Phospho‐tyrosine dependent protein–protein interaction network
Arndt Grossmann,Nouhad Benlasfer,Petra Birth,Anna Hegele,Franziska Wachsmuth,Luise Apelt,Ulrich Stelzl +6 more
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TLDR
Network analysis revealed that pY‐mediated recognition events are tied to a highly connected protein module dedicated to signaling and cell growth pathways related to cancer, exemplarily providing evidence that the two pY-dependent PPIs dictate cellular cancer phenotypes.Abstract:
Post-translational protein modifications, such as tyrosine phosphorylation, regulate protein–protein interactions (PPIs) critical for signal processing and cellular phenotypes. We extended an established yeast two-hybrid system employing human protein kinases for the analyses of phospho-tyrosine (pY)-dependent PPIs in a direct experimental, large-scale approach. We identified 292 mostly novel pY-dependent PPIs which showed high specificity with respect to kinases and interacting proteins and validated a large fraction in co-immunoprecipitation experiments from mammalian cells. About one-sixth of the interactions are mediated by known linear sequence binding motifs while the majority of pY-PPIs are mediated by other linear epitopes or governed by alternative recognition modes. Network analysis revealed that pY-mediated recognition events are tied to a highly connected protein module dedicated to signaling and cell growth pathways related to cancer. Using binding assays, protein complementation and phenotypic readouts to characterize the pY-dependent interactions of TSPAN2 (tetraspanin 2) and GRB2 or PIK3R3 (p55γ), we exemplarily provide evidence that the two pY-dependent PPIs dictate cellular cancer phenotypes.read more
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References
More filters
Journal ArticleDOI
Clustering by Passing Messages Between Data Points
Brendan J. Frey,Delbert Dueck +1 more
TL;DR: A method called “affinity propagation,” which takes as input measures of similarity between pairs of data points, which found clusters with much lower error than other methods, and it did so in less than one-hundredth the amount of time.
Journal ArticleDOI
Oncogenic kinase signalling
Peter Blume-Jensen,Tony Hunter +1 more
TL;DR: How oncogenic conversion of protein kinases results from perturbation of the normal autoinhibitory constraints on kinase activity is emphasized and an update is provided on the role of deregulated PI(3)K/Akt and mammalian target of rapamycin/p70S6K signalling in human malignancies.
Journal ArticleDOI
A census of human cancer genes
P. Andrew Futreal,Lachlan J. M. Coin,Mhairi Marshall,Thomas A. Down,Tim Hubbard,Richard Wooster,Nazneen Rahman,Michael R. Stratton +7 more
TL;DR: A 'census' of cancer genes is conducted that indicates that mutations in more than 1% of genes contribute to human cancer.
Journal ArticleDOI
SH2 domains recognize specific phosphopeptide sequences
Songyang Zhou,Songyang Zhou,Steven E. Shoelson,Manas Chaudhuri,Gerald D. Gish,Tony Pawson,Wayne G. Haser,Frederick J. King,Thomas M. Roberts,Sheldon Ratnofsky,Robert J. Lechleider,Benjamin G. Neel,Raymond B. Birge,J. Eduardo Fajardo,Margaret M. Chou,Hidesaburo Hanafusa,Brian Schaffhausen,Lewis C. Cantley +17 more
TL;DR: The variability in SH2 domain sequences at likely sites of contact provides a structural basis for the phosphopeptide selectivity of these families.
Journal ArticleDOI
A human protein-protein interaction network : a resource for annotating the proteome
Ulrich Stelzl,Uwe Worm,Maciej Lalowski,Christian Haenig,Felix H. Brembeck,Heike Goehler,Martin Stroedicke,Martina Zenkner,Anke Schoenherr,Susanne Koeppen,Jan Timm,Sascha Mintzlaff,Claudia Abraham,Nicole Bock,Silvia Kietzmann,Astrid Goedde,Engin Toksöz,Anja Droege,Sylvia Krobitsch,Bernhard Korn,Walter Birchmeier,Hans Lehrach,Erich E. Wanker +22 more
TL;DR: A large, highly connected network of interacting pairs of human proteins was identified, characterizing ANP32A and CRMP1 as modulators of Wnt signaling and two novel Axin-1 interactions were validated experimentally.
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