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Article Addendum

A comprehensive strategy to identify stoichiometric membrane protein interactomes

, , , &
Pages 189-196 | Published online: 31 Dec 2012

References

  • Perez-Cornejo P, Gokhale A, Duran C, Cui Y, Xiao Q, Hartzell HC, et al. Anoctamin 1 (Tmem16A) Ca2+-activated chloride channel stoichiometrically interacts with an ezrin-radixin-moesin network. Proc Natl Acad Sci U S A 2012; 109:10376 - 81; http://dx.doi.org/10.1073/pnas.1200174109; PMID: 22685202
  • Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567 - 80; http://dx.doi.org/10.1006/jmbi.2000.4315; PMID: 11152613
  • Wallin E, von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 1998; 7:1029 - 38; http://dx.doi.org/10.1002/pro.5560070420; PMID: 9568909
  • Xia Y, Lu LJ, Gerstein M. Integrated prediction of the helical membrane protein interactome in yeast. J Mol Biol 2006; 357:339 - 49; http://dx.doi.org/10.1016/j.jmb.2005.12.067; PMID: 16413578
  • Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabási AL. The human disease network. Proc Natl Acad Sci U S A 2007; 104:8685 - 90; http://dx.doi.org/10.1073/pnas.0701361104; PMID: 17502601
  • Overington JP, Al-Lazikani B, Hopkins AL. How many drug targets are there?. Nat Rev Drug Discov 2006; 5:993 - 6; http://dx.doi.org/10.1038/nrd2199; PMID: 17139284
  • Yildirim MA, Goh KI, Cusick ME, Barabási AL, Vidal M. Drug-target network. Nat Biotechnol 2007; 25:1119 - 26; http://dx.doi.org/10.1038/nbt1338; PMID: 17921997
  • Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 2009; 19:1316 - 23; http://dx.doi.org/10.1101/gr.080531.108; PMID: 19498102
  • Fredriksson R, Lagerström MC, Lundin LG, Schiöth HB. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 2003; 63:1256 - 72; http://dx.doi.org/10.1124/mol.63.6.1256; PMID: 12761335
  • Kroeze WK, Sheffler DJ, Roth BL. G-protein-coupled receptors at a glance. J Cell Sci 2003; 116:4867 - 9; http://dx.doi.org/10.1242/jcs.00902; PMID: 14625380
  • Sharman JL, Mpamhanga CP, Spedding M, Germain P, Staels B, Dacquet C, et al, NC-IUPHAR. IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data. Nucleic Acids Res 2011; 39:Database issue D534 - 8; http://dx.doi.org/10.1093/nar/gkq1062; PMID: 21087994
  • Jegla TJ, Zmasek CM, Batalov S, Nayak SK. Evolution of the human ion channel set. Comb Chem High Throughput Screen 2009; 12:2 - 23; http://dx.doi.org/10.2174/138620709787047957; PMID: 19149488
  • Yu FH, Catterall WA. The VGL-chanome: a protein superfamily specialized for electrical signaling and ionic homeostasis. Sci STKE 2004; 2004:re15; http://dx.doi.org/10.1126/stke.2532004re15; PMID: 15467096
  • Yu K, Duran C, Qu Z, Cui YY, Hartzell HC. Explaining calcium-dependent gating of anoctamin-1 chloride channels requires a revised topology. Circ Res 2012; 110:990 - 9; http://dx.doi.org/10.1161/CIRCRESAHA.112.264440; PMID: 22394518
  • Sanchez C, Lachaize C, Janody F, Bellon B, Röder L, Euzenat J, et al. Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database. Nucleic Acids Res 1999; 27:89 - 94; http://dx.doi.org/10.1093/nar/27.1.89; PMID: 9847149
  • Satagopam VP, Theodoropoulou MC, Stampolakis CK, Pavlopoulos GA, Papandreou NC, Bagos PG, et al. GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. Database (Oxford) 2010; 2010:baq019; http://dx.doi.org/10.1093/database/baq019; PMID: 20689020
  • Müller CS, Haupt A, Bildl W, Schindler J, Knaus HG, Meissner M, et al. Quantitative proteomics of the Cav2 channel nano-environments in the mammalian brain. Proc Natl Acad Sci U S A 2010; 107:14950 - 7; http://dx.doi.org/10.1073/pnas.1005940107; PMID: 20668236
  • Miller JP, Lo RS, Ben-Hur A, Desmarais C, Stagljar I, Noble WS, et al. Large-scale identification of yeast integral membrane protein interactions. Proc Natl Acad Sci U S A 2005; 102:12123 - 8; http://dx.doi.org/10.1073/pnas.0505482102; PMID: 16093310
  • Brito GC, Andrews DW. Removing bias against membrane proteins in interaction networks. BMC Syst Biol 2011; 5:169; http://dx.doi.org/10.1186/1752-0509-5-169; PMID: 22011625
  • Tarassov K, Messier V, Landry CR, Radinovic S, Serna Molina MM, Shames I, et al. An in vivo map of the yeast protein interactome. Science 2008; 320:1465 - 70; http://dx.doi.org/10.1126/science.1153878; PMID: 18467557
  • Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, et al. The genetic landscape of a cell. Science 2010; 327:425 - 31; http://dx.doi.org/10.1126/science.1180823; PMID: 20093466
  • Babu M, Vlasblom J, Pu S, Guo X, Graham C, Bean BD, et al. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature 2012; 489:585 - 9; http://dx.doi.org/10.1038/nature11354; PMID: 22940862
  • Yang YD, Cho H, Koo JY, Tak MH, Cho Y, Shim WS, et al. TMEM16A confers receptor-activated calcium-dependent chloride conductance. Nature 2008; 455:1210 - 5; http://dx.doi.org/10.1038/nature07313; PMID: 18724360
  • Schroeder BC, Cheng T, Jan YN, Jan LY. Expression cloning of TMEM16A as a calcium-activated chloride channel subunit. Cell 2008; 134:1019 - 29; http://dx.doi.org/10.1016/j.cell.2008.09.003; PMID: 18805094
  • Caputo A, Caci E, Ferrera L, Pedemonte N, Barsanti C, Sondo E, et al. TMEM16A, a membrane protein associated with calcium-dependent chloride channel activity. Science 2008; 322:590 - 4; http://dx.doi.org/10.1126/science.1163518; PMID: 18772398
  • Hartzell HC, Yu K, Xiao Q, Chien LT, Qu Z. Anoctamin/TMEM16 family members are Ca2+-activated Cl- channels. J Physiol 2009; 587:2127 - 39; http://dx.doi.org/10.1113/jphysiol.2008.163709; PMID: 19015192
  • Kunzelmann K, Tian Y, Martins JR, Faria D, Kongsuphol P, Ousingsawat J, et al. Anoctamins. Pflugers Arch 2011; 462:195 - 208; http://dx.doi.org/10.1007/s00424-011-0975-9; PMID: 21607626
  • Romanenko VG, Catalán MA, Brown DA, Putzier I, Hartzell HC, Marmorstein AD, et al. Tmem16A encodes the Ca2+-activated Cl- channel in mouse submandibular salivary gland acinar cells. J Biol Chem 2010; 285:12990 - 3001; http://dx.doi.org/10.1074/jbc.M109.068544; PMID: 20177062
  • Huang F, Rock JR, Harfe BD, Cheng T, Huang X, Jan YN, et al. Studies on expression and function of the TMEM16A calcium-activated chloride channel. Proc Natl Acad Sci U S A 2009; 106:21413 - 8; http://dx.doi.org/10.1073/pnas.0911935106; PMID: 19965375
  • Lentz TL. Cell Fine Structure Saunders (W.B.) Co Ltd 1971.
  • Duran C, Hartzell HC. Physiological roles and diseases of Tmem16/Anoctamin proteins: are they all chloride channels?. Acta Pharmacol Sin 2011; 32:685 - 92; http://dx.doi.org/10.1038/aps.2011.48; PMID: 21642943
  • Tarran R, Loewen ME, Paradiso AM, Olsen JC, Gray MA, Argent BE, et al. Regulation of murine airway surface liquid volume by CFTR and Ca2+-activated Cl- conductances. J Gen Physiol 2002; 120:407 - 18; http://dx.doi.org/10.1085/jgp.20028599; PMID: 12198094
  • Stephan AB, Shum EY, Hirsh S, Cygnar KD, Reisert J, Zhao H. ANO2 is the cilial calcium-activated chloride channel that may mediate olfactory amplification. Proc Natl Acad Sci U S A 2009; 106:11776 - 81; http://dx.doi.org/10.1073/pnas.0903304106; PMID: 19561302
  • Hengl T, Kaneko H, Dauner K, Vocke K, Frings S, Möhrlen F. Molecular components of signal amplification in olfactory sensory cilia. Proc Natl Acad Sci U S A 2010; 107:6052 - 7; http://dx.doi.org/10.1073/pnas.0909032107; PMID: 20231443
  • Stöhr H, Heisig JB, Benz PM, Schöberl S, Milenkovic VM, Strauss O, et al. TMEM16B, a novel protein with calcium-dependent chloride channel activity, associates with a presynaptic protein complex in photoreceptor terminals. J Neurosci 2009; 29:6809 - 18; http://dx.doi.org/10.1523/JNEUROSCI.5546-08.2009; PMID: 19474308
  • Liu B, Linley JE, Du X, Zhang X, Ooi L, Zhang H, et al. The acute nociceptive signals induced by bradykinin in rat sensory neurons are mediated by inhibition of M-type K+ channels and activation of Ca2+-activated Cl- channels. J Clin Invest 2010; 120:1240 - 52; http://dx.doi.org/10.1172/JCI41084; PMID: 20335661
  • Pifferi S, Cenedese V, Menini A. Anoctamin 2/TMEM16B: a calcium-activated chloride channel in olfactory transduction. Exp Physiol 2012; 97:193 - 9; PMID: 21890523
  • Large WA, Wang Q. Characteristics and physiological role of the Ca(2+)-activated Cl- conductance in smooth muscle. Am J Physiol 1996; 271:C435 - 54; PMID: 8769982
  • Duan D. Phenomics of cardiac chloride channels: the systematic study of chloride channel function in the heart. J Physiol 2009; 587:2163 - 77; http://dx.doi.org/10.1113/jphysiol.2008.165860; PMID: 19171656
  • Xiang CC, Mezey E, Chen M, Key S, Ma L, Brownstein MJ. Using DSP, a reversible cross-linker, to fix tissue sections for immunostaining, microdissection and expression profiling. Nucleic Acids Res 2004; 32:e185; http://dx.doi.org/10.1093/nar/gnh185; PMID: 15604454
  • Gokhale A, Larimore J, Werner E, So L, Moreno-De-Luca A, Lese-Martin C, et al. Quantitative proteomic and genetic analyses of the schizophrenia susceptibility factor dysbindin identify novel roles of the biogenesis of lysosome-related organelles complex 1. J Neurosci 2012; 32:3697 - 711; http://dx.doi.org/10.1523/JNEUROSCI.5640-11.2012; PMID: 22423091
  • Salazar G, Zlatic S, Craige B, Peden AA, Pohl J, Faundez V. Hermansky-Pudlak syndrome protein complexes associate with phosphatidylinositol 4-kinase type II alpha in neuronal and non-neuronal cells. J Biol Chem 2009; 284:1790 - 802; http://dx.doi.org/10.1074/jbc.M805991200; PMID: 19010779
  • Nesvizhskii AI. Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics 2012; 12:1639 - 55; http://dx.doi.org/10.1002/pmic.201100537; PMID: 22611043
  • Gingras AC, Gstaiger M, Raught B, Aebersold R. Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 2007; 8:645 - 54; http://dx.doi.org/10.1038/nrm2208; PMID: 17593931
  • Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002; 1:376 - 86; http://dx.doi.org/10.1074/mcp.M200025-MCP200; PMID: 12118079
  • Trinkle-Mulcahy L, Boulon S, Lam YW, Urcia R, Boisvert FM, Vandermoere F, et al. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J Cell Biol 2008; 183:223 - 39; http://dx.doi.org/10.1083/jcb.200805092; PMID: 18936248
  • Mann M. Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 2006; 7:952 - 8; http://dx.doi.org/10.1038/nrm2067; PMID: 17139335
  • Ong SE, Mann M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat Protoc 2006; 1:2650 - 60; http://dx.doi.org/10.1038/nprot.2006.427; PMID: 17406521
  • Zlatic SA, Ryder PV, Salazar G, Faundez V. Isolation of labile multi-protein complexes by in vivo controlled cellular cross-linking and immuno-magnetic affinity chromatography. J Vis Exp 2010; 1855; PMID: 20216526
  • Fehon RG, McClatchey AI, Bretscher A. Organizing the cell cortex: the role of ERM proteins. Nat Rev Mol Cell Biol 2010; 11:276 - 87; http://dx.doi.org/10.1038/nrm2866; PMID: 20308985
  • Tsukita S, Yonemura S. ERM (ezrin/radixin/moesin) family: from cytoskeleton to signal transduction. Curr Opin Cell Biol 1997; 9:70 - 5; http://dx.doi.org/10.1016/S0955-0674(97)80154-8; PMID: 9013673
  • Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tatar D, Benita Y, et al, International Inflammatory Bowel Disease Genetics Constortium. Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet 2011; 7:e1001273; http://dx.doi.org/10.1371/journal.pgen.1001273; PMID: 21249183
  • Jeong H, Mason SP, Barabási AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001; 411:41 - 2; http://dx.doi.org/10.1038/35075138; PMID: 11333967
  • Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005; 122:957 - 68; http://dx.doi.org/10.1016/j.cell.2005.08.029; PMID: 16169070
  • Jackson LP, Kelly BT, McCoy AJ, Gaffry T, James LC, Collins BM, et al. A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex. Cell 2010; 141:1220 - 9; http://dx.doi.org/10.1016/j.cell.2010.05.006; PMID: 20603002
  • Höning S, Ricotta D, Krauss M, Späte K, Spolaore B, Motley A, et al. Phosphatidylinositol-(4,5)-bisphosphate regulates sorting signal recognition by the clathrin-associated adaptor complex AP2. Mol Cell 2005; 18:519 - 31; http://dx.doi.org/10.1016/j.molcel.2005.04.019; PMID: 15916959
  • Lomant AJ, Fairbanks G. Chemical probes of extended biological structures: synthesis and properties of the cleavable protein cross-linking reagent [35S]dithiobis(succinimidyl propionate). J Mol Biol 1976; 104:243 - 61; http://dx.doi.org/10.1016/0022-2836(76)90011-5; PMID: 957432
  • Craige B, Salazar G, Faundez V. Phosphatidylinositol-4-kinase type II alpha contains an AP-3-sorting motif and a kinase domain that are both required for endosome traffic. Mol Biol Cell 2008; 19:1415 - 26; http://dx.doi.org/10.1091/mbc.E07-12-1239; PMID: 18256276
  • Benashski SE, King SM. Investigation of protein-protein interactions within flagellar dynein using homobifunctional and zero-length crosslinking reagents. Methods 2000; 22:365 - 71; http://dx.doi.org/10.1006/meth.2000.1088; PMID: 11133242
  • Huotari J, Helenius A. Endosome maturation. EMBO J 2011; 30:3481 - 500; http://dx.doi.org/10.1038/emboj.2011.286; PMID: 21878991
  • van Meel E, Klumperman J. Imaging and imagination: understanding the endo-lysosomal system. Histochem Cell Biol 2008; 129:253 - 66; http://dx.doi.org/10.1007/s00418-008-0384-0; PMID: 18274773
  • Galli T, Chilcote T, Mundigl O, Binz T, Niemann H, De Camilli P. Tetanus toxin-mediated cleavage of cellubrevin impairs exocytosis of transferrin receptor-containing vesicles in CHO cells. J Cell Biol 1994; 125:1015 - 24; http://dx.doi.org/10.1083/jcb.125.5.1015; PMID: 8195285
  • Veale KJ, Offenhäuser C, Whittaker SP, Estrella RP, Murray RZ. Recycling endosome membrane incorporation into the leading edge regulates lamellipodia formation and macrophage migration. Traffic 2010; 11:1370 - 9; http://dx.doi.org/10.1111/j.1600-0854.2010.01094.x; PMID: 20604897