메뉴 건너뛰기




Volumn 7, Issue , 2011, Pages

The multiple-specificity landscape of modular peptide recognition domains

Author keywords

binding specificity; PDZ; peptide recognition domains; phage display; residue correlations

Indexed keywords

DROSOPHILA PROTEIN; PDZ PROTEIN; PDZ1 PROTEIN; PEPTIDE; PROTEIN DLG1; PROTEIN KINASE; PROTEIN SH3; PROTEIN WW; UNCLASSIFIED DRUG; DLG1 PROTEIN, HUMAN; MEMBRANE PROTEIN; SCRIB PROTEIN, HUMAN; SIGNAL TRANSDUCING ADAPTOR PROTEIN; TUMOR SUPPRESSOR PROTEIN;

EID: 79955569676     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2011.18     Document Type: Article
Times cited : (69)

References (54)
  • 3
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36
    • (1994) Proc Int Conf Intell Syst Mol Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 5
    • 15944375458 scopus 로고    scopus 로고
    • PDZBase: A protein-protein interaction database for PDZ-domains
    • DOI 10.1093/bioinformatics/bti098
    • Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H (2005) PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics 21: 827-828 (Pubitemid 40439423)
    • (2005) Bioinformatics , vol.21 , Issue.6 , pp. 827-828
    • Beuming, T.1    Skrabanek, L.2    Niv, M.Y.3    Mukherjee, P.4    Weinstein, H.5
  • 7
    • 0033579464 scopus 로고    scopus 로고
    • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
    • DOI 10.1006/jmbi.1999.3310
    • Blom N, Gammeltoft S, Brunak S (1999) Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol 294: 1351-1362 (Pubitemid 30008805)
    • (1999) Journal of Molecular Biology , vol.294 , Issue.5 , pp. 1351-1362
    • Blom, N.1    Gammeltoft, S.2    Brunak, S.3
  • 9
    • 0031825709 scopus 로고    scopus 로고
    • Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network
    • Brusic V, Rudy G, Honeyman G, Hammer J, Harrison L (1998) Prediction of MHC class II-binding peptides using an evolutionary algorithmand artificial neural network. Bioinformatics 14: 121-130 (Pubitemid 28395870)
    • (1998) Bioinformatics , vol.14 , Issue.2 , pp. 121-130
    • Brusic, V.1    Rudy, G.2    Honeyman, M.3    Hammer, J.4    Harrison, L.5
  • 13
    • 0030604722 scopus 로고    scopus 로고
    • Crystal structures of a complexed and peptide-free membrane protein- binding domain: Molecular basis of peptide recognition by PDZ
    • DOI 10.1016/S0092-8674(00)81307-0
    • Doyle DA, Lee A, Lewis J, Kim E, Sheng M, MacKinnon R (1996) Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell 85: 1067-1076 (Pubitemid 26231173)
    • (1996) Cell , vol.85 , Issue.7 , pp. 1067-1076
    • Doyle, D.A.1    Lee, A.2    Lewis, J.3    Kim, E.4    Sheng, M.5    MacKinnon, R.6
  • 14
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797 (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 17
    • 0034697980 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
    • Emanuelsson O, Nielsen H, Brunak S, von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016
    • (2000) J Mol Biol , vol.300 , pp. 1005-1016
    • Emanuelsson, O.1    Nielsen, H.2    Brunak, S.3    Von Heijne, G.4
  • 18
    • 77956544553 scopus 로고    scopus 로고
    • Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing
    • Ernst A, Gfeller D, Kan Z, Seshagiri S, Kim PM, Bader GD, Sidhu SS (2010) Coevolution of PDZ domain-ligand interactions analyzed by high-throughput phage display and deep sequencing. Mol Biosyst 6: 1782-1790
    • (2010) Mol Biosyst , vol.6 , pp. 1782-1790
    • Ernst, A.1    Gfeller, D.2    Kan, Z.3    Seshagiri, S.4    Kim, P.M.5    Bader, G.D.6    Sidhu, S.S.7
  • 19
    • 0027962645 scopus 로고
    • Two binding orientations for peptides to the Src SH3 domain: Development of a general model for SH3-ligand interactions
    • Feng S, Chen JK, Yu H, Simon JA, Schreiber SL (1994) Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. Science 18: 1241-1247 (Pubitemid 24371282)
    • (1994) Science , vol.266 , Issue.5188 , pp. 1241-1247
    • Feng, S.1    Chen, J.K.2    Yu, H.3    Simon, J.A.4    Schreiber, S.L.5
  • 23
    • 0030974119 scopus 로고    scopus 로고
    • In vitro selection and evolution of functional proteins by using ribosome display
    • Hanes J, Pluckthun A (1997) In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci USA 94: 4937-4942
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 4937-4942
    • Hanes, J.1    Pluckthun, A.2
  • 24
    • 29144484156 scopus 로고    scopus 로고
    • Enhanced position weight matrices using mixture models
    • DOI 10.1093/bioinformatics/bti1001
    • Hannenhalli S, Wang LS (2005) Enhanced position weight matrices using mixture models. Bioinformatics 21(Suppl 1): i204-i212 (Pubitemid 41794491)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Hannenhalli, S.1    Wang, L.-S.2
  • 25
    • 77952913083 scopus 로고    scopus 로고
    • The plastic energy landscape of protein folding: A triangular folding mechanism with an equilibrium intermediate for a small protein domain
    • Haq SR, Jurgens MC, Chi CN, Koh CS, Elfstrom L, Selmer M, Gianni S, Jemth P (2010) The plastic energy landscape of protein folding: a triangular folding mechanism with an equilibrium intermediate for a small protein domain. J Biol Chem 285: 18051-18059
    • (2010) J Biol Chem , vol.285 , pp. 18051-18059
    • Haq, S.R.1    Jurgens, M.C.2    Chi, C.N.3    Koh, C.S.4    Elfstrom, L.5    Selmer, M.6    Gianni, S.7    Jemth, P.8
  • 26
    • 0034740693 scopus 로고    scopus 로고
    • Mechanisma and role of PDZ domains in signaling complex assembly
    • Harris BZ, Lim WA (2001) Mechanism and role of PDZ domains in signaling complex assembly. J Cell Sci 114: 3219-3231 (Pubitemid 32998900)
    • (2001) Journal of Cell Science , vol.114 , Issue.18 , pp. 3219-3231
    • Harris, B.Z.1    Lim, W.A.2
  • 27
    • 0033617473 scopus 로고    scopus 로고
    • Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex
    • DOI 10.1126/science.284.5415.812
    • Hillier BJ, Christopherson KS, Prehoda KE, Bredt DS, Lim WA (1999) Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. Science 284: 812-815 (Pubitemid 29291348)
    • (1999) Science , vol.284 , Issue.5415 , pp. 812-815
    • Hillier, B.J.1    Christopherson, K.S.2    Prehoda, K.E.3    Bredt, D.S.4    Lim, W.A.5
  • 29
    • 77957737014 scopus 로고    scopus 로고
    • Proteome scanning to predict PDZ domain interactions using support vector machines
    • Hui S, Bader GD (2010) Proteome scanning to predict PDZ domain interactions using support vector machines. BMC Bioinformatics 11: 507
    • (2010) BMC Bioinformatics , vol.11 , pp. 507
    • Hui, S.1    Bader, G.D.2
  • 31
    • 0028148629 scopus 로고
    • Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains
    • DOI 10.1038/372375a0
    • Lim WA, Richards FM, Fox RO (1994) Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature 372: 375-379 (Pubitemid 24363441)
    • (1994) Nature , vol.372 , Issue.6504 , pp. 375-379
    • Lim, W.A.1    Richards, F.M.2    Fox, R.O.3
  • 32
    • 0035030510 scopus 로고    scopus 로고
    • SH3 domains: Complexity in moderation
    • Mayer BJ (2001) SH3 domains: complexity in moderation. J Cell Sci 114: 1253-1263 (Pubitemid 32409462)
    • (2001) Journal of Cell Science , vol.114 , Issue.7 , pp. 1253-1263
    • Mayer, B.J.1
  • 34
    • 0033044637 scopus 로고    scopus 로고
    • Machine learning approaches for the prediction of signal peptides and other protein sorting signals
    • Nielsen H, Brunak S, von Heijne G (1999) Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng 12: 3-9 (Pubitemid 29050535)
    • (1999) Protein Engineering , vol.12 , Issue.1 , pp. 3-9
    • Nielsen, H.1    Brunak, S.2    Von Heijne, G.3
  • 36
    • 0042622251 scopus 로고    scopus 로고
    • Scansite 2.0: Proteome-wide prediction of cell signalling interactions using short sequence motifs
    • DOI 10.1093/nar/gkg584
    • Obenauer JC, Cantley LC, YaffeMB(2003) Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31: 3635-3641 (Pubitemid 37442212)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3635-3641
    • Obenauer, J.C.1    Cantley, L.C.2    Yaffe, M.B.3
  • 39
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • DOI 10.1126/science.1083653
    • Pawson T, Nash P (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300: 445-452 (Pubitemid 36444318)
    • (2003) Science , vol.300 , Issue.5618 , pp. 445-452
    • Pawson, T.1    Nash, P.2
  • 40
    • 7544232779 scopus 로고    scopus 로고
    • Internal recognition through PDZ domain plasticity in the Par-6-Pals1 complex
    • DOI 10.1038/nsmb839
    • Penkert RR, DiVittorio HM, Prehoda KE (2004) Internal recognition through PDZ domain plasticity in the Par-6-Pals1 complex. Nat Struct Mol Biol 11: 1122-1127 (Pubitemid 39453342)
    • (2004) Nature Structural and Molecular Biology , vol.11 , Issue.11 , pp. 1122-1127
    • Penkert, R.R.1    DiVittorio, H.M.2    Prehoda, K.E.3
  • 42
    • 79551614773 scopus 로고    scopus 로고
    • A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence
    • Shao X, Tan CS, Voss C, Li SS, Deng N, Bader GD (2010) A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence. Bioinformatics 27: 383-390
    • (2010) Bioinformatics , vol.27 , pp. 383-390
    • Shao, X.1    Tan, C.S.2    Voss, C.3    Li, S.S.4    Deng, N.5    Bader, G.D.6
  • 43
    • 50949097456 scopus 로고    scopus 로고
    • A feature-based approach to modeling protein-DNA interactions
    • Sharon E, Lubliner S, Segal E (2008) A feature-based approach to modeling protein-DNA interactions. PLoS Comput Biol 4: e1000154
    • (2008) PLoS Comput Biol , vol.4
    • Sharon, E.1    Lubliner, S.2    Segal, E.3
  • 44
    • 77956730468 scopus 로고    scopus 로고
    • Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains
    • Smith CA, Kortemme T (2010) Structure-based prediction of the peptide sequence space recognized by natural and synthetic PDZ domains. J Mol Biol 402: 460-474
    • (2010) J Mol Biol , vol.402 , pp. 460-474
    • Smith, C.A.1    Kortemme, T.2
  • 45
    • 77954249974 scopus 로고    scopus 로고
    • Detecting interactions with membrane proteins using a membrane two-hybrid assay in yeast
    • Snider J, Kittanakom S, Damjanovic D, Curak J, Wong V, Stagljar I (2010) Detecting interactions with membrane proteins using a membrane two-hybrid assay in yeast. Nat Protoc 5: 1281-1293
    • (2010) Nat Protoc , vol.5 , pp. 1281-1293
    • Snider, J.1    Kittanakom, S.2    Damjanovic, D.3    Curak, J.4    Wong, V.5    Stagljar, I.6
  • 50
    • 34250748507 scopus 로고    scopus 로고
    • Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries
    • DOI 10.1038/nprot.2007.151, PII NPROT.2007.151
    • Tonikian R, Zhang Y, Boone C, Sidhu SS (2007) Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries. Nat Protoc 2: 1368-1386 (Pubitemid 46952319)
    • (2007) Nature Protocols , vol.2 , Issue.6 , pp. 1368-1386
    • Tonikian, R.1    Zhang, Y.2    Boone, C.3    Sidhu, S.S.4
  • 52
    • 34548861782 scopus 로고    scopus 로고
    • Protein-protein docking with backbone flexibility
    • DOI 10.1016/j.jmb.2007.07.050, PII S0022283607010030
    • Wang C, Bradley P, Baker D (2007) Protein-protein docking with backbone flexibility. J Mol Biol 373: 503-519 (Pubitemid 47445567)
    • (2007) Journal of Molecular Biology , vol.373 , Issue.2 , pp. 503-519
    • Wang, C.1    Bradley, P.2    Baker, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.