Microscopy approaches to investigate protein dynamics and lipid organization

References

• Akihiro K, Sakot Y. 1996. Cell surface organization by the membrane skeleton. Curr Opin Cell Biol 8:566–574
   Google Scholar
• Antollini SS, Barrantes FJ. 1998. Disclosure of discrete sites for phospholipid and sterols at the protein-lipid interface in native acetylcholine receptor-rich membrane. Biochemistry 37:16653–16662
   Google Scholar
• Axelrod D, Koppel DE, Schlessinger J, Elson E, Webb WW. 1976. Mobility measurement by analysis of fluorescence photobleaching recovery kinetics. Biophys J 16:1055–1069
   PubMed Web of Science ®Google Scholar
• Bagatolli LA, Parasassi T, Fidelio GD, Gratton E. 1999. A model for the interaction of 6-lauroyl-2-(N,N-dimethylamino)naphthalene with lipid environments: Implications for spectral properties. Photochem Photobiol 70:557–564
   PubMed Web of Science ®Google Scholar
• Benda A, Benes M, Marec V, Lhotsky A, Hermens W, Heyrovsky J. 2003. How to determine diffusion coefficients in planar phospholipid systems by confocal fluorescence correlation spectroscopy. Langmuir 9:4120–4126
   Google Scholar
• Benda A, Hof M, Wahl M, Patting M, Erdmann R, Kapusta P. 2005. TCSPC upgrade of a confocal FCS microscope. Rev Sci Instrum 76:033106–4
   Google Scholar
• Benes M, Billy D, Speijer H, Hof M, Hermens WT. 2004. Phospholipid membranes on mica, silica and glass. Langmuir 20:10129–10137
   Google Scholar
• Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, et al. 2006. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–1645
   PubMed Web of Science ®Google Scholar
• Bohmer M. 2002. Time-resolved fluorescence correlation spectroscopy. Chem Phys Lett 353:439–445
   Google Scholar
• Bückers J, Wildanger D, Vicidomini G, Kastrup L, Hell SW. 2011. Simultaneous multi-lifetime multi-color STED imaging for colocalization analyses. Opt Express 19:3130–3143
   PubMed Web of Science ®Google Scholar
• Chen Y, Mills JD, Periasamy A. 2003. Protein localization in living cells and tissues using FRET and FLIM. Differentiation 71:528–541
   Google Scholar
• Clegg RM, Breusegam S, Barry N, Holub O, Govindjee G, Redford G. 2005. How Can one choose the best method for measuring FRET in a microscope with my biological system? Microsc Microanal 11:272–273
   Google Scholar
• Digman MA, Caiolfa VR, Zamai M, Gratton E. 2008. The phasor approach to fluorescence lifetime imaging analysis. Biophys J 94:L14–L16
   PubMed Web of Science ®Google Scholar
• Digman MA, Sengupta P, Wiseman PW, Brown CM, Horwitz AR, Gratton E. 2005. Fluctuation correlation spectroscopy with a laser-scanning microscope: Exploiting the hidden time structure. Biophys J 88:L33–L36
   Google Scholar
• Digman MA, Wiseman PW, Horwitz AR, Gratton E. 2009. Detecting protein complexes in living cells from laser scanning confocal image sequences by the cross correlation raster image spectroscopy method. Biophys J 96:707–716
   Google Scholar
• Douglass AD, Vale RD. 2005. Single-molecule microscopy reveals plasma membrane microdomains created by protein-protein networks that exclude or trap signaling molecules in T cells. Cell 121:937–950
   PubMed Web of Science ®Google Scholar
• Eggeling C, Ringemann C, Medda R, Schwarzmann G, Sandhoff K, Polyakova S, et al. 2009. Direct observation of the nanoscale dynamics of membrane lipids in a living cell. Nature 457:1159–1162
   PubMed Web of Science ®Google Scholar
• Ehrig J, Petrov EP, Schwille P. 2011. Near-critical fluctuations and cytoskeleton-assisted phase separation lead to subdiffusion in cell membranes. Biophys J 100:80–89
   Google Scholar
• Enderlein J, Gregor I. 2005. Using fluorescence lifetime for discriminating detector afterpulsing in fluorescence-correlation spectroscopy. Rev Sci Instrum 76:033102–5
   Google Scholar
• Engelman DM. 2005. Membranes are more mosaic than fluid. Nature 438:578–80
   PubMed Web of Science ®Google Scholar
• Feder TJ, Brust-Mascher I, Slattery JP, Baird B, Webb WW. 1996. Constrained diffusion or immobile fraction on cell surfaces: A new interpretation. Biophys J 70:2767–2773
   PubMed Web of Science ®Google Scholar
• Fereidouni F, Bader AN, Gerritsen HC. 2012. Spectral phasor analysis allows rapid and reliable unmixing of fluorescence microscopy spectral images. Opt Express 20:12729–12741
   PubMed Web of Science ®Google Scholar
• Fujiwara T, Ritchie K, Murakoshi H, Jacobson K, Kusumi A. 2002. Phospholipids undergo hop diffusion in compartmentalized cell membrane. J Cell Biol 157:1071–1081
   PubMed Web of Science ®Google Scholar
• Garg S, Tang JX, Rühe J, Naumann C. 2009. Actin-induced perturbation of PS lipid-cholesterol interaction: A possible mechanism of cytoskeleton-based regulation of membrane organization. J Struct Biol 168:11–20
   PubMed Web of Science ®Google Scholar
• Gaus K, Chklovskaia E, Fazekas de St Groth B, Jessup W, Harder T. 2005. Condensation of the plasma membrane at the site of T lymphocyte activation. J Cell Biol 171:121–131
   PubMed Web of Science ®Google Scholar
• Gaus K, Gratton E, Kable EPW, Jones AS, Gelissen I, Kritharides L, Jessup W. 2003. Visualizing lipid structure and raft domains in living cells with two-photon microscopy. Proc Natl Acad Sci USA 100:15554–15559
   PubMed Web of Science ®Google Scholar
• Geumann U, Schäfer C, Riedel D, Jahn R, Rizzoli S. 2010. Synaptic membrane proteins form stable microdomains in early endosomes. Microsc Res Tech 73:606–617
   Google Scholar
• Golfetto O, Hinde E, Gratton E. 2013. Laurdan fluorescence lifetime discriminates cholesterol content from changes in fluidity in living cell membranes. Biophys J 104:1238–1247
   Google Scholar
• Goswami D, Gowrishankar K, Bilgrami S, Ghosh S, Raghupathy R, Chadda R, et al. 2008. Nanoclusters of GPI-anchored proteins are formed by cortical actin-driven activity. Cell 135:1085–1097
   PubMed Web of Science ®Google Scholar
• Gowrishankar K, Ghosh S, Saha SCR, Mayor S, Rao M. 2012. Active remodeling of cortical actin regulates spatiotemporal organization of cell surface molecules. Cell 149:1353–1367
   PubMed Web of Science ®Google Scholar
• Halemani ND, Bethani I, Rizzoli SO, Lang T. 2010. Structure and dynamics of a two-helix SNARE complex in live cells. Traffic 11:394–404
   Google Scholar
• He H-T, Marguet D. 2011. Detecting nanodomains in living cell membrane by fluorescence correlation spectroscopy. Ann Rev Phys Chem 62:417–436
   Google Scholar
• Hell SW, Wichmann J. 1994. Breaking the diffraction resolution limit by stimulated emission: Stimulated-emission-depletion fluorescence microscopy. Opt Lett 19:780–782
   PubMed Web of Science ®Google Scholar
• Hinde E, Digman MA, Hahn KM, Gratton E. 2012. Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM. Proc Natl Acad Sci USA 110:135–40
   Google Scholar
• Hof M. 2012. Springer Series on Fluorescence Methods and Applications. Berlin: Springer Heidelberg
   Google Scholar
• Holowka D. 1997. Compartmentalized activation of the high affinity immunoglobulin E receptor within membrane domains. J Biol Chem 272:4276–4280
   Google Scholar
• Ishikawa-Ankerhold HC, Ankerhold R, Drummen GPC. 2012. Advanced fluorescence microscopy techniques – FRAP, FLIP, FLAP, FRET and FLIM. Molecules 17:4047–4132
   PubMed Web of Science ®Google Scholar
• Jacobson K, Mouritsen O, Anderson R. 2007. Lipid rafts: At a crossroad between cell biology and physics. Nat Cell Biol 9:7–14
   PubMed Web of Science ®Google Scholar
• Jin L, Millard AC, Wuskell JP, Clark HA, Loew LM. 2005. Cholesterol-enriched lipid domains can be visualized by di-4-ANEPPDHQ with linear and nonlinear optics. Biophys J 89:L04–6
   Google Scholar
• Jin L, Millard AC, Wuskell JP, Dong X, Wu D, Clark HA, Loew LM. 2006. Characterization and application of a new optical probe for membrane lipid domains. Biophys J 90:2563–2575
   PubMed Web of Science ®Google Scholar
• Kasper R, Harke B, Forthmann C, Tinnefeld P, Hell SW, Sauer M. 2010. Single-molecule STED microscopy with photostable organic fluorophores. Small 6:1379–1384
   Google Scholar
• Kenworthy AK, Petranova N, Edidin M. 2000. High-resolution FRET microscopy of cholera toxin B-subunit and GPI-anchored proteins in cell plasma membranes. Mol Biol Cell 11:1645–1655
   PubMed Web of Science ®Google Scholar
• Kenworthy A, Edidin M. 1998. A glycosylphosphatidylinositol-anchored protein at the apical surface of MDCK cells examined at a resolution of <100 Å using imaging fluorescence resonance energy. J Cell Biol 142:69–84
   PubMed Web of Science ®Google Scholar
• Kusumi A, Koyama-Honda I, Suzuki K. 2004. Molecular dynamics and interactions for creation of stimulation-induced stabilized rafts from small unstable steady-state rafts. Traffic 5:213–230
   PubMed Web of Science ®Google Scholar
• Kusumi A, Suzuki KGN, Kasai RS, Ritchie K, Fujiwara TK. 2011. Hierarchical mesoscale domain organization of the plasma membrane. Trends Biochem Sci 36:604–615
   Google Scholar
• Kwiatek JM, Owen DM, Abu-Siniyeh A, Yan P, Loew LM, Gaus K. 2013. Characterization of a new series of fluorescent probes for imaging membrane order. PLoS One 8:e52960
   Google Scholar
• Liang Y, Fotiadis D, Filipek S, Saperstein DA, Palczewski K, Engel A. 2003. Organization of the G protein-coupled receptors rhodopsin and opsin in native membranes. J Biol Chem 278:21655–21662
   PubMed Web of Science ®Google Scholar
• Liebman P, Entine G. 1974. Lateral diffusion of visual pigment in photoreceptor disk membranes. Science 185:457–459
   PubMed Web of Science ®Google Scholar
• Lippincott-Schwartz J, Snapp E, Kenworthy A. 2001. Studying protein dynamics in living cells. Nat Rev Mol Cell Biol 2:444–456
   PubMed Web of Science ®Google Scholar
• Magde D, Elson E, Webb W. 1972. Thermodynamic fluctuations in a reacting system – measurement by fluorescence correlation spectroscopy. Phys Rev Lett 29:705–708
   Web of Science ®Google Scholar
• Mueller V, Ringemann C, Honigmann A, Schwarzmann G, Medda R, Leutenegger M, et al. 2011. STED nanoscopy reveals molecular details of cholesterol- and cytoskeleton-modulated lipid interactions in living cells. Biophys J 101:1651–1660
   PubMedGoogle Scholar
• Obaid AL, Loew LM, Wuskell JP, Salzberg BM. 2004. Novel naphthylstyryl-pyridium potentiometric dyes offer advantages for neural network analysis. J Neurosci Meth 134:179–190
   PubMedGoogle Scholar
• Owen D, Lanigan PMP, Dunsby C, Munro I, Grant D, Neil MAA, et al. 2006. Fluorescence lifetime imaging provides enhanced contrast when imaging the phase-sensitive dye di-4-ANEPPDHQ in model membranes and live cells. Biophys J 90:L80–L82
   Google Scholar
• Owen D, Magenau A, Majumdar A, Gaus K. 2010. Imaging membrane lipid order in whole, living vertebrate organisms. Biophys J 99:L7–L9
   PubMed Web of Science ®Google Scholar
• Owen D, Rentero C, Magenau A, Abu-Siniyeh A, Gaus K. 2012a. Quantitative imaging of membrane lipid order in cells and organisms. Nat Protoc 7:24–35
   Web of Science ®Google Scholar
• Owen D, Williamson D, Magenau A, Gaus K. 2012b. Sub-resolution lipid domains exist in the plasma membrane and regulate protein diffusion and distribution. Nat Commun 3:1256
   PubMed Web of Science ®Google Scholar
• Parasassi T, De Stasio G, d’Ubaldo A, Gratton E. 1990. Phase fluctuation in phospholipid membranes revealed by Laurdan fluorescence. Biophys J 57:1179–1186
   PubMed Web of Science ®Google Scholar
• Parasassi T, Gratton E. 1995. Membrane lipid domains and dynamics as detected by Laurdan fluorescence. J Fluoresc 5:59–69
   PubMedGoogle Scholar
• Parasassi T, Gratton E, Yu WM, Wilson P, Levi M. 1997. Two-photon fluorescence microscopy of laurdan generalized polarization domains in model and natural membranes. Biophys J 72:2413–2429
   PubMed Web of Science ®Google Scholar
• Parasassi T, Krasnowska EK, Bagatolli L, Gratton E. 1998. Laurdan and prodan as polarity-sensitive fluorescent membrane probes. J Fluoresc 8:365–373
   Web of Science ®Google Scholar
• Parasassi T, Ravagnan G, Rusch RM, Gratton E. 1993. Modulation and dynamics of phase properties in phospholipid mixtures detected by Laurdan fluorescence. Photochem Photobiol 57:403–410
   PubMed Web of Science ®Google Scholar
• Pasenkiewicz Gierula M, Subczynski WK, Kusumi A. 1991. Influence of phospholipid unsaturation on the cholesterol distribution in membranes. Biochimie 73:1311–1316
   Google Scholar
• Pike LJ. 2006. Rafts defined: a report on the Keystone Symposium on Lipid Rafts and Cell Function. J Lipid Res 47:1597–1598
   PubMed Web of Science ®Google Scholar
• Quinn P, Griffiths G, Warren G. 1984. Density of newly synthesized plasma membrane proteins in intracellular membranes II. Biochemical studies. J Cell Biol 98:2142–2147
   Google Scholar
• Rossy J, Ma Y, Gaus K. 2014. The organisation of the cell membrane: do proteins rule lipids? Curr Opin Chem Biol 20C:54–59
   Google Scholar
• Rossy J, Owen DM, Williamson DJ, Yang Z, Gaus K. 2013. Conformational states of the kinase Lck regulate clustering in early T cell signaling. Nat Immunol 14:82–89
   Google Scholar
• Rothberg KG, Ying YS, Kamen B a, Anderson RG. 1990. Cholesterol controls the clustering of the glycophospholipid-anchored membrane receptor for 5-methyltetrahydrofolate. J Cell Biol 111:2931–2938
   PubMed Web of Science ®Google Scholar
• Rust MJ, Bates M, Zhuang X. 2006. Imaging by stochastic optical reconstruction microscopy (STORM). Nature Methods 3:793–795
   PubMed Web of Science ®Google Scholar
• Sako Y, Nagafuchi A, Tsukita S, Takeichi M, Kusumi A. 1998. Cytoplasmic regulation of the movement of E-cadherin on the free cell surface as studied by optical tweezers and single particle tracking: corralling and tethering by the membrane skeleton. J Cell Biol 140:1227–1240
   PubMed Web of Science ®Google Scholar
• Sengupta P, Jovanovic-Talisman T, Skoko D, Renz M, Veatch SL, Lippincott-Schwartz J. 2011. Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis. Nat Methods 8:969–975
   PubMed Web of Science ®Google Scholar
• Sezgin E, Levental I, Grzybek M, Schwarzmann G, Mueller V, Honigmann A, et al. 2012. Partitioning, diffusion, and ligand binding of raft lipid analogs in model and cellular plasma membranes. Biochim Biophys Acta 1818:1777–1784
   Google Scholar
• Sharma P, Varma R, Sarasij RC, Ira RC, Gousset K, Krishnamoorthy G, et al. 2004. Nanoscale organization of multiple GPI-anchored proteins in living cell membranes. Cell 116:577–589
   PubMed Web of Science ®Google Scholar
• Siegel RM. 2000. Fas preassociation required for apoptosis signaling and dominant inhibition by pathogenic mutations. Science 288:2354–2357
   PubMed Web of Science ®Google Scholar
• Simons K, Ikonen E. 1997. Functional rafts in cell membranes. Nature 387:569–572
   PubMed Web of Science ®Google Scholar
• Simons K, Vaz WLC. 2004. Model systems, lipid rafts, and cell membranes. Ann Rev Biophys Biomol Struct 33:269–295
   PubMedGoogle Scholar
• Singer S, Nicolson G. 1972. The fluid mosaic model of the structure of cells membranes. Science 175:720–731
   PubMed Web of Science ®Google Scholar
• Singh H, Lu R, Rodríguez PFG, Wu Y, Bopassa JC, Stefani E, Toro L. 2012. Visualization and quantification of cardiac mitochondrial protein clusters with STED microscopy. Mitochondrion 12:230–236
   PubMed Web of Science ®Google Scholar
• Sohn HW, Tolar P, Pierce SK. 2008. Membrane heterogeneities in the formation of B cell receptor-Lyn kinase microclusters and the immune synapse. J Cell Biol 182:367–379
   PubMed Web of Science ®Google Scholar
• Subczynski WK, Hyde JS, Kusumi A. 1991. Effect of alkyl chain unsaturation and cholesterol intercalation on oxygen transport in membranes: a pulse ESR spin labeling study. Biochemistry 30:8578–8590
   Google Scholar
• Suzuki K, Ritchie K, Kajikawa E, Fujiwara T, Kusumi A. 2005. Rapid hop diffusion of a G-protein-coupled receptor in the plasma membrane as revealed by single-molecule techniques. Biophys J 88:3659–3680
   Google Scholar
• Suzuki KGN, Kasai RS, Hirosawa KM, Nemoto YL, Ishibashi M, Miwa Y, et al. 2012. Transient GPI-anchored protein homodimers are units for raft organization and function. Nat Chem Biol 8:774–783
   PubMed Web of Science ®Google Scholar
• Tavano R, Contento RL, Baranda SJ, Soligo M, Tuosto L, Manes S, Viola A. 2006. CD28 interaction with filamin-A controls lipid raft accumulation at the T-cell immunological synapse. Nat. Cell Biol 8:1270–1276
   PubMed Web of Science ®Google Scholar
• Tomishige M, Sako Y, Kusumi A. 1998. Regulation mechanism of the lateral diffusion of band 3 in erythrocyte membranes by the membrane skeleton. J Cell Biol 142:989–1000
   Google Scholar
• Varma R, Mayor S. 1998. GPI-anchored proteins are organized in submicron domains at the cell surface. Nature 394:798–801
   PubMed Web of Science ®Google Scholar
• Weber G, Farris FJ. 1979. Synthesis and spectral properties of a hydrophobic fluorescent probe: 6-propionyl-2-(dimethylamino)naphthalene. Biochemistry 18:3075–3078
   PubMed Web of Science ®Google Scholar
• White J, Stelzer E. 1999. Photobleaching GFP reveals protein dynamics inside live cells. Trends Cell Biol 9:61–65
   PubMed Web of Science ®Google Scholar
• Williamson DJ, Owen DM, Rossy J, Magenau A, Wehrmann M, Gooding JJ, Gaus K. 2011. Pre-existing clusters of the adaptor Lat do not participate in early T cell signaling events. Nat Immunol 12:655–662
   PubMed Web of Science ®Google Scholar
• Willig KI, Harke B, Medda R, Hell SW. 2007. STED microscopy with continuous wave beams. Nat Methods 4:915–918
   PubMed Web of Science ®Google Scholar
• Wurm CA, Neumann D, Lauterbach M, Harke B, Egner A, Hell SW, Jakobs S. 2011. Nanoscale distribution of mitochondrial import receptor Tom20 is adjusted to cellular conditions and exhibits an inner-cellular gradient. Proc Natl Acad Sci USA 108:13546–13551
   PubMed Web of Science ®Google Scholar
• Yan P, Acker CD, Zhou W-L, Lee P, Bollensdorff C, Negrean A, et al. 2012. Palette of fluorinated voltage-sensitive hemicyanine dyes. Proc Natl Acad Sci USA 109:20443–8.
   Google Scholar
• Yechiel E, Edidin M. 1987. Micrometer-scale domains in fibroblast plasma membranes. J Cell Biol 105:755–760
   PubMed Web of Science ®Google Scholar
• Yokosuka T, Saito T. 2009. Dynamic regulation of T-cell costimulation through TCR-CD28 microclusters. Immunol Rev 229:27–40
   Google Scholar