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For: Jin J, Xie X, Chen C, Park JG, Stark C, James DA, Olhovsky M, Linding R, Mao Y, Pawson T. Eukaryotic protein domains as functional units of cellular evolution. Sci Signal 2009;2:ra76. [PMID: 19934434 DOI: 10.1126/scisignal.2000546] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Number Cited by Other Article(s)
51
Zhao B, Tan PH, Li SSC, Pei D. Systematic characterization of the specificity of the SH2 domains of cytoplasmic tyrosine kinases. J Proteomics 2013;81:56-69. [PMID: 23313216 DOI: 10.1016/j.jprot.2012.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 12/18/2012] [Accepted: 12/29/2012] [Indexed: 01/26/2023]
52
Bornberg-Bauer E, Albà MM. Dynamics and adaptive benefits of modular protein evolution. Curr Opin Struct Biol 2013;23:459-66. [PMID: 23562500 DOI: 10.1016/j.sbi.2013.02.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 02/15/2013] [Accepted: 02/15/2013] [Indexed: 11/29/2022]
53
Uhart M, Bustos DM. Human 14-3-3 paralogs differences uncovered by cross-talk of phosphorylation and lysine acetylation. PLoS One 2013;8:e55703. [PMID: 23418452 PMCID: PMC3572099 DOI: 10.1371/journal.pone.0055703] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 12/28/2012] [Indexed: 01/24/2023]  Open
54
Moore AD, Grath S, Schüler A, Huylmans AK, Bornberg-Bauer E. Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013;1834:898-907. [PMID: 23376183 DOI: 10.1016/j.bbapap.2013.01.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/06/2013] [Accepted: 01/09/2013] [Indexed: 12/24/2022]
55
Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD. SH3 interactome conserves general function over specific form. Mol Syst Biol 2013;9:652. [PMID: 23549480 PMCID: PMC3658277 DOI: 10.1038/msb.2013.9] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 02/20/2013] [Indexed: 12/20/2022]  Open
56
Liu BA, Nash PD. Evolution of SH2 domains and phosphotyrosine signalling networks. Philos Trans R Soc Lond B Biol Sci 2012;367:2556-73. [PMID: 22889907 DOI: 10.1098/rstb.2012.0107] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
57
Jin J, Pawson T. Modular evolution of phosphorylation-based signalling systems. Philos Trans R Soc Lond B Biol Sci 2012;367:2540-55. [PMID: 22889906 DOI: 10.1098/rstb.2012.0106] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
58
Zmasek CM, Godzik A. This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes. PLoS Comput Biol 2012;8:e1002701. [PMID: 23166479 PMCID: PMC3499355 DOI: 10.1371/journal.pcbi.1002701] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 07/27/2012] [Indexed: 12/31/2022]  Open
59
Kaneko T, Joshi R, Feller SM, Li SS. Phosphotyrosine recognition domains: the typical, the atypical and the versatile. Cell Commun Signal 2012;10:32. [PMID: 23134684 PMCID: PMC3507883 DOI: 10.1186/1478-811x-10-32] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022]  Open
60
Liu BA, Engelmann BW, Nash PD. High-throughput analysis of peptide-binding modules. Proteomics 2012;12:1527-46. [PMID: 22610655 DOI: 10.1002/pmic.201100599] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
61
Callebaut I, Mornon JP. The PWAPA cassette: Intimate association of a PHD-like finger and a winged-helix domain in proteins included in histone-modifying complexes. Biochimie 2012;94:2006-12. [DOI: 10.1016/j.biochi.2012.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/14/2012] [Indexed: 12/11/2022]
62
Zhang L, Ma H. Complex evolutionary history and diverse domain organization of SET proteins suggest divergent regulatory interactions. THE NEW PHYTOLOGIST 2012;195:248-63. [PMID: 22510098 DOI: 10.1111/j.1469-8137.2012.04143.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
63
Sacco F, Perfetto L, Castagnoli L, Cesareni G. The human phosphatase interactome: An intricate family portrait. FEBS Lett 2012;586:2732-9. [PMID: 22626554 PMCID: PMC3437441 DOI: 10.1016/j.febslet.2012.05.008] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/08/2012] [Accepted: 05/08/2012] [Indexed: 11/17/2022]
64
Cardone RA, Greco MR, Capulli M, Weinman EJ, Busco G, Bellizzi A, Casavola V, Antelmi E, Ambruosi B, Dell'Aquila ME, Paradiso A, Teti A, Rucci N, Reshkin SJ. NHERF1 acts as a molecular switch to program metastatic behavior and organotropism via its PDZ domains. Mol Biol Cell 2012;23:2028-40. [PMID: 22496422 PMCID: PMC3364169 DOI: 10.1091/mbc.e11-11-0911] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
65
Swift J, Discher DE. Subcellular organization: change of phase in partitioning the cellular milieu. Curr Biol 2012;22:R188-90. [PMID: 22440801 DOI: 10.1016/j.cub.2012.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
66
Phase transitions in the assembly of multivalent signalling proteins. Nature 2012;483:336-40. [PMID: 22398450 PMCID: PMC3343696 DOI: 10.1038/nature10879] [Citation(s) in RCA: 1809] [Impact Index Per Article: 139.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 01/20/2012] [Indexed: 01/20/2023]
67
Kim J, Kim I, Yang JS, Shin YE, Hwang J, Park S, Choi YS, Kim S. Rewiring of PDZ domain-ligand interaction network contributed to eukaryotic evolution. PLoS Genet 2012;8:e1002510. [PMID: 22346764 PMCID: PMC3276551 DOI: 10.1371/journal.pgen.1002510] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 12/12/2011] [Indexed: 12/04/2022]  Open
68
Ying M, Chen D. Tudor domain-containing proteins of Drosophila melanogaster. Dev Growth Differ 2012;54:32-43. [DOI: 10.1111/j.1440-169x.2011.01308.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
69
Conserved BK channel-protein interactions reveal signals relevant to cell death and survival. PLoS One 2011;6:e28532. [PMID: 22174833 PMCID: PMC3235137 DOI: 10.1371/journal.pone.0028532] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 11/09/2011] [Indexed: 12/28/2022]  Open
70
Liu BA, Shah E, Jablonowski K, Stergachis A, Engelmann B, Nash PD. The SH2 domain-containing proteins in 21 species establish the provenance and scope of phosphotyrosine signaling in eukaryotes. Sci Signal 2011;4:ra83. [PMID: 22155787 DOI: 10.1126/scisignal.2002105] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
71
Steirer LM, Moe GR. An antibody to de-N-acetyl sialic acid containing-polysialic acid identifies an intracellular antigen and induces apoptosis in human cancer cell lines. PLoS One 2011;6:e27249. [PMID: 22096542 PMCID: PMC3212545 DOI: 10.1371/journal.pone.0027249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 10/12/2011] [Indexed: 02/01/2023]  Open
72
Parikesit AA, Stadler PF, Prohaska SJ. Evolution and quantitative comparison of genome-wide protein domain distributions. Genes (Basel) 2011;2:912-24. [PMID: 24710298 PMCID: PMC3927604 DOI: 10.3390/genes2040912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 10/07/2011] [Accepted: 10/25/2011] [Indexed: 02/01/2023]  Open
73
Chen C, Nott TJ, Jin J, Pawson T. Deciphering arginine methylation: Tudor tells the tale. Nat Rev Mol Cell Biol 2011;12:629-42. [PMID: 21915143 DOI: 10.1038/nrm3185] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
74
Xie X, Jin J, Mao Y. Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks. BMC Evol Biol 2011;11:242. [PMID: 21849086 PMCID: PMC3167776 DOI: 10.1186/1471-2148-11-242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 08/18/2011] [Indexed: 11/21/2022]  Open
75
Wiedenhoeft J, Krause R, Eulenstein O. The plexus model for the inference of ancestral multidomain proteins. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011;8:890-901. [PMID: 21282868 DOI: 10.1109/tcbb.2011.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
76
Cohen-Gihon I, Sharan R, Nussinov R. Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement. Phys Biol 2011;8:035009. [PMID: 21572172 PMCID: PMC3140765 DOI: 10.1088/1478-3975/8/3/035009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
77
Kaneko T, Sidhu SS, Li SSC. Evolving specificity from variability for protein interaction domains. Trends Biochem Sci 2011;36:183-90. [PMID: 21227701 DOI: 10.1016/j.tibs.2010.12.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 12/07/2010] [Accepted: 12/08/2010] [Indexed: 12/18/2022]
78
Lasko P. Tudor domain. Curr Biol 2010;20:R666-7. [PMID: 20728048 DOI: 10.1016/j.cub.2010.05.056] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
79
Yap KL, Zhou MM. Keeping it in the family: diverse histone recognition by conserved structural folds. Crit Rev Biochem Mol Biol 2010;45:488-505. [PMID: 20923397 PMCID: PMC2988946 DOI: 10.3109/10409238.2010.512001] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
80
Mesquita RD, Woods NT, Seabra-Junior ES, Monteiro ANA. Tandem BRCT Domains: DNA's Praetorian Guard. Genes Cancer 2010;1:1140-6. [PMID: 21533002 PMCID: PMC3082952 DOI: 10.1177/1947601910392988] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
81
Modularity in the Hippo signaling pathway. Trends Biochem Sci 2010;35:627-33. [DOI: 10.1016/j.tibs.2010.05.010] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Revised: 05/25/2010] [Accepted: 05/26/2010] [Indexed: 01/15/2023]
82
Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain. Proc Natl Acad Sci U S A 2010;107:18398-403. [PMID: 20937909 DOI: 10.1073/pnas.1013106107] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
83
Apic G, Russell RB. Domain Recombination: A Workhorse for Evolutionary Innovation. Sci Signal 2010;3:pe30. [DOI: 10.1126/scisignal.3139pe30] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
84
Lim WA, Pawson T. Phosphotyrosine signaling: evolving a new cellular communication system. Cell 2010;142:661-7. [PMID: 20813250 PMCID: PMC2950826 DOI: 10.1016/j.cell.2010.08.023] [Citation(s) in RCA: 267] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
85
Grassi L, Fusco D, Sellerio A, Corà D, Bassetti B, Caselle M, Lagomarsino MC. Identity and divergence of protein domain architectures after the yeast whole-genome duplication event. MOLECULAR BIOSYSTEMS 2010;6:2305-15. [PMID: 20820472 DOI: 10.1039/c003507f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
86
Arkov AL, Ramos A. Building RNA-protein granules: insight from the germline. Trends Cell Biol 2010;20:482-90. [PMID: 20541937 PMCID: PMC2929181 DOI: 10.1016/j.tcb.2010.05.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 05/17/2010] [Accepted: 05/17/2010] [Indexed: 11/30/2022]
87
Callebaut I, Mornon JP. LOTUS, a new domain associated with small RNA pathways in the germline. Bioinformatics 2010;26:1140-4. [DOI: 10.1093/bioinformatics/btq122] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
88
Challenges and Approaches for Assay Development of Membrane and Membrane-Associated Proteins in Drug Discovery. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2010. [DOI: 10.1016/s1877-1173(10)91007-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
89
Pawson T, VanHook AM. Science Signaling Podcast: 24 November 2009. Sci Signal 2009. [DOI: 10.1126/scisignal.298pc21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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