Live cell single-molecule detection in systems biology

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Volumn 4, Issue 2, 2012, Pages 183-192

  Sako, Yasushi ^a   Hiroshima, Michio ^a   Pack, Chan Gi ^a   Okamoto, Kenji ^a   Hibino, Kayo ^a   Yamamoto, Akihiro ^a  

^a RIKEN   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN;

BACTERIAL CELL; CELL STRUCTURE; CHEMICAL REACTION KINETICS; CYTOPLASM; ESCHERICHIA COLI; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; LIVE CELL SINGLE MOLECULE DETECTION; MICROSCOPY; MOLECULAR DYNAMICS; MOLECULAR IMAGING; MOLECULAR INTERACTION; MOLECULE; NONHUMAN; REVIEW; SINGLE CELL ANALYSIS; SYSTEMS BIOLOGY;

FLUORESCENT DYES; HELA CELLS; HUMANS; KINETICS; MICROSCOPY, FLUORESCENCE; MODELS, BIOLOGICAL; MOLECULAR DYNAMICS SIMULATION; NANOTECHNOLOGY; PHOTONS; RECEPTOR, EPIDERMAL GROWTH FACTOR; SYSTEMS BIOLOGY;

EID: 84857072115     PISSN: 19395094     EISSN: 1939005X     Source Type: Journal    
DOI: 10.1002/wsbm.161     Document Type: Review

References (43)

1. Selvin PR, Ha T, eds. Single-Molecule Techniques. A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press; 2008.
2. Ishii Y, Yanagida T, eds. Single Molecule Dynamics in Life Science. Weinheim: Wiley-VCH; 2009.
3. Sako Y, Yanagida T. Single-molecule visualization in cell biology. Nat Rev Cell Biol 2003, 4:SS1-SS5.
4. Sako Y. Imaging single molecules for systems biology. Mol Syst Biol 2006, 2. doi:10.1038/msb4100100.
5. Sako Y, Ueda M, eds. Cell Signaling Reactions: Single-Molecular Kinetic Analysis. London: Springer; 2010.
6. Gratton ELV. Exploring dynamics in living cells by tracking single particles. Cell Biochem Biophys 2007, 48:1-15.
7. Bacia K, Kim SA, Schwille P. Fluorescence cross-correlation spectroscopy in living cells. Nat Methods 2006, 3:83-89.
8. Tani T, Miyamoto Y, Fujimori K, Taguchi T, Yanagida T, Sako Y, Harada Y. Trafficking of ligand-receptor complex on the growth cones as an essential step for the uptake of nerve growth factor at the distal end of the axon: a single-molecule analysis. J Neurosci 2005, 25:2181-2191.
9. Ueda M, Sako Y, Tanaka T, Devreotes PN, Yanagida T. Single molecule analysis of chemotactic signaling in Dictyostelium cells. Science 2001, 294:864-867.
10. Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science 2002, 297:1183-1186.
11. Hell SW. Microscopy and its focal switch. Nat Methods 2009, 6:24-32.
12. Wazawa T, Ueda M. Total internal reflection fluorescence microscopy in single molecule nanobioscience. Adv Biochem Eng Biotechnol 2005, 95:77-106.
13. Tokunaga M, Imamoto N, Sakata-Sogawa K. Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat Methods 2008, 5:159-161.
14. Schmidt T, Kubitscheck U, Rohler D, Nienhaus U. Photostability data for fluorescent dyes: an update. Singl Mol 2002, 3:5-6.
15. Murakoshi H, Iino R, Kobayashi T, Fujiwara T, Ohshima C, Yoshimura A, Kusumi A. Single-molecule imaging analysis of Ras activation in living cells. Proc Natl Acad Sci USA 2004, 101:7317-7322.
16. Nguyen VT, Kamio Y, Higuchi H. Single-molecule imaging of cooperative assembly of γ-hemolysin on erythrocyte membranes. EMBO J 2003, 22:4968-4979.
17. Teramura Y, Ichinose J, Takagi H, Nishida K, Yanagida T, Sako Y. Single-molecule analysis of epidermal growth factor binding on the surface of living cells. EMBO J 2006, 25:4215-4222.
18. Webb SED, Roberts SK, Needham SR, Tynan CJ, Rolfe DJ, Winn MD, Clarke DT, Barraclough R, Martin-Fernandez ML. Single-molecule imaging and fluorescence lifetime imaging microscopy show different structures for high- and low-affinity epidermal growth factor receptors in A431 cells. Biophys J 2008, 94:803-819.
19. Matsuoka S, Iijima M, Watanabe TM, Kuwayama H, Yanagida T, Devreotes PN, Ueda M. Single-molecule analysis of chemoattractant-stimulated membrane recruitment of a PH-domain-containing protein. J Cell Sci 2005, 119:1071-1079.
20. 2+ signaling: single-molecule tracking study 2. J Cell Biol 2007, 177:731-742.
21. Hibino K, Shibata T, Yanagida T, Sako Y. A RasGTP-induced conformational change in C-RAF is essential for accurate molecular recognition. Biophys J 2009, 97:1277-1287.
22. Yang W, Gelles J, Musser SM. Imaging of single-molecule translocation through nuclear pore complexes. Proc Natl Acad Sci USA 2004, 101:12887-12892.
23. Douglass AD, Vale RD. Single-molecule microscopy reveals plasma membrane microdomains created by protein-protein networks that exclude or trap signaling molecules in T cells. Cell 2005, 121:937-950.
24. Yokosuka T, Sakata-Sogawa K, Kobayashi W, Hiroshima M, Hashimoto-Tane A, Tokunaga M, Dustin ML, Saito T. Newly generated T cell receptor microclusters initiate and sustain T cell activation by recruitment of Zap70 and SLP-76. Nat Immunol 2005, 6:1253-1262.
25. Jacquier V, Prummer M, Segura J-M, Pick H, Vogel H. Visualizing odorant receptor trafficking in living cells down to the single-molecule level. Proc Natl Acad Sci USA 2006, 103:14325-14330.
26. Drbal K, Moertelmaier M, Holzhauser C, Muhammad A, Fuertbauer E, Howorka S, Hinterberger M, Stockinger H, Schütz GJ. Single-molecule microscopy reveals heterogeneous dynamics of lipid raft components upon TCR engagement. Int Immunol 2007, 19:675-684.
27. James JR, White SS, Clarke RW, Johansen AM, Dunne PD, Sleep DL, Fitzgerald WJ, Davis SJ, Klenerman D. Single-molecule level analysis of the subunit composition of the T cell receptor on live T cells. Proc Natl Acad Sci USA 2007, 104:17662-17667.
28. Schaaf MJ, Koopmans WJ, Meckel T, van Noort J, Snaar-Jagalska BE, Schmidt TS, Spaink HP. Single-molecule microscopy reveals membrane microdomain organization of cells in a living vertebrate. Biophys J 2009, 97:1206-1214.
29. Shibata SC, Hibino K, Mashimo T, Yanagida T, Sako Y. Formation of signal transduction complexes during immobile phase of NGFR movements. Biochem Biophys Res Comm 2006, 342:316-322.
30. Simson R, Sheets ED, Jacobson K. Detection of temporary lateral confinement of membrane proteins using single-particle tracking analysis. Biophys J 1995, 69:989-993.
31. Chung I, Akita R, Vandlen R, Toomre D, Schles singer J, Mellman I. Spatial control of EGF receptor activation by reversible dimerization on living cells. Nature 2010, 464:783-787.
32. Vazquez F, Matsuoka. Sellers S, Yanagida WR, Ueda T, Devreotes M. PN Tumor suppressor PTEN acts through dynamic interaction with the plasma membrane. Proc Natl Acad Sci USA 2006, 103:3633-3638.
33. Xie SX, Choi PJ, Li G-W, Lee NK, Lia G. Single-molecule approach to molecular biology in living bacteria cells. Ann Rev Biophys 2008, 37:417-444.
34. Pack C, Saito K, Tamura M, Kinjo M. Microenvironment and effect of energy depletion in the nucleus analyzed by mobility of multiple oligomeric EGFPs. Biophys J 2006, 91:3921-3936.
35. Bancaud A, Huet S, Daigle N, Mozziconacci J, Beaudouin J, Ellenberg J. Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. EMBO J 2009, 28:3785-3798.
36. Vukojevic V, Papadopoulos DK, Terenius L, Gehring WJ, Rigler R. Quantitative study of synthetic Hox transcription factor-DNA interactions in live cells. Proc Natl Acad Sci USA 2010, 107:4093-4098.
37. Yu SR, Burkhardt M, Nowak M, Ries J, Petrásek Z, Scholpp S, Schwille P, Brand M. Fgf8 morphogen gradient forms by a source-sink mechanism with freely diffusing molecules. Nature 2009, 461:533-536.
38. Malengo G, Andolfo A, Sidenius N, Gratton E, Zamai M, Caiolfa VR. Fluorescence correlation spectroscopy and photon counting histogram on membrane proteins: functional dynamics of the GPI-anchored urokinase plasminogen activator receptor. J Biomed Opt 2008, 13:031215.
39. Chen Y, Müller JD. Determining the stoichiometry of protein heterocomplexes in living cells with fluorescence fluctuation spectroscopy. Proc Natl Acad Sci USA 2006, 104:3147-3152.
40. Yilidiz A, Forkey JN, McKinney SA, Ha T, Goldman YE, Selvin PR. Myosin V walks hand-over-hand: single fluorephore imaging with 1.5-nm localization. Science 2003, 300:2061-2065.
41. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz J, Hess HF. Imaging intracellular fluorescent proteins at nanometer resolution. Science 2006, 313:1642-1645.
42. Bates M, Huang B, Dempsey GT, Zhuang XW. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 2007, 317:1749-1753.
43. Dertinger T, Colyer R, Iyer G, Weiss S, Enderlein J. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). Proc Natl Acad Sci USA 2009, 106:22287-22292.