An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells

Aoh, 2009, SCAMP3 negatively regulates epidermal growth factor receptor degradation and promotes receptor recycling, Mol Biol Cell., 20, 1816, 10.1091/mbc.e08-09-0894 Ashburner, 2000, Gene ontology: tool for the unification of biology, Nat. Genet., 25, 25, 10.1038/75556 Bernatchez, 2007, Myoferlin regulates vascular endothelial growth factor receptor-2 stability and function, J. Biol. Chem., 282, 30745, 10.1074/jbc.M704798200 Bisson, 2011, Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor, Nat. Biotechnol., 29, 653, 10.1038/nbt.1905 Brangwynne, 2013, Phase transitions and size scaling of membrane-less organelles, J. Cell Biol., 203, 875, 10.1083/jcb.201308087 Cheng, 2000, beta-arrestin differentially regulates the chemokine receptor CXCR4-mediated signaling and receptor internalization, and this implicates multiple interaction sites between beta-arrestin and CXCR4, J. Biol. Chem., 275, 2479, 10.1074/jbc.275.4.2479 Choi, 2011, SAINT: probabilistic scoring of affinity purification-mass spectrometry data, Nat. Methods, 8, 70, 10.1038/nmeth.1541 Choi, 2012, Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT, Curr. Protoc. Bioinformatics, Chapter 8 Choi, 2014, MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments, Bioinformatics, 30, 2524, 10.1093/bioinformatics/btu305 Collins, 2013, Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system, Nat. Methods, 10, 1246, 10.1038/nmeth.2703 Cox, 2008, MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification, Nat. Biotechnol., 26, 1367, 10.1038/nbt.1511 de Hoon, 2004, Open source clustering software, Bioinformatics, 20, 1453, 10.1093/bioinformatics/bth078 Dores, 2015, The α-arrestin ARRDC3 mediates ALIX ubiquitination and G protein-coupled receptor lysosomal sorting, Mol. Biol. Cell, 26, 4660, 10.1091/mbc.E15-05-0284 Eichel, 2016, β-Arrestin drives MAP kinase signalling from clathrin-coated structures after GPCR dissociation, Nat. Cell Biol., 18, 303, 10.1038/ncb3307 Eulalio, 2007, P bodies: at the crossroads of post-transcriptional pathways, Nat. Rev. Mol. Cell Biol., 8, 9, 10.1038/nrm2080 Falguières, 2012, Regulation of the MVB pathway by SCAMP3, Traffic, 13, 131, 10.1111/j.1600-0854.2011.01291.x Foltz, 2006, The human CENP-A centromeric nucleosome-associated complex, Nat. Cell Biol., 8, 458, 10.1038/ncb1397 Gavin, 2006, Proteome survey reveals modularity of the yeast cell machinery, Nature, 440, 631, 10.1038/nature04532 Gendron, 2016, Molecular Pharmacology of δ-Opioid Receptors, Pharmacol. Rev., 68, 631, 10.1124/pr.114.008979 2015, Gene Ontology Consortium: going forward, Nucleic Acids Res., 43, D1049, 10.1093/nar/gku1179 Gillooly, 2000, Localization of phosphatidylinositol 3-phosphate in yeast and mammalian cells, EMBO J., 19, 4577, 10.1093/emboj/19.17.4577 Gurevich, 2015, Arrestins: critical players in trafficking of many GPCRs, Prog. Mol. Biol. Transl. Sci., 132, 1, 10.1016/bs.pmbts.2015.02.010 Henry, 2011, The role of ubiquitination in lysosomal trafficking of δ-opioid receptors, Traffic, 12, 170, 10.1111/j.1600-0854.2010.01145.x Hislop, 2009, Ubiquitination regulates proteolytic processing of G protein-coupled receptors after their sorting to lysosomes, J. Biol. Chem., 284, 19361, 10.1074/jbc.M109.001644 Hung, 2014, Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging, Mol. Cell, 55, 332, 10.1016/j.molcel.2014.06.003 Hung, 2016, Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2, Nat. Protoc., 11, 456, 10.1038/nprot.2016.018 Ideker, 2012, Differential network biology, Mol. Syst. Biol., 8, 565, 10.1038/msb.2011.99 Inoue, 2005, An inducible translocation strategy to rapidly activate and inhibit small GTPase signaling pathways, Nat. Methods, 2, 415, 10.1038/nmeth763 Irannejad, 2015, Effects of endocytosis on receptor-mediated signaling, Curr. Opin. Cell Biol., 35, 137, 10.1016/j.ceb.2015.05.005 Itzhak, 2016, Global, quantitative and dynamic mapping of protein subcellular localization, eLife, 5, 5, 10.7554/eLife.16950 Jäger, 2011, Global landscape of HIV-human protein complexes, Nature, 481, 365, 10.1038/nature10719 Kennedy, 2015, Regulation of GPCR trafficking by ubiquitin, Prog. Mol. Biol. Transl. Sci., 132, 15, 10.1016/bs.pmbts.2015.02.005 Kholodenko, 2006, Cell-signalling dynamics in time and space, Nat. Rev. Mol. Cell Biol., 7, 165, 10.1038/nrm1838 Kim, 2016, Filling the void: proximity-based labeling of proteins in living cells, Trends Cell Biol., 26, 804, 10.1016/j.tcb.2016.09.004 Krogan, 2006, Global landscape of protein complexes in the yeast Saccharomyces cerevisiae, Nature, 440, 637, 10.1038/nature04670 Lam, 2015, Directed evolution of APEX2 for electron microscopy and proximity labeling, Nat. Methods, 12, 51, 10.1038/nmeth.3179 Lauffer, 2010, SNX27 mediates PDZ-directed sorting from endosomes to the plasma membrane, J. Cell Biol., 190, 565, 10.1083/jcb.201004060 Lavallée-Adam, 2013, Discovery of cell compartment specific protein-protein interactions using affinity purification combined with tandem mass spectrometry, J. Proteome Res., 12, 272, 10.1021/pr300778b Lohse, 2008, Kinetics of G-protein-coupled receptor signals in intact cells, Br. J. Pharmacol., 153, S125, 10.1038/sj.bjp.0707656 Lundberg, 2010, Creation of an antibody-based subcellular protein atlas, Proteomics, 10, 3984, 10.1002/pmic.201000125 Luttrell, 1999, Beta-arrestin-dependent formation of beta2 adrenergic receptor-Src protein kinase complexes, Science, 283, 655, 10.1126/science.283.5402.655 MacLean, 2010, Skyline: an open source document editor for creating and analyzing targeted proteomics experiments, Bioinformatics, 26, 966, 10.1093/bioinformatics/btq054 Martell, 2012, Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy, Nat. Biotechnol., 30, 1143, 10.1038/nbt.2375 Marx, 2015, Mapping proteins with spatial proteomics, Nat. Methods, 12, 815, 10.1038/nmeth.3555 McMahon, 2011, Molecular mechanism and physiological functions of clathrin-mediated endocytosis, Nat. Rev. Mol. Cell Biol., 12, 517, 10.1038/nrm3151 Mick, 2015, Proteomics of Primary Cilia by Proximity Labeling, Dev. Cell, 35, 497, 10.1016/j.devcel.2015.10.015 Navaroli, 2012, Rabenosyn-5 defines the fate of the transferrin receptor following clathrin-mediated endocytosis, Proc. Natl. Acad. Sci. USA, 109, E471, 10.1073/pnas.1115495109 Oo, 2011, Engagement of S1P1-degradative mechanisms leads to vascular leak in mice, J. Clin. Invest., 121, 2290, 10.1172/JCI45403 Perini, 2014, Mammalian CORVET is required for fusion and conversion of distinct early endosome subpopulations, Traffic, 15, 1366, 10.1111/tra.12232 Perry, 2002, Targeting of cyclic AMP degradation to beta 2-adrenergic receptors by beta-arrestins, Science, 298, 834, 10.1126/science.1074683 Rhee, 2013, Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging, Science, 339, 1328, 10.1126/science.1230593 Ritter, 2009, Fine-tuning of GPCR activity by receptor-interacting proteins, Nat. Rev. Mol. Cell Biol., 10, 819, 10.1038/nrm2803 Rosenbaum, 2009, The structure and function of G-protein-coupled receptors, Nature, 459, 356, 10.1038/nature08144 Saldanha, 2004, Java Treeview--extensible visualization of microarray data, Bioinformatics, 20, 3246, 10.1093/bioinformatics/bth349 Schmidt, 2012, The ESCRT machinery, Curr. Biol., 22, R116, 10.1016/j.cub.2012.01.028 Scott, 2009, Cell signaling in space and time: where proteins come together and when they’re apart, Science, 326, 1220, 10.1126/science.1175668 Seet, 2004, Endofin recruits TOM1 to endosomes, J. Biol. Chem., 279, 4670, 10.1074/jbc.M311228200 Sharma, 2014, Panorama: a targeted proteomics knowledge base, J. Proteome Res., 13, 4205, 10.1021/pr5006636 Sorkin, 2009, Endocytosis and signalling: intertwining molecular networks, Nat. Rev. Mol. Cell Biol., 10, 609, 10.1038/nrm2748 Temkin, 2011, SNX27 mediates retromer tubule entry and endosome-to-plasma membrane trafficking of signalling receptors, Nat. Cell Biol., 13, 715, 10.1038/ncb2252 Tsao, 2000, Type-specific sorting of G protein-coupled receptors after endocytosis, J. Biol. Chem., 275, 11130, 10.1074/jbc.275.15.11130 Vizcaíno, 2016, 2016 update of the PRIDE database and its related tools, Nucleic Acids Res., 44, D447, 10.1093/nar/gkv1145 Wang, 2010, The emerging role of VHS domain-containing Tom1, Tom1L1 and Tom1L2 in membrane trafficking, Traffic, 11, 1119, 10.1111/j.1600-0854.2010.01098.x Yamakami, 2003, Tom1, a VHS domain-containing protein, interacts with tollip, ubiquitin, and clathrin, J. Biol. Chem., 278, 52865, 10.1074/jbc.M306740200