• 1
    Komander D, Rape M (2012) The ubiquitin code. Annu Rev Biochem 81:203229.
  • 2
    Hospenthal MK, Freund SM, Komander D (2013) Assembly, analysis and architecture of atypical ubiquitin chains. Nat Struct Mol Biol 20:555565.
  • 3
    Ikeda H, Kerppola TK (2008) Lysosomal localization of ubiquitinated Jun requires multiple determinants in a lysine-27-linked polyubiquitin conjugate. Mol Biol Cell 19:45884601.
  • 4
    Oshikawa K, Matsumoto M, Nakayama KI (2012) Comprehensive study of protein ubiquitylation sites by conjugation of engineered lysine-less ubiquitin. Seikagaku 84:479487.
  • 5
    Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI (2012) Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin. J Proteome Res 11:796807.
  • 6
    Sun T, Guo J, Shallow H, Yang T, Xu J, Li W, Hanson C, Wu JG, Li X, Massaeli H, Zhang S (2011) The role of monoubiquitination in endocytic degradation of human ether-a-go-go-related gene (hERG) channels under low K+ conditions. J Biol Chem 286:67516759.
  • 7
    Ziv I, Matiuhin Y, Kirkpatrick DS, Erpapazoglou Z, Leon S, Pantazopoulou M, Kim W, Gygi SP, Haguenauer-Tsapis R, Reis N, Glickman MH, Kleifeld O (2011) A perturbed ubiquitin landscape distinguishes between ubiquitin in trafficking and in proteolysis. Mol Cell Proteomics 10:M111 009753.
  • 8
    Eddins MJ, Waradan R, Fushman D, Pickart CM, Wolberger C (2007) Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH. J Mol Biol 367:204211.
  • 9
    Zhang N, Wang Q, Ehlinger A, Randles L, Lary JW, Kang Y, Harirnia A, Storaska AJ, Cole JL, Fushman D, Walters KJ (2009) Structure of the S5a:k48-linked diubiquitin complex and its interactions with rpn13. Mol Cell 35:280290.
  • 10
    Johnson EC, Handel TM (1999) Effect of hydrophobic core packing on sidechain dynamics. J Biomol NMR 15:135143.
  • 11
    Johnson EC, Lazar GA, Desjarlais JR, Handel TM (1999) Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin. Structure 7:967976.
  • 12
    Lazar GA, Desjarlais JR, Handel TM (1997) De novo design of the hydrophobic core of ubiquitin. Protein Sci 6:11671178.
  • 13
    Lazar GA, Johnson EC, Desjarlais JR, Handel TM (1999) Rotamer strain as a determinant of protein structural specificity. Protein Sci 8:25982610.
  • 14
    Haririnai A, Verma R, Purohit N, Twarog MZ, Deshaies RJ, Bolon D, Fushman D (2008) Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins. J Mol Biol 375:979996.
  • 15
    Hirano T, Serve O, Yagi-Utsumi M, Takemoto E, Hiromoto T, Satoh T, Mizushima T, Kato K (2011) Conformational dynamics of wild-type Lys-48-linked diubiquitin in solution. J Biol Chem 286:3749637502.
  • 16
    Lai MY, Zhang D, Laronde-Leblanc N, Fushman D (2012) Structural and biochemical studies of the open state of Lys48-linked diubiquitin. Biochim Biophys Acta 1823:20462056.
  • 17
    Castaneda CA, Kashyap TR, Nakasone MA, Krueger S, Fushman D (2013) Unique structural, dynamical, and functional properties of k11-linked polyubiquitin chains. Structure 21:11681181.
  • 18
    Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120:68366837.
  • 19
    Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 194:531544.
  • 20
    Esadze A, Li DW, Wang T, Bruschweiler R, Iwahara J (2011) Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H-15N NMR spectroscopy. J Am Chem Soc 133:909919.
  • 21
    Eghbalnia HR, Wang L, Bahrami A, Assadi A, Markley JL (2005) Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR 32:7181.
  • 22
    Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS plus : a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213223.
  • 23
    Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:46854690.
  • 24
    Zweckstetter M, Bax A (2000) Prediction of sterically induced alignment in a dilute liquid crystalline phase: aid to protein structure determination by NMR. J Am Chem Soc 122:37913792.
  • 25
    Das R, Mariano J, Tsai YC, Kalathur RC, Kostova Z, Li J, Tarasov SG, McFeeters RL, Altieri AS, Ji X, Byrd RA, Weissman AM (2009) Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78. Mol Cell 34:674685.
  • 26
    Stagno JR, Altieri AS, Bubunenko M, Tarasov SG, Li J, Court DL, Byrd RA, Ji X (2011) Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination. Nucleic Acids Res 39:78037815.
  • 27
    Das R, Liang YH, Mariano J, Li J, Huang T, King A, Tarasov SG, Weissman AM, Ji X, Byrd RA (2013) Allosteric regulation of E2-E3 interactions promote a processive ubiquitination machine. EMBO J 32:25042516.
  • 28
    Sattler M, Schleucher J, Griesinger C (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog Nucl Mag Res Sp 34:93158.
  • 29
    Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) Nmrpipe—a multidimensional spectral processing system based on Unix pipes. J Biomol NMR 6:277293.
  • 30
    Goddard TD, Kneller DG SPARKY 3, San Francisco: University of California.
  • 31
    Cordier F, Dingley AJ, Grzesiek S (1999) A doublet-separated sensitivity-enhanced HSQC for the determination of scalar and dipolar one-bond J-couplings. J Biomol NMR 13:175180.
  • 32
    Ruckert M, Otting G (2000) Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. J Am Chem Soc 122:77937797.
  • 33
    Sgourakis NG, Lange OF, DiMaio F, Andre I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D (2011) Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings. J Am Chem Soc 133:62886298.