System-wide Analysis Reveals Intrinsically Disordered Proteins Are Prone to Ubiquitylation after Misfolding Stress
Tài liệu tham khảo
Balch, 2008, Adapting proteostasis for disease intervention, Science, 319, 916, 10.1126/science.1141448
Hartl, 2011, Molecular chaperones in protein folding and proteostasis, Nature, 475, 324, 10.1038/nature10317
Pickart, 2004, Ubiquitin: structures, functions, mechanisms, Biochim. Biophys. Acta, 1695, 55, 10.1016/j.bbamcr.2004.09.019
Finley, 2009, Recognition and processing of ubiquitin-protein conjugates by the proteasome, Ann. Rev. Biochem, 78, 477, 10.1146/annurev.biochem.78.081507.101607
Berke, 2003, Protein aggregation and the ubiquitin proteasome pathway: gaining the UPPer hand on neurodegeneration, Curr. Opin. Genet. Dev, 13, 253, 10.1016/S0959-437X(03)00053-4
Carrard, 2002, Impairment of proteasome structure and function in aging, Int. J. Biochem. Cell Biol, 34, 1461, 10.1016/S1357-2725(02)00085-7
Vembar, 2008, One step at a time: endoplasmic reticulum-associated degradation, Nat. Rev. Mol. Cell Biol, 9, 944, 10.1038/nrm2546
Connell, 2001, The co-chaperone CHIP regulates protein triage decisions mediated by heat-shock proteins, Nat. Cell Biol, 3, 93, 10.1038/35050618
Hough, 1986, Ubiquitin-lysozyme conjugates, J. Biol. Chem, 261, 2400, 10.1016/S0021-9258(17)35950-1
Parag, 1987, Effect of heat shock on protein degradation in mammalian cells: involvement of the ubiquitin system, EMBO J, 6, 55, 10.1002/j.1460-2075.1987.tb04718.x
Fang, 2011, Hul5 HECT ubiquitin ligase plays a major role in the ubiquitylation and turnover of cytosolic misfolded proteins, Nat. Cell Biol, 13, 1344, 10.1038/ncb2343
Fang, 2012, Hul5 ubiquitin ligase: good riddance to bad proteins, Prion, 6, 240, 10.4161/pri.19929
Carlson, 1987, Microinjection of ubiquitin: changes in protein degradation in HeLa cells subjected to heat-shock, J. Cell Biol, 104, 547, 10.1083/jcb.104.3.547
Dantuma, 2006, A dynamic ubiquitin equilibrium couples proteasomal activity to chromatin remodeling, J. Cell Biol, 173, 19, 10.1083/jcb.200510071
Cherry, 2012, Saccharomyces Genome Database: the genomics resource of budding yeast, Nucleic Acids Res, 40, 10.1093/nar/gkr1029
Ihaka, 1996, R: a language for data analysis and graphics, Journal of Computational and Graphical Statistics, 5, 299
Ward, 2004, Prediction and functional analysis of native disorder in proteins from the three kingdoms of life, J. Mol. Biol, 337, 635, 10.1016/j.jmb.2004.02.002
Petersen, 2009, A generic method for assignment of reliability scores applied to solvent accessibility predictions, BMC Struct. Biol, 9, 51, 10.1186/1472-6807-9-51
Mayor, 2007, Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway, Mol. Cell. Proteomics, 6, 1885, 10.1074/mcp.M700264-MCP200
Mayor, 2005, Analysis of polyubiquitin conjugates reveals that the Rpn10 substrate receptor contributes to the turnover of multiple proteasome targets, Mol. Cell. Proteomics, 4, 741, 10.1074/mcp.M400220-MCP200
Rappsilber, 2007, Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips, Nat. Protoc, 2, 1896, 10.1038/nprot.2007.261
Wilde, 2011, Proteomic characterization of aggregating proteins after the inhibition of the ubiquitin proteasome system, J. Proteome Res, 10, 1062, 10.1021/pr1008543
Kim, 2011, Systematic and quantitative assessment of the ubiquitin-modified proteome, Mol. Cell, 44, 325, 10.1016/j.molcel.2011.08.025
Wagner, 2011, A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles, Mol. Cell. Proteomics, 10, 10.1074/mcp.M111.013284
Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat Soc. Series B Stat. Methodol, 57, 289
Gsponer, 2008, Tight regulation of unstructured proteins: from transcript synthesis to protein degradation, Science, 322, 1365, 10.1126/science.1163581
Vavouri, 2009, Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity, Cell, 138, 198, 10.1016/j.cell.2009.04.029
Radivojac, 2007, Intrinsic disorder and functional proteomics, Biophys. J, 92, 1439, 10.1529/biophysj.106.094045
Dosztanyi, 2005, The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins, J. Mol. Biol, 347, 827, 10.1016/j.jmb.2005.01.071
Ghaemmaghami, 2003, Global analysis of protein expression in yeast, Nature, 425, 737, 10.1038/nature02046
Alberti, 2009, A systematic survey identifies prions and illuminates sequence features of prionogenic proteins, Cell, 137, 146, 10.1016/j.cell.2009.02.044
Harrison, 2003, A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes, Genome Biol, 4, 10.1186/gb-2003-4-6-r40
Michelitsch, 2000, A census of glutamine/asparagine-rich regions: implications for their conserved function and the prediction of novel prions, Proc. Natl. Acad. Sci. U.S.A, 97, 11910, 10.1073/pnas.97.22.11910
Chernova, 2011, Prion induction by the short-lived, stress-induced protein Lsb2 is regulated by ubiquitination and association with the actin cytoskeleton, Mol. Cell, 43, 242, 10.1016/j.molcel.2011.07.001
Kim, 2008, The role of disorder in interaction networks: a structural analysis, Mol. Syst. Biol, 4, 179, 10.1038/msb.2008.16
Buljan, 2012, Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks, Mol. Cell, 46, 871, 10.1016/j.molcel.2012.05.039
Babu, 2011, Intrinsically disordered proteins: regulation and disease, Curr. Opin. Struct. Biol, 21, 432, 10.1016/j.sbi.2011.03.011
Obenauer, 2003, Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs, Nucleic Acids Res, 31, 3635, 10.1093/nar/gkg584
Dinkel, 2012, ELM—the database of eukaryotic linear motifs, Nucleic Acids Res, 40, 10.1093/nar/gkr1064
Mészáros, 2009, Prediction of protein binding regions in disordered proteins, PLoS Comput. Biol, 5, e1000376, 10.1371/journal.pcbi.1000376
Crosas, 2006, Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities, Cell, 127, 1401, 10.1016/j.cell.2006.09.051
Galea, 2009, Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome, J. Proteome Res, 8, 211, 10.1021/pr800308v
Iakoucheva, 2002, Intrinsic disorder in cell-signaling and cancer-associated proteins, J. Mol. Biol, 323, 573, 10.1016/S0022-2836(02)00969-5
Tsvetkov, 2009, The nanny model for IDPs, Nat. Chem. Biol, 5, 778, 10.1038/nchembio.233