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Volumn 392, Issue 1, 2009, Pages 228-241

A Computationally Guided Protein-Interaction Screen Uncovers Coiled-Coil Interactions Involved in Vesicular Trafficking

Author keywords

coiled coils; computational prediction; protein interactions; vesicular trafficking; yeast two hybrid

Indexed keywords

CARRIER PROTEIN; GREEN FLUORESCENT PROTEIN; SNARE PROTEIN;

EID: 68949183221     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.07.006     Document Type: Article
Times cited : (16)

References (68)
  • 1
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in S. cerevisiae
    • Uetz P., Giot L., Cagney G., Mansfield T., Judson R., Knight J., et al. A comprehensive analysis of protein-protein interactions in S. cerevisiae. Nature 403 (2000) 623-627
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3    Mansfield, T.4    Judson, R.5    Knight, J.6
  • 3
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin A., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415 (2002) 141-147
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.1    Bosche, M.2    Krause, R.3    Grandi, P.4    Marzioch, M.5    Bauer, A.6
  • 4
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • Ho Y., Gruhler A., Heilbut A., Bader G., Moore L., Adams S., et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415 (2002) 180-183
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3    Bader, G.4    Moore, L.5    Adams, S.6
  • 5
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin A.C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440 (2006) 631-636
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1    Aloy, P.2    Grandi, P.3    Krause, R.4    Boesche, M.5    Marzioch, M.6
  • 6
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440 (2006) 637-643
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4    Guo, X.5    Ignatchenko, A.6
  • 8
    • 53349117774 scopus 로고    scopus 로고
    • High-quality binary protein interaction map of the yeast interactome network
    • Yu H., Braun P., Yildirim M.A., Lemmens I., Venkatesan K., Sahalie J., et al. High-quality binary protein interaction map of the yeast interactome network. Science 322 (2008) 104-110
    • (2008) Science , vol.322 , pp. 104-110
    • Yu, H.1    Braun, P.2    Yildirim, M.A.3    Lemmens, I.4    Venkatesan, K.5    Sahalie, J.6
  • 9
    • 33847744247 scopus 로고    scopus 로고
    • How complete are current yeast and human protein-interaction networks?
    • Hart G.T., Ramani A.K., and Marcotte E.M. How complete are current yeast and human protein-interaction networks?. Genome Biol. 7 (2006) 120
    • (2006) Genome Biol. , vol.7 , pp. 120
    • Hart, G.T.1    Ramani, A.K.2    Marcotte, E.M.3
  • 11
    • 48649096489 scopus 로고    scopus 로고
    • A protein domain-based interactome network for C. elegans early embryogenesis
    • Boxem M., Maliga Z., Klitgord N., Li N., Lemmens I., Mana M., et al. A protein domain-based interactome network for C. elegans early embryogenesis. Cell 134 (2008) 534-545
    • (2008) Cell , vol.134 , pp. 534-545
    • Boxem, M.1    Maliga, Z.2    Klitgord, N.3    Li, N.4    Lemmens, I.5    Mana, M.6
  • 12
    • 49049114813 scopus 로고    scopus 로고
    • Domains mediate protein-protein interactions and nucleate protein assemblies
    • Costa S., and Cesareni G. Domains mediate protein-protein interactions and nucleate protein assemblies. Handb. Exp. Pharmacol. 186 (2008) 383-405
    • (2008) Handb. Exp. Pharmacol. , vol.186 , pp. 383-405
    • Costa, S.1    Cesareni, G.2
  • 15
    • 0034700087 scopus 로고    scopus 로고
    • A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae
    • Newman J.R., Wolf E., and Kim P.S. A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 97 (2000) 13203-13208
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 13203-13208
    • Newman, J.R.1    Wolf, E.2    Kim, P.S.3
  • 16
    • 30544449081 scopus 로고    scopus 로고
    • A quantitative protein interaction network for the ErbB receptors using protein microarrays
    • Jones R.B., Gordus A., Krall J.A., and MacBeath G. A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439 (2006) 168-174
    • (2006) Nature , vol.439 , pp. 168-174
    • Jones, R.B.1    Gordus, A.2    Krall, J.A.3    MacBeath, G.4
  • 17
    • 0034808117 scopus 로고    scopus 로고
    • Comparing function and structure between entire proteomes
    • Liu J., and Rost B. Comparing function and structure between entire proteomes. Protein Sci. 10 (2001) 1970-1979
    • (2001) Protein Sci. , vol.10 , pp. 1970-1979
    • Liu, J.1    Rost, B.2
  • 18
    • 17444424974 scopus 로고    scopus 로고
    • The structure of alpha-helical coiled coils
    • Lupas A.N., and Gruber M. The structure of alpha-helical coiled coils. Adv. Protein Chem. 70 (2005) 37-78
    • (2005) Adv. Protein Chem. , vol.70 , pp. 37-78
    • Lupas, A.N.1    Gruber, M.2
  • 19
    • 0036558277 scopus 로고    scopus 로고
    • A journey through the exocytic pathway
    • Beraud-Dufour S., and Balch W. A journey through the exocytic pathway. J. Cell Sci. 115 (2002) 1779-1780
    • (2002) J. Cell Sci. , vol.115 , pp. 1779-1780
    • Beraud-Dufour, S.1    Balch, W.2
  • 21
    • 33845704018 scopus 로고    scopus 로고
    • The budding yeast endocytic pathway
    • Toret C.P., and Drubin D.G. The budding yeast endocytic pathway. J. Cell Sci. 119 (2006) 4585-4587
    • (2006) J. Cell Sci. , vol.119 , pp. 4585-4587
    • Toret, C.P.1    Drubin, D.G.2
  • 22
    • 0842324801 scopus 로고    scopus 로고
    • The mechanisms of vesicle budding and fusion
    • Bonifacino J.S., and Glick B.S. The mechanisms of vesicle budding and fusion. Cell 116 (2004) 153-166
    • (2004) Cell , vol.116 , pp. 153-166
    • Bonifacino, J.S.1    Glick, B.S.2
  • 24
    • 0043162027 scopus 로고    scopus 로고
    • Long coiled-coil proteins and membrane traffic
    • Gillingham A.K., and Munro S. Long coiled-coil proteins and membrane traffic. Biochim. Biophys. Acta 1641 (2003) 71-85
    • (2003) Biochim. Biophys. Acta , vol.1641 , pp. 71-85
    • Gillingham, A.K.1    Munro, S.2
  • 25
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25 (2000) 25-29
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5    Cherry, J.M.6
  • 26
    • 9144257282 scopus 로고    scopus 로고
    • The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
    • Ruepp A., Zollner A., Maier D., Albermann K., Hani J., Mokrejs M., et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32 (2004) 5539-5545
    • (2004) Nucleic Acids Res. , vol.32 , pp. 5539-5545
    • Ruepp, A.1    Zollner, A.2    Maier, D.3    Albermann, K.4    Hani, J.5    Mokrejs, M.6
  • 27
    • 32144456009 scopus 로고    scopus 로고
    • Paircoil2: improved prediction of coiled coils from sequence
    • McDonnell A.V., Jiang T., Keating A.E., and Berger B. Paircoil2: improved prediction of coiled coils from sequence. Bioinformatics 22 (2006) 356-358
    • (2006) Bioinformatics , vol.22 , pp. 356-358
    • McDonnell, A.V.1    Jiang, T.2    Keating, A.E.3    Berger, B.4
  • 28
    • 25444434087 scopus 로고    scopus 로고
    • AVID: an integrative framework for discovering functional relationships among proteins
    • Jiang T., and Keating A.E. AVID: an integrative framework for discovering functional relationships among proteins. BMC Bioinformatics 6 (2005) 136
    • (2005) BMC Bioinformatics , vol.6 , pp. 136
    • Jiang, T.1    Keating, A.E.2
  • 29
    • 3042569597 scopus 로고    scopus 로고
    • Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs
    • Yu H., Luscombe N.M., Lu H.X., Zhu X., Xia Y., Han J.D., et al. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 14 (2004) 1107-1118
    • (2004) Genome Res. , vol.14 , pp. 1107-1118
    • Yu, H.1    Luscombe, N.M.2    Lu, H.X.3    Zhu, X.4    Xia, Y.5    Han, J.D.6
  • 30
    • 4143058720 scopus 로고    scopus 로고
    • Predicting specificity in bZIP coiled-coil protein interactions
    • Fong J.H., Keating A.E., and Singh M. Predicting specificity in bZIP coiled-coil protein interactions. Genome Biol. 5 (2004) R11
    • (2004) Genome Biol. , vol.5
    • Fong, J.H.1    Keating, A.E.2    Singh, M.3
  • 32
    • 0024406857 scopus 로고
    • A novel genetic system to detect protein-protein interactions
    • Fields S., and Song O. A novel genetic system to detect protein-protein interactions. Nature 340 (1989) 245-246
    • (1989) Nature , vol.340 , pp. 245-246
    • Fields, S.1    Song, O.2
  • 33
    • 0037595546 scopus 로고    scopus 로고
    • Comprehensive identification of human bZIP interactions with coiled-coil arrays
    • Newman J.R., and Keating A.E. Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science 300 (2003) 2097-2101
    • (2003) Science , vol.300 , pp. 2097-2101
    • Newman, J.R.1    Keating, A.E.2
  • 34
    • 11844252081 scopus 로고    scopus 로고
    • Detecting protein-protein interactions with a green fluorescent protein fragment reassembly: scope and mechanism
    • Magliery T.J., Wilson C.G.M., Pan W., Mishler D., Ghosh I., Hamilton A.D., and Regan L. Detecting protein-protein interactions with a green fluorescent protein fragment reassembly: scope and mechanism. J. Am. Chem. Soc. 127 (2005) 146-157
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 146-157
    • Magliery, T.J.1    Wilson, C.G.M.2    Pan, W.3    Mishler, D.4    Ghosh, I.5    Hamilton, A.D.6    Regan, L.7
  • 35
    • 0037415752 scopus 로고    scopus 로고
    • Retromer and the sorting nexins Snx4/41/42 mediate distinct retrieval pathways from yeast endosomes
    • Hettema E.H., Lewis M.J., Black M.W., and Pelham H.R. Retromer and the sorting nexins Snx4/41/42 mediate distinct retrieval pathways from yeast endosomes. EMBO J. 22 (2003) 548-557
    • (2003) EMBO J. , vol.22 , pp. 548-557
    • Hettema, E.H.1    Lewis, M.J.2    Black, M.W.3    Pelham, H.R.4
  • 36
    • 0037119448 scopus 로고    scopus 로고
    • Cooperative binding of the cytoplasm to vacuole targeting pathway proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-autophagosomal structure is required for selective autophagy
    • Nice D.C., Sato T.K., Stromhaug P.E., Emr S.D., and Klionsky D.J. Cooperative binding of the cytoplasm to vacuole targeting pathway proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-autophagosomal structure is required for selective autophagy. J. Biol. Chem. 277 (2002) 30198-30207
    • (2002) J. Biol. Chem. , vol.277 , pp. 30198-30207
    • Nice, D.C.1    Sato, T.K.2    Stromhaug, P.E.3    Emr, S.D.4    Klionsky, D.J.5
  • 37
    • 0034004749 scopus 로고    scopus 로고
    • The yeast kinesin-related protein Smy1p exerts its effects on the class V myosin Myo2p via a physical interaction
    • Beningo K.A., Lillie S.H., and Brown S.S. The yeast kinesin-related protein Smy1p exerts its effects on the class V myosin Myo2p via a physical interaction. Mol. Biol. Cell 11 (2000) 691-702
    • (2000) Mol. Biol. Cell , vol.11 , pp. 691-702
    • Beningo, K.A.1    Lillie, S.H.2    Brown, S.S.3
  • 38
    • 34247342216 scopus 로고    scopus 로고
    • The emerging shape of the ESCRT machinery
    • Williams R.L., and Urbe S. The emerging shape of the ESCRT machinery. Nat. Rev. Mol. Cell Biol. 8 (2007) 355-368
    • (2007) Nat. Rev. Mol. Cell Biol. , vol.8 , pp. 355-368
    • Williams, R.L.1    Urbe, S.2
  • 40
    • 33646010475 scopus 로고    scopus 로고
    • The ESCRT complexes: structure and mechanism of a membrane-trafficking network
    • Hurley J.H., and Emr S.D. The ESCRT complexes: structure and mechanism of a membrane-trafficking network. Annu. Rev. Biophys. Biomol. Struct. 35 (2006) 277-298
    • (2006) Annu. Rev. Biophys. Biomol. Struct. , vol.35 , pp. 277-298
    • Hurley, J.H.1    Emr, S.D.2
  • 43
    • 0035918302 scopus 로고    scopus 로고
    • Homo- and heterooligomeric SNARE complexes studied by site-directed spin labeling
    • Margittai M., Fasshauer D., Pabst S., Jahn R., and Langen R. Homo- and heterooligomeric SNARE complexes studied by site-directed spin labeling. J. Biol. Chem. 276 (2001) 13169-13177
    • (2001) J. Biol. Chem. , vol.276 , pp. 13169-13177
    • Margittai, M.1    Fasshauer, D.2    Pabst, S.3    Jahn, R.4    Langen, R.5
  • 44
    • 0035798661 scopus 로고    scopus 로고
    • Crystal structure and biophysical properties of a complex between the N-terminal SNARE region of SNAP25 and syntaxin 1a
    • Misura K.M., Gonzalez Jr. L.C., May A.P., Scheller R.H., and Weis W.I. Crystal structure and biophysical properties of a complex between the N-terminal SNARE region of SNAP25 and syntaxin 1a. J. Biol. Chem. 276 (2001) 41301-41309
    • (2001) J. Biol. Chem. , vol.276 , pp. 41301-41309
    • Misura, K.M.1    Gonzalez Jr., L.C.2    May, A.P.3    Scheller, R.H.4    Weis, W.I.5
  • 45
    • 0035918229 scopus 로고    scopus 로고
    • Self-association of the H3 region of syntaxin 1A. Implications for intermediates in SNARE complex assembly
    • Misura K.M., Scheller R.H., and Weis W.I. Self-association of the H3 region of syntaxin 1A. Implications for intermediates in SNARE complex assembly. J. Biol. Chem. 276 (2001) 13273-13282
    • (2001) J. Biol. Chem. , vol.276 , pp. 13273-13282
    • Misura, K.M.1    Scheller, R.H.2    Weis, W.I.3
  • 46
    • 60149107964 scopus 로고    scopus 로고
    • Phylogeny of the SNARE vesicle fusion machinery yields insights into the conservation of the secretory pathway in fungi
    • Kienle N., Kloepper T.H., and Fasshauer D. Phylogeny of the SNARE vesicle fusion machinery yields insights into the conservation of the secretory pathway in fungi. BMC Evol. Biol. 9 (2009) 19
    • (2009) BMC Evol. Biol. , vol.9 , pp. 19
    • Kienle, N.1    Kloepper, T.H.2    Fasshauer, D.3
  • 47
    • 0033749565 scopus 로고    scopus 로고
    • Testing the 3Q:1R "rule": mutational analysis of the ionic "zero" layer in the yeast exocytic SNARE complex reveals no requirement for arginine
    • Katz L., and Brennwald P. Testing the 3Q:1R "rule": mutational analysis of the ionic "zero" layer in the yeast exocytic SNARE complex reveals no requirement for arginine. Mol. Biol. Cell 11 (2000) 3849-3858
    • (2000) Mol. Biol. Cell , vol.11 , pp. 3849-3858
    • Katz, L.1    Brennwald, P.2
  • 48
    • 0034669052 scopus 로고    scopus 로고
    • Exocytosis requires asymmetry in the central layer of the SNARE complex
    • Ossig R., Schmitt H.D., de Groot B., Riedel D., Keranen S., Ronne H., et al. Exocytosis requires asymmetry in the central layer of the SNARE complex. EMBO J. 19 (2000) 6000-6010
    • (2000) EMBO J. , vol.19 , pp. 6000-6010
    • Ossig, R.1    Schmitt, H.D.2    de Groot, B.3    Riedel, D.4    Keranen, S.5    Ronne, H.6
  • 49
    • 16344389389 scopus 로고    scopus 로고
    • Single molecule observation of liposome-bilayer fusion thermally induced by soluble N-ethyl maleimide sensitive-factor attachment protein receptors (SNAREs)
    • Bowen M.E., Weninger K., Brunger A.T., and Chu S. Single molecule observation of liposome-bilayer fusion thermally induced by soluble N-ethyl maleimide sensitive-factor attachment protein receptors (SNAREs). Biophys. J. 87 (2004) 3569-3584
    • (2004) Biophys. J. , vol.87 , pp. 3569-3584
    • Bowen, M.E.1    Weninger, K.2    Brunger, A.T.3    Chu, S.4
  • 51
    • 29444447288 scopus 로고    scopus 로고
    • Structure-based prediction of bZIP partnering specificity
    • Grigoryan G., and Keating A.E. Structure-based prediction of bZIP partnering specificity. J. Mol. Biol. 355 (2006) 1125-1142
    • (2006) J. Mol. Biol. , vol.355 , pp. 1125-1142
    • Grigoryan, G.1    Keating, A.E.2
  • 52
    • 55849119883 scopus 로고    scopus 로고
    • Analysis of coiled-coil interactions between core proteins of the spindle pole body
    • Zizlsperger N., Malashkevich V.N., Pillay S., and Keating A.E. Analysis of coiled-coil interactions between core proteins of the spindle pole body. Biochemistry 47 (2008) 11858-11868
    • (2008) Biochemistry , vol.47 , pp. 11858-11868
    • Zizlsperger, N.1    Malashkevich, V.N.2    Pillay, S.3    Keating, A.E.4
  • 53
    • 49549094267 scopus 로고    scopus 로고
    • Structural specificity in coiled-coil interactions
    • Grigoryan G., and Keating A.E. Structural specificity in coiled-coil interactions. Curr. Opin. Struct. Biol. 18 (2008) 477-483
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 477-483
    • Grigoryan, G.1    Keating, A.E.2
  • 54
    • 0036087548 scopus 로고    scopus 로고
    • Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
    • Dwight S.S., Harris M.A., Dolinski K., Ball C.A., Binkley G., Christie K.R., et al. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30 (2002) 69-72
    • (2002) Nucleic Acids Res. , vol.30 , pp. 69-72
    • Dwight, S.S.1    Harris, M.A.2    Dolinski, K.3    Ball, C.A.4    Binkley, G.5    Christie, K.R.6
  • 57
    • 0037245913 scopus 로고    scopus 로고
    • BIND: the Biomolecular Interaction Network Database
    • Bader G.D., Betel D., and Hogue C.W. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31 (2003) 248-250
    • (2003) Nucleic Acids Res. , vol.31 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.3
  • 62
    • 0035853291 scopus 로고    scopus 로고
    • Socket: a program for identifying and analysing coiled-coil motifs within protein structures
    • Walshaw J., and Woolfson D.N. Socket: a program for identifying and analysing coiled-coil motifs within protein structures. J. Mol. Biol. 307 (2001) 1427-1450
    • (2001) J. Mol. Biol. , vol.307 , pp. 1427-1450
    • Walshaw, J.1    Woolfson, D.N.2
  • 64
    • 0032169688 scopus 로고    scopus 로고
    • PQS: a protein quaternary structure file server
    • Henrick K., and Thornton J.M. PQS: a protein quaternary structure file server. Trends Biochem. Sci. 23 (1998) 358-361
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 67
    • 3242876311 scopus 로고    scopus 로고
    • BLAST: at the core of a powerful and diverse set of sequence analysis tools
    • McGinnis S., and Madden T.L. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32 (2004) W20-W25
    • (2004) Nucleic Acids Res. , vol.32
    • McGinnis, S.1    Madden, T.L.2


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