Linear motif atlas for phosphorylation-dependent signaling

Martin Lee Miller; Lars Juhl Jensen; Francesca Diella; Claus Jørgensen; Michele Tinti; Lei Li; Marilyn Hsiung; Sirlester A Parker; Jennifer Bordeaux; Thomas Sicheritz-Ponten; Marina Olhovsky; Adrian Pasculescu; Jes Alexander; Stefan Knapp; Nikolaj Blom; Peer Bork; Shawn Li; Gianni Cesareni; Tony Pawson; Benjamin E Turk; Michael B Yaffe; Søren Brunak; Rune Linding

doi:10.1126/scisignal.1159433

Linear motif atlas for phosphorylation-dependent signaling

Martin Lee Miller, Lars Juhl Jensen, Francesca Diella, Claus Jørgensen, Michele Tinti, Lei Li, Marilyn Hsiung, Sirlester A Parker, Jennifer Bordeaux, Thomas Sicheritz-Ponten, Marina Olhovsky, Adrian Pasculescu, Jes Alexander, Stefan Knapp, Nikolaj Blom, Peer Bork, Shawn Li, Gianni Cesareni, Tony Pawson, Benjamin E TurkMichael B Yaffe, Søren Brunak, Rune Linding

325 Citations (Scopus)

Abstract

Systematic and quantitative analysis of protein phosphorylation is revealing dynamic regulatory networks underlying cellular responses to environmental cues. However, matching these sites to the kinases that phosphorylate them and the phosphorylation-dependent binding domains that may subsequently bind to them remains a challenge. NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding domains [Src homology 2 (SH2), phosphotyrosine binding (PTB), BRCA1 C-terminal (BRCT), WW, and 14-3-3]. The atlas reveals new aspects of signaling systems, including the observation that tyrosine kinases mutated in cancer have lower specificity than their non-oncogenic relatives. The resource is maintained by an automated pipeline, which uses phylogenetic trees to structure the currently available in vivo and in vitro data to derive probabilistic sequence models of linear motifs. The atlas is available as a community resource (http://netphorest.info).

Original language	English
Journal	Science Signaling
Volume	1
Issue number	35
Pages (from-to)	ra2
DOIs	https://doi.org/10.1126/scisignal.1159433
Publication status	Published - 2008

Keywords

14-3-3 Proteins
Amino Acid Motifs
Animals
BRCA1 Protein
Consensus Sequence
Databases, Protein
Humans
Phosphorylation
Phosphotransferases
Phosphotyrosine
Protein Binding
Signal Transduction
src Homology Domains

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1126/scisignal.1159433

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Miller, M. L., Jensen, L. J., Diella, F., Jørgensen, C., Tinti, M., Li, L., Hsiung, M., Parker, S. A., Bordeaux, J., Sicheritz-Ponten, T., Olhovsky, M., Pasculescu, A., Alexander, J., Knapp, S., Blom, N., Bork, P., Li, S., Cesareni, G., Pawson, T., ... Linding, R. (2008). Linear motif atlas for phosphorylation-dependent signaling. Science Signaling, 1(35), ra2. https://doi.org/10.1126/scisignal.1159433

Miller, ML, Jensen, LJ, Diella, F, Jørgensen, C, Tinti, M, Li, L, Hsiung, M, Parker, SA, Bordeaux, J, Sicheritz-Ponten, T, Olhovsky, M, Pasculescu, A, Alexander, J, Knapp, S, Blom, N, Bork, P, Li, S, Cesareni, G, Pawson, T, Turk, BE, Yaffe, MB, Brunak, S & Linding, R 2008, 'Linear motif atlas for phosphorylation-dependent signaling', Science Signaling, vol. 1, no. 35, pp. ra2. https://doi.org/10.1126/scisignal.1159433

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abstract = "Systematic and quantitative analysis of protein phosphorylation is revealing dynamic regulatory networks underlying cellular responses to environmental cues. However, matching these sites to the kinases that phosphorylate them and the phosphorylation-dependent binding domains that may subsequently bind to them remains a challenge. NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding domains [Src homology 2 (SH2), phosphotyrosine binding (PTB), BRCA1 C-terminal (BRCT), WW, and 14-3-3]. The atlas reveals new aspects of signaling systems, including the observation that tyrosine kinases mutated in cancer have lower specificity than their non-oncogenic relatives. The resource is maintained by an automated pipeline, which uses phylogenetic trees to structure the currently available in vivo and in vitro data to derive probabilistic sequence models of linear motifs. The atlas is available as a community resource (http://netphorest.info).",

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AU - Knapp, Stefan

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AU - Li, Shawn

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AB - Systematic and quantitative analysis of protein phosphorylation is revealing dynamic regulatory networks underlying cellular responses to environmental cues. However, matching these sites to the kinases that phosphorylate them and the phosphorylation-dependent binding domains that may subsequently bind to them remains a challenge. NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding domains [Src homology 2 (SH2), phosphotyrosine binding (PTB), BRCA1 C-terminal (BRCT), WW, and 14-3-3]. The atlas reveals new aspects of signaling systems, including the observation that tyrosine kinases mutated in cancer have lower specificity than their non-oncogenic relatives. The resource is maintained by an automated pipeline, which uses phylogenetic trees to structure the currently available in vivo and in vitro data to derive probabilistic sequence models of linear motifs. The atlas is available as a community resource (http://netphorest.info).

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KW - Animals

KW - BRCA1 Protein

KW - Consensus Sequence

KW - Databases, Protein

KW - Humans

KW - Phosphorylation

KW - Phosphotransferases

KW - Phosphotyrosine

KW - Protein Binding

KW - Signal Transduction

KW - src Homology Domains

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VL - 1

SP - ra2

JO - Science Signaling

JF - Science Signaling

IS - 35

ER -

Linear motif atlas for phosphorylation-dependent signaling

Abstract

Keywords

UN SDGs

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