Artículo

Dinkel, H.; Van Roey, K.; Michael, S.; Davey, N.E.; Weatheritt, R.J.; Born, D.; Speck, T.; Krüger, D.; Grebnev, G.; Kubań, M.; Strumillo, M.; Uyar, B.; Budd, A.; Altenberg, B.; Seiler, M.; Chemes, L.B.; Glavina, J.; Sánchez, I.E. (...) Gibson, T.J. "The eukaryotic linear motif resource ELM: 10 years and counting" (2014) Nucleic Acids Research. 42(D1):D259-D266
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Abstract:

The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). For >10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear motifs. The current version of ELM contains ∼200 different motif classes with over 2400 experimentally validated instances manually curated from >2000 scientific publications. Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange formats. Where appropriate, links are provided to resources such as switches.elm.eu.org and KEGG pathways. © 2013 The Author(s). Published by Oxford University Press.

Registro:

Documento: Artículo
Título:The eukaryotic linear motif resource ELM: 10 years and counting
Autor:Dinkel, H.; Van Roey, K.; Michael, S.; Davey, N.E.; Weatheritt, R.J.; Born, D.; Speck, T.; Krüger, D.; Grebnev, G.; Kubań, M.; Strumillo, M.; Uyar, B.; Budd, A.; Altenberg, B.; Seiler, M.; Chemes, L.B.; Glavina, J.; Sánchez, I.E.; Diella, F.; Gibson, T.J.
Filiación:Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Department of Physiology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, United States
Structural Studies Division, Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
Ruprecht-Karls-Universität, 69117 Heidelberg, Germany
School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Co. Dublin, Ireland
Laboratory of Bioinformatics and Biostatistics, Maria Sklodowska-Curie Memorial Cancer Center, Institute of Oncology, WK Roentgena 5, 02-781 Warsaw, Poland
Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos, Avenida Patricias Argentinas 435, CP 1405 Buenos Aires, Argentina
Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Gúiraldes 2160, Argentina
Idioma: Inglés
Año:2014
Volumen:42
Número:D1
Página de inicio:D259
Página de fin:D266
DOI: http://dx.doi.org/10.1093/nar/gkt1047
Título revista:Nucleic Acids Research
Título revista abreviado:Nucleic Acids Res.
ISSN:03051048
CODEN:NARHA
Registro:http://digital.bl.fcen.uba.ar/collection/paper/document/paper_03051048_v42_nD1_pD259_Dinkel

Referencias:

  • Tompa, P., Intrinsically disordered proteins: A 10-year recap (2012) Trends Biochem. Sci., 37, pp. 509-516
  • Dunker, A.K., Lawson, J.D., Brown, C.J., Williams, R.M., Romero, P., Oh, J.S., Oldfield, C.J., Hipps, K.W., Intrinsically disordered protein (2001) J. Mol. Graph. Model., 19, pp. 26-59
  • Uversky, V.N., Gillespie, J.R., Fink, A.L., Why are "natively unfolded" proteins unstructured under physiologic conditions? (2000) Proteins, 41, pp. 415-427
  • Wright, P.E., Dyson, H.J., Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm (1999) J. Mol. Biol., 293, pp. 321-331
  • Fuxreiter, M., Tompa, P., Simon, I., Local structural disorder imparts plasticity on linear motifs (2007) Bioinformatics, 23, pp. 950-956
  • Dyson, H.J., Wright, P.E., Intrinsically unstructured proteins and their functions (2005) Nat. Rev. Mol. Cell Biol., 6, pp. 197-208
  • Neduva, V., Russell, R.B., Linear motifs: Evolutionary interaction switches (2005) FEBS Lett., 579, pp. 3342-3345
  • Diella, F., Haslam, N., Chica, C., Budd, A., Michael, S., Brown, N.P., Trave, G., Gibson, T., Understanding eukaryotic linear motifs and their role in cell signaling and regulation (2008) Front. Biosci., 13, pp. 6580-6603
  • Davey, N.E., Van Roey, K., Weatheritt, R.J., Toedt, G., Uyar, B., Altenberg, B., Budd, A., Gibson, T.J., Attributes of short linear motifs (2012) Mol. Biosyst., 8, pp. 268-281
  • Ladbury, J.E., Lemmon, M.A., Zhou, M., Green, J., Botfield, M.C., Schlessinger, J., Measurement of the binding of tyrosyl phosphopeptides to SH2 domains: A reappraisal (1995) Proc. Natl Acad. Sci. USA, 92, pp. 3199-3203
  • Meszaros, B., Tompa, P., Simon, I., Dosztanyi, Z., Molecular principles of the interactions of disordered proteins (2007) J. Mol. Biol., 372, pp. 549-561
  • Haslam, N.J., Shields, D.C., Peptide-binding domains: Are limp handshakes safest? (2012) Sci. Signal., 5, pp. pe40
  • Davey, N.E., Trave, G., Gibson, T.J., How viruses hijack cell regulation (2011) Trends Biochem. Sci., 36, pp. 159-169
  • Kadaveru, K., Vyas, J., Schiller, M.R., Viral infection and human disease-insights from minimotifs (2008) Front. Biosci., 13, pp. 6455-6471
  • 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 (2013) Sci. Signal., 6, pp. rs7
  • Van Roey, K., Orchard, S., Kerrien, S., Dumousseau, M., Ricard-Blum, S., Hermjakob, H., Gibson, T.J., Capturing cooperative interactions with the PSI-MI format (2013) Database, 2013, pp. bat066. , Oxford
  • Van Roey, K., Gibson, T.J., Davey, N.E., Motif switches: Decision-making in cell regulation (2012) Curr. Opin. Struct. Biol., 22, pp. 378-385
  • Puntervoll, P., Linding, R., Gemund, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D.M.A., Costantini, A., ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins (2003) Nucleic Acids Res., 31, pp. 3625-3630
  • Gibson, T.J., Seiler, M., Veitia, R.A., The transience of transient overexpression (2013) Nat. Methods, 10, pp. 715-721
  • Dinkel, H., Michael, S., Weatheritt, R.J., Davey, N.E., Van Roey, K., Altenberg, B., Toedt, G., Budd, A., ELM-the database of eukaryotic linear motifs (2012) Nucleic Acids Res., 40, pp. D242-D251
  • Gould, C.M., Diella, F., Via, A., Puntervoll, P., Gemund, C., Chabanis-Davidson, S., Michael, S., Chica, C., ELM: The status of the 2010 eukaryotic linear motif resource (2010) Nucleic Acids Res., 38, pp. D167-D180
  • Remenyi, A., Good, M.C., Lim, W.A., Docking interactions in protein kinase and phosphatase networks (2006) Curr. Opin. Struct. Biol., 16, pp. 676-685
  • Schrader, E.K., Harstad, K.G., Matouschek, A., Targeting proteins for degradation (2009) Nat. Chem. Biol., 5, pp. 815-822
  • Weatheritt, R.J., Jehl, P., Dinkel, H., Gibson, T.J., IELM-A web server to explore short linear motif-mediated interactions (2012) Nucleic Acids Res., 40, pp. W364-W369
  • Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Clements, J., The Pfam protein families database (2012) Nucleic Acids Res., 40, pp. D290-D301
  • Letunic, I., Doerks, T., Bork, P., SMART 7: Recent updates to the protein domain annotation resource (2012) Nucleic Acids Res., 40, pp. D302-D305
  • Kerrien, S., Orchard, S., Montecchi-Palazzi, L., Aranda, B., Quinn, A.F., Vinod, N., Bader, G.D., Sherman, D., Broadening the horizon-level 2.5 of the HUPO-PSI format for molecular interactions (2007) BMC Biol., 5, p. 44
  • Labit, H., Fujimitsu, K., Bayin, N.S., Takaki, T., Gannon, J., Yamano, H., Dephosphorylation of Cdc20 is required for its C-box-dependent activation of the APC/C (2012) EMBO J., 31, pp. 3351-3362
  • Peters, J.-M., The anaphase promoting complex/cyclosome: A machine designed to destroy (2006) Nat.Rev. Mol. Cell Biol., 7, pp. 644-656
  • Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E., UCSF Chimera-A visualization system for exploratory research and analysis (2004) J. Comput. Chem., 25, pp. 1605-1612
  • Da Fonseca, P.C.A., Kong, E.H., Zhang, Z., Schreiber, A., Williams, M.A., Morris, E.P., Barford, D., Structures of APC/C(Cdh1) with substrates identify Cdh1 and Apc10 as the D-box co-receptor (2011) Nature, 470, pp. 274-278
  • Passmore, L.A., McCormack, E.A., Au, S.W., Paul, A., Willison, K.R., Harper, J.W., Barford, D., Doc1 mediates the activity of the anaphase-promoting complex by contributing to substrate recognition (2003) EMBO J., 22, pp. 786-796
  • Glotzer, M., Murray, A.W., Kirschner, M.W., Cyclin is degraded by the ubiquitin pathway (1991) Nature, 349, pp. 132-138
  • Pfleger, C.M., Kirschner, M.W., The KEN box: An APC recognition signal distinct from the D box targeted by Cdh1 (2000) Genes Dev., 14, pp. 655-665
  • Michael, S., Trave, G., Ramu, C., Chica, C., Gibson, T.J., Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation (2008) Bioinformatics, 24, pp. 453-457
  • Listovsky, T., Oren, Y.S., Yudkovsky, Y., Mahbubani, H.M., Weiss, A.M., Lebendiker, M., Brandeis, M., Mammalian Cdh1/Fzr mediates its own degradation (2004) EMBO J., 23, pp. 1619-1626
  • Choi, E., Dial, J.M., Jeong, D.-E., Hall, M.C., Unique D box and KEN box sequences limit ubiquitination of Acm 1 and promote pseudosubstrate inhibition of the anaphase-promoting complex (2008) J. Biol. Chem., 283, pp. 23701-23710
  • Martinez, J.S., Jeong, D.-E., Choi, E., Billings, B.M., Hall, M.C., Acm1 is a negative regulator of the CDH1-dependent anaphase-promoting complex/cyclosome in budding yeast (2006) Mol. Cell Biol., 26, pp. 9162-9176
  • Rape, M., Reddy, S.K., Kirschner, M.W., The processivity of multiubiquitination by the APC determines the order of substrate degradation (2006) Cell, 124, pp. 89-103
  • Arakawa, K., Kono, N., Yamada, Y., Mori, H., Tomita, M., KEGG-based pathway visualization tool for complex omics data (2005) Silico Biol., 5, pp. 419-423
  • Fielding, R.T., Taylor, R.N., Principled design of the modern Web architecture (2002) ACM Trans. Internet Technol., 2, pp. 115-150
  • De Oliveira, E.A.G., Romeiro, N.C., Ribeiro, E.D.S., Santa-Catarina, C., Oliveira, A.E.A., Silveira, V., De Souza Filho, G.A., Cruz, M.A.L., Structural and functional characterization of the protein kinase Mps1 in Arabidopsis thaliana (2012) PLoS One, 7, pp. e45707
  • Rawat, R., Takahashi, N., Hsu, P.Y., Jones, M.A., Schwartz, J., Salemi, M.R., Phinney, B.S., Harmer, S.L., REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock (2011) PLoS Genet., 7, pp. e1001350
  • Wang, R., Li, K.-M., Zhou, C.-H., Xue, J.-L., Ji, C.-N., Chen, J.-Z., Cdc20 mediates D-box-dependent degradation of Sp100 (2011) Biochem. Biophys. Res. Commun., 415, pp. 702-706
  • Lauck, M., Sibley, S.D., Lara, J., Purdy, M.A., Khudyakov, Y., Hyeroba, D., Tumukunde, A., Chapman, C.A., A novel hepacivirus with an unusually long and intrinsically disordered NS5A protein in a wild old world primate (2013) J. Virol., 87, pp. 8971-8981
  • Perfetto, L., Gherardini, P.F., Davey, N.E., Diella, F., Helmer-Citterich, M., Cesareni, G., Exploring the diversity of SPRY/B30.2-mediated interactions (2013) Trends Biochem. Sci., 38, pp. 38-46
  • Rigden, D.J., Woodhead, D.D., Wong, P.W.H., Galperin, M.Y., New structural and functional contexts of the Dx[DN]xDG linear motif: Insights into evolution of calcium-binding proteins (2011) PLoS One, 6, pp. e21507
  • Luck, K., Charbonnier, S., Trave, G., The emerging contribution of sequence context to the specificity of protein interactions mediated by PDZ domains (2012) FEBS Lett., 586, pp. 2648-2661
  • Stavropoulos, I., Khaldi, N., Davey, N.E., O'Brien, K., Martin, F., Shields, D.C., Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins (2012) PLoS One, 7, pp. e44389
  • Kobe, B., Boden, M., Computational modelling of linear motif-mediated protein interactions (2012) Curr. Top. Med. Chem., 12, pp. 1553-1561
  • Trabuco, L.G., Lise, S., Petsalaki, E., Russell, R.B., PepSite: Prediction of peptide-binding sites from protein surfaces (2012) Nucleic Acids Res., 40, pp. W423-W427

Citas:

---------- APA ----------
Dinkel, H., Van Roey, K., Michael, S., Davey, N.E., Weatheritt, R.J., Born, D., Speck, T.,..., Gibson, T.J. (2014) . The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Research, 42(D1), D259-D266.
http://dx.doi.org/10.1093/nar/gkt1047
---------- CHICAGO ----------
Dinkel, H., Van Roey, K., Michael, S., Davey, N.E., Weatheritt, R.J., Born, D., et al. "The eukaryotic linear motif resource ELM: 10 years and counting" . Nucleic Acids Research 42, no. D1 (2014) : D259-D266.
http://dx.doi.org/10.1093/nar/gkt1047
---------- MLA ----------
Dinkel, H., Van Roey, K., Michael, S., Davey, N.E., Weatheritt, R.J., Born, D., et al. "The eukaryotic linear motif resource ELM: 10 years and counting" . Nucleic Acids Research, vol. 42, no. D1, 2014, pp. D259-D266.
http://dx.doi.org/10.1093/nar/gkt1047
---------- VANCOUVER ----------
Dinkel, H., Van Roey, K., Michael, S., Davey, N.E., Weatheritt, R.J., Born, D., et al. The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res. 2014;42(D1):D259-D266.
http://dx.doi.org/10.1093/nar/gkt1047