Split-protein systems: beyond binary protein–protein interactions

Current Opinion in Chemical Biology - Tập 15 - Trang 789-797 - 2011
Sujan S Shekhawat1, Indraneel Ghosh1
1Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Blvd, Tucson, AZ 85721, United States

Tài liệu tham khảo

Stumpf, 2008, Estimating the size of the human interactome, Proc Natl Acad Sci USA, 105, 6959, 10.1073/pnas.0708078105 Fields, 1989, A novel genetic system to detect protein–protein interactions, Nature, 340, 245, 10.1038/340245a0 Licitra, 1996, A three-hybrid system for detecting small ligand–protein receptor interactions, Proc Natl Acad Sci USA, 93, 12817, 10.1073/pnas.93.23.12817 Zhang, 2002, Creating new fluorescent probes for cell biology, Nat Rev Mol Biol, 3, 906, 10.1038/nrm976 Richards, 1958, On the enzymic activity of subtilisin-modified ribonuclease, Proc Natl Acad Sci USA, 44, 162, 10.1073/pnas.44.2.162 Ullmann, 1967, Characterization by in vitro complementation of a peptide corresponding to an operator-proximal segment of beta-galactosidase structural gene of Escherichia coli, J Mol Biol, 24, 339, 10.1016/0022-2836(67)90341-5 Johnsson, 1994, Split ubiquitin as a sensor of protein interactions in vivo, Proc Natl Acad Sci USA, 91, 10340, 10.1073/pnas.91.22.10340 Ostermeier, 1999, Combinatorial protein engineering by incremental truncation, Proc Natl Acad Sci USA, 96, 3562, 10.1073/pnas.96.7.3562 Ghosh, 2000, Antiparallel leucine zipper-directed protein reassembly: application to the green fluorescent protein, J Am Chem Soc, 122, 5658, 10.1021/ja994421w Hu, 2003, Simultaneous visualization of multiple protein interactions in living cells using multicolor fluorescence complementation analysis, Nat Biotechnol, 21, 539, 10.1038/nbt816 Pelletier, 1998, Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments, Proc Natl Acad Sci USA, 95, 12141, 10.1073/pnas.95.21.12141 Galarneau, 2002, beta-Lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein–protein interactions, Nat Biotechnol, 20, 619, 10.1038/nbt0602-619 Luker, 2004, Kinetics of regulated protein–protein interactions revealed with firefly luciferase complementation imaging in cells and living animals, Proc Natl Acad Sci USA, 101, 12288, 10.1073/pnas.0404041101 Remy, 2006, A highly sensitive protein–protein interaction assay based on Gaussia luciferase, Nat Methods, 3, 977, 10.1038/nmeth979 Paulmurugan, 2003, Monitoring protein–protein interactions using split synthetic renilla luciferase protein-fragment-assisted complementation, Anal Chem, 759, 1584, 10.1021/ac020731c Wehr, 2006, Monitoring regulated protein–protein interactions using split TEV, Nat Methods, 3, 985, 10.1038/nmeth967 Massoud, 2010, A molecularly engineered split reporter for imaging protein–protein interactions with positron emission tomography, Nat Med, 16, 921, 10.1038/nm.2185 Muller, 2010, Design, selection, and characterization of a split chorismate mutase, Protein Sci, 19, 1000, 10.1002/pro.377 Pelletier, 1999, An in vivo library-versus-library selection of optimized protein–protein interactions, Nat Biotechnol, 17, 683, 10.1038/10897 Amstutz, 2006, Rapid selection of specific MAP kinase-binders from designed ankyrin repeat protein libraries, Protein Eng Des Sel, 19, 219, 10.1093/protein/gzl004 Mossner, 2001, Fast selection of antibodies without antigen purification: adaptation of the protein fragment complementation assay to select antigen-antibody pairs, J Mol Biol, 308, 115, 10.1006/jmbi.2001.4575 Campbell-Valois, 2005, Massive sequence perturbation of a small protein, Proc Natl Acad Sci USA, 102, 14988, 10.1073/pnas.0500465102 Jackrel, 2010, Screening libraries to identify proteins with desired binding activities using a split-GFP reassembly assay, ACS Chem Biol, 5, 553, 10.1021/cb900272j Michnick, 2007, Universal strategies in research and drug discovery based on protein-fragment complementation assays, Nat Rev Drug Discov, 6, 569, 10.1038/nrd2311 Muller, 2008, Split-ubiquitin and the split-protein sensors: chessman for the endgame, ChemBioChem, 9, 2029, 10.1002/cbic.200800190 Magliery, 2005, Detecting protein–protein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism, J Am Chem Soc, 127, 146, 10.1021/ja046699g Nyfeler, 2005, Capturing protein interactions in the secretory pathway of living cells, Proc Natl Acad Sci USA, 102, 6350, 10.1073/pnas.0501976102 Lindman, 2010, In vivo protein stabilization based on fragment complementation and a split GFP system, Proc Natl Acad Sci USA, 107, 19826, 10.1073/pnas.1005689107 Porter, 2008, A general and rapid cell-free approach for the interrogation of protein–protein, protein–DNA, and protein–RNA interactions and their antagonists utilizing split-protein reporters, J Am Chem Soc, 130, 6488, 10.1021/ja7114579 Hida, 2009, High-sensitivity real-time imaging of dual protein–protein interactions in living subjects using multicolor luciferases, PLoS ONE, 4, e5868, 10.1371/journal.pone.0005868 Dupre, 2006, Seven transmembrane receptor core signaling complexes are assembled prior to plasma membrane trafficking, J Biol Chem, 281, 34561, 10.1074/jbc.M605012200 Heroux, 2007, Functional calcitonin gene-related peptide receptors are formed by the asymmetric assembly of a calcitonin receptor-like receptor homo-oligomer and a monomer of receptor activity-modifying protein-1, J Biol Chem, 282, 31610, 10.1074/jbc.M701790200 Shyu, 2008, Visualization of AP-1-NF-kappa B ternary complexes in living cells by using a BiFC-based FRET, Proc Natl Acad Sci USA, 105, 151, 10.1073/pnas.0705181105 Porter, 2010, Profiling small molecule inhibitors against helix-receptor interactions: the Bcl-2 family inhibitor BH3I-1 potently inhibits p53/hDM2, Chem Commun, 46, 8020, 10.1039/c0cc02969f MacDonald, 2006, Identifying off-target effects and hidden phenotypes of drugs in human cells, Nat Chem Biol, 2, 329, 10.1038/nchembio790 Stains, 2010, A general approach for receptor and antibody-targeted detection of native proteins utilizing split-luciferase reassembly, ACS Chem Biol, 5, 943, 10.1021/cb100143m Stains, 2005, DNA sequence-enabled reassembly of the green fluorescent protein, J Am Chem Soc, 127, 10782, 10.1021/ja051969w Porter, 2007, Split beta-lactamase sensor for the sequence-specific detection of DNA methylation, Anal Chem, 79, 6702, 10.1021/ac071163+ Stains, 2006, Site-specific detection of DNA methylation utilizing mCpG-SEER, J Am Chem Soc, 128, 9761, 10.1021/ja060681j Furman, 2011, Turn-on DNA damage sensors for the direct detection of 8-oxoguanine and photoproducts in native DNA, J Am Chem Soc, 133, 12518, 10.1021/ja1116606 Badran, 2011, Evaluating the global CpG methylation status of native DNA utilizing a bipartite split-luciferase sensor, Anal Chem, 83, 7151, 10.1021/ac2015239 Rackham, 2004, Visualization of RNA–protein interactions in living cells: FMRP and IMP1 interact on mRNAs, EMBO J, 23, 3346, 10.1038/sj.emboj.7600341 Ozawa, 2007, Imaging dynamics of endogenous mitochondrial RNA in single living cell, Nat Methods, 4, 413, 10.1038/nmeth1030 Furman, 2010, Toward a general approach for RNA-templated hierarchical assembly of split-proteins, J Am Chem Soc, 132, 11692, 10.1021/ja104395b Takeda, 2008, Covalent split protein fragment–DNA hybrids generated through N-terminus-specific modification of proteins by oligonucleotides, Org Biomol Chem, 6, 2187, 10.1039/b720013g Demidov, 2006, Fast complementation of split fluorescent protein triggered by DNA hybridization, Proc Natl Acad Sci USA, 103, 2052, 10.1073/pnas.0511078103 Hoff, 2009, In vivo fluorescent detection of Fe–S clusters coordinated by human GRX2, Chem Biol, 16, 1299, 10.1016/j.chembiol.2009.11.011 Furman, 2011, A turn-on split-luciferase sensor for the direct detection of poly(ADP-ribose) as a marker for DNA repair and cell death, Chem Commun, 47, 397, 10.1039/C0CC02229B Spencer, 1993, Controlling signal-transduction with synthetic ligands, Science, 262, 1019, 10.1126/science.7694365 Fegan, 2010, Chemically controlled protein assembly: techniques and applications, Chem Rev, 110, 3315, 10.1021/cr8002888 Pratt, 2007, Small molecule-mediated rescue of protein function by an inducible proteolytic shunt, Proc Natl Acad Sci USA, 104, 11209, 10.1073/pnas.0700816104 Williams, 2009, Rapid modification of proteins using a rapamycin-inducible tobacco etch virus protease system, PLoS ONE, 4, 14, 10.1371/journal.pone.0007474 Gray, 2010, Activation of specific apoptotic caspases with an engineered small-molecule-activated protease, Cell, 142, 637, 10.1016/j.cell.2010.07.014 Dirnberger, 2006, A small-molecule–protein interaction system with split-ubiquitin as sensor, ChemBioChem, 7, 936, 10.1002/cbic.200500544 Jester, 2010, A coiled-coil enabled split-luciferase three-hybrid system: applied toward profiling inhibitors of protein kinases, J Am Chem Soc, 132, 11727, 10.1021/ja104491h Shekhawat, 2009, An autoinhibited coiled-coil design strategy for split-protein protease sensors, J Am Chem Soc, 131, 15284, 10.1021/ja9050857 Shekhawat SS, Campbell, ST, Ghosh I: A comprehensive panel of turn-on caspase biosensors for investigating caspase specificity and caspase activation pathways. ChemBioChem, doi:10.1002/cbic.201100372. Sakamoto, 2008, Supramolecular control of split-GFP reassembly by conjugation of beta-cyclodextrin and coumarin units, J Am Chem Soc, 130, 9574, 10.1021/ja802313a Callahan, 2010, Protease activation of split green fluorescent protein, ChemBioChem, 11, 2259, 10.1002/cbic.201000453