Open Access
Issue |
Med Sci (Paris)
Volume 35, Number 3, Mars 2019
|
|
---|---|---|
Page(s) | 223 - 231 | |
Section | M/S Revues | |
DOI | https://doi.org/10.1051/medsci/2019035 | |
Published online | 01 April 2019 |
- Urh M, Simpson D, Zhao K. Affinity chromatography: general methods. Methods Enzymol 2009 ; 463 : 417–438. [CrossRef] [PubMed] [Google Scholar]
- ten Have S, Boulon S, Ahmad Y, Lamond AI. Mass spectrometry-based immuno-precipitation proteomics - the user’s guide. Proteomics 2011 ; 11 : 1153–1159. [CrossRef] [PubMed] [Google Scholar]
- Hein MY, Hubner NC, Poser I et al. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 2015 ; 163 : 712–723. [CrossRef] [PubMed] [Google Scholar]
- Ewing RM, Chu P, Elisma F et al. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol 2007 ; 3 : 89. [Google Scholar]
- Huttlin EL, Bruckner RJ, Paulo JA et al. Architecture of the human interactome defines protein communities and disease networks. Nature 2017 ; 545 : 505–509. [CrossRef] [PubMed] [Google Scholar]
- Huttlin EL, Ting L, Bruckner RJ et al. The BioPlex network: a systematic exploration of the human interactome. Cell 2015 ; 162 : 425–440. [CrossRef] [PubMed] [Google Scholar]
- Gerace E, Moazed D. Affinity purification of protein complexes using TAP tags. Methods Enzymol 2015 ; 559 : 37–52. [CrossRef] [PubMed] [Google Scholar]
- Fields S, Song O. A novel genetic system to detect protein-protein interactions. Nature 1989 ; 340 : 245–246. [Google Scholar]
- Hamdi A, Colas P. Yeast two-hybrid methods and their applications in drug discovery. Trends Pharmacol Sci 2012 ; 33 : 109–118. [Google Scholar]
- Uetz P, Giot L, Cagney G et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000 ; 403 : 623–627. [CrossRef] [PubMed] [Google Scholar]
- Ito T, Chiba T, Ozawa R et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 2001 ; 98 : 4569–4574. [CrossRef] [Google Scholar]
- Tourette C, Li B, Bell R et al. A large scale Huntingtin protein interaction network implicates Rho GTPase signaling pathways in Huntington disease. J Biol Chem 2014 ; 289 : 6709–6726. [PubMed] [Google Scholar]
- Shahheydari H, Frost S, Smith BJ et al. Identification of PLP2 and RAB5C as novel TPD52 binding partners through yeast two-hybrid screening. Mol Biol Rep 2014 ; 41 : 4565–4572. [CrossRef] [PubMed] [Google Scholar]
- Huang H, Jedynak BM, Bader JS. Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput Biol 2007 ; 3 : e214. [Google Scholar]
- Zhang J, Lautar S. A Yeast three-hybrid method to clone ternary protein complex components. Anal Biochem 1996 ; 242 : 68–72. [CrossRef] [PubMed] [Google Scholar]
- Johnsson N, Varshavsky A. Split ubiquitin as a sensor of protein interactions in vivo. Proc Natl Acad Sci USA 1994 ; 91 : 10340–10344. [CrossRef] [Google Scholar]
- Brückner A, Polge C, Lentze N et al. Yeast two-hybrid, a powerful tool for systems biology. Int J Mol Sci 2009 ; 10 : 2763–2788. [Google Scholar]
- Gingras A-C, Abe KT, Raught B. Getting to know the neighborhood: using proximity-dependent biotinylation to characterize protein complexes and map organelles. Curr Opin Chem Biol 2018 ; 48 : 44–54. [Google Scholar]
- Kim DI, Roux KJ. Filling the void: proximity-based labeling of proteins in living cells. Trends Cell Biol 2016 ; 26 : 804–817. [Google Scholar]
- Roux KJ, Kim DI, Raida M et al. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol 2012 ; 196 : 801–810. [CrossRef] [PubMed] [Google Scholar]
- Kim DI, Kc B, Zhu W et al. Probing nuclear pore complex architecture with proximity-dependent biotinylation. Proc Natl Acad Sci USA 2014 ; 111 : E2453–E2461. [CrossRef] [Google Scholar]
- Couzens AL, Knight JDR, Kean MJ, et al. Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions. Sci Signal 2013; 6 : rs15. [Google Scholar]
- Gupta GD, Coyaud E, Gonçalves J et al. A Dynamic protein interaction landscape of the human centrosome-cilium interface. Cell 2015 ; 163 : 1484–1499. [CrossRef] [PubMed] [Google Scholar]
- Kim BR, Coyaud E, Laurent EMN et al. Identification of the SOX2 interactome by BioID reveals EP300 as a mediator of SOX2-dependent squamous differentiation and lung squamous cell carcinoma growth. Mol Cell Proteomics 2017 ; 16 : 1864–1888. [CrossRef] [PubMed] [Google Scholar]
- Dingar D, Kalkat M, Chan PK et al. BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors. J Proteomics 2015 ; 118 : 95–111. [CrossRef] [PubMed] [Google Scholar]
- Meyer N, Penn LZ. Reflecting on 25 years with MYC. Nat Rev Cancer 2008 ; 8 : 976–990. [Google Scholar]
- Kehrer J, Frischknecht F, Mair GR. Proteomic analysis of the Plasmodium berghei gametocyte egressome and vesicular bioID of osmiophilic body proteins identifies merozoite TRAP-like protein (MTRAP) as an essential factor for parasite transmission. Mol Cell Proteomics MCP 2016 ; 15 : 2852–2862. [CrossRef] [Google Scholar]
- Lin Q, Zhou Z, Luo W et al. Screening of proximal and interacting proteins in rice protoplasts by proximity-dependent biotinylation. Front Plant Sci 2017 ; 8 : 749. [CrossRef] [PubMed] [Google Scholar]
- Lampugnani ER, Wink RH, Persson S et al. The toolbox to study protein-protein interactions in plants. Crit Rev Plant Sci 2018 ; 1–27. [Google Scholar]
- Khan M, Youn JY, Gingras AC et al. In planta proximity dependent biotin identification (BioID). Sci Rep 2018 ; 8 : 9212. [CrossRef] [PubMed] [Google Scholar]
- Branon TC, Bosch JA, Sanchez AD et al. Efficient proximity labeling in living cells and organisms with TurboID. Nat Biotechnol 2018 ; 36 : 880–887. [CrossRef] [PubMed] [Google Scholar]
- Liu X, Salokas K, Tamene F et al. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nat Commun 2018 ; 9 : 1188. [CrossRef] [PubMed] [Google Scholar]
- Schopp IM, Amaya Ramirez CC, Debeljak J et al. Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes. Nat Commun 2017 ; 8 : 15690. [CrossRef] [PubMed] [Google Scholar]
- De Munter S, Görnemann J, Derua R et al. Split-BioID: a proximity biotinylation assay for dimerization-dependent protein interactions. FEBS Lett 2017 ; 591 : 415–424. [CrossRef] [PubMed] [Google Scholar]
- Rhee H-W, Zou P, Udeshi ND et al. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. Science 2013 ; 339 : 1328–1331. [Google Scholar]
- Lam SS, Martell JD, Kamer KJ et al. Directed evolution of APEX2 for electron microscopy and proximity labeling. Nat Methods 2015 ; 12 : 51–54. [CrossRef] [PubMed] [Google Scholar]
- Markmiller S, Soltanieh S, Server KL et al. Context-dependent and disease-specific diversity in protein interactions within stress granules. Cell 2018 ; 172 : 590–04 e13. [CrossRef] [PubMed] [Google Scholar]
- Bersuker K, Peterson CWH, To M et al. A Proximity labeling strategy provides insights into the composition and dynamics of lipid droplet proteomes. Dev Cell 2018 ; 44 : 97–112 e7. [CrossRef] [PubMed] [Google Scholar]
- Chen CL, Hu Y, Udeshi ND et al. Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase. Proc Natl Acad Sci USA 2015 ; 112 : 12093–12098. [CrossRef] [Google Scholar]
- Hung V, Zou P, Rhee H-W et al. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Mol Cell 2014 ; 55 : 332–341. [CrossRef] [PubMed] [Google Scholar]
- Tyanova S, Temu T, Cox J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc 2016 ; 11 : 2301–2319. [CrossRef] [PubMed] [Google Scholar]
- Choi H, Larsen B, Lin ZY et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat Methods 2011 ; 8 : 70–73. [CrossRef] [PubMed] [Google Scholar]
- Söderberg O, Gullberg M, Jarvius M et al. Direct observation of individual endogenous protein complexes in situ by proximity ligation. Nat Methods 2006 ; 3 : 995–1 000. [Google Scholar]
- Söderberg O, Leuchowius K-J, Gullberg M et al. Characterizing proteins and their interactions in cells and tissues using the in situ proximity ligation assay. Methods San Diego Calif 2008 ; 45 : 227–232. [CrossRef] [Google Scholar]
- Bobrich MA, Schwabe SA, Brobeil A et al. PTPIP51: a new interaction partner of the insulin receptor and PKA in adipose tissue. J Obes 2013 ; 2013 : 476240. [CrossRef] [PubMed] [Google Scholar]
- Poulard C, Treilleux I, Lavergne E et al. Activation of rapid oestrogen signalling in aggressive human breast cancers. EMBO Mol Med 2012 ; 4 : 1200–1213. [CrossRef] [PubMed] [Google Scholar]
- Smith MA, Hall R, Fisher K, et al. Annotation of human cancers with EGFR signaling-associated protein complexes using proximity ligation assays. Sci Signal 2015; 8 : ra4. [Google Scholar]
- Sekar RB, Periasamy A. Fluorescence resonance energy transfer (FRET) microscopy imaging of live cell protein localizations. J Cell Biol 2003 ; 160 : 629–633. [CrossRef] [PubMed] [Google Scholar]
- Xu Y, Piston DW, Johnson CH. A bioluminescence resonance energy transfer (BRET) system: application to interacting circadian clock proteins. Proc Natl Acad Sci USA 1999 ; 96 : 151–156. [CrossRef] [Google Scholar]
- Couturier C, Deprez B. Setting up a bioluminescence resonance energy transfer high throughput screening assay to search for protein/protein interaction inhibitors in mammalian cells. Front Endocrinol 2012 ; 3 : 100. [CrossRef] [Google Scholar]
- Malovannaya A, Lanz RB, Jung SY et al. Analysis of the human endogenous coregulator complexome. Cell 2011 ; 145 : 787–799. [CrossRef] [PubMed] [Google Scholar]
- Rual JF, Venkatesan K, Hao T et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005 ; 437 : 1173–1178. [CrossRef] [PubMed] [Google Scholar]
- Stelzl U, Worm U, Lalowski M et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005 ; 122 : 957–968. [CrossRef] [PubMed] [Google Scholar]
- Vinayagam A, Stelzl U, Foulle R, et al. A directed protein interaction network for investigating intracellular signal transduction. Sci Signal 2011; 4 : rs8. [Google Scholar]
- Wang J, Huo K, Ma L et al. Toward an understanding of the protein interaction network of the human liver. Mol Syst Biol 2011 ; 7 : 536. [Google Scholar]
- Rolland T, TaŞan M, Charloteaux B et al. A proteome-scale map of the human interactome network. Cell 2014 ; 159 : 1212–1226. [CrossRef] [PubMed] [Google Scholar]
- Lambert JP, Tucholska M, Go C et al. Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. J Proteomics 2015 ; 118 : 81–94. [CrossRef] [PubMed] [Google Scholar]
- Mackmull MT, Klaus B, Heinze I et al. Landscape of nuclear transport receptor cargo specificity. Mol Syst Biol 2017 ; 13 : 962. [Google Scholar]
- Youn JY, Dunham WH, Hong SJ et al. High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies. Mol Cell 2018 ; 69 : 517–32 e11. [CrossRef] [PubMed] [Google Scholar]
- Jing J, He L, Sun A et al. Proteomic mapping of ER-PM junctions identifies STIMATE as a regulator of Ca2+ influx. Nat Cell Biol 2015 ; 17 : 1339–1347. [CrossRef] [PubMed] [Google Scholar]
- Mick DU, Rodrigues RB, Leib RD et al. Proteomics of primary cilia by proximity labeling. Dev Cell 2015 ; 35 : 497–512. [CrossRef] [PubMed] [Google Scholar]
Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.
Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.
Initial download of the metrics may take a while.