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Volumn 7, Issue 7, 2012, Pages

Loop 7 of E2 enzymes: An ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade

Author keywords

[No Author keywords available]

Indexed keywords

RING FINGER PROTEIN; RING FINGER PROTEIN RBX1; UBIQUITIN; UBIQUITIN ACTIVATING ENZYME E1; UBIQUITIN CONJUGATING ENZYME E2; UBIQUITIN PROTEIN LIGASE; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG;

EID: 84864021794     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040786     Document Type: Article
Times cited : (25)

References (80)
  • 1
    • 79955484976 scopus 로고    scopus 로고
    • The spatial and temporal organization of ubiquitin networks
    • Grabbe C, Husnjak K, Dikic I, (2011) The spatial and temporal organization of ubiquitin networks. Nat Rev Mol Cell Biol 12: 295-307.
    • (2011) Nat Rev Mol Cell Biol , vol.12 , pp. 295-307
    • Grabbe, C.1    Husnjak, K.2    Dikic, I.3
  • 2
    • 70349441058 scopus 로고    scopus 로고
    • Ubiquitin-binding domains - from structures to functions
    • Dikic I, Wakatsuki S, Walters KJ, (2009) Ubiquitin-binding domains- from structures to functions. Nat Rev Mol Cell Biol 10: 659-671.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 659-671
    • Dikic, I.1    Wakatsuki, S.2    Walters, K.J.3
  • 3
    • 70350150000 scopus 로고    scopus 로고
    • The emerging complexity of protein ubiquitination
    • Komander D, (2009) The emerging complexity of protein ubiquitination. Biochem Soc Trans 37: 937-953.
    • (2009) Biochem Soc Trans , vol.37 , pp. 937-953
    • Komander, D.1
  • 4
    • 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
  • 5
    • 78650100616 scopus 로고    scopus 로고
    • Ubiquitin: Same Molecule, Different Degradation Pathways
    • Clague MJ, Urbe S, (2010) Ubiquitin: Same Molecule, Different Degradation Pathways. Cell 143: 682-685.
    • (2010) Cell , vol.143 , pp. 682-685
    • Clague, M.J.1    Urbe, S.2
  • 6
    • 10744227299 scopus 로고    scopus 로고
    • Specific and covalent targeting of conjugating and deconjugating enzymes of ubiquitin-like proteins
    • Hemelaar J, Borodovsky A, Kessler BM, Reverter D, Cook J, et al. (2004) Specific and covalent targeting of conjugating and deconjugating enzymes of ubiquitin-like proteins. Mol Cell Biol 24: 84-95.
    • (2004) Mol Cell Biol , vol.24 , pp. 84-95
    • Hemelaar, J.1    Borodovsky, A.2    Kessler, B.M.3    Reverter, D.4    Cook, J.5
  • 7
    • 79251482771 scopus 로고    scopus 로고
    • What Determines the Specificity and Outcomes of Ubiquitin Signaling?
    • Ikeda F, Crosetto N, Dikic I, (2010) What Determines the Specificity and Outcomes of Ubiquitin Signaling? Cell 143: 677-681.
    • (2010) Cell , vol.143 , pp. 677-681
    • Ikeda, F.1    Crosetto, N.2    Dikic, I.3
  • 8
    • 71449096063 scopus 로고    scopus 로고
    • Ubiquitin linkages make a difference
    • Dikic I, Dotsch V, (2009) Ubiquitin linkages make a difference. Nat Struct Mol Biol 16: 1208-1210.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 1208-1210
    • Dikic, I.1    Dotsch, V.2
  • 9
    • 67349231313 scopus 로고    scopus 로고
    • Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains
    • Komander D, Reyes-Turcu F, Licchesi JDF, Odenwaelder P, Wilkinson KD, et al. (2009) Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains. Embo Rep 10: 466-473.
    • (2009) Embo Rep , vol.10 , pp. 466-473
    • Komander, D.1    Reyes-Turcu, F.2    Licchesi, J.D.F.3    Odenwaelder, P.4    Wilkinson, K.D.5
  • 10
    • 77955417276 scopus 로고    scopus 로고
    • Lys11-linked ubiquitin chains adopt compact conformations and are preferentially hydrolyzed by the deubiquitinase Cezanne
    • Bremm A, Freund SMV, Komander D, (2010) Lys11-linked ubiquitin chains adopt compact conformations and are preferentially hydrolyzed by the deubiquitinase Cezanne. Nat Struct Mol Biol 17: 939-U947.
    • (2010) Nat Struct Mol Biol , vol.17
    • Bremm, A.1    Freund, S.M.V.2    Komander, D.3
  • 12
    • 79955620198 scopus 로고    scopus 로고
    • Constructing and decoding unconventional ubiquitin chains
    • Behrends C, Harper JW, (2011) Constructing and decoding unconventional ubiquitin chains. Nat Struct Mol Biol 18: 520-528.
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 520-528
    • Behrends, C.1    Harper, J.W.2
  • 13
    • 79551625633 scopus 로고    scopus 로고
    • Ubiquitin networks in cancer
    • Kirkin V, Dikic I, (2011) Ubiquitin networks in cancer. Curr Op Gen & Devel 21: 21-28.
    • (2011) Curr Op Gen & Devel , vol.21 , pp. 21-28
    • Kirkin, V.1    Dikic, I.2
  • 14
    • 54249104026 scopus 로고    scopus 로고
    • The ubiquitin system, disease, and drug discovery
    • Petroski MD, (2008) The ubiquitin system, disease, and drug discovery. BMC Biochem 9.
    • (2008) BMC Biochem , vol.9
    • Petroski, M.D.1
  • 15
    • 79151485014 scopus 로고    scopus 로고
    • Role of ubiquitin-proteasome-mediated proteolysis in nervous system disease
    • Hegde AN, Upadhya SC, (2011) Role of ubiquitin-proteasome-mediated proteolysis in nervous system disease. Biochim Et Biophys Acta 1809: 128-140.
    • (2011) Biochim Et Biophys Acta , vol.1809 , pp. 128-140
    • Hegde, A.N.1    Upadhya, S.C.2
  • 16
    • 78650824534 scopus 로고    scopus 로고
    • Ubiquitin-like protein conjugation and the ubiquitin-proteasome system as drug targets
    • Bedford L, Lowe J, Dick LR, Mayer RJ, Brownell JE, (2011) Ubiquitin-like protein conjugation and the ubiquitin-proteasome system as drug targets. Nat Rev Drug Discov 10: 29-46.
    • (2011) Nat Rev Drug Discov , vol.10 , pp. 29-46
    • Bedford, L.1    Lowe, J.2    Dick, L.R.3    Mayer, R.J.4    Brownell, J.E.5
  • 17
    • 61749102005 scopus 로고    scopus 로고
    • Targeting the SUMO E2 conjugating enzyme Ubc9 interaction for anti-cancer drug design
    • Duan X, Trent JO, Ye H, (2009) Targeting the SUMO E2 conjugating enzyme Ubc9 interaction for anti-cancer drug design. Anti Agents Med Chem 9: 51-54.
    • (2009) Anti Agents Med Chem , vol.9 , pp. 51-54
    • Duan, X.1    Trent, J.O.2    Ye, H.3
  • 18
    • 79959656754 scopus 로고    scopus 로고
    • An Allosteric Inhibitor of the Human Cdc34 Ubiquitin-Conjugating Enzyme
    • Ceccarelli DF, Tang XJ, Pelletier B, Orlicky S, Xie WL, et al. (2011) An Allosteric Inhibitor of the Human Cdc34 Ubiquitin-Conjugating Enzyme. Cell 145: 1075-1087.
    • (2011) Cell , vol.145 , pp. 1075-1087
    • Ceccarelli, D.F.1    Tang, X.J.2    Pelletier, B.3    Orlicky, S.4    Xie, W.L.5
  • 19
    • 67449110736 scopus 로고    scopus 로고
    • Allosteric Activation of E2-RING Finger-Mediated Ubiquitylation by a Structurally Defined Specific E2-Binding Region of gp78
    • Das R, Mariano J, Tsai YC, Kalathur RC, Kostova Z, et al. (2009) Allosteric Activation of E2-RING Finger-Mediated Ubiquitylation by a Structurally Defined Specific E2-Binding Region of gp78. Mol Cell 34: 674-685.
    • (2009) Mol Cell , vol.34 , pp. 674-685
    • Das, R.1    Mariano, J.2    Tsai, Y.C.3    Kalathur, R.C.4    Kostova, Z.5
  • 20
    • 80054680999 scopus 로고    scopus 로고
    • Anti-Ro52 Autoantibodies from Patients with Sjogren's Syndrome Inhibit the Ro52 E3 Ligase Activity by Blocking the E3/E2 Interface
    • Espinosa A, Hennig J, Ambrosi A, Anandapadmanaban M, Abelius MS, et al. (2011) Anti-Ro52 Autoantibodies from Patients with Sjogren's Syndrome Inhibit the Ro52 E3 Ligase Activity by Blocking the E3/E2 Interface. J Biol Chem 286: 36478-36491.
    • (2011) J Biol Chem , vol.286 , pp. 36478-36491
    • Espinosa, A.1    Hennig, J.2    Ambrosi, A.3    Anandapadmanaban, M.4    Abelius, M.S.5
  • 21
    • 79951672720 scopus 로고    scopus 로고
    • Alternative Allosteric Mechanisms Can Regulate the Substrate and E2 in SUMO Conjugation
    • Karaca E, Tozluoglu M, Nussinov R, Haliloglu T, (2011) Alternative Allosteric Mechanisms Can Regulate the Substrate and E2 in SUMO Conjugation. J Mol Biol 406: 620-630.
    • (2011) J Mol Biol , vol.406 , pp. 620-630
    • Karaca, E.1    Tozluoglu, M.2    Nussinov, R.3    Haliloglu, T.4
  • 22
    • 81755171430 scopus 로고    scopus 로고
    • Flexible cullins in cullin-ring E3 ligases allosterically regulate ubiquitination
    • Liu J, Nussinov R, (2011) Flexible cullins in cullin-ring E3 ligases allosterically regulate ubiquitination. J Biol Chem. 286: 40934-42.
    • (2011) J Biol Chem , vol.286 , pp. 40934-40942
    • Liu, J.1    Nussinov, R.2
  • 23
    • 77649272268 scopus 로고    scopus 로고
    • Molecular Dynamics Reveal the Essential Role of Linker Motions in the Function of Cullin-RING E3 Ligases
    • Liu J, Nussinov R, (2010) Molecular Dynamics Reveal the Essential Role of Linker Motions in the Function of Cullin-RING E3 Ligases. J Mol Biol 396: 1508-1523.
    • (2010) J Mol Biol , vol.396 , pp. 1508-1523
    • Liu, J.1    Nussinov, R.2
  • 25
    • 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
  • 26
    • 77950579617 scopus 로고    scopus 로고
    • The E2 Ubiquitin-conjugating Enzymes Direct Polyubiquitination to Preferred Lysines
    • David Y, Ziv T, Admon A, Navon A, (2010) The E2 Ubiquitin-conjugating Enzymes Direct Polyubiquitination to Preferred Lysines. J Biol Chem 285: 8595-8604.
    • (2010) J Biol Chem , vol.285 , pp. 8595-8604
    • David, Y.1    Ziv, T.2    Admon, A.3    Navon, A.4
  • 27
    • 77955990685 scopus 로고    scopus 로고
    • Catalysis of Lysine 48-Specific Ubiquitin Chain Assembly by Residues in E2 and Ubiquitin
    • Rodrigo-Brenni MC, Foster SA, Morgan DO, (2010) Catalysis of Lysine 48-Specific Ubiquitin Chain Assembly by Residues in E2 and Ubiquitin. Mol Cell 39: 548-559.
    • (2010) Mol Cell , vol.39 , pp. 548-559
    • Rodrigo-Brenni, M.C.1    Foster, S.A.2    Morgan, D.O.3
  • 28
    • 77955493107 scopus 로고    scopus 로고
    • Mechanisms of mono- and poly-ubiquitination: Ubiquitination specificity depends on compatibility between the E2 catalytic core and amino acid residues proximal to the lysine
    • Sadowski M, Sarcevic B, (2010) Mechanisms of mono- and poly-ubiquitination: Ubiquitination specificity depends on compatibility between the E2 catalytic core and amino acid residues proximal to the lysine. Cell Div 5: 19.
    • (2010) Cell Div , vol.5 , pp. 19
    • Sadowski, M.1    Sarcevic, B.2
  • 29
    • 38949212916 scopus 로고    scopus 로고
    • Two different classes of E2 ubiquitin-conjugating enzymes are required for the mono-ubiquitination of proteins and elongation by polyubiquitin chains with a specific topology
    • Windheim M, Peggle M, Cohen P, (2008) Two different classes of E2 ubiquitin-conjugating enzymes are required for the mono-ubiquitination of proteins and elongation by polyubiquitin chains with a specific topology. Biochem J 409: 723-729.
    • (2008) Biochem J , vol.409 , pp. 723-729
    • Windheim, M.1    Peggle, M.2    Cohen, P.3
  • 30
    • 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
  • 31
    • 67449091213 scopus 로고    scopus 로고
    • What was the set of ubiquitin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor?
    • Michelle C, Vourc'h P, Mignon L, Andres CR, (2009) What was the set of ubiquitin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor? J Mol Evol 68: 616-628.
    • (2009) J Mol Evol , vol.68 , pp. 616-628
    • Michelle, C.1    Vourc'h, P.2    Mignon, L.3    Andres, C.R.4
  • 32
    • 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
  • 33
    • 34347240365 scopus 로고    scopus 로고
    • Structural and electrostatic properties of ubiquitination and related pathways
    • Winn PJ, Zahran M, Battey JND, Zhou YX, Wade RC, et al. (2007) Structural and electrostatic properties of ubiquitination and related pathways. Front Biosci 12: 3419-3430.
    • (2007) Front Biosci , vol.12 , pp. 3419-3430
    • Winn, P.J.1    Zahran, M.2    Battey, J.N.D.3    Zhou, Y.X.4    Wade, R.C.5
  • 34
    • 79952407243 scopus 로고    scopus 로고
    • Ubiquitin in Motion: Structural Studies of the Ubiquitin-Conjugating Enzyme similar to Ubiquitin Conjugate
    • Pruneda JN, Stoll KE, Bolton LJ, Brzovic PS, Klevit RE, (2011) Ubiquitin in Motion: Structural Studies of the Ubiquitin-Conjugating Enzyme similar to Ubiquitin Conjugate. Biochemistry 50: 1624-1633.
    • (2011) Biochemistry , vol.50 , pp. 1624-1633
    • Pruneda, J.N.1    Stoll, K.E.2    Bolton, L.J.3    Brzovic, P.S.4    Klevit, R.E.5
  • 35
    • 28944435024 scopus 로고    scopus 로고
    • Mechanism of lysine 48-linked ubiquitin-chain synthesis by the cullin-RING ubiquitin-ligase complex SCF-Cdc34
    • Petroski MD, Deshaies RJ, (2005) Mechanism of lysine 48-linked ubiquitin-chain synthesis by the cullin-RING ubiquitin-ligase complex SCF-Cdc34. Cell 123: 1107-1120.
    • (2005) Cell , vol.123 , pp. 1107-1120
    • Petroski, M.D.1    Deshaies, R.J.2
  • 36
    • 35148869981 scopus 로고    scopus 로고
    • Human Cdc34 employs distinct sites to coordinate attachment of ubiquitin to a substrate and assembly of polyubiquitin chains
    • Gazdoiu S, Yamoah K, Wu K, Pan Z-Q, (2007) Human Cdc34 employs distinct sites to coordinate attachment of ubiquitin to a substrate and assembly of polyubiquitin chains. Mol Cell Biol 27: 7041-7052.
    • (2007) Mol Cell Biol , vol.27 , pp. 7041-7052
    • Gazdoiu, S.1    Yamoah, K.2    Wu, K.3    Pan, Z.-Q.4
  • 37
    • 79953178278 scopus 로고    scopus 로고
    • The loop-less (tm)Cdc34 E2 mutant defective in polyubiquitination in vitro and in vivo supports yeast growth in a manner dependent on Ubp14 and Cka2
    • Lass A, Cocklin R, Scaglione KM, Skowyra M, Korolev S, et al. (2011) The loop-less (tm)Cdc34 E2 mutant defective in polyubiquitination in vitro and in vivo supports yeast growth in a manner dependent on Ubp14 and Cka2. Cell Div 6.
    • (2011) Cell Div , vol.6
    • Lass, A.1    Cocklin, R.2    Scaglione, K.M.3    Skowyra, M.4    Korolev, S.5
  • 38
    • 45749091661 scopus 로고    scopus 로고
    • The CK2 phosphorylation of catalytic domain of Cdc34 modulates its activity at the G1 to S transition in Saccharomyces cerevisiae
    • Coccetti P, Tripodi F, Tedeschi G, Nonnis S, Marin O, et al. (2008) The CK2 phosphorylation of catalytic domain of Cdc34 modulates its activity at the G1 to S transition in Saccharomyces cerevisiae. Cell Cycle 7: 1391-1401.
    • (2008) Cell Cycle , vol.7 , pp. 1391-1401
    • Coccetti, P.1    Tripodi, F.2    Tedeschi, G.3    Nonnis, S.4    Marin, O.5
  • 39
    • 79958155322 scopus 로고    scopus 로고
    • An Acidic Loop and Cognate Phosphorylation Sites Define a Molecular Switch That Modulates Ubiquitin Charging Activity in Cdc34-Like Enzymes
    • Papaleo E, Ranzani V, Tripodi F, Vitriolo A, Cirulli C, et al. (2011) An Acidic Loop and Cognate Phosphorylation Sites Define a Molecular Switch That Modulates Ubiquitin Charging Activity in Cdc34-Like Enzymes. PLoS Comput Biol 7: e100256.
    • (2011) PLoS Comput Biol , vol.7
    • Papaleo, E.1    Ranzani, V.2    Tripodi, F.3    Vitriolo, A.4    Cirulli, C.5
  • 40
    • 0035174874 scopus 로고    scopus 로고
    • Identification of molecular determinants required for interaction of ubiquitin-conjugating enzymes and RING finger proteins
    • Martinez-Noel G, Muller U, Harbers K, (2001) Identification of molecular determinants required for interaction of ubiquitin-conjugating enzymes and RING finger proteins. Eur J Biochem 268: 5912-5919.
    • (2001) Eur J Biochem , vol.268 , pp. 5912-5919
    • Martinez-Noel, G.1    Muller, U.2    Harbers, K.3
  • 41
  • 42
    • 79955058214 scopus 로고    scopus 로고
    • Active-site residues move independently from the rest of the protein in a 200 ns molecular dynamics simulation of cytochrome P450 CYP119
    • Brandman R, Lampe JN, Brandman Y, de Montellano PRO, (2011) Active-site residues move independently from the rest of the protein in a 200 ns molecular dynamics simulation of cytochrome P450 CYP119. Arch Biochem Biophys 509: 127-132.
    • (2011) Arch Biochem Biophys , vol.509 , pp. 127-132
    • Brandman, R.1    Lampe, J.N.2    Brandman, Y.3    de Montellano, P.R.O.4
  • 43
    • 79953671764 scopus 로고    scopus 로고
    • "Fluctuograms" Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution
    • Silvestre-Ryan J, Lin YC, Chu JW, (2011) "Fluctuograms" Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution. PLoS Comput Biol 7: e100023.
    • (2011) PLoS Comput Biol , vol.7
    • Silvestre-Ryan, J.1    Lin, Y.C.2    Chu, J.W.3
  • 44
    • 77955682724 scopus 로고    scopus 로고
    • Rbx1 Flexible Linker Facilitates Cullin-RING Ligase Function Before Neddylation and After Deneddylation
    • Liu J, Nussinov R, (2010) Rbx1 Flexible Linker Facilitates Cullin-RING Ligase Function Before Neddylation and After Deneddylation. Biophys J 99: 736-744.
    • (2010) Biophys J , vol.99 , pp. 736-744
    • Liu, J.1    Nussinov, R.2
  • 46
    • 0031037265 scopus 로고    scopus 로고
    • Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution
    • Cook WJ, Martin PD, Edwards BF, Yamazaki RK, Chau V, (1997) Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution. Biochemistry 36: 1621-1627.
    • (1997) Biochemistry , vol.36 , pp. 1621-1627
    • Cook, W.J.1    Martin, P.D.2    Edwards, B.F.3    Yamazaki, R.K.4    Chau, V.5
  • 47
    • 77951244767 scopus 로고    scopus 로고
    • Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2
    • Ju T, Bocik W, Majumdar A, Tolman JR, (2010) Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2. Proteins 78: 1291-1301.
    • (2010) Proteins , vol.78 , pp. 1291-1301
    • Ju, T.1    Bocik, W.2    Majumdar, A.3    Tolman, J.R.4
  • 48
    • 33747818007 scopus 로고    scopus 로고
    • CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    • Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, et al. (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34: W116-W118.
    • (2006) Nucleic Acids Res , vol.34
    • Dundas, J.1    Ouyang, Z.2    Tseng, J.3    Binkowski, A.4    Turpaz, Y.5
  • 49
    • 33748684383 scopus 로고    scopus 로고
    • Identification of function-associated loop motifs and application to protein function prediction
    • Espadaler J, Querol E, Aviles FX, Oliva B, (2006) Identification of function-associated loop motifs and application to protein function prediction. Bioinformatics 22: 2237-2243.
    • (2006) Bioinformatics , vol.22 , pp. 2237-2243
    • Espadaler, J.1    Querol, E.2    Aviles, F.X.3    Oliva, B.4
  • 50
    • 0029070171 scopus 로고
    • PROTEIN MOTIFS.6. OMEGA-LOOPS - NONREGULAR SECONDARY STRUCTURES SIGNIFICANT IN PROTEIN FUNCTION AND STABILITY
    • Fetrow JS, (1995) PROTEIN MOTIFS.6. OMEGA-LOOPS- NONREGULAR SECONDARY STRUCTURES SIGNIFICANT IN PROTEIN FUNCTION AND STABILITY. FASEB J 9: 708-717.
    • (1995) FASEB J , vol.9 , pp. 708-717
    • Fetrow, J.S.1
  • 51
    • 0022981913 scopus 로고
    • LOOPS IN GLOBULAR-PROTEINS - A NOVEL CATEGORY OF SECONDARY STRUCTURE
    • Leszczynski JF, Rose GD, (1986) LOOPS IN GLOBULAR-PROTEINS- A NOVEL CATEGORY OF SECONDARY STRUCTURE. Science 234: 849-855.
    • (1986) Science , vol.234 , pp. 849-855
    • Leszczynski, J.F.1    Rose, G.D.2
  • 52
    • 0026530262 scopus 로고
    • TAXONOMY AND CONFORMATIONAL-ANALYSIS OF LOOPS IN PROTEINS
    • Ring CS, Kneller DG, Langridge R, Cohen FE, (1992) TAXONOMY AND CONFORMATIONAL-ANALYSIS OF LOOPS IN PROTEINS. J Mol Biol 224: 685-699.
    • (1992) J Mol Biol , vol.224 , pp. 685-699
    • Ring, C.S.1    Kneller, D.G.2    Langridge, R.3    Cohen, F.E.4
  • 54
    • 0037334895 scopus 로고    scopus 로고
    • One-thousand-and-one substrates of protein kinase CK2?
    • Meggio F, Pinna LA, (2003) One-thousand-and-one substrates of protein kinase CK2? FASEB J 17: 349-368.
    • (2003) FASEB J , vol.17 , pp. 349-368
    • Meggio, F.1    Pinna, L.A.2
  • 55
    • 0034788322 scopus 로고    scopus 로고
    • Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail
    • Hamilton KS, Ellison MJ, Barber KR, Williams RS, Huzil JT, et al. (2001) Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail. Structure 9: 897-904.
    • (2001) Structure , vol.9 , pp. 897-904
    • Hamilton, K.S.1    Ellison, M.J.2    Barber, K.R.3    Williams, R.S.4    Huzil, J.T.5
  • 56
    • 56149122833 scopus 로고    scopus 로고
    • Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase itch and the E2 UbcH7
    • Raimondo D, Giorgetti A, Bernassola F, Melino G, Tramontano A, (2008) Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase itch and the E2 UbcH7. Biochem Pharmacol 76: 1620-1627.
    • (2008) Biochem Pharmacol , vol.76 , pp. 1620-1627
    • Raimondo, D.1    Giorgetti, A.2    Bernassola, F.3    Melino, G.4    Tramontano, A.5
  • 57
    • 79958694800 scopus 로고    scopus 로고
    • E2 Conjugating Enzyme Selectivity and Requirements for Function of the E3 Ubiquitin Ligase CHIP
    • Soss SE, Yue YY, Dhe-Paganon S, Chazin WJ, (2011) E2 Conjugating Enzyme Selectivity and Requirements for Function of the E3 Ubiquitin Ligase CHIP. J Biol Chem 286: 21277-21286.
    • (2011) J Biol Chem , vol.286 , pp. 21277-21286
    • Soss, S.E.1    Yue, Y.Y.2    Dhe-Paganon, S.3    Chazin, W.J.4
  • 58
    • 0033591242 scopus 로고    scopus 로고
    • Identification of rabbit reticulocyte E2(17K) as a UBC7 homologue and functional characterization of its core domain loop
    • Lin HJ, Wing SS, (1999) Identification of rabbit reticulocyte E2(17K) as a UBC7 homologue and functional characterization of its core domain loop. J Biol Chem 274: 14685-14691.
    • (1999) J Biol Chem , vol.274 , pp. 14685-14691
    • Lin, H.J.1    Wing, S.S.2
  • 59
    • 0029143644 scopus 로고
    • Intragenic suppression among CDC34 (UBC3) mutations defines a class of ubiquitin-conjugating catalytic domains
    • Liu Y, Mathias N, Steussy CN, Goebl MG, (1995) Intragenic suppression among CDC34 (UBC3) mutations defines a class of ubiquitin-conjugating catalytic domains. Mol Cell Biol 15: 5635-5644.
    • (1995) Mol Cell Biol , vol.15 , pp. 5635-5644
    • Liu, Y.1    Mathias, N.2    Steussy, C.N.3    Goebl, M.G.4
  • 60
    • 34547447215 scopus 로고    scopus 로고
    • Cdc34 C-terminal tail phosphorylation regulates Skp1/cullin/F-box (SCF)-mediated ubiquitination and cell cycle progression
    • Sadowski M, Mawson A, Baker R, Sarcevic B, (2007) Cdc34 C-terminal tail phosphorylation regulates Skp1/cullin/F-box (SCF)-mediated ubiquitination and cell cycle progression. Biochem J 405: 569-581.
    • (2007) Biochem J , vol.405 , pp. 569-581
    • Sadowski, M.1    Mawson, A.2    Baker, R.3    Sarcevic, B.4
  • 61
    • 33646266474 scopus 로고    scopus 로고
    • Conformational changes in protein loops and helices induced by post-translational phosphorylation
    • Groban ES, Narayanan A, Jacobson MP, (2006) Conformational changes in protein loops and helices induced by post-translational phosphorylation. PLoS Comput Biol 2: 238-250.
    • (2006) PLoS Comput Biol , vol.2 , pp. 238-250
    • Groban, E.S.1    Narayanan, A.2    Jacobson, M.P.3
  • 62
    • 0035815288 scopus 로고    scopus 로고
    • Dynamic coupling between the SH2 and SH3 domains of c-Src and hck underlies their inactivation by C-terminal tyrosine phosphorylation
    • Young MA, Gonfloni S, Superti-Furga G, Roux B, Kuriyan J, (2001) Dynamic coupling between the SH2 and SH3 domains of c-Src and hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105: 115-126.
    • (2001) Cell , vol.105 , pp. 115-126
    • Young, M.A.1    Gonfloni, S.2    Superti-Furga, G.3    Roux, B.4    Kuriyan, J.5
  • 63
    • 78650805323 scopus 로고    scopus 로고
    • Chemical states of the N-terminal "lid" of MDM2 regulate p53 binding Simulations reveal complexities of modulation
    • Dastidar SG, Raghunathan D, Nicholson J, Hupp TR, Lane DP, et al. (2011) Chemical states of the N-terminal "lid" of MDM2 regulate p53 binding Simulations reveal complexities of modulation. Cell Cycle 10: 82-89.
    • (2011) Cell Cycle , vol.10 , pp. 82-89
    • Dastidar, S.G.1    Raghunathan, D.2    Nicholson, J.3    Hupp, T.R.4    Lane, D.P.5
  • 64
    • 64549122329 scopus 로고    scopus 로고
    • Computational studies of protein regulation by post-translational phosphorylation
    • Narayanan A, Jacobson MP, (2009) Computational studies of protein regulation by post-translational phosphorylation. Curr Op Struct Biol19: 156-163.
    • (2009) Curr Op Struct Biol , vol.19 , pp. 156-163
    • Narayanan, A.1    Jacobson, M.P.2
  • 65
    • 62549151081 scopus 로고    scopus 로고
    • Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations
    • Berteotti A, Cavalli A, Branduardi D, Gervasio FL, Recanatini M, et al. (2009) Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations. J Am Chem Soc 131: 244-250.
    • (2009) J Am Chem Soc , vol.131 , pp. 244-250
    • Berteotti, A.1    Cavalli, A.2    Branduardi, D.3    Gervasio, F.L.4    Recanatini, M.5
  • 66
    • 24744450560 scopus 로고    scopus 로고
    • Ubiquitin manipulation by an E2 conjugating enzyme using a novel covalent intermediate
    • Merkley N, Barber KR, Shaw GS, (2005) Ubiquitin manipulation by an E2 conjugating enzyme using a novel covalent intermediate. J Biol Chem 280: 31732-31738.
    • (2005) J Biol Chem , vol.280 , pp. 31732-31738
    • Merkley, N.1    Barber, K.R.2    Shaw, G.S.3
  • 67
    • 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
  • 68
    • 33947243954 scopus 로고    scopus 로고
    • A ubiquitin ligase transfers preformed polyubiquitin chains from a conjugating enzyme to a substrate
    • Li W, Tu D, Brunger AT, Ye Y, (2007) A ubiquitin ligase transfers preformed polyubiquitin chains from a conjugating enzyme to a substrate. Nature 446: 333-337.
    • (2007) Nature , vol.446 , pp. 333-337
    • Li, W.1    Tu, D.2    Brunger, A.T.3    Ye, Y.4
  • 69
    • 33748309025 scopus 로고    scopus 로고
    • DivergentSet, a tool for picking non-redundant sequences from large sequence collections
    • Widmann J, Hamady M, Knight R, (2006) DivergentSet, a tool for picking non-redundant sequences from large sequence collections. Mol Cell Proteomics 5: 1520-1532.
    • (2006) Mol Cell Proteomics , vol.5 , pp. 1520-1532
    • Widmann, J.1    Hamady, M.2    Knight, R.3
  • 70
    • 78650567599 scopus 로고    scopus 로고
    • A performance enhanced PSI-BLAST based on hybrid alignment
    • Li YH, Chia N, Lauria M, Bundschuh R, (2011) A performance enhanced PSI-BLAST based on hybrid alignment. Bioinformatics 27: 31-37.
    • (2011) Bioinformatics , vol.27 , pp. 31-37
    • Li, Y.H.1    Chia, N.2    Lauria, M.3    Bundschuh, R.4
  • 72
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa J, (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217.
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 73
    • 0036681416 scopus 로고    scopus 로고
    • Scoring residue conservation
    • Valdar WSJ, (2002) Scoring residue conservation. Proteins 48: 227-241.
    • (2002) Proteins , vol.48 , pp. 227-241
    • Valdar, W.S.J.1
  • 74
    • 77953513118 scopus 로고    scopus 로고
    • Improved side-chain torsion potentials for the Amber ff99SB protein force field
    • Lindorff-Larsen K, Piana S, Palmo K, Maragakis P, Klepeis JL, et al. (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78: 1950-1958.
    • (2010) Proteins , vol.78 , pp. 1950-1958
    • Lindorff-Larsen, K.1    Piana, S.2    Palmo, K.3    Maragakis, P.4    Klepeis, J.L.5
  • 76
    • 0034500645 scopus 로고    scopus 로고
    • Similarities between principal components of protein dynamics and random diffusion
    • Hess
    • Hess (2000) Similarities between principal components of protein dynamics and random diffusion. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 62: 8438-8448.
    • (2000) Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics , vol.62 , pp. 8438-8448
  • 77
    • 67349196001 scopus 로고    scopus 로고
    • Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case
    • Papaleo E, Mereghetti P, Fantucci P, Grandori R, De Gioia L, (2009) Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case. J Mol Graph Model 27: 889-899.
    • (2009) J Mol Graph Model , vol.27 , pp. 889-899
    • Papaleo, E.1    Mereghetti, P.2    Fantucci, P.3    Grandori, R.4    de Gioia, L.5
  • 78
    • 0029092698 scopus 로고
    • Fluctuation And Cross-Correlation Analysis Of Protein Motions Observed In Nanosecond Molecular-Dynamics Simulations
    • Hunenberger PH, Mark AE, Vangunsteren WF, (1995) Fluctuation And Cross-Correlation Analysis Of Protein Motions Observed In Nanosecond Molecular-Dynamics Simulations. J Mol Biol 252: 492-503.
    • (1995) J Mol Biol , vol.252 , pp. 492-503
    • Hunenberger, P.H.1    Mark, A.E.2    Vangunsteren, W.F.3
  • 79
    • 79952455148 scopus 로고    scopus 로고
    • Dynamic properties of extremophilic subtilisin-like serine-proteases
    • Tiberti M, Papaleo E, (2011) Dynamic properties of extremophilic subtilisin-like serine-proteases. J Struct Biol. 174: 69-83.
    • (2011) J Struct Biol , vol.174 , pp. 69-83
    • Tiberti, M.1    Papaleo, E.2
  • 80
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, et al. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80: 505-515.
    • (2001) Biophys J , vol.80 , pp. 505-515
    • Atilgan, A.R.1    Durell, S.R.2    Jernigan, R.L.3    Demirel, M.C.4    Keskin, O.5


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