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Volumn 123, Issue 2, 2010, Pages 159-163

Understanding large multiprotein complexes: Applying a multiple allosteric networks model to explain the function of the Mediator transcription complex

Author keywords

Graph theory; Mediator; Networks; Transcription

Indexed keywords

CYCLIN DEPENDENT KINASE 7; CYCLIN DEPENDENT KINASE 8; DNA BINDING PROTEIN; G PROTEIN COUPLED RECEPTOR; HEMOGLOBIN; LIVER X RECEPTOR; MULTIPROTEIN COMPLEX; RNA POLYMERASE II; SERINE PROTEINASE; TRANSCRIPTION FACTOR IID; TRANSCRIPTION FACTOR IIH; VITAMIN D RECEPTOR;

EID: 73849144383     PISSN: 00219533     EISSN: None     Source Type: Journal    
DOI: 10.1242/jcs.057216     Document Type: Article
Times cited : (5)

References (46)
  • 2
  • 3
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabasi, A. L. and Oltvai, Z. N. (2004). Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113.
    • (2004) Nat. Rev. Genet , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 4
    • 18844427874 scopus 로고    scopus 로고
    • The yeast Mediator complex and its regulation
    • Bjorklund, S. and Gustafsson, C. M. (2005). The yeast Mediator complex and its regulation. Trends Biochem. Sci. 30, 240-244.
    • (2005) Trends Biochem. Sci , vol.30 , pp. 240-244
    • Bjorklund, S.1    Gustafsson, C.M.2
  • 5
    • 3042651100 scopus 로고    scopus 로고
    • Conformational spread: The propagation of allosteric states in large multiprotein complexes
    • Bray, D. and Duke, T. (2004). Conformational spread: the propagation of allosteric states in large multiprotein complexes. Annu. Rev. Biophys. Biomol. Struct. 33, 53-73.
    • (2004) Annu. Rev. Biophys. Biomol. Struct , vol.33 , pp. 53-73
    • Bray, D.1    Duke, T.2
  • 6
    • 0035477093 scopus 로고    scopus 로고
    • Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs
    • Butler, J. E. and Kadonaga, J. T. (2001). Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev. 15, 2515-2519.
    • (2001) Genes Dev , vol.15 , pp. 2515-2519
    • Butler, J.E.1    Kadonaga, J.T.2
  • 7
    • 18844385514 scopus 로고    scopus 로고
    • Structure of eukaryotic Mediator complexes
    • Chadick, J. Z. and Asturias, F. J. (2005). Structure of eukaryotic Mediator complexes. Trends Biochem. Sci. 30, 264-271.
    • (2005) Trends Biochem. Sci , vol.30 , pp. 264-271
    • Chadick, J.Z.1    Asturias, F.J.2
  • 8
    • 18844378166 scopus 로고    scopus 로고
    • The mammalian Mediator complex and its role in transcriptional regulation
    • Conaway, R. C., Sato, S., Tomomori-Sato, C., Yao, T. and Conaway, J. W. (2005). The mammalian Mediator complex and its role in transcriptional regulation. Trends Biochem. Sci. 30, 250-255.
    • (2005) Trends Biochem. Sci , vol.30 , pp. 250-255
    • Conaway, R.C.1    Sato, S.2    Tomomori-Sato, C.3    Yao, T.4    Conaway, J.W.5
  • 9
    • 0036671095 scopus 로고    scopus 로고
    • Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction
    • Davis, J. A., Takagi, Y., Kornberg, R. D. and Asturias, F. A. (2002). Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol. Cell 10, 409-415.
    • (2002) Mol. Cell , vol.10 , pp. 409-415
    • Davis, J.A.1    Takagi, Y.2    Kornberg, R.D.3    Asturias, F.A.4
  • 10
    • 12944331889 scopus 로고    scopus 로고
    • Small-world network approach to identify key residues in protein-protein interaction
    • del Sol, A. and O'Meara, P. (2005). Small-world network approach to identify key residues in protein-protein interaction. Proteins 58, 672-682.
    • (2005) Proteins , vol.58 , pp. 672-682
    • del Sol, A.1    O'Meara, P.2
  • 11
    • 33745461893 scopus 로고    scopus 로고
    • del Sol, A., Fujihashi, H., Amoros, D. and Nussinov, R. (2006). Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol. Syst. Biol. 2, 2006.0019.
    • del Sol, A., Fujihashi, H., Amoros, D. and Nussinov, R. (2006). Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol. Syst. Biol. 2, 2006.0019.
  • 13
    • 9944220618 scopus 로고    scopus 로고
    • Rewiring cell signaling: The logic and plasticity of eukaryotic protein circuitry
    • Dueber, J. E., Yeh, B. J., Bhattacharyya, R. P. and Lim, W. A. (2004). Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. Curr. Opin. Struct. Biol. 14, 690-699.
    • (2004) Curr. Opin. Struct. Biol , vol.14 , pp. 690-699
    • Dueber, J.E.1    Yeh, B.J.2    Bhattacharyya, R.P.3    Lim, W.A.4
  • 14
    • 0035804929 scopus 로고    scopus 로고
    • Conformational spread in a ring of proteins: A stochastic approach to allostery
    • Duke, T. A., Le Novere, N. and Bray, D. (2001). Conformational spread in a ring of proteins: a stochastic approach to allostery. J. Mol. Biol. 308, 541-553.
    • (2001) J. Mol. Biol , vol.308 , pp. 541-553
    • Duke, T.A.1    Le Novere, N.2    Bray, D.3
  • 15
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • Greene, L. H. and Higman, V. A. (2003). Uncovering network systems within protein structures. J. Mol. Biol. 334, 781-791.
    • (2003) J. Mol. Biol , vol.334 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 17
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong, H., Mason, S. P., Barabasi, A. L. and Oltvai, Z. N. (2001). Lethality and centrality in protein networks. Nature 411, 41-42.
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 18
    • 0028930099 scopus 로고
    • Regulation of HIS4 expression by the Saccharomyces cerevisiae SIN4 transcriptional regulator
    • Jiang, Y. W. and Stillman, D. J. (1995). Regulation of HIS4 expression by the Saccharomyces cerevisiae SIN4 transcriptional regulator. Genetics 140, 103-114.
    • (1995) Genetics , vol.140 , pp. 103-114
    • Jiang, Y.W.1    Stillman, D.J.2
  • 19
    • 0028949055 scopus 로고
    • Genetic and physical interactions between yeast RGR1 and SIN4 in chromatin organization and transcriptional regulation
    • Jiang, Y. W., Dohrmann, P. R. and Stillman, D. J. (1995). Genetic and physical interactions between yeast RGR1 and SIN4 in chromatin organization and transcriptional regulation. Genetics 140, 47-54.
    • (1995) Genetics , vol.140 , pp. 47-54
    • Jiang, Y.W.1    Dohrmann, P.R.2    Stillman, D.J.3
  • 20
    • 0037694964 scopus 로고    scopus 로고
    • Assembly of a Mediator/TFIID/ TFIIA complex bypasses the need for an activator
    • Johnson, K. M. and Carey, M. (2003). Assembly of a Mediator/TFIID/ TFIIA complex bypasses the need for an activator. Curr. Biol. 13, 772-777.
    • (2003) Curr. Biol , vol.13 , pp. 772-777
    • Johnson, K.M.1    Carey, M.2
  • 21
    • 0037099312 scopus 로고    scopus 로고
    • TFIID and human Mediator coactivator complexes assemble cooperatively on promoter DNA
    • Johnson, K. M., Wang, J., Smallwood, A., Arayata, C. and Carey, M. (2002). TFIID and human Mediator coactivator complexes assemble cooperatively on promoter DNA. Genes Dev. 16, 1852-1863.
    • (2002) Genes Dev , vol.16 , pp. 1852-1863
    • Johnson, K.M.1    Wang, J.2    Smallwood, A.3    Arayata, C.4    Carey, M.5
  • 22
    • 18844461272 scopus 로고    scopus 로고
    • Interactions between subunits of Drosophila Mediator and activator proteins
    • Kim, Y. J. and Lis, J. T. (2005). Interactions between subunits of Drosophila Mediator and activator proteins. Trends Biochem. Sci. 30, 245-249.
    • (2005) Trends Biochem. Sci , vol.30 , pp. 245-249
    • Kim, Y.J.1    Lis, J.T.2
  • 23
    • 0028282551 scopus 로고
    • A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II
    • Kim, Y. J., Bjorklund, S., Li, Y., Sayre, M. H. and Kornberg, R. D. (1994). A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77, 599-608.
    • (1994) Cell , vol.77 , pp. 599-608
    • Kim, Y.J.1    Bjorklund, S.2    Li, Y.3    Sayre, M.H.4    Kornberg, R.D.5
  • 24
    • 0032059891 scopus 로고    scopus 로고
    • An activator target in the RNA polymerase II holoenzyme
    • Koh, S. S., Ansari, A. Z., Ptashne, M. and Young, R. A. (1998). An activator target in the RNA polymerase II holoenzyme. Mol. Cell 1, 895-904.
    • (1998) Mol. Cell , vol.1 , pp. 895-904
    • Koh, S.S.1    Ansari, A.Z.2    Ptashne, M.3    Young, R.A.4
  • 25
    • 18844451820 scopus 로고    scopus 로고
    • Mediator and the mechanism of transcriptional activation
    • Kornberg, R. D. (2005). Mediator and the mechanism of transcriptional activation. Trends Biochem. Sci. 30, 235-239.
    • (2005) Trends Biochem. Sci , vol.30 , pp. 235-239
    • Kornberg, R.D.1
  • 26
    • 0001603028 scopus 로고    scopus 로고
    • An activator binding module of yeast RNA polymerase II holoenzyme
    • Lee, Y. C., Park, J. M., Min, S., Han, S. J. and Kim, Y. J. (1999). An activator binding module of yeast RNA polymerase II holoenzyme. Mol. Cell. Biol. 19, 2967-2976.
    • (1999) Mol. Cell. Biol , vol.19 , pp. 2967-2976
    • Lee, Y.C.1    Park, J.M.2    Min, S.3    Han, S.J.4    Kim, Y.J.5
  • 27
    • 0141725524 scopus 로고    scopus 로고
    • The mediator coactivator complex: Functional and physical roles in transcriptional regulation
    • Lewis, B. A. and Reinberg, D. (2003). The mediator coactivator complex: functional and physical roles in transcriptional regulation. J. Cell Sci. 116, 3667-3675.
    • (2003) J. Cell Sci , vol.116 , pp. 3667-3675
    • Lewis, B.A.1    Reinberg, D.2
  • 28
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless, S. W. and Ranganathan, R. (1999). Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286, 295-299.
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 29
    • 18844394569 scopus 로고    scopus 로고
    • Dynamic regulation of pol II transcription by the mammalian Mediator complex
    • Malik, S. and Roeder, R. G. (2005). Dynamic regulation of pol II transcription by the mammalian Mediator complex. Trends Biochem. Sci. 30, 256-263.
    • (2005) Trends Biochem. Sci , vol.30 , pp. 256-263
    • Malik, S.1    Roeder, R.G.2
  • 30
    • 0842310355 scopus 로고    scopus 로고
    • Ras induces Mediator complex exchange on C/EBP beta
    • Mo, X., Kowenz-Leutz, E., Xu, H. and Leutz, A. (2004). Ras induces Mediator complex exchange on C/EBP beta. Mol. Cell 13, 241-250.
    • (2004) Mol. Cell , vol.13 , pp. 241-250
    • Mo, X.1    Kowenz-Leutz, E.2    Xu, H.3    Leutz, A.4
  • 31
    • 0033786937 scopus 로고    scopus 로고
    • Mediator of transcriptional regulation
    • Myers, L. C. and Kornberg, R. D. (2000). Mediator of transcriptional regulation. Annu. Rev. Biochem. 69, 729-749.
    • (2000) Annu. Rev. Biochem , vol.69 , pp. 729-749
    • Myers, L.C.1    Kornberg, R.D.2
  • 33
    • 0036606879 scopus 로고    scopus 로고
    • Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation
    • Naar, A. M., Taatjes, D. J., Zhai, W., Nogales, E. and Tjian, R. (2002). Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation. Genes Dev. 16, 1339-1344.
    • (2002) Genes Dev , vol.16 , pp. 1339-1344
    • Naar, A.M.1    Taatjes, D.J.2    Zhai, W.3    Nogales, E.4    Tjian, R.5
  • 34
    • 18744389789 scopus 로고    scopus 로고
    • Assortative mixing in networks
    • Newman, M. E. (2002). Assortative mixing in networks. Phys. Rev. Lett. 89, 208701.
    • (2002) Phys. Rev. Lett , vol.89 , pp. 208701
    • Newman, M.E.1
  • 37
    • 0033928379 scopus 로고    scopus 로고
    • Specific structural motifs determine TRAP220 interactions with nuclear hormone receptors
    • Ren, Y., Behre, E., Ren, Z., Zhang, J., Wang, Q. and Fondell, J. D. (2000). Specific structural motifs determine TRAP220 interactions with nuclear hormone receptors. Mol. Cell. Biol. 20, 5433-5446.
    • (2000) Mol. Cell. Biol , vol.20 , pp. 5433-5446
    • Ren, Y.1    Behre, E.2    Ren, Z.3    Zhang, J.4    Wang, Q.5    Fondell, J.D.6
  • 38
    • 1642304065 scopus 로고    scopus 로고
    • Structural determinants of allosteric ligand activation in RXR heterodimers
    • Shulman, A. I., Larson, C., Mangelsdorf, D. J. and Ranganathan, R. (2004). Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 116, 417-429.
    • (2004) Cell , vol.116 , pp. 417-429
    • Shulman, A.I.1    Larson, C.2    Mangelsdorf, D.J.3    Ranganathan, R.4
  • 39
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin, V. and Mirny, L. A. (2003). Protein complexes and functional modules in molecular networks. Proc. Natl. Acad. Sci. USA 100, 12123-12128.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 40
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • Suel, G. M., Lockless, S. W., Wall, M. A. and Ranganathan, R. (2003). Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10, 59-69.
    • (2003) Nat. Struct. Biol , vol.10 , pp. 59-69
    • Suel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 41
    • 2942577583 scopus 로고    scopus 로고
    • Structure and function of CRSP/Med2; a promoter-selective transcriptional coactivator complex
    • Taatjes, D. J. and Tjian, R. (2004). Structure and function of CRSP/Med2; a promoter-selective transcriptional coactivator complex. Mol. Cell 14, 675-683.
    • (2004) Mol. Cell , vol.14 , pp. 675-683
    • Taatjes, D.J.1    Tjian, R.2
  • 42
    • 0037039776 scopus 로고    scopus 로고
    • Taatjes, D. J., Naar, A. M., Andel, F., 3rd, Nogales, E. and Tjian, R. (2002). Structure, function, and activator-induced conformations of the CRSP coactivator. Science 295, 1058-1062.
    • Taatjes, D. J., Naar, A. M., Andel, F., 3rd, Nogales, E. and Tjian, R. (2002). Structure, function, and activator-induced conformations of the CRSP coactivator. Science 295, 1058-1062.
  • 43
    • 3042692982 scopus 로고    scopus 로고
    • Distinct conformational states of nuclear receptor-bound CRSP-Med complexes
    • Taatjes, D. J., Schneider-Poetsch, T. and Tjian, R. (2004). Distinct conformational states of nuclear receptor-bound CRSP-Med complexes. Nat. Struct. Mol. Biol. 11, 664-671.
    • (2004) Nat. Struct. Mol. Biol , vol.11 , pp. 664-671
    • Taatjes, D.J.1    Schneider-Poetsch, T.2    Tjian, R.3
  • 44
    • 0033525687 scopus 로고    scopus 로고
    • Competition between thyroid hormone receptor-associated protein (TRAP) 220 and transcriptional intermediary factor (TIF) 2 for binding to nuclear receptors. Implications for the recruitment of TRAP and p160 coactivator complexes
    • Treuter, E., Johansson, L., Thomsen, J. S., Warnmark, A., Leers, J., Pelto-Huikko, M., Sjoberg, M., Wright, A. P., Spyrou, G. and Gustafsson, J. A. (1999). Competition between thyroid hormone receptor-associated protein (TRAP) 220 and transcriptional intermediary factor (TIF) 2 for binding to nuclear receptors. Implications for the recruitment of TRAP and p160 coactivator complexes. J. Biol. Chem. 274, 6667-6777.
    • (1999) J. Biol. Chem , vol.274 , pp. 6667-6777
    • Treuter, E.1    Johansson, L.2    Thomsen, J.S.3    Warnmark, A.4    Leers, J.5    Pelto-Huikko, M.6    Sjoberg, M.7    Wright, A.P.8    Spyrou, G.9    Gustafsson, J.A.10
  • 45
    • 23744490065 scopus 로고    scopus 로고
    • Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets
    • van de Peppel, J., Kettelarij, N., van Bakel, H., Kockelkorn, T. T., van Leenen, D. and Holstege, F. C. (2005). Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets. Mol. Cell 19, 511-522.
    • (2005) Mol. Cell , vol.19 , pp. 511-522
    • van de Peppel, J.1    Kettelarij, N.2    van Bakel, H.3    Kockelkorn, T.T.4    van Leenen, D.5    Holstege, F.C.6
  • 46
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • Watts, D. J. and Strogatz, S. H. (1998). Collective dynamics of 'small-world' networks. Nature 393, 440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2


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