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Volumn 15, Issue 7, 2016, Pages 2476-2490

Global membrane protein interactome analysis using in vivo crosslinking and mass spectrometry-based protein correlation profiling

Author keywords

[No Author keywords available]

Indexed keywords

BUFFER; FORMALDEHYDE; MEMBRANE PROTEIN; PROTEIN; PROTEOME; CROSS LINKING REAGENT;

EID: 84977272330     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O115.055467     Document Type: Article
Times cited : (56)

References (53)
  • 2
    • 84878659212 scopus 로고    scopus 로고
    • Mass spectrometry of membrane proteins: A focus on aquaporins
    • Schey, K. L., Grey, A. C., and Nicldayt, J. J. (2013) Mass Spectrometry of Membrane Proteins: A Focus on Aquaporins. Biochemistry 52, 3807-3817
    • (2013) Biochemistry , vol.52 , pp. 3807-3817
    • Schey, K.L.1    Grey, A.C.2    Nicldayt, J.J.3
  • 3
    • 84929129370 scopus 로고    scopus 로고
    • Multidimensional proteomics for cell biology
    • Larance, M., and Lamond, A. I. (2015) Multidimensional proteomics for cell biology. Nat. Rev. Mol. Cell Biol. 16, 269-280
    • (2015) Nat. Rev. Mol. Cell Biol. , vol.16 , pp. 269-280
    • Larance, M.1    Lamond, A.I.2
  • 4
    • 84860270506 scopus 로고    scopus 로고
    • A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells
    • Roux, K. J., Kim, D. I., Raida, M., and Burke, B. (2012) A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J. Cell Biol. 196, 801-810
    • (2012) J. Cell Biol. , vol.196 , pp. 801-810
    • Roux, K.J.1    Kim, D.I.2    Raida, M.3    Burke, B.4
  • 5
    • 84874956967 scopus 로고    scopus 로고
    • Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging
    • Rhee, H. W., Zou, P., Udeshi, N. D., Martell, J. D., Mootha, V. K., Carr, S. A., and Ting, A. Y. (2013) Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging. Science 339, 1328-1331
    • (2013) Science , vol.339 , pp. 1328-1331
    • Rhee, H.W.1    Zou, P.2    Udeshi, N.D.3    Martell, J.D.4    Mootha, V.K.5    Carr, S.A.6    Ting, A.Y.7
  • 6
    • 84890669750 scopus 로고    scopus 로고
    • Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics
    • Kirkwood, K. J., Ahmad, Y., Larance, M., and Lamond, A. I. (2013) Char-acterization of Native Protein Complexes and Protein Isoform Variation Using Size-fractionation-based Quantitative Proteomics. Mol. Cell. Pro-teomics 12, 3851-3873
    • (2013) Mol. Cell. Pro-teomics , vol.12 , pp. 3851-3873
    • Kirkwood, K.J.1    Ahmad, Y.2    Larance, M.3    Lamond, A.I.4
  • 7
    • 0346874342 scopus 로고    scopus 로고
    • Proteomic characterization of the human centrosome by protein correlation profiling
    • Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P., Nigg, E. A., and Mann, M. (2003) Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570-574
    • (2003) Nature , vol.426 , pp. 570-574
    • Andersen, J.S.1    Wilkinson, C.J.2    Mayor, T.3    Mortensen, P.4    Nigg, E.A.5    Mann, M.6
  • 11
    • 84866134921 scopus 로고    scopus 로고
    • A high-throughput approach for measuring temporal changes in the interactome
    • Kristensen, A. R., Gsponer, J., and Foster, L. J. (2012) A high-throughput approach for measuring temporal changes in the interactome. Nat. Meth. 9, 907-909
    • (2012) Nat. Meth. , vol.9 , pp. 907-909
    • Kristensen, A.R.1    Gsponer, J.2    Foster, L.J.3
  • 12
    • 77951153298 scopus 로고    scopus 로고
    • Proteomic analysis of integrin-associ-ated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6
    • Humphries, J. D., Byron, A., Bass, M. D., Craig, S. E., Pinney, J. W., Knight, D., and Humphries, M. J. (2009) Proteomic analysis of integrin-associ-ated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6. Sci Signal. 2, ra51
    • (2009) Sci Signal. , vol.2 , pp. ra51
    • Humphries, J.D.1    Byron, A.2    Bass, M.D.3    Craig, S.E.4    Pinney, J.W.5    Knight, D.6    Humphries, M.J.7
  • 13
  • 14
    • 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
  • 16
    • 33644670152 scopus 로고    scopus 로고
    • An Integrated Mass Spectrometry-based Proteomic Approach: Quantitative Analysis of Tandem Affinity-purified in vivo Cross-linked Protein Complexes (qtax) to Decipher the 26 s Proteasome-interacting Network
    • Guerrero, C., Tagwerker, C., Kaiser, P., and Huang, L. (2006) An Integrated Mass Spectrometry-based Proteomic Approach: Quantitative Analysis of Tandem Affinity-purified in vivo Cross-linked Protein Complexes (qtax) to Decipher the 26 s Proteasome-interacting Network. Mol. Cell. Proteom-ics 5, 366-378
    • (2006) Mol. Cell. Proteom-ics , vol.5 , pp. 366-378
    • Guerrero, C.1    Tagwerker, C.2    Kaiser, P.3    Huang, L.4
  • 17
    • 0033388858 scopus 로고    scopus 로고
    • In vivo Cross-Linking and Immunopre-cipitation for Studying Dynamic Protein:DNA Associations in a Chromatin Environment
    • Kuo, M.-H., and Allis, C. D. (1999) In vivo Cross-Linking and Immunopre-cipitation for Studying Dynamic Protein:DNA Associations in a Chromatin Environment. Methods 19, 425-433
    • (1999) Methods , vol.19 , pp. 425-433
    • Kuo, M.-H.1    Allis, C.D.2
  • 18
    • 0034161329 scopus 로고    scopus 로고
    • Mapping chromosomal proteins in vivo by formalde-hyde-crosslinked-chromatin immunoprecipitation
    • Orlando, V. (2000) Mapping chromosomal proteins in vivo by formalde-hyde-crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 25, 99-104
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 99-104
    • Orlando, V.1
  • 20
    • 33645703441 scopus 로고    scopus 로고
    • A Tandem Affinity Tag for Two-step Purification under Fully Denaturing Conditions: Application in Ubiquitin Profiling and Protein Complex Identification Combined with in vivoCross-Linking
    • Tagwerker, C., Flick, K., Cui, M., Guerrero, C., Dou, Y., Auer, B., Baldi, P., Huang, L., and Kaiser, P. (2006) A Tandem Affinity Tag for Two-step Purification under Fully Denaturing Conditions: Application in Ubiquitin Profiling and Protein Complex Identification Combined with in vivoCross-Linking. Mol. Cell. Proteomics 5, 737-748
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 737-748
    • Tagwerker, C.1    Flick, K.2    Cui, M.3    Guerrero, C.4    Dou, Y.5    Auer, B.6    Baldi, P.7    Huang, L.8    Kaiser, P.9
  • 21
    • 10644254712 scopus 로고    scopus 로고
    • Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry
    • Vasilescu, J., Guo, X., and Kast, J. (2004) Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry. Proteom-ics 4, 3845-3854
    • (2004) Proteom-ics , vol.4 , pp. 3845-3854
    • Vasilescu, J.1    Guo, X.2    Kast, J.3
  • 22
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotech. 26, 1367-1372
    • (2008) Nat. Biotech. , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 24
    • 84907197082 scopus 로고    scopus 로고
    • Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
    • Cox, J., Hein, M. Y., Luber, C. A., Paron, I., Nagaraj, N., and Mann, M. (2014) Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ. Mol. Cell. Proteomics 13, 2513-2526
    • (2014) Mol. Cell. Proteomics , vol.13 , pp. 2513-2526
    • Cox, J.1    Hein, M.Y.2    Luber, C.A.3    Paron, I.4    Nagaraj, N.5    Mann, M.6
  • 26
    • 34247500374 scopus 로고    scopus 로고
    • Python for scientific computing
    • Oliphant, T. E. (2007) Python for scientific computing. Comput. Sci. Eng. 9, 10-20
    • (2007) Comput. Sci. Eng. , vol.9 , pp. 10-20
    • Oliphant, T.E.1
  • 29
    • 84881455143 scopus 로고    scopus 로고
    • Mentha: A resource for browsing integrated protein-interaction networks
    • Calderone, A., Castagnoli, L., and Cesareni, G. (2013) mentha: a resource for browsing integrated protein-interaction networks. Nat. Methods 10, 690-691
    • (2013) Nat. Methods , vol.10 , pp. 690-691
    • Calderone, A.1    Castagnoli, L.2    Cesareni, G.3
  • 30
    • 84860361165 scopus 로고    scopus 로고
    • Detecting overlapping protein complexes in protein-protein interaction networks
    • Nepusz, T., Yu, H. Y., and Paccanaro, A. (2012) Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods 9, 471-U481
    • (2012) Nat Methods , vol.9 , pp. 471U481
    • Nepusz, T.1    Yu, H.Y.2    Paccanaro, A.3
  • 31
    • 77949786295 scopus 로고    scopus 로고
    • Value of using multiple proteases for large-scale mass spectrometry-based proteomics
    • Swaney, D. L., Wenger, C. D., and Coon, J. J. (2010) Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics. J. Proteome Res. 9, 1323-1329
    • (2010) J. Proteome Res. , vol.9 , pp. 1323-1329
    • Swaney, D.L.1    Wenger, C.D.2    Coon, J.J.3
  • 32
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. L. (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305, 567-580
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    Von Heijne, G.3    Sonnhammer, E.L.L.4
  • 33
    • 3343011406 scopus 로고    scopus 로고
    • NG2 proteogly-can promotes endothelial cell motility and angiogenesis via engagement of galectin-3 and alpha3beta1 integrin
    • Fukushi, J., Makagiansar, I. T., and Stallcup, W. B. (2004) NG2 proteogly-can promotes endothelial cell motility and angiogenesis via engagement of galectin-3 and alpha3beta1 integrin. Mol. Biol. Cell 15, 3580-3590
    • (2004) Mol. Biol. Cell , vol.15 , pp. 3580-3590
    • Fukushi, J.1    Makagiansar, I.T.2    Stallcup, W.B.3
  • 36
    • 11244304502 scopus 로고    scopus 로고
    • Palmitoylation supports assembly and function of integrin-tetraspanin complexes
    • Yang, X., Kovalenko, O. V., Tang, W., Claas, C., Stipp, C. S., and Hemler, M. E. (2004) Palmitoylation supports assembly and function of integrin-tetraspanin complexes. J. Cell Biol. 167, 1231-1240
    • (2004) J. Cell Biol. , vol.167 , pp. 1231-1240
    • Yang, X.1    Kovalenko, O.V.2    Tang, W.3    Claas, C.4    Stipp, C.S.5    Hemler, M.E.6
  • 38
    • 84945298509 scopus 로고    scopus 로고
    • Three steps forward, two steps back: Mechanistic insights into the assembly and disassembly of the SNARE complex
    • Bombardier, J. P., and Munson, M. (2015) Three steps forward, two steps back: mechanistic insights into the assembly and disassembly of the SNARE complex. Curr. Opin. Chem. Biol. 29, 66-71
    • (2015) Curr. Opin. Chem. Biol. , vol.29 , pp. 66-71
    • Bombardier, J.P.1    Munson, M.2
  • 39
    • 0022824304 scopus 로고
    • G proteins: A family of signal transduc-ers
    • Stryer, L., and Bourne, H. R. (1986) G proteins: a family of signal transduc-ers. Annu. Rev. Cell Biol. 2, 391-419
    • (1986) Annu. Rev. Cell Biol. , vol.2 , pp. 391-419
    • Stryer, L.1    Bourne, H.R.2
  • 41
    • 1942535218 scopus 로고    scopus 로고
    • Boca-dependent maturation of beta-propeller/EGF modules in low-density lipoprotein receptor proteins
    • Culi, J., Springer, T. A., and Mann, R. S. (2004) Boca-dependent maturation of beta-propeller/EGF modules in low-density lipoprotein receptor proteins. EMBO J. 23, 1372-1380
    • (2004) EMBO J. , vol.23 , pp. 1372-1380
    • Culi, J.1    Springer, T.A.2    Mann, R.S.3
  • 43
    • 0023911134 scopus 로고
    • Beta-Hydroxyaspartic acid or beta-hydroxyasparagine in bovine low density lipoprotein receptor and in bovine thrombomodulin
    • Stenflo, J., Ohlin, A. K., Owen, W. G., and Schneider, W. J. (1988) beta-Hydroxyaspartic acid or beta-hydroxyasparagine in bovine low density lipoprotein receptor and in bovine thrombomodulin. J. Biol. Chem. 263, 21-24
    • (1988) J. Biol. Chem. , vol.263 , pp. 21-24
    • Stenflo, J.1    Ohlin, A.K.2    Owen, W.G.3    Schneider, W.J.4
  • 44
    • 34848823742 scopus 로고    scopus 로고
    • Mitochon-drial protein-import machinery: Correlating structure with function
    • Baker, M. J., Frazier, A. E., Gulbis, J. M., and Ryan, M. T. (2007) Mitochon-drial protein-import machinery: correlating structure with function. Trends Cell Biol. 17, 456-464
    • (2007) Trends Cell Biol. , vol.17 , pp. 456-464
    • Baker, M.J.1    Frazier, A.E.2    Gulbis, J.M.3    Ryan, M.T.4
  • 45
    • 67349234086 scopus 로고    scopus 로고
    • The Miro GTPases: At the heart of the mitochondrial transport machinery
    • Reis, K., Fransson, A., and Aspenstrom, P. (2009) The Miro GTPases: at the heart of the mitochondrial transport machinery. FEBS Lett. 583, 1391-1398
    • (2009) FEBS Lett. , vol.583 , pp. 1391-1398
    • Reis, K.1    Fransson, A.2    Aspenstrom, P.3
  • 47
    • 0030479325 scopus 로고    scopus 로고
    • Molecular cloning and characterization of a full-length complementary DNA encoding human acid ceramidase. Identification of the first molecular lesion causing Farber disease
    • Koch, J., Gartner, S., Li, C. M., Quintern, L. E., Bernardo, K., Levran, O., Schnabel, D., Desnick, R. J., Schuchman, E. H., and Sandhoff, K. (1996) Molecular cloning and characterization of a full-length complementary DNA encoding human acid ceramidase. Identification Of the first molecular lesion causing Farber disease. J. Biol. Chem. 271, 33110-33115
    • (1996) J. Biol. Chem. , vol.271 , pp. 33110-33115
    • Koch, J.1    Gartner, S.2    Li, C.M.3    Quintern, L.E.4    Bernardo, K.5    Levran, O.6    Schnabel, D.7    Desnick, R.J.8    Schuchman, E.H.9    Sandhoff, K.10
  • 48
    • 0041355473 scopus 로고    scopus 로고
    • Purification and characterization of recom-binant, human acid ceramidase. Catalytic reactions and interactions with acid sphingomyelinase
    • He, X., Okino, N., Dhami, R., Dagan, A., Gatt, S., Schulze, H., Sandhoff, K., and Schuchman, E. H. (2003) Purification and characterization of recom-binant, human acid ceramidase. Catalytic reactions and interactions with acid sphingomyelinase. J. Biol. Chem. 278, 32978-32986
    • (2003) J. Biol. Chem. , vol.278 , pp. 32978-32986
    • He, X.1    Okino, N.2    Dhami, R.3    Dagan, A.4    Gatt, S.5    Schulze, H.6    Sandhoff, K.7    Schuchman, E.H.8
  • 49
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protocols 4, 44-57
    • (2008) Nat. Protocols , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 50
    • 79960610118 scopus 로고    scopus 로고
    • REVIGO summa-rizes and visualizes long lists of gene ontology terms
    • Supek, F., Bosnjak, M., Skunca, N., and Smuc, T. (2011) REVIGO summa-rizes and visualizes long lists of gene ontology terms. PloS One. 6, e21800
    • (2011) PloS One. , vol.6 , pp. e21800
    • Supek, F.1    Bosnjak, M.2    Skunca, N.3    Smuc, T.4
  • 51
    • 84874642970 scopus 로고    scopus 로고
    • Global subcellular characterization of protein degradation using quantitative proteomics
    • Larance, M., Ahmad, Y., Kirkwood, K. J., Ly, T., and Lamond, A. I. (2013) Global Subcellular Characterization of Protein Degradation Using Quantitative Proteomics. Mol. Cell. Proteomics 12, 638-650
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 638-650
    • Larance, M.1    Ahmad, Y.2    Kirkwood, K.J.3    Ly, T.4    Lamond, A.I.5
  • 52
    • 0019082582 scopus 로고
    • A nondenaturing zwitterionic detergent for mem-brane biochemistry: Design and synthesis
    • Hjelmeland, L. M. (1980) A nondenaturing zwitterionic detergent for mem-brane biochemistry: design and synthesis. Proc. Natl. Acad. Sci. U.S.A. 77, 6368-6370
    • (1980) Proc. Natl. Acad. Sci. U.S.A. , vol.77 , pp. 6368-6370
    • Hjelmeland, L.M.1
  • 53
    • 84905702834 scopus 로고    scopus 로고
    • Using VisANT to analyze networks
    • Hu, Z. (2014) Using VisANT to Analyze Networks. Curr. Protoc. Bioinfor-matics 8, 8.8.1-8.8.39
    • (2014) Curr. Protoc. Bioinfor-matics , vol.8 , pp. 881-8839
    • Hu, Z.1


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