Self-recognition behavior of a helix–loop–helix domain by a fragment scan

Michael Beisswenger1, Chiara Cabrele1,2
1Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
2Department of Molecular Biology, Division of Chemistry and Bioanalytics, Paris-Lodron University Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria

Tài liệu tham khảo

Benezra, 2001, The Id proteins: targets for inhibiting tumor cells and their blood supply, Biochim. Biophys. Acta, 1551, F39 Hasskarl, 2002, Id proteins — tumor markers or oncogenes?, Cancer Biol. Ther., 1, 91, 10.4161/cbt.50 Iavarone, 2006, ID proteins as targets in cancer and tools in neurobiology, Trends Mol. Med., 12, 588, 10.1016/j.molmed.2006.10.007 Ling, 2006, The multiple roles of Id-1 in cancer progression, Differentiation, 74, 481, 10.1111/j.1432-0436.2006.00083.x Perk, 2005, Id family of helix–loop–helix proteins in cancer, Nat. Rev. Cancer, 5, 603, 10.1038/nrc1673 Ruzinova, 2003, Id proteins in development, cell cycle and cancer, Trends Cell Biol., 13, 410, 10.1016/S0962-8924(03)00147-8 Sikder, 2003, Id proteins in cell growth and tumorigenesis, Cancer Cell, 3, 525, 10.1016/S1535-6108(03)00141-7 Massari, 2000, Helix–loop–helix proteins: regulators of transcription in eucaryotic organisms, Mol. Cell Biol., 20, 429, 10.1128/MCB.20.2.429-440.2000 Ellenberger, 1994, Crystal structure of transcription factor E47: E-box recognition by a basic region helix–loop–helix dimer, Genes Dev., 8, 970, 10.1101/gad.8.8.970 O'Toole, 2003, Id proteins negatively regulate basic helix–loop–helix transcription factor function by disrupting subnuclear compartmentalization, J. Biol. Chem., 278, 45770, 10.1074/jbc.M306056200 Forrest, 2004, Id family of transcription factors and vascular lesion formation, Arterioscler. Thromb. Vasc. Biol., 24, 2014, 10.1161/01.ATV.0000143932.03151.ad Forrest, 2004, Intron retention generates a novel Id3 isoform that inhibits vascular lesion formation, J. Biol. Chem., 279, 32897, 10.1074/jbc.M404882200 Henke, 2008, Peptide-conjugated antisense oligonucleotides for targeted inhibition of a transcriptional regulator in vivo, Nat. Biotechnol., 26, 91, 10.1038/nbt1366 Mern, 2010, Targeting Id1 and Id3 by a specific peptide aptamer induces E-box promoter activity, cell cycle arrest, and apoptosis in breast cancer cells, Breast Cancer Res. Treat., 124, 623, 10.1007/s10549-010-0810-6 Ruzinova, 2003, Effect of angiogenesis inhibition by Id loss and the contribution of bone-marrow-derived endothelial cells in spontaneous murine tumors, Cancer Cell, 4, 277, 10.1016/S1535-6108(03)00240-X Jang, 2006, Id-1 gene downregulation by sulindac sulfide and its upregulation during tumor development in gastric cancer, Int. J. Cancer, 118, 1356, 10.1002/ijc.21503 Fong, 2003, Id-1 as a molecular target in therapy for breast cancer cell invasion and metastasis, Proc. Natl. Acad. Sci. U. S. A., 100, 13543, 10.1073/pnas.2230238100 Cheung, 2004, Id-1-induced Raf/MEK pathway activation is essential for its protective role against taxol-induced apoptosis in nasopharyngeal carcinoma cells, Carcinogenesis, 25, 881, 10.1093/carcin/bgh087 Lin, 2005, The association of Id-1, MIF and GSTpi with acquired drug resistance in hormone independent prostate cancer cells, Oncol. Rep., 13, 983 Zhang, 2006, Inactivation of Id-1 in prostate cancer cells: a potential therapeutic target in inducing chemosensitization to taxol through activation of JNK pathway, Int. J. Cancer, 118, 2072, 10.1002/ijc.21592 Zhang, 2007, Evidence of a novel antiapoptotic factor: role of inhibitor of differentiation or DNA binding (Id-1) in anticancer drug-induced apoptosis, Cancer Sci., 98, 308, 10.1111/j.1349-7006.2007.00400.x Mern, 2010, Inhibition of Id proteins by a peptide aptamer induces cell-cycle arrest and apoptosis in ovarian cancer cells, Br. J. Cancer, 103, 1237, 10.1038/sj.bjc.6605897 Ciarapica, 2009, Targeting Id protein interactions by an engineered HLH domain induces human neuroblastoma cell differentiation, Oncogene, 28, 1881, 10.1038/onc.2009.56 Ciarapica, 2003, Molecular recognition in helix–loop–helix and helix–loop–helix–leucine zipper domains. Design of repertoires and selection of high affinity ligands for natural proteins, J. Biol. Chem., 278, 12182, 10.1074/jbc.M211991200 Chen, 2010, Affinity of synthetic peptide fragments of MyoD for Id1 protein and their biological effects in several cancer cells, J. Pept. Sci., 16, 231 Pellegrino, 2009, Synthetic peptides containing a conserved sequence motif of the Id protein family modulate vascular smooth muscle cell phenotype, Bioorg. Med. Chem. Lett., 19, 6298, 10.1016/j.bmcl.2009.09.105 Fairman, 1993, Multiple oligomeric states regulate the DNA binding of helix–loop–helix peptides, Proc. Natl. Acad. Sci. U. S. A., 90, 10429, 10.1073/pnas.90.22.10429 Kiewitz, 2005, Synthesis and conformational properties of protein fragments based on the Id family of DNA-binding and cell-differentiation inhibitors, Biopolymers (Pept. Sci.), 80, 762, 10.1002/bip.20287 Sarver, 2001, Analysis of peptides and proteins containing nitrotyrosine by matrix-assisted laser desorption/ionization mass spectrometry, J. Am. Soc. Mass Spectrom., 12, 439, 10.1016/S1044-0305(01)00213-6 Mach, 1992, Statistical determination of the average values of the extinction coefficients of tryptophan and tyrosine in native proteins, Anal. Biochem., 200, 74, 10.1016/0003-2697(92)90279-G Ito, 2001, Fluorescence study of conformational properties of melanotropins labeled with aminobenzoic acid, Biophys. J., 81, 1180, 10.1016/S0006-3495(01)75775-X Chavali, 2001, Analysis of sequence signature defining functional specificity and structural stability in helix–loop–helix proteins, Proteins, 42, 471, 10.1002/1097-0134(20010301)42:4<471::AID-PROT60>3.0.CO;2-P Eletsky, 2012 Wong, 2012, A divalent ion is crucial in the structure and dominant-negative function of ID proteins, a class of helix–loop–helix transcription regulators, PLoS One, 7, e48591, 10.1371/journal.pone.0048591 Abello, 2009, Protein tyrosine nitration: selectivity, physicochemical and biological consequences, denitration, and proteomics methods for the identification of tyrosine-nitrated proteins, J. Proteome Res., 8, 3222, 10.1021/pr900039c Riordan, 1967, Environmentally sensitive tyrosyl residues. Nitration with tetranitromethane, Biochemistry, 6, 358, 10.1021/bi00853a053 Sokolovsky, 1967, Conversion of 3-nitrotyrosine to 3-aminotyrosine in peptides and proteins, Biochem. Biophys. Res. Commun., 27, 20, 10.1016/S0006-291X(67)80033-0 Bandekar, 1982, Conformations of cyclo(l-alanyl-l-alanyl-epsilon-aminocaproyl) and of cyclo(l-alanyl-d-alanyl-epsilon-aminocaproyl); cyclized dipeptide models for specific types of beta-bends, Int. J. Pept. Protein Res., 19, 187, 10.1111/j.1399-3011.1982.tb02608.x Perczel, 1991, Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins, Protein Eng., 4, 669, 10.1093/protein/4.6.669 Woody, 1985 Dunker, 2008, Function and structure of inherently disordered proteins, Curr. Opin. Struct. Biol., 18, 756, 10.1016/j.sbi.2008.10.002 Mittag, 2010, Protein dynamics and conformational disorder in molecular recognition, J. Mol. Recognit., 23, 105 Tompa, 2008, Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions, Trends Biochem. Sci., 33, 2, 10.1016/j.tibs.2007.10.003 Uversky, 2011, Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes, Chem. Soc. Rev., 40, 1623, 10.1039/C0CS00057D Dyson, 2011, Expanding the proteome: disordered and alternatively folded proteins, Q. Rev. Biophys., 44, 467, 10.1017/S0033583511000060 Minezaki, 2006, Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation, J. Mol. Biol., 359, 1137, 10.1016/j.jmb.2006.04.016 Liu, 2006, Intrinsic disorder in transcription factors, Biochemistry, 45, 6873, 10.1021/bi0602718 Fuxreiter, 2011, Dynamic protein–DNA recognition: beyond what can be seen, Trends Biochem. Sci., 36, 415, 10.1016/j.tibs.2011.04.006 Guo, 2012, Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors, Pac. Symp. Biocomput., 104 Beisswenger, 2010, Synthesis and conformation of an analog of the helix–loop–helix domain of the Id1 protein containing the O-acyl iso-prolyl-seryl switch motif, J. Pept. Sci., 16, 303, 10.1002/psc.1239 Kiewitz, 2008, Switching from the unfolded to the folded state of the helix–loop–helix domain of the Id proteins based on the O-acyl isopeptide method, J. Pept. Sci., 14, 1209, 10.1002/psc.1059 Colombo, 2006, Synthesis and conformational analysis of Id2 protein fragments: impact of chain length and point mutations on the structural HLH motif, J. Pept. Sci., 12, 550, 10.1002/psc.764 Linding, 2003, Protein disorder prediction: implications for structural proteomics, Structure, 11, 1453, 10.1016/j.str.2003.10.002 Obradovic, 2005, Exploiting heterogeneous sequence properties improves prediction of protein disorder, Proteins, 61, 176, 10.1002/prot.20735 Broglia, 2006, A folding inhibitor of the HIV-1 protease, Proteins, 62, 928, 10.1002/prot.20849 Dunker, 2005, Flexible nets. The roles of intrinsic disorder in protein interaction networks, FEBS J., 272, 5129, 10.1111/j.1742-4658.2005.04948.x Perkins, 2010, Transient protein–protein interactions: structural, functional, and network properties, Structure, 18, 1233, 10.1016/j.str.2010.08.007 Swadesh, 1984, Local structure involving histidine-12 in reduced S-sulfonated ribonuclease A detected by proton NMR spectroscopy under folding conditions, Proc. Natl. Acad. Sci. U. S. A., 81, 4606, 10.1073/pnas.81.14.4606 Follis, 2008, Structural rationale for the coupled binding and unfolding of the c-Myc oncoprotein by small molecules, Chem. Biol., 15, 1149, 10.1016/j.chembiol.2008.09.011 Bounpheng, 1999, Degradation of Id proteins by the ubiquitin–proteasome pathway, FASEB J., 13, 2257, 10.1096/fasebj.13.15.2257 Trausch-Azar, 2004, Ubiquitin–proteasome-mediated degradation of Id1 is modulated by MyoD, J. Biol. Chem., 279, 32614, 10.1074/jbc.M403794200 Butler, 2009, Phospho-ablated Id2 is growth suppressive and pro-apoptotic in proliferating myoblasts, PLoS One, 4, e6302, 10.1371/journal.pone.0006302 Deed, 1997, Regulation of Id3 cell cycle function by Cdk-2-dependent phosphorylation, Mol. Cell. Biol., 17, 6815, 10.1128/MCB.17.12.6815 Forrest, 2004, Phosphorylation regulates Id3 function in vascular smooth muscle cells, Circ. Res., 95, 557, 10.1161/01.RES.0000142735.67542.5a Hara, 1997, Cdk2-dependent phosphorylation of Id2 modulates activity of E2A-related transcription factors, EMBO J., 16, 332, 10.1093/emboj/16.2.332 Florio, 1998, Id2 promotes apoptosis by a novel mechanism independent of dimerization to basic helix–loop–helix factors, Mol. Cell. Biol., 18, 5435, 10.1128/MCB.18.9.5435 Lasorella, 2006, Degradation of Id2 by the anaphase-promoting complex couples cell cycle exit and axonal growth, Nature, 442, 471, 10.1038/nature04895 Nguewa, 2014, Id-1B, an alternatively spliced isoform of the inhibitor of differentiation-1, impairs cancer cell malignancy through inhibition of proliferation and angiogenesis, Curr. Mol. Med., 14, 151, 10.2174/1566524013666131203100643 Tamura, 1998, Differential activity of a variant form of the human Id-1 protein generated by alternative splicing, FEBS Lett., 436, 169, 10.1016/S0014-5793(98)01117-X Svobodova, 2006, Stepwise solid-phase synthesis and spontaneous homodimerization of the helix–loop–helix protein Id3, Chembiochem, 7, 1164, 10.1002/cbic.200600059