메뉴 건너뛰기




Volumn 9, Issue 1, 2010, Pages 25-31

Finding chimeras: A bioinformatics strategy for identification of cross-linked peptides

Author keywords

[No Author keywords available]

Indexed keywords

HETERODIMER; HOMODIMER;

EID: 76649135167     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M800555-MCP200     Document Type: Article
Times cited : (69)

References (29)
  • 1
    • 33644555054 scopus 로고    scopus 로고
    • Gavin, A. C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., Edelmann, A., Heurtier, M. A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A. M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J. M., Kuster, B., Bork, P., Russell, R. B., and Superti-Furga, G. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636
    • Gavin, A. C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., Edelmann, A., Heurtier, M. A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A. M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J. M., Kuster, B., Bork, P., Russell, R. B., and Superti-Furga, G. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636
  • 2
    • 33645453254 scopus 로고    scopus 로고
    • Krogan, N. J, Cagney, G, Yu, H, Zhong, G, Guo, X, Ignatchenko, A, Li, J, Pu, S, Datta, N, Tikuisis, A. P, Punna, T, Peregrín-Alvarez, J. M, Shales, M, Zhang, X, Davey, M, Robinson, M. D, Paccanaro, A, Bray, J. E, Sheung, A, Beattie, B, Richards, D. P, Canadien, V, Lalev, A, Mena, F, Wong, P, Starostine, A, Canete, M. M, Vlasblom, J, Wu, S, Orsi, C, Collins, S. R, Chandran, S, Haw, R, Rilstone, J. J, Gandi, K, Thompson, N. J, Musso, G, St Onge, P, Ghanny, S, Lam, M. H, Butland, G, Altaf-Ul, A. M, Kanaya, S, Shilatifard, A, O'Shea, E, Weissman, J. S, Ingles, C. J, Hughes, T. R, Parkinson, J, Gerstein, M, Wodak, S. J, Emili, A, and Greenblatt, J. F, 2006 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643
    • Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A. P., Punna, T., Peregrín-Alvarez, J. M., Shales, M., Zhang, X., Davey, M., Robinson, M. D., Paccanaro, A., Bray, J. E., Sheung, A., Beattie, B., Richards, D. P., Canadien, V., Lalev, A., Mena, F., Wong, P., Starostine, A., Canete, M. M., Vlasblom, J., Wu, S., Orsi, C., Collins, S. R., Chandran, S., Haw, R., Rilstone, J. J., Gandi, K., Thompson, N. J., Musso, G., St Onge, P., Ghanny, S., Lam, M. H., Butland, G., Altaf-Ul, A. M., Kanaya, S., Shilatifard, A., O'Shea, E., Weissman, J. S., Ingles, C. J., Hughes, T. R., Parkinson, J., Gerstein, M., Wodak, S. J., Emili, A., and Greenblatt, J. F. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643
  • 4
    • 33745742438 scopus 로고    scopus 로고
    • Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions
    • Sinz, A. (2006) Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom. Rev. 25, 663-682
    • (2006) Mass Spectrom. Rev , vol.25 , pp. 663-682
    • Sinz, A.1
  • 5
    • 0041846956 scopus 로고    scopus 로고
    • MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides
    • Schilling, B., Row, R. H., Gibson, B. W., Guo, X., and Young, M. M. (2003) MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. J. Am. Soc. Mass Spectrom. 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
  • 6
    • 0035800080 scopus 로고    scopus 로고
    • Mapping protein interfaces with a fluorogenic cross-linker and mass spectrometry: Application to nebulin-calmodulin complexes
    • Sinz, A., and Wang, K. (2001) Mapping protein interfaces with a fluorogenic cross-linker and mass spectrometry: application to nebulin-calmodulin complexes. Biochemistry 40, 7903-7913
    • (2001) Biochemistry , vol.40 , pp. 7903-7913
    • Sinz, A.1    Wang, K.2
  • 7
    • 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., and Steinmetz, M. O. (2001) Isotope-tagged cross-linking reagents. A new tool in mass spectrometric protein interaction analysis. Anal. Chem. 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
  • 8
    • 0036007815 scopus 로고    scopus 로고
    • Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method
    • Pearson, K. M., Pannell, L. K., and Fales, H. M. (2002) Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method. Rapid Commun. Mass Spectrom. 16, 149-159
    • (2002) Rapid Commun. Mass Spectrom , vol.16 , pp. 149-159
    • Pearson, K.M.1    Pannell, L.K.2    Fales, H.M.3
  • 9
    • 0033837787 scopus 로고    scopus 로고
    • Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping-a novel approach to assess intermolecular protein contacts
    • Bennett, K. L., Kussmann, M., Björk, P., Godzwon, M., Mikkelsen, M., Sørensen, P., and Roepstorff, P. (2000) Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping-a novel approach to assess intermolecular protein contacts. Protein Sci. 9, 1503-1518
    • (2000) Protein Sci , vol.9 , pp. 1503-1518
    • Bennett, K.L.1    Kussmann, M.2    Björk, P.3    Godzwon, M.4    Mikkelsen, M.5    Sørensen, P.6    Roepstorff, P.7
  • 10
    • 0034725391 scopus 로고    scopus 로고
    • Mapping protein-protein interactions in the bacteriophage T4 DNA polymerase holoenzyme using a novel trifunctional photo-cross-linking and affinity reagent
    • Alley, S. C., Ishmael, F. T., Jones, D., and Benkovic, S. J. (2000) Mapping protein-protein interactions in the bacteriophage T4 DNA polymerase holoenzyme using a novel trifunctional photo-cross-linking and affinity reagent. J. Am. Chem. Soc. 122, 6126-6127
    • (2000) J. Am. Chem. Soc , vol.122 , pp. 6126-6127
    • Alley, S.C.1    Ishmael, F.T.2    Jones, D.3    Benkovic, S.J.4
  • 11
    • 2442604553 scopus 로고    scopus 로고
    • Mass spectrometric detection of affinity purified crosslinked peptides
    • Hurst, G. B., Lankford, T. K., and Kennel, S. J. (2004) Mass spectrometric detection of affinity purified crosslinked peptides. J. Am. Soc. Mass Spectrom. 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
  • 13
    • 0035942229 scopus 로고    scopus 로고
    • Mapping of contact sites in complex formation between light-activated rhodopsin and transducin by covalent crosslinking: Use of a chemically preactivated reagent
    • Itoh, Y., Cai, K., and Khorana, H. G. (2001) Mapping of contact sites in complex formation between light-activated rhodopsin and transducin by covalent crosslinking: use of a chemically preactivated reagent. Proc. Natl. Acad. Sci. U.S.A. 98, 4883-4887
    • (2001) Proc. Natl. Acad. Sci. U.S.A , vol.98 , pp. 4883-4887
    • Itoh, Y.1    Cai, K.2    Khorana, H.G.3
  • 14
    • 0035942238 scopus 로고    scopus 로고
    • Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking: Use of a photoactivatable reagent
    • Cai, K., Itoh, Y., and Khorana, H. G. (2001) Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking: use of a photoactivatable reagent. Proc. Natl. Acad. Sci. U.S.A. 98, 4877-4882
    • (2001) Proc. Natl. Acad. Sci. U.S.A , vol.98 , pp. 4877-4882
    • Cai, K.1    Itoh, Y.2    Khorana, H.G.3
  • 16
    • 33747618271 scopus 로고    scopus 로고
    • Isotopecoded and affinity-tagged cross-linking (ICATXL): An efficient strategy to probe protein interaction surfaces
    • Chu, F., Mahrus, S., Craik, C. S., and Burlingame, A. L. (2006) Isotopecoded and affinity-tagged cross-linking (ICATXL): an efficient strategy to probe protein interaction surfaces. J. Am. Chem. Soc. 128, 10362-10363
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 10362-10363
    • Chu, F.1    Mahrus, S.2    Craik, C.S.3    Burlingame, A.L.4
  • 18
    • 33645682750 scopus 로고    scopus 로고
    • Pro-CrossLink. Software tool for protein crosslinking and mass spectrometry
    • Gao, Q., Xue, S., Doneanu, C. E., Shaffer, S. A., Goodlett, D. R., and Nelson, S. D. (2006) Pro-CrossLink. Software tool for protein crosslinking and mass spectrometry. Anal. Chem. 78, 2145-2149
    • (2006) Anal. Chem , vol.78 , pp. 2145-2149
    • Gao, Q.1    Xue, S.2    Doneanu, C.E.3    Shaffer, S.A.4    Goodlett, D.R.5    Nelson, S.D.6
  • 21
    • 24044491542 scopus 로고    scopus 로고
    • Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: II. new developments in Protein Prospector allow for reliable and comprehensive automatic analysis of large datasets
    • Chalkley, R. J., Baker, P. R., Huang, L., Hansen, K. C., Allen, N. P., Rexach, M., and Burlingame, A. L. (2005) Comprehensive analysis of a multidimensional liquid chromatography mass spectrometry dataset acquired on a quadrupole selecting, quadrupole collision cell, time-of-flight mass spectrometer: II. new developments in Protein Prospector allow for reliable and comprehensive automatic analysis of large datasets. Mol. Cell. Proteomics 4, 1194-1204
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1194-1204
    • Chalkley, R.J.1    Baker, P.R.2    Huang, L.3    Hansen, K.C.4    Allen, N.P.5    Rexach, M.6    Burlingame, A.L.7
  • 23
    • 9344221072 scopus 로고    scopus 로고
    • Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry
    • Chu, F., Shan, S. O., Moustakas, D. T., Alber, F., Egea, P. F., Stroud, R. M., Walter, P., and Burlingame, A. L. (2004) Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 101, 16454-16459
    • (2004) Proc. Natl. Acad. Sci. U.S.A , vol.101 , pp. 16454-16459
    • Chu, F.1    Shan, S.O.2    Moustakas, D.T.3    Alber, F.4    Egea, P.F.5    Stroud, R.M.6    Walter, P.7    Burlingame, A.L.8
  • 24
    • 0034912563 scopus 로고    scopus 로고
    • Novel inter-protein cross-link identified in the GGH-ecotin D137Y dimer
    • Person, M. D., Brown, K. C., Mahrus, S., Craik, C. S., and Burlingame, A. L. (2001) Novel inter-protein cross-link identified in the GGH-ecotin D137Y dimer. Protein Sci. 10, 1549-1562
    • (2001) Protein Sci , vol.10 , pp. 1549-1562
    • Person, M.D.1    Brown, K.C.2    Mahrus, S.3    Craik, C.S.4    Burlingame, A.L.5
  • 25
    • 33744489349 scopus 로고    scopus 로고
    • Identification of novel quaternary domain interactions in the Hsp90 chaperone, GRP94
    • Chu, F., Maynard, J. C., Chiosis, G., Nicchitta, C. V., and Burlingame, A. L. (2006) Identification of novel quaternary domain interactions in the Hsp90 chaperone, GRP94. Protein Sci. 15, 1260-1269
    • (2006) Protein Sci , vol.15 , pp. 1260-1269
    • Chu, F.1    Maynard, J.C.2    Chiosis, G.3    Nicchitta, C.V.4    Burlingame, A.L.5
  • 28
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • Elias, J. E., and Gygi, S. P. (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214
    • (2007) Nat. Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 29
    • 17044419154 scopus 로고    scopus 로고
    • Targeting proteins to membranes: Structure of the signal recognition particle
    • Egea, P. F., Stroud, R. M., and Walter, P. (2005) Targeting proteins to membranes: structure of the signal recognition particle. Curr. Opin. Struct. Biol. 15, 213-220
    • (2005) Curr. Opin. Struct. Biol , vol.15 , pp. 213-220
    • Egea, P.F.1    Stroud, R.M.2    Walter, P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.