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Volumn 8, Issue 11, 2012, Pages

Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DYNAMICS; ENZYMES; PLANTS (BOTANY);

EID: 84870667444     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002754     Document Type: Article
Times cited : (16)

References (38)
  • 1
    • 70350482286 scopus 로고    scopus 로고
    • Evolution of biomolecular networks: lessons from metabolic and protein interactions
    • Yamada T, Bork P, (2009) Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nat Rev Mol Cell Biol 10: 791-803.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 791-803
    • Yamada, T.1    Bork, P.2
  • 3
    • 34347265174 scopus 로고    scopus 로고
    • Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins
    • Dye BT, Schulman BA, (2007) Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins. Annu Rev Biophys Biomol Struct 36: 131-150.
    • (2007) Annu Rev Biophys Biomol Struct , vol.36 , pp. 131-150
    • Dye, B.T.1    Schulman, B.A.2
  • 4
    • 0034915764 scopus 로고    scopus 로고
    • Mechanisms underlying ubiquitination
    • Pickart CM, (2001) Mechanisms underlying ubiquitination. Annu Rev Biochem 70: 503-533.
    • (2001) Annu Rev Biochem , vol.70 , pp. 503-533
    • Pickart, C.M.1
  • 5
    • 67349109115 scopus 로고    scopus 로고
    • Ubiquitin, infinitely seductive: symposium on the many faces of ubiquitin
    • Rape M, (2009) Ubiquitin, infinitely seductive: symposium on the many faces of ubiquitin. EMBO Rep 10: 558-562.
    • (2009) EMBO Rep , vol.10 , pp. 558-562
    • Rape, M.1
  • 6
    • 34347329214 scopus 로고    scopus 로고
    • Dual E1 activation systems for ubiquitin differentially regulate E2 enzyme charging
    • Jin J, Li X, Gygi SP, Harper JW, (2007) Dual E1 activation systems for ubiquitin differentially regulate E2 enzyme charging. Nature 447: 1135-1138.
    • (2007) Nature , vol.447 , pp. 1135-1138
    • Jin, J.1    Li, X.2    Gygi, S.P.3    Harper, J.W.4
  • 7
    • 34748884321 scopus 로고    scopus 로고
    • E1-L2 activates both ubiquitin and FAT10
    • Chiu YH, Sun Q, Chen ZJ, (2007) E1-L2 activates both ubiquitin and FAT10. Mol Cell 27: 1014-1023.
    • (2007) Mol Cell , vol.27 , pp. 1014-1023
    • Chiu, Y.H.1    Sun, Q.2    Chen, Z.J.3
  • 8
    • 70350461507 scopus 로고    scopus 로고
    • Building ubiquitin chains: E2 enzymes at work
    • Ye Y, Rape M, (2009) Building ubiquitin chains: E2 enzymes at work. Nat Rev Mol Cell Biol 10: 755-764.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 755-764
    • Ye, Y.1    Rape, M.2
  • 9
    • 70349645557 scopus 로고    scopus 로고
    • Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network
    • Markson G, Kiel C, Hyde R, Brown S, Charalabous P, et al. (2009) Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res 19: 1905-1911.
    • (2009) Genome Res , vol.19 , pp. 1905-1911
    • Markson, G.1    Kiel, C.2    Hyde, R.3    Brown, S.4    Charalabous, P.5
  • 10
    • 77951651753 scopus 로고    scopus 로고
    • The family of ubiquitin-conjugating enzymes (E2s): deciding between life and death of proteins
    • van Wijk SJ, Timmers HT, (2010) The family of ubiquitin-conjugating enzymes (E2s): deciding between life and death of proteins. Faseb J 24: 981-993.
    • (2010) Faseb J , vol.24 , pp. 981-993
    • van Wijk, S.J.1    Timmers, H.T.2
  • 11
    • 78751498823 scopus 로고    scopus 로고
    • E2s: structurally economical and functionally replete
    • Wenzel DM, Stoll KE, Klevit RE, (2011) E2s: structurally economical and functionally replete. Biochem J 433: 31-42.
    • (2011) Biochem J , vol.433 , pp. 31-42
    • Wenzel, D.M.1    Stoll, K.E.2    Klevit, R.E.3
  • 12
    • 42649124278 scopus 로고    scopus 로고
    • Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation
    • Burroughs AM, Jaffee M, Iyer LM, Aravind L, (2008) Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. J Struct Biol 162: 205-218.
    • (2008) J Struct Biol , vol.162 , pp. 205-218
    • Burroughs, A.M.1    Jaffee, M.2    Iyer, L.M.3    Aravind, L.4
  • 13
    • 69249150517 scopus 로고    scopus 로고
    • A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system
    • van Wijk SJ, de Vries SJ, Kemmeren P, Huang A, Boelens R, et al. (2009) A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system. Mol Syst Biol 5: 295.
    • (2009) Mol Syst Biol , vol.5 , pp. 295
    • van Wijk, S.J.1    de Vries, S.J.2    Kemmeren, P.3    Huang, A.4    Boelens, R.5
  • 14
    • 79952290609 scopus 로고    scopus 로고
    • The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2
    • Wickliffe KE, Lorenz S, Wemmer DE, Kuriyan J, Rape M, (2011) The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2. Cell 144: 769-781.
    • (2011) Cell , vol.144 , pp. 769-781
    • Wickliffe, K.E.1    Lorenz, S.2    Wemmer, D.E.3    Kuriyan, J.4    Rape, M.5
  • 15
    • 1842510658 scopus 로고    scopus 로고
    • An altered-specificity ubiquitin-conjugating enzyme/ubiquitin-protein ligase pair
    • Winkler GS, Albert TK, Dominguez C, Legtenberg YI, Boelens R, et al. (2004) An altered-specificity ubiquitin-conjugating enzyme/ubiquitin-protein ligase pair. J Mol Biol 337: 157-165.
    • (2004) J Mol Biol , vol.337 , pp. 157-165
    • Winkler, G.S.1    Albert, T.K.2    Dominguez, C.3    Legtenberg, Y.I.4    Boelens, R.5
  • 16
    • 40949086767 scopus 로고    scopus 로고
    • Identification of conjugation specificity determinants unmasks vestigial preference for ubiquitin within the NEDD8 E2
    • Huang DT, Zhuang M, Ayrault O, Schulman BA, (2008) Identification of conjugation specificity determinants unmasks vestigial preference for ubiquitin within the NEDD8 E2. Nat Struct Mol Biol 15: 280-287.
    • (2008) Nat Struct Mol Biol , vol.15 , pp. 280-287
    • Huang, D.T.1    Zhuang, M.2    Ayrault, O.3    Schulman, B.A.4
  • 17
    • 53049083773 scopus 로고    scopus 로고
    • The basis for selective E1-E2 interactions in the ISG15 conjugation system
    • Durfee LA, Kelley ML, Huibregtse JM, (2008) The basis for selective E1-E2 interactions in the ISG15 conjugation system. J Biol Chem 283: 23895-23902.
    • (2008) J Biol Chem , vol.283 , pp. 23895-23902
    • Durfee, L.A.1    Kelley, M.L.2    Huibregtse, J.M.3
  • 18
    • 77955391393 scopus 로고    scopus 로고
    • The HADDOCK web server for data-driven biomolecular docking
    • de Vries SJ, van Dijk M, Bonvin AM, (2010) The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 5: 883-897.
    • (2010) Nat Protoc , vol.5 , pp. 883-897
    • de Vries, S.J.1    van Dijk, M.2    Bonvin, A.M.3
  • 19
    • 36748998784 scopus 로고    scopus 로고
    • HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets
    • de Vries SJ, van Dijk AD, Krzeminski M, van Dijk M, Thureau A, et al. (2007) HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69: 726-733.
    • (2007) Proteins , vol.69 , pp. 726-733
    • de Vries, S.J.1    van Dijk, A.D.2    Krzeminski, M.3    van Dijk, M.4    Thureau, A.5
  • 20
    • 0028896619 scopus 로고
    • Measurement of yeast intracellular pH by image processing and the change it undergoes during growth phase
    • Imai T, Ohno T, (1995) Measurement of yeast intracellular pH by image processing and the change it undergoes during growth phase. J Biotechnol 38: 165-172.
    • (1995) J Biotechnol , vol.38 , pp. 165-172
    • Imai, T.1    Ohno, T.2
  • 21
    • 0036143771 scopus 로고    scopus 로고
    • A novel mechanism of tumorigenesis involving pH-dependent destabilization of a mutant p53 tetramer
    • DiGiammarino EL, Lee AS, Cadwell C, Zhang W, Bothner B, et al. (2002) A novel mechanism of tumorigenesis involving pH-dependent destabilization of a mutant p53 tetramer. Nat Struct Biol 9: 12-16.
    • (2002) Nat Struct Biol , vol.9 , pp. 12-16
    • DiGiammarino, E.L.1    Lee, A.S.2    Cadwell, C.3    Zhang, W.4    Bothner, B.5
  • 22
    • 66149124079 scopus 로고    scopus 로고
    • Cooperative regulation of p53 by modulation of ternary complex formation with CBP/p300 and HDM2
    • Ferreon JC, Lee CW, Arai M, Martinez-Yamout MA, Dyson HJ, et al. (2009) Cooperative regulation of p53 by modulation of ternary complex formation with CBP/p300 and HDM2. Proc Natl Acad Sci U S A 106: 6591-6596.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 6591-6596
    • Ferreon, J.C.1    Lee, C.W.2    Arai, M.3    Martinez-Yamout, M.A.4    Dyson, H.J.5
  • 23
    • 0033536637 scopus 로고    scopus 로고
    • The tyrosine kinase negative regulator c-Cbl as a RING-type, E2-dependent ubiquitin-protein ligase
    • Joazeiro CA, Wing SS, Huang H, Leverson JD, Hunter T, et al. (1999) The tyrosine kinase negative regulator c-Cbl as a RING-type, E2-dependent ubiquitin-protein ligase. Science 286: 309-312.
    • (1999) Science , vol.286 , pp. 309-312
    • Joazeiro, C.A.1    Wing, S.S.2    Huang, H.3    Leverson, J.D.4    Hunter, T.5
  • 24
    • 1842607157 scopus 로고    scopus 로고
    • Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches
    • Dominguez C, Bonvin AM, Winkler GS, van Schaik FM, Timmers HT, et al. (2004) Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Structure 12: 633-644.
    • (2004) Structure , vol.12 , pp. 633-644
    • Dominguez, C.1    Bonvin, A.M.2    Winkler, G.S.3    van Schaik, F.M.4    Timmers, H.T.5
  • 25
    • 4444314569 scopus 로고    scopus 로고
    • Determinants of functionality in the ubiquitin conjugating enzyme family
    • Winn PJ, Religa TL, Battey JN, Banerjee A, Wade RC, (2004) Determinants of functionality in the ubiquitin conjugating enzyme family. Structure 12: 1563-1574.
    • (2004) Structure , vol.12 , pp. 1563-1574
    • Winn, P.J.1    Religa, T.L.2    Battey, J.N.3    Banerjee, A.4    Wade, R.C.5
  • 27
    • 84864117363 scopus 로고    scopus 로고
    • Genome scale analysis of interaction dynamics reveals organization of biological networks
    • Das J, Mohammed J, Yu H, (2012) Genome scale analysis of interaction dynamics reveals organization of biological networks. Bioinformatics 28: 1873-8.
    • (2012) Bioinformatics , vol.28 , pp. 1873-1878
    • Das, J.1    Mohammed, J.2    Yu, H.3
  • 28
    • 37049014272 scopus 로고    scopus 로고
    • Version 1.2 of the Crystallography and NMR system
    • Brunger AT, (2007) Version 1.2 of the Crystallography and NMR system. Nat Protoc 2: 2728-2733.
    • (2007) Nat Protoc , vol.2 , pp. 2728-2733
    • Brunger, A.T.1
  • 32
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • Bussi G, Donadio D, Parrinello M, (2007) Canonical sampling through velocity rescaling. J Chem Phys 126: 014101.
    • (2007) J Chem Phys , vol.126 , pp. 014101
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 34
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • Tironi IG, Sperb R, Smith PE, van Gunsteren WF, (1995) A generalized reaction field method for molecular dynamics simulations. J Chem Phys 102: 5451-5459.
    • (1995) J Chem Phys , vol.102 , pp. 5451-5459
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    van Gunsteren, W.F.4
  • 35
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N [center-dot] log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: An N [center-dot] log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.