) Methods Mol. Biol. , vol.146 , pp. 113-131
    • Bennett, K.L.1    Matthiesen, T.2    Roepstorff, P.3
  • 2
    • 0027203297 scopus 로고
    • New photolabeling and cross-linking methods
    • Brunner, J. New photolabeling and cross-linking methods. Annu. Rev. Biochem. 1993, 62, 483-514.
    • (1993) Annu. Rev. Biochem. , vol.62 , pp. 483-514
    • Brunner, J.1
  • 3
    • 0034705128 scopus 로고    scopus 로고
    • High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry
    • 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.
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 5802-5806
    • Young, M.M.1    Tang, N.2    Hempel, J.C.3    Oshiro, C.M.4    Taylor, E.W.5    Kuntz, I.D.6    Gibson, B.W.7    Dollinger, G.8
  • 4
    • 0034650492 scopus 로고    scopus 로고
    • A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry
    • Rappsilber, J.; Siniossolou, 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.
    • (2000) Anal. Chem. , vol.72 , pp. 267-275
    • Rappsilber, J.1    Siniossolou, S.2    Hurt, E.C.3    Mann, M.4
  • 5
    • 0041846956 scopus 로고    scopus 로고
    • MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically cross-linked peptides
    • Schilling, B.; Row, R. H.; Gibson, B. W.; Guo, X.; Young, M. M. MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically cross-linked peptides. J. Am. Soc. Mass Spectrom. 2003, 14, 834-850.
    • (2003) J. Am. Soc. Mass Spectrom. , vol.14 , pp. 834-850
    • Schilling, B.1    Row, R.H.2    Gibson, B.W.3    Guo, X.4    Young, M.M.5
  • 7
    • 0347286732 scopus 로고    scopus 로고
    • Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes
    • Sinz, A. Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes. J. Mass. Spectrom. 2003, 38, 1225-1237.
    • (2003) J. Mass. Spectrom. , vol.38 , pp. 1225-1237
    • Sinz, A.1
  • 8
    • 19444371218 scopus 로고    scopus 로고
    • A novel strategy for the identification of protein-DNA contacts by photo-cross-linking and mass spectrometry
    • Geyer, H.; Geyer, R.; Pingoud, V. A novel strategy for the identification of protein-DNA contacts by photo-cross-linking and mass spectrometry. Nucleic Acids Res. 2004, 32, e132.
    • (2004) Nucleic Acids Res. , vol.32
    • Geyer, H.1    Geyer, R.2    Pingoud, V.3
  • 9
    • 0042349690 scopus 로고    scopus 로고
    • Chemical cross-linking and mass spectrometry for protein structural modeling
    • Back, J. W.; de Jong, L.; Muijsers, A. O.; de Koster, C. G. Chemical Cross-linking and Mass Spectrometry for Protein Structural Modeling. J. Mol. Biol. 2003, 331, 303-313.
    • (2003) J. Mol. Biol. , vol.331 , pp. 303-313
    • Back, J.W.1    De Jong, L.2    Muijsers, A.O.3    De Koster, C.G.4
  • 10
    • 24044520965 scopus 로고    scopus 로고
    • Isotopically coded cleavable cross-linker for studying protein-protein interaction and protein complexes
    • Petrochenko, E. V.; Olkhovik, V. K.; Borchers, C. H. Isotopically Coded Cleavable Cross-linker for Studying Protein-Protein Interaction and Protein Complexes. Mol. Cell. Proteomics 2005, 4, 1167-79.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1167-1179
    • Petrochenko, E.V.1    Olkhovik, V.K.2    Borchers, C.H.3
  • 11
    • 33745742438 scopus 로고    scopus 로고
    • Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions
    • Sinz, A. Chemical Cross-linking and Mass Spectrometry to Map Three-Dimensional Protein Structures and Protein-Protein Interactions. Mass Spectrom. Rev. 2006, 25, 663-682.
    • (2006) Mass Spectrom. Rev. , vol.25 , pp. 663-682
    • Sinz, A.1
  • 13
    • 2442604553 scopus 로고    scopus 로고
    • Mass spectrometric detection of affinity purified cross-linked peptides
    • Hurst, G. B.; Lankford, T. K.; Kennel, S. J. Mass spectrometric detection of affinity purified cross-linked peptides. J. Am. Soc. Mass Spectrom. 2004, 15, 832-839.
    • (2004) J. Am. Soc. Mass Spectrom. , vol.15 , pp. 832-839
    • Hurst, G.B.1    Lankford, T.K.2    Kennel, S.J.3
  • 14
    • 0035326345 scopus 로고    scopus 로고
    • Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis
    • Müller, D. R.; Schindler, P.; Towbin, H.; Wirth, U.; Voshol, H.; Hoving, S.; Steinmetz, M. O. Isotope-Tagged Cross-Linking Reagents. A New Tool in Mass Spectrometric Protein Interaction Analysis. Anal. Chem. 2001, 73, 1927-1934.
    • (2001) Anal. Chem. , vol.73 , pp. 1927-1934
    • Müller, D.R.1    Schindler, P.2    Towbin, H.3    Wirth, U.4    Voshol, H.5    Hoving, S.6    Steinmetz, M.O.7
  • 15
    • 0242317292 scopus 로고    scopus 로고
    • Isotopically labeled cross-linking reagents: Resolution of mass degeneracy in the identification of cross-linked peptides
    • Collins, C. J.; Schilling, B.; Young, M.; Dollinger, G.; Guy, R. K. Isotopically labeled cross-linking reagents: resolution of mass degeneracy in the identification of cross-linked peptides. Bioorg. Med. Chem. Lett. 2003, 13, 4023-4026.
    • (2003) Bioorg. Med. Chem. Lett. , vol.13 , pp. 4023-4026
    • Collins, C.J.1    Schilling, B.2    Young, M.3    Dollinger, G.4    Guy, R.K.5
  • 16
    • 3042818018 scopus 로고    scopus 로고
    • The international protein index: An integrated database for proteomics experiments
    • Kersey, P. J.; Duarte, J.; Williams, A.; Karavidopoulou, Y.; Birney, E.; Apweiler, R. The International Protein Index: An integrated database for proteomics experiments. Proteomics 2004, 4 (7), 1985-1988.
    • (2004) Proteomics , vol.4 , Issue.7 , pp. 1985-1988
    • Kersey, P.J.1    Duarte, J.2    Williams, A.3    Karavidopoulou, Y.4    Birney, E.5    Apweiler, R.6
  • 18
    • 0036808207 scopus 로고    scopus 로고
    • A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data
    • Zhang, N.; Aebersold, R.; Schwikowski, B. A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics 2002, 2, 1406-1412.
    • (2002) Proteomics , vol.2 , pp. 1406-1412
    • Zhang, N.1    Aebersold, R.2    Schwikowski, B.3
  • 19
    • 0033565832 scopus 로고    scopus 로고
    • Role of accurate mass measurement (± 10 ppm) in protein identification strategies employing MS or MS/MS and database searching
    • Clauser, K. R.; Baker, P. R.; Burlingame, A. L. Role of accurate mass measurement (± 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 1999, 71, 2871-2882.
    • (1999) Anal. Chem. , vol.71 , pp. 2871-2882
    • Clauser, K.R.1    Baker, P.R.2    Burlingame, A.L.3
  • 20
    • 33748325067 scopus 로고    scopus 로고
    • center of advanced european studies and research (caesar), Bonn, Germany
    • Wefing, S.; Schnaible, V.; Hoffmann, D. SearchXLinks, http://www.searchxlinks.de/, center of advanced european studies and research (caesar), Bonn, Germany, 2001.
    • (2001)
    • Wefing, S.1    Schnaible, V.2    Hoffmann, D.3
  • 21
    • 27644497319 scopus 로고    scopus 로고
    • CLPM: A cross-linked peptide mapping algorithm for mass spectrometric analysis
    • Jul 15
    • Tang, Y.; Chen, Y.; Lichti, C. F.; Hall, R. A.; Raney, K. D.; Jennings, S. F. CLPM: a cross-linked peptide mapping algorithm for mass spectrometric analysis BMC Bioinformatics 2005 Jul 15; 6 Suppl 2: S9.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 2
    • Tang, Y.1    Chen, Y.2    Lichti, C.F.3    Hall, R.A.4    Raney, K.D.5    Jennings, S.F.6
  • 22
    • 33645016907 scopus 로고    scopus 로고
    • Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes
    • de Koning, L. J.; Kasper, P. T.; Back, J. W.; Nessen, M. A.; Vanrobaeys, F.; Van Beeumen, J.; Gherardi, E.; de Koster, C. G.; de long, L. Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes FEBS J. 2006, 273, 281-91.
    • (2006) FEBS J. , vol.273 , pp. 281-291
    • De Koning, L.J.1    Kasper, P.T.2    Back, J.W.3    Nessen, M.A.4    Vanrobaeys, F.5    Van Beeumen, J.6    Gherardi, E.7    De Koster, C.G.8    De Long, L.9
  • 23
    • 33344463891 scopus 로고    scopus 로고
    • Influence of Cross-linker Identity and Position on Gas-Phase Dissociation of Lys-Lys Cross-linked Peptides
    • Gaucher, S. P.; Hadi, M. Z.; Young, M. M. Influence of Cross-linker Identity and Position on Gas-Phase Dissociation of Lys-Lys Cross-linked Peptides. J. Am. Soc. Mass Spectrom. 2006, 17, 395-405.
    • (2006) J. Am. Soc. Mass Spectrom. , vol.17 , pp. 395-405
    • Gaucher, S.P.1    Hadi, M.Z.2    Young, M.M.3
  • 24
    • 21844457685 scopus 로고    scopus 로고
    • Fragmentation pathways of protonated peptides
    • Paizs, B.; Suhai, S, Fragmentation pathways of protonated peptides. Mass Spectrom. Rev. 2005, 24, 508-548.
    • (2005) Mass Spectrom. Rev. , vol.24 , pp. 508-548
    • Paizs, B.1    Suhai, S.2
  • 25
    • 0034973193 scopus 로고    scopus 로고
    • Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulers
    • Green, N. S.; Reisler, E.; Houk, K. N. Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulers. Protein Sci. 2001, 10, 1293-1304.
    • (2001) Protein Sci. , vol.10 , pp. 1293-1304
    • Green, N.S.1    Reisler, E.2    Houk, K.N.3
  • 26
    • 18844423484 scopus 로고    scopus 로고
    • Probing conformational changes of human serum albumin due to unsaturated fatty acid binding by chemical cross-linking and mass spectrometry
    • Huang, B. X.; Dass, C.; Kim, H. Y. Probing conformational changes of human serum albumin due to unsaturated fatty acid binding by chemical cross-linking and mass spectrometry. Biochem. J. 2005, 387, 695-702.
    • (2005) Biochem. J. , vol.387 , pp. 695-702
    • Huang, B.X.1    Dass, C.2    Kim, H.Y.3
  • 27
    • 0032828715 scopus 로고
    • A generic protein purification method for protein complex characterization and proteome exploration
    • Rigaut, G.; Shevchenko, A.; Rutz, B.; Wilm, M.; Mann, M.; Seraphin, B. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 1899, 17, 1030-1032.
    • (1899) Nat. Biotechnol. , vol.17 , pp. 1030-1032
    • Rigaut, G.1    Shevchenko, A.2    Rutz, B.3    Wilm, M.4    Mann, M.5    Seraphin, B.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.