메뉴 건너뛰기




Volumn 55, Issue 2, 2014, Pages 161-169

A Million peptide motifs for the molecular biologist

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEOME;

EID: 84904469894     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2014.05.032     Document Type: Review
Times cited : (386)

References (80)
  • 1
    • 5044235050 scopus 로고    scopus 로고
    • Ten thousand interactions for the molecular biologist
    • Aloy P., Russell R.B. Ten thousand interactions for the molecular biologist. Nat. Biotechnol. 2004, 22:1317-1321.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1317-1321
    • Aloy, P.1    Russell, R.B.2
  • 2
    • 84866463338 scopus 로고    scopus 로고
    • Structural biology. Versatility from protein disorder
    • Babu M.M., Kriwacki R.W., Pappu R.V. Structural biology. Versatility from protein disorder. Science 2012, 337:1460-1461.
    • (2012) Science , vol.337 , pp. 1460-1461
    • Babu, M.M.1    Kriwacki, R.W.2    Pappu, R.V.3
  • 6
    • 84902031172 scopus 로고    scopus 로고
    • Evolution and functional cross-talk of protein post-translational modifications
    • Beltrao P., Bork P., Krogan N.J., van Noort V. Evolution and functional cross-talk of protein post-translational modifications. Mol. Syst. Biol. 2013, 9:714.
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 714
    • Beltrao, P.1    Bork, P.2    Krogan, N.J.3    van Noort, V.4
  • 7
    • 33746363486 scopus 로고    scopus 로고
    • Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits
    • Bhattacharyya R.P., Reményi A., Yeh B.J., Lim W.A. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu. Rev. Biochem. 2006, 75:655-680.
    • (2006) Annu. Rev. Biochem. , vol.75 , pp. 655-680
    • Bhattacharyya, R.P.1    Reményi, A.2    Yeh, B.J.3    Lim, W.A.4
  • 8
    • 84878437599 scopus 로고    scopus 로고
    • Functional diversity and structural disorder in the human ubiquitination pathway
    • Bhowmick P., Pancsa R., Guharoy M., Tompa P. Functional diversity and structural disorder in the human ubiquitination pathway. PLoS ONE 2013, 8:e65443.
    • (2013) PLoS ONE , vol.8
    • Bhowmick, P.1    Pancsa, R.2    Guharoy, M.3    Tompa, P.4
  • 9
    • 34250865564 scopus 로고    scopus 로고
    • CDC25 phosphatases in cancer cells: key players? Good targets?
    • Boutros R., Lobjois V., Ducommun B. CDC25 phosphatases in cancer cells: key players? Good targets?. Nat. Rev. Cancer 2007, 7:495-507.
    • (2007) Nat. Rev. Cancer , vol.7 , pp. 495-507
    • Boutros, R.1    Lobjois, V.2    Ducommun, B.3
  • 10
    • 84862992463 scopus 로고    scopus 로고
    • Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks
    • Buljan M., Chalancon G., Eustermann S., Wagner G.P., Fuxreiter M., Bateman A., Babu M.M. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol. Cell 2012, 46:871-883.
    • (2012) Mol. Cell , vol.46 , pp. 871-883
    • Buljan, M.1    Chalancon, G.2    Eustermann, S.3    Wagner, G.P.4    Fuxreiter, M.5    Bateman, A.6    Babu, M.M.7
  • 12
    • 36749037699 scopus 로고    scopus 로고
    • Mining alpha-helix-forming molecular recognition features with cross species sequence alignments
    • Cheng Y., Oldfield C.J., Meng J., Romero P., Uversky V.N., Dunker A.K. Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry 2007, 46:13468-13477.
    • (2007) Biochemistry , vol.46 , pp. 13468-13477
    • Cheng, Y.1    Oldfield, C.J.2    Meng, J.3    Romero, P.4    Uversky, V.N.5    Dunker, A.K.6
  • 13
    • 0027122748 scopus 로고
    • Proteins. One thousand families for the molecular biologist
    • Chothia C. Proteins. One thousand families for the molecular biologist. Nature 1992, 357:543-544.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 14
    • 77952956167 scopus 로고    scopus 로고
    • Decoding signalling networks by mass spectrometry-based proteomics
    • Choudhary C., Mann M. Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. Mol. Cell Biol. 2010, 11:427-439.
    • (2010) Nat. Rev. Mol. Cell Biol. , vol.11 , pp. 427-439
    • Choudhary, C.1    Mann, M.2
  • 16
    • 84870600202 scopus 로고    scopus 로고
    • SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions
    • Davey N.E., Cowan J.L., Shields D.C., Gibson T.J., Coldwell M.J., Edwards R.J. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic Acids Res. 2012, 40:10628-10641.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 10628-10641
    • Davey, N.E.1    Cowan, J.L.2    Shields, D.C.3    Gibson, T.J.4    Coldwell, M.J.5    Edwards, R.J.6
  • 20
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • Dyson H.J., Wright P.E. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 2005, 6:197-208.
    • (2005) Nat. Rev. Mol. Cell Biol. , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 23
    • 2142757231 scopus 로고    scopus 로고
    • Preformed structural elements feature in partner recognition by intrinsically unstructured proteins
    • Fuxreiter M., Simon I., Friedrich P., Tompa P. Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J.Mol. Biol. 2004, 338:1015-1026.
    • (2004) J.Mol. Biol. , vol.338 , pp. 1015-1026
    • Fuxreiter, M.1    Simon, I.2    Friedrich, P.3    Tompa, P.4
  • 24
    • 34249695447 scopus 로고    scopus 로고
    • Local structural disorder imparts plasticity on linear motifs
    • Fuxreiter M., Tompa P., Simon I. Local structural disorder imparts plasticity on linear motifs. Bioinformatics 2007, 23:950-956.
    • (2007) Bioinformatics , vol.23 , pp. 950-956
    • Fuxreiter, M.1    Tompa, P.2    Simon, I.3
  • 25
    • 47649102449 scopus 로고    scopus 로고
    • Regulation of cell division by intrinsically unstructured proteins: intrinsic flexibility, modularity, and signaling conduits
    • Galea C.A., Wang Y., Sivakolundu S.G., Kriwacki R.W. Regulation of cell division by intrinsically unstructured proteins: intrinsic flexibility, modularity, and signaling conduits. Biochemistry 2008, 47:7598-7609.
    • (2008) Biochemistry , vol.47 , pp. 7598-7609
    • Galea, C.A.1    Wang, Y.2    Sivakolundu, S.G.3    Kriwacki, R.W.4
  • 26
    • 84881437733 scopus 로고    scopus 로고
    • The transience of transient overexpression
    • Gibson T.J., Seiler M., Veitia R.A. The transience of transient overexpression. Nat. Methods 2013, 10:715-721.
    • (2013) Nat. Methods , vol.10 , pp. 715-721
    • Gibson, T.J.1    Seiler, M.2    Veitia, R.A.3
  • 27
    • 79958071006 scopus 로고    scopus 로고
    • Attributing functions to genes and gene products
    • Greenspan N.S. Attributing functions to genes and gene products. Trends Biochem. Sci. 2011, 36:293-297.
    • (2011) Trends Biochem. Sci. , vol.36 , pp. 293-297
    • Greenspan, N.S.1
  • 28
    • 83255171058 scopus 로고    scopus 로고
    • Structural basis and sequence rules for substrate recognition by Tankyrase explain the basis for cherubism disease
    • Guettler S., LaRose J., Petsalaki E., Gish G., Scotter A., Pawson T., Rottapel R., Sicheri F. Structural basis and sequence rules for substrate recognition by Tankyrase explain the basis for cherubism disease. Cell 2011, 147:1340-1354.
    • (2011) Cell , vol.147 , pp. 1340-1354
    • Guettler, S.1    LaRose, J.2    Petsalaki, E.3    Gish, G.4    Scotter, A.5    Pawson, T.6    Rottapel, R.7    Sicheri, F.8
  • 29
    • 84902318220 scopus 로고    scopus 로고
    • Use of host-like peptide motifs in viral proteins is a prevalent strategy in host-virus interactions
    • Hagai T., Azia A., Babu M.M., Andino R. Use of host-like peptide motifs in viral proteins is a prevalent strategy in host-virus interactions. Cell Rep 2014, 7:1729-1739.
    • (2014) Cell Rep , vol.7 , pp. 1729-1739
    • Hagai, T.1    Azia, A.2    Babu, M.M.3    Andino, R.4
  • 30
    • 33847744247 scopus 로고    scopus 로고
    • How complete are current yeast and human protein-interaction networks?
    • Hart G.T., Ramani A.K., Marcotte E.M. How complete are current yeast and human protein-interaction networks?. Genome Biol. 2006, 7:120.
    • (2006) Genome Biol. , vol.7 , pp. 120
    • Hart, G.T.1    Ramani, A.K.2    Marcotte, E.M.3
  • 33
    • 47549083849 scopus 로고    scopus 로고
    • Positive feedback sharpens the anaphase switch
    • Holt L.J., Krutchinsky A.N., Morgan D.O. Positive feedback sharpens the anaphase switch. Nature 2008, 454:353-357.
    • (2008) Nature , vol.454 , pp. 353-357
    • Holt, L.J.1    Krutchinsky, A.N.2    Morgan, D.O.3
  • 34
    • 70349546862 scopus 로고    scopus 로고
    • Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution
    • Holt L.J., Tuch B.B., Villén J., Johnson A.D., Gygi S.P., Morgan D.O. Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science 2009, 325:1682-1686.
    • (2009) Science , vol.325 , pp. 1682-1686
    • Holt, L.J.1    Tuch, B.B.2    Villén, J.3    Johnson, A.D.4    Gygi, S.P.5    Morgan, D.O.6
  • 35
    • 84857047339 scopus 로고    scopus 로고
    • PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
    • Hornbeck P.V., Kornhauser J.M., Tkachev S., Zhang B., Skrzypek E., Murray B., Latham V., Sullivan M. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2012, 40(Database issue):D261-D270.
    • (2012) Nucleic Acids Res. , vol.40
    • Hornbeck, P.V.1    Kornhauser, J.M.2    Tkachev, S.3    Zhang, B.4    Skrzypek, E.5    Murray, B.6    Latham, V.7    Sullivan, M.8
  • 36
    • 1042275615 scopus 로고    scopus 로고
    • Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry
    • Jensen O.N. Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr. Opin. Chem. Biol. 2004, 8:33-41.
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 33-41
    • Jensen, O.N.1
  • 37
  • 42
    • 84862642911 scopus 로고    scopus 로고
    • High-throughput analysis of peptide-binding modules
    • Liu B.A., Engelmann B.W., Nash P.D. High-throughput analysis of peptide-binding modules. Proteomics 2012, 12:1527-1546.
    • (2012) Proteomics , vol.12 , pp. 1527-1546
    • Liu, B.A.1    Engelmann, B.W.2    Nash, P.D.3
  • 43
    • 52649141086 scopus 로고    scopus 로고
    • Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini
    • Mahrus S., Trinidad J.C., Barkan D.T., Sali A., Burlingame A.L., Wells J.A. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 2008, 134:866-876.
    • (2008) Cell , vol.134 , pp. 866-876
    • Mahrus, S.1    Trinidad, J.C.2    Barkan, D.T.3    Sali, A.4    Burlingame, A.L.5    Wells, J.A.6
  • 45
    • 0037334895 scopus 로고    scopus 로고
    • One-thousand-and-one substrates of protein kinase CK2?
    • Meggio F., Pinna L.A. One-thousand-and-one substrates of protein kinase CK2?. FASEB J. 2003, 17:349-368.
    • (2003) FASEB J. , vol.17 , pp. 349-368
    • Meggio, F.1    Pinna, L.A.2
  • 46
    • 67049119327 scopus 로고    scopus 로고
    • Prediction of protein binding regions in disordered proteins
    • Mészáros B., Simon I., Dosztányi Z. Prediction of protein binding regions in disordered proteins. PLoS Comput. Biol. 2009, 5:e1000376.
    • (2009) PLoS Comput. Biol. , vol.5
    • Mészáros, B.1    Simon, I.2    Dosztányi, Z.3
  • 48
    • 84862987797 scopus 로고    scopus 로고
    • The role of structural disorder in the rewiring of protein interactions through evolution
    • Mosca R., Pache R.A., Aloy P. The role of structural disorder in the rewiring of protein interactions through evolution. Mol. Cell. Proteomics 2012, 11:014969.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 014969
    • Mosca, R.1    Pache, R.A.2    Aloy, P.3
  • 49
    • 20444414545 scopus 로고    scopus 로고
    • Linear motifs: evolutionary interaction switches
    • Neduva V., Russell R.B. Linear motifs: evolutionary interaction switches. FEBS Lett. 2005, 579:3342-3345.
    • (2005) FEBS Lett. , vol.579 , pp. 3342-3345
    • Neduva, V.1    Russell, R.B.2
  • 50
    • 33748953868 scopus 로고    scopus 로고
    • Peptides mediating interaction networks: new leads at last
    • Neduva V., Russell R.B. Peptides mediating interaction networks: new leads at last. Curr. Opin. Biotechnol. 2006, 17:465-471.
    • (2006) Curr. Opin. Biotechnol. , vol.17 , pp. 465-471
    • Neduva, V.1    Russell, R.B.2
  • 51
    • 82955239916 scopus 로고    scopus 로고
    • Phosphorylation in protein-protein binding: effect on stability and function
    • Nishi H., Hashimoto K., Panchenko A.R. Phosphorylation in protein-protein binding: effect on stability and function. Structure 2011, 19:1807-1815.
    • (2011) Structure , vol.19 , pp. 1807-1815
    • Nishi, H.1    Hashimoto, K.2    Panchenko, A.R.3
  • 52
    • 82655175478 scopus 로고    scopus 로고
    • Is there a biological cost of protein disorder? Analysis of cancer-associated mutations
    • Pajkos M., Mészáros B., Simon I., Dosztányi Z. Is there a biological cost of protein disorder? Analysis of cancer-associated mutations. Mol. Biosyst. 2012, 8:296-307.
    • (2012) Mol. Biosyst. , vol.8 , pp. 296-307
    • Pajkos, M.1    Mészáros, B.2    Simon, I.3    Dosztányi, Z.4
  • 53
    • 33745314092 scopus 로고    scopus 로고
    • Genetics: what is a gene?
    • Pearson H. Genetics: what is a gene?. Nature 2006, 441:398-401.
    • (2006) Nature , vol.441 , pp. 398-401
    • Pearson, H.1
  • 55
    • 77957771797 scopus 로고    scopus 로고
    • Transient protein-protein interactions: structural, functional, and network properties
    • Perkins J.R., Diboun I., Dessailly B.H., Lees J.G., Orengo C. Transient protein-protein interactions: structural, functional, and network properties. Structure 2010, 18:1233-1243.
    • (2010) Structure , vol.18 , pp. 1233-1243
    • Perkins, J.R.1    Diboun, I.2    Dessailly, B.H.3    Lees, J.G.4    Orengo, C.5
  • 56
    • 84873802661 scopus 로고    scopus 로고
    • Systematic analysis of somatic mutationsin phosphorylation signaling predicts novel cancer drivers
    • Reimand J., Bader G.D. Systematic analysis of somatic mutationsin phosphorylation signaling predicts novel cancer drivers. Mol. Syst. Biol. 2013, 9:637.
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 637
    • Reimand, J.1    Bader, G.D.2
  • 58
    • 43149094164 scopus 로고    scopus 로고
    • Pfam 10 years on: 10,000 families and still growing
    • Sammut S.J., Finn R.D., Bateman A. Pfam 10 years on: 10,000 families and still growing. Brief. Bioinform. 2008, 9:210-219.
    • (2008) Brief. Bioinform. , vol.9 , pp. 210-219
    • Sammut, S.J.1    Finn, R.D.2    Bateman, A.3
  • 59
    • 65249099497 scopus 로고    scopus 로고
    • Fundamental aspects of protein-protein association kinetics
    • Schreiber G., Haran G., Zhou H.X. Fundamental aspects of protein-protein association kinetics. Chem. Rev. 2009, 109:839-860.
    • (2009) Chem. Rev. , vol.109 , pp. 839-860
    • Schreiber, G.1    Haran, G.2    Zhou, H.X.3
  • 60
    • 79953071469 scopus 로고    scopus 로고
    • Three-dimensional modeling of protein interactions and complexes is going 'omics
    • Stein A., Mosca R., Aloy P. Three-dimensional modeling of protein interactions and complexes is going 'omics. Curr. Opin. Struct. Biol. 2011, 21:200-208.
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 200-208
    • Stein, A.1    Mosca, R.2    Aloy, P.3
  • 62
    • 79551562879 scopus 로고    scopus 로고
    • Genome-wide analysis of PDZ domain binding reveals inherent functional overlap within the PDZ interaction network
    • te Velthuis A.J., Sakalis P.A., Fowler D.A., Bagowski C.P. Genome-wide analysis of PDZ domain binding reveals inherent functional overlap within the PDZ interaction network. PLoS ONE 2011, 6:e16047.
    • (2011) PLoS ONE , vol.6
    • te Velthuis, A.J.1    Sakalis, P.A.2    Fowler, D.A.3    Bagowski, C.P.4
  • 63
    • 84870057622 scopus 로고    scopus 로고
    • Intrinsically disordered proteins: a 10-year recap
    • Tompa P. Intrinsically disordered proteins: a 10-year recap. Trends Biochem. Sci. 2012, 37:509-516.
    • (2012) Trends Biochem. Sci. , vol.37 , pp. 509-516
    • Tompa, P.1
  • 64
    • 84904005219 scopus 로고    scopus 로고
    • Hydrogel formation by multivalent IDPs. A reincarnation of the microtrabecular lattice?
    • Tompa P. Hydrogel formation by multivalent IDPs. A reincarnation of the microtrabecular lattice?. Intrinsically Disordered Proteins 2013, 1:e24068.
    • (2013) Intrinsically Disordered Proteins , vol.1
    • Tompa, P.1
  • 65
    • 65249102824 scopus 로고    scopus 로고
    • Close encounters of the third kind: disordered domains and the interactions of proteins
    • Tompa P., Fuxreiter M., Oldfield C.J., Simon I., Dunker A.K., Uversky V.N. Close encounters of the third kind: disordered domains and the interactions of proteins. Bioessays 2009, 31:328-335.
    • (2009) Bioessays , vol.31 , pp. 328-335
    • Tompa, P.1    Fuxreiter, M.2    Oldfield, C.J.3    Simon, I.4    Dunker, A.K.5    Uversky, V.N.6
  • 67
    • 84874724662 scopus 로고    scopus 로고
    • Update on activities at the Universal Protein Resource (UniProt) in 2013
    • UniProt Consortium
    • Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 2013, 41(Database issue):D43-D47. UniProt Consortium.
    • (2013) Nucleic Acids Res. , vol.41
  • 71
    • 84876158670 scopus 로고    scopus 로고
    • The switches.ELM resource: a compendium of conditional regulatory interaction interfaces
    • Van Roey K., Dinkel H., Weatheritt R.J., Gibson T.J., Davey N.E. The switches.ELM resource: a compendium of conditional regulatory interaction interfaces. Sci. Signal. 2013, 6:rs7.
    • (2013) Sci. Signal. , vol.6
    • Van Roey, K.1    Dinkel, H.2    Weatheritt, R.J.3    Gibson, T.J.4    Davey, N.E.5
  • 73
    • 79953153131 scopus 로고    scopus 로고
    • Extensions of PDZ domains as important structural and functional elements
    • Wang C.K., Pan L., Chen J., Zhang M. Extensions of PDZ domains as important structural and functional elements. Protein Cell 2010, 1:737-751.
    • (2010) Protein Cell , vol.1 , pp. 737-751
    • Wang, C.K.1    Pan, L.2    Chen, J.3    Zhang, M.4
  • 75
    • 84863928687 scopus 로고    scopus 로고
    • Linear motifs confer functional diversity onto splice variants
    • Weatheritt R.J., Davey N.E., Gibson T.J. Linear motifs confer functional diversity onto splice variants. Nucleic Acids Res. 2012, 40:7123-7131.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 7123-7131
    • Weatheritt, R.J.1    Davey, N.E.2    Gibson, T.J.3
  • 77
    • 84876221513 scopus 로고    scopus 로고
    • Higher-order assemblies in a new paradigm of signal transduction
    • Wu H. Higher-order assemblies in a new paradigm of signal transduction. Cell 2013, 153:287-292.
    • (2013) Cell , vol.153 , pp. 287-292
    • Wu, H.1
  • 78
    • 0346555269 scopus 로고    scopus 로고
    • Optimization of specificity in a cellular protein interaction network by negative selection
    • Zarrinpar A., Park S.H., Lim W.A. Optimization of specificity in a cellular protein interaction network by negative selection. Nature 2003, 426:676-680.
    • (2003) Nature , vol.426 , pp. 676-680
    • Zarrinpar, A.1    Park, S.H.2    Lim, W.A.3
  • 79
    • 84856708599 scopus 로고    scopus 로고
    • Intrinsic disorder: signaling via highly specific but short-lived association
    • Zhou H.X. Intrinsic disorder: signaling via highly specific but short-lived association. Trends Biochem. Sci. 2012, 37:43-48.
    • (2012) Trends Biochem. Sci. , vol.37 , pp. 43-48
    • Zhou, H.X.1
  • 80
    • 77953240454 scopus 로고    scopus 로고
    • Precision mapping of an invivo N-glycoproteome reveals rigid topological and sequence constraints
    • Zielinska D.F., Gnad F., Wiśniewski J.R., Mann M. Precision mapping of an invivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 2010, 141:897-907.
    • (2010) Cell , vol.141 , pp. 897-907
    • Zielinska, D.F.1    Gnad, F.2    Wiśniewski, J.R.3    Mann, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.