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Volumn 7, Issue 5, 2012, Pages

Peptide array X-linking (PAX): A new peptide-protein identification approach

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANALYTIC METHOD; ANIMAL CELL; ARTICLE; CONTROLLED STUDY; IMMUNOPRECIPITATION; LIQUID CHROMATOGRAPHY; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTIDE ARRAY X LINKING; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CROSS LINKING; PROTEIN DENATURATION; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN SYNTHESIS; SEQUENCE HOMOLOGY; TANDEM MASS SPECTROMETRY; ANIMAL; BRAIN LEVEL; CHEMISTRY; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PEPTIDE LIBRARY; PROTEOMICS;

EID: 84861013042     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037035     Document Type: Article
Times cited : (15)

References (50)
  • 1
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • Pawson T, Nash P, (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300: 445-452.
    • (2003) Science , vol.300 , pp. 445-452
    • Pawson, T.1    Nash, P.2
  • 4
    • 2542463049 scopus 로고    scopus 로고
    • Selectivity and promiscuity in the interaction network mediated by protein recognition modules
    • Castagnoli L, Costantini A, Dall'Armi C, Gonfloni S, Montecchi-Palazzi L, et al. (2004) Selectivity and promiscuity in the interaction network mediated by protein recognition modules. FEBS letters 567: 74-79.
    • (2004) FEBS Letters , vol.567 , pp. 74-79
    • Castagnoli, L.1    Costantini, A.2    Dall'Armi, C.3    Gonfloni, S.4    Montecchi-Palazzi, L.5
  • 5
    • 33845729059 scopus 로고    scopus 로고
    • The WASP-WAVE protein network: connecting the membrane to the cytoskeleton
    • Takenawa T, Suetsugu S, (2007) The WASP-WAVE protein network: connecting the membrane to the cytoskeleton. Nat Rev Mol Cell Biol 8: 37-48.
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 37-48
    • Takenawa, T.1    Suetsugu, S.2
  • 6
    • 77949834455 scopus 로고    scopus 로고
    • A nucleator arms race: cellular control of actin assembly
    • Campellone KG, Welch MD, (2010) A nucleator arms race: cellular control of actin assembly. Nat Rev Mol Cell Biol 11: 237-251.
    • (2010) Nat Rev Mol Cell Biol , vol.11 , pp. 237-251
    • Campellone, K.G.1    Welch, M.D.2
  • 7
    • 0037138411 scopus 로고    scopus 로고
    • WW and SH3 domains, two different scaffolds to recognize proline-rich ligands
    • Macias MJ, Wiesner S, Sudol M, (2002) WW and SH3 domains, two different scaffolds to recognize proline-rich ligands. FEBS letters 513: 30-37.
    • (2002) FEBS Letters , vol.513 , pp. 30-37
    • Macias, M.J.1    Wiesner, S.2    Sudol, M.3
  • 8
    • 24044540256 scopus 로고    scopus 로고
    • Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction
    • Li SS, (2005) Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction. Biochem J 390: 641-653.
    • (2005) Biochem J , vol.390 , pp. 641-653
    • Li, S.S.1
  • 9
    • 0036469131 scopus 로고    scopus 로고
    • Doing (F/L)PPPPs: EVH1 domains and their proline-rich partners in cell polarity and migration
    • Renfranz PJ, Beckerle MC, (2002) Doing (F/L)PPPPs: EVH1 domains and their proline-rich partners in cell polarity and migration. Current opinion in cell biology 14: 88-103.
    • (2002) Current Opinion in Cell Biology , vol.14 , pp. 88-103
    • Renfranz, P.J.1    Beckerle, M.C.2
  • 11
    • 79959424627 scopus 로고    scopus 로고
    • Quantitative, high-resolution proteomics for data-driven systems biology
    • Cox J, Mann M, (2011) Quantitative, high-resolution proteomics for data-driven systems biology. Annual review of biochemistry 80: 273-299.
    • (2011) Annual Review of Biochemistry , vol.80 , pp. 273-299
    • Cox, J.1    Mann, M.2
  • 13
    • 0023006043 scopus 로고
    • p-Benzoyl-L-phenylalanine, a new photoreactive amino acid. Photolabeling of calmodulin with a synthetic calmodulin-binding peptide
    • Kauer JC, Erickson-Viitanen S, Wolfe HR Jr, DeGrado WF, (1986) p-Benzoyl-L-phenylalanine, a new photoreactive amino acid. Photolabeling of calmodulin with a synthetic calmodulin-binding peptide. J Biol Chem 261: 10695-10700.
    • (1986) J Biol Chem , vol.261 , pp. 10695-10700
    • Kauer, J.C.1    Erickson-Viitanen, S.2    Wolfe Jr., H.R.3    DeGrado, W.F.4
  • 14
    • 0024384873 scopus 로고
    • Photolabeling of calmodulin with basic, amphiphilic alpha-helical peptides containing p-benzoylphenylalanine
    • O'Neil KT, Erickson-Viitanen S, DeGrado WF, (1989) Photolabeling of calmodulin with basic, amphiphilic alpha-helical peptides containing p-benzoylphenylalanine. J Biol Chem 264: 14571-14578.
    • (1989) J Biol Chem , vol.264 , pp. 14571-14578
    • O'Neil, K.T.1    Erickson-Viitanen, S.2    DeGrado, W.F.3
  • 15
    • 0036849244 scopus 로고    scopus 로고
    • Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells
    • Sakamoto K, Hayashi A, Sakamoto A, Kiga D, Nakayama H, et al. (2002) Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res 30: 4692-4699.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4692-4699
    • Sakamoto, K.1    Hayashi, A.2    Sakamoto, A.3    Kiga, D.4    Nakayama, H.5
  • 16
    • 18744396951 scopus 로고    scopus 로고
    • Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid
    • Hino N, Okazaki Y, Kobayashi T, Hayashi A, Sakamoto K, et al. (2005) Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid. Nat Methods 2: 201-206.
    • (2005) Nat Methods , vol.2 , pp. 201-206
    • Hino, N.1    Okazaki, Y.2    Kobayashi, T.3    Hayashi, A.4    Sakamoto, K.5
  • 17
    • 23644445334 scopus 로고    scopus 로고
    • Photo-cross-linking interacting proteins with a genetically encoded benzophenone
    • Farrell IS, Toroney R, Hazen JL, Mehl RA, Chin JW, (2005) Photo-cross-linking interacting proteins with a genetically encoded benzophenone. Nat Methods 2: 377-384.
    • (2005) Nat Methods , vol.2 , pp. 377-384
    • Farrell, I.S.1    Toroney, R.2    Hazen, J.L.3    Mehl, R.A.4    Chin, J.W.5
  • 18
    • 34547502435 scopus 로고    scopus 로고
    • Genetically encoding unnatural amino acids for cellular and neuronal studies
    • Wang W, Takimoto JK, Louie GV, Baiga TJ, Noel JP, et al. (2007) Genetically encoding unnatural amino acids for cellular and neuronal studies. Nat Neurosci 10: 1063-1072.
    • (2007) Nat Neurosci , vol.10 , pp. 1063-1072
    • Wang, W.1    Takimoto, J.K.2    Louie, G.V.3    Baiga, T.J.4    Noel, J.P.5
  • 19
    • 33847648384 scopus 로고    scopus 로고
    • Genetic incorporation of unnatural amino acids into proteins in mammalian cells
    • Liu W, Brock A, Chen S, Schultz PG, (2007) Genetic incorporation of unnatural amino acids into proteins in mammalian cells. Nat Methods 4: 239-244.
    • (2007) Nat Methods , vol.4 , pp. 239-244
    • Liu, W.1    Brock, A.2    Chen, S.3    Schultz, P.G.4
  • 20
    • 82555191167 scopus 로고    scopus 로고
    • SH3 domain-based phototrapping in living cells reveals Rho family GAP signaling complexes
    • Okada H, Uezu A, Mason FM, Soderblom EJ, Moseley MA, 3rd, et al. (2011) SH3 domain-based phototrapping in living cells reveals Rho family GAP signaling complexes. Science signaling 4: rs13.
    • (2011) Science Signaling , vol.4
    • Okada, H.1    Uezu, A.2    Mason, F.M.3    Soderblom, E.J.4    Moseley 3rd, M.A.5
  • 21
    • 0036903024 scopus 로고    scopus 로고
    • The WRP component of the WAVE-1 complex attenuates Rac-mediated signalling
    • Soderling SH, Binns KL, Wayman GA, Davee SM, Ong SH, et al. (2002) The WRP component of the WAVE-1 complex attenuates Rac-mediated signalling. Nat Cell Biol 4: 970-975.
    • (2002) Nat Cell Biol , vol.4 , pp. 970-975
    • Soderling, S.H.1    Binns, K.L.2    Wayman, G.A.3    Davee, S.M.4    Ong, S.H.5
  • 23
    • 0033679292 scopus 로고    scopus 로고
    • Structure of the Homer EVH1 domain-peptide complex reveals a new twist in polyproline recognition
    • Beneken J, Tu JC, Xiao B, Nuriya M, Yuan JP, et al. (2000) Structure of the Homer EVH1 domain-peptide complex reveals a new twist in polyproline recognition. Neuron 26: 143-154.
    • (2000) Neuron , vol.26 , pp. 143-154
    • Beneken, J.1    Tu, J.C.2    Xiao, B.3    Nuriya, M.4    Yuan, J.P.5
  • 24
    • 0028675698 scopus 로고
    • NMR structure of the N-terminal SH3 domain of GRB2 and its complex with a proline-rich peptide from Sos
    • Goudreau N, Cornille F, Duchesne M, Parker F, Tocque B, et al. (1994) NMR structure of the N-terminal SH3 domain of GRB2 and its complex with a proline-rich peptide from Sos. Nature structural biology 1: 898-907.
    • (1994) Nature Structural Biology , vol.1 , pp. 898-907
    • Goudreau, N.1    Cornille, F.2    Duchesne, M.3    Parker, F.4    Tocque, B.5
  • 25
    • 0028675576 scopus 로고
    • Structure of the N-terminal SH3 domain of GRB2 complexed with a peptide from the guanine nucleotide releasing factor Sos
    • Terasawa H, Kohda D, Hatanaka H, Tsuchiya S, Ogura K, et al. (1994) Structure of the N-terminal SH3 domain of GRB2 complexed with a peptide from the guanine nucleotide releasing factor Sos. Nature structural biology 1: 891-897.
    • (1994) Nature Structural Biology , vol.1 , pp. 891-897
    • Terasawa, H.1    Kohda, D.2    Hatanaka, H.3    Tsuchiya, S.4    Ogura, K.5
  • 26
    • 38949137887 scopus 로고    scopus 로고
    • Structure of the Eps15-stonin2 complex provides a molecular explanation for EH-domain ligand specificity
    • Rumpf J, Simon B, Jung N, Maritzen T, Haucke V, et al. (2008) Structure of the Eps15-stonin2 complex provides a molecular explanation for EH-domain ligand specificity. The EMBO journal 27: 558-569.
    • (2008) The EMBO Journal , vol.27 , pp. 558-569
    • Rumpf, J.1    Simon, B.2    Jung, N.3    Maritzen, T.4    Haucke, V.5
  • 27
    • 17544384658 scopus 로고    scopus 로고
    • The endocytic protein intersectin is a major binding partner for the Ras exchange factor mSos1 in rat brain
    • Tong XK, Hussain NK, de Heuvel E, Kurakin A, Abi-Jaoude E, et al. (2000) The endocytic protein intersectin is a major binding partner for the Ras exchange factor mSos1 in rat brain. The EMBO journal 19: 1263-1271.
    • (2000) The EMBO Journal , vol.19 , pp. 1263-1271
    • Tong, X.K.1    Hussain, N.K.2    de Heuvel, E.3    Kurakin, A.4    Abi-Jaoude, E.5
  • 29
    • 0032552056 scopus 로고    scopus 로고
    • Epsin is an EH-domain-binding protein implicated in clathrin-mediated endocytosis
    • Chen H, Fre S, Slepnev VI, Capua MR, Takei K, et al. (1998) Epsin is an EH-domain-binding protein implicated in clathrin-mediated endocytosis. Nature 394: 793-797.
    • (1998) Nature , vol.394 , pp. 793-797
    • Chen, H.1    Fre, S.2    Slepnev, V.I.3    Capua, M.R.4    Takei, K.5
  • 30
    • 0031008152 scopus 로고    scopus 로고
    • A new member of the amphiphysin family connecting endocytosis and signal transduction pathways
    • Leprince C, Romero F, Cussac D, Vayssiere B, Berger R, et al. (1997) A new member of the amphiphysin family connecting endocytosis and signal transduction pathways. The Journal of biological chemistry 272: 15101-15105.
    • (1997) The Journal of Biological Chemistry , vol.272 , pp. 15101-15105
    • Leprince, C.1    Romero, F.2    Cussac, D.3    Vayssiere, B.4    Berger, R.5
  • 31
    • 33846196143 scopus 로고    scopus 로고
    • A WAVE-1 and WRP signaling complex regulates spine density, synaptic plasticity, and memory
    • Soderling SH, Guire ES, Kaech S, White J, Zhang F, et al. (2007) A WAVE-1 and WRP signaling complex regulates spine density, synaptic plasticity, and memory. J Neurosci 27: 355-365.
    • (2007) J Neurosci , vol.27 , pp. 355-365
    • Soderling, S.H.1    Guire, E.S.2    Kaech, S.3    White, J.4    Zhang, F.5
  • 32
    • 0035002333 scopus 로고    scopus 로고
    • N-WASP, WAVE and Mena play different roles in the organization of actin cytoskeleton in lamellipodia
    • Nakagawa H, Miki H, Ito M, Ohashi K, Takenawa T, et al. (2001) N-WASP, WAVE and Mena play different roles in the organization of actin cytoskeleton in lamellipodia. Journal of cell science 114: 1555-1565.
    • (2001) Journal of Cell Science , vol.114 , pp. 1555-1565
    • Nakagawa, H.1    Miki, H.2    Ito, M.3    Ohashi, K.4    Takenawa, T.5
  • 33
    • 0037305940 scopus 로고    scopus 로고
    • Functional genomics of intracellular peptide recognition domains with combinatorial biology methods
    • Sidhu SS, Bader GD, Boone C, (2003) Functional genomics of intracellular peptide recognition domains with combinatorial biology methods. Current opinion in chemical biology 7: 97-102.
    • (2003) Current Opinion in Chemical Biology , vol.7 , pp. 97-102
    • Sidhu, S.S.1    Bader, G.D.2    Boone, C.3
  • 35
    • 34250379613 scopus 로고    scopus 로고
    • Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening
    • Wu C, Ma MH, Brown KR, Geisler M, Li L, et al. (2007) Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. Proteomics 7: 1775-1785.
    • (2007) Proteomics , vol.7 , pp. 1775-1785
    • Wu, C.1    Ma, M.H.2    Brown, K.R.3    Geisler, M.4    Li, L.5
  • 36
    • 70350404403 scopus 로고    scopus 로고
    • Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
    • Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, et al. (2009) Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol 7: e1000218.
    • (2009) PLoS Biol , vol.7
    • Tonikian, R.1    Xin, X.2    Toret, C.P.3    Gfeller, D.4    Landgraf, C.5
  • 37
    • 68949183227 scopus 로고    scopus 로고
    • Ena/VASP: towards resolving a pointed controversy at the barbed end
    • Bear JE, Gertler FB, (2009) Ena/VASP: towards resolving a pointed controversy at the barbed end. Journal of cell science 122: 1947-1953.
    • (2009) Journal of Cell Science , vol.122 , pp. 1947-1953
    • Bear, J.E.1    Gertler, F.B.2
  • 38
    • 0037459075 scopus 로고    scopus 로고
    • Cellular motility driven by assembly and disassembly of actin filaments
    • Pollard TD, Borisy GG, (2003) Cellular motility driven by assembly and disassembly of actin filaments. Cell 112: 453-465.
    • (2003) Cell , vol.112 , pp. 453-465
    • Pollard, T.D.1    Borisy, G.G.2
  • 39
    • 46449098660 scopus 로고    scopus 로고
    • WAVE and Arp2/3 jointly inhibit filopodium formation by entering into a complex with mDia2
    • Beli P, Mascheroni D, Xu D, Innocenti M, (2008) WAVE and Arp2/3 jointly inhibit filopodium formation by entering into a complex with mDia2. Nat Cell Biol 10: 849-857.
    • (2008) Nat Cell Biol , vol.10 , pp. 849-857
    • Beli, P.1    Mascheroni, D.2    Xu, D.3    Innocenti, M.4
  • 40
    • 0034705317 scopus 로고    scopus 로고
    • Negative regulation of fibroblast motility by Ena/VASP proteins
    • Bear JE, Loureiro JJ, Libova I, Fassler R, Wehland J, et al. (2000) Negative regulation of fibroblast motility by Ena/VASP proteins. Cell 101: 717-728.
    • (2000) Cell , vol.101 , pp. 717-728
    • Bear, J.E.1    Loureiro, J.J.2    Libova, I.3    Fassler, R.4    Wehland, J.5
  • 41
    • 0034282711 scopus 로고    scopus 로고
    • Scar/WAVE-1, a Wiskott-Aldrich syndrome protein, assembles an actin-associated multi-kinase scaffold
    • Westphal RS, Soderling SH, Alto NM, Langeberg LK, Scott JD, (2000) Scar/WAVE-1, a Wiskott-Aldrich syndrome protein, assembles an actin-associated multi-kinase scaffold. Embo J 19: 4589-4600.
    • (2000) Embo J , vol.19 , pp. 4589-4600
    • Westphal, R.S.1    Soderling, S.H.2    Alto, N.M.3    Langeberg, L.K.4    Scott, J.D.5
  • 42
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller A, Nesvizhskii AI, Kolker E, Aebersold R, (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74: 5383-5392.
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 43
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii AI, Keller A, Kolker E, Aebersold R, (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75: 4646-4658.
    • (2003) Anal Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 45
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • Liu H, Sadygov RG, Yates JR, 3rd, (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76: 4193-4201.
    • (2004) Anal Chem , vol.76 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates 3rd, J.R.3
  • 46
    • 77949695293 scopus 로고    scopus 로고
    • Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies
    • Searle BC, (2010) Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies. Proteomics 10: 1265-1269.
    • (2010) Proteomics , vol.10 , pp. 1265-1269
    • Searle, B.C.1
  • 48
    • 9444225935 scopus 로고    scopus 로고
    • Java Treeview-extensible visualization of microarray data
    • Saldanha AJ, (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
    • (2004) Bioinformatics , vol.20 , pp. 3246-3248
    • Saldanha, A.J.1
  • 49
    • 78651324347 scopus 로고    scopus 로고
    • The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
    • Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2010) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-568.
    • (2010) Nucleic Acids Res , vol.39
    • Szklarczyk, D.1    Franceschini, A.2    Kuhn, M.3    Simonovic, M.4    Roth, A.5
  • 50
    • 0030592559 scopus 로고    scopus 로고
    • Mena, a relative of VASP and Drosophila Enabled, is implicated in the control of microfilament dynamics
    • Gertler FB, Niebuhr K, Reinhard M, Wehland J, Soriano P, (1996) Mena, a relative of VASP and Drosophila Enabled, is implicated in the control of microfilament dynamics. Cell 87: 227-239.
    • (1996) Cell , vol.87 , pp. 227-239
    • Gertler, F.B.1    Niebuhr, K.2    Reinhard, M.3    Wehland, J.4    Soriano, P.5


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