Measuring colocalization by dual color single molecule imaging. Thresholds, error rates, and sensitivity

Advances in Planar Lipid Bilayers and Liposomes

Volumn 12, Issue C, 2010, Pages 21-40

  Ruprecht, Verena ^a   Weghuber, Julian ^a   Wieser, Stefan ^b   Schütz, Gerhard J ^a  

^a JOHANNES KEPLER UNIVERSITY LINZ   (Austria)

^b CENTRE D IMMUNOLOGIE DE MARSEILLE LUMINY   (France)

Author keywords

Association; Diffusion; Fluorescence; Plasma membrane; Protein interaction; Single molecule microscopy; Single particle tracking

Indexed keywords

EID: 77958138174     PISSN: 15544516     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381266-7.00002-X     Document Type: Book

References (77)

1. Yetukuri L., et al. Informatics and computational strategies for the study of lipids. Mol. Biosyst. 2008, 4(2):121-127.
2. Wallin E., von Heijne G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 1998, 7(4):1029-1038.
3. Kusumi A., Koyama-Honda I., Suzuki K. Molecular dynamics and interactions for creation of stimulation-induced stabilized rafts from small unstable steady-state rafts. Traffic 2004, 5(4):213-230.
4. Schwarzenbacher M., et al. Micropatterning for quantitative analysis of protein-protein interactions in living cells. Nat. Methods 2008, 5(12):1053-1060.
5. Bolte S., Cordelieres F.P. A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 2006, 224(Pt 3):213-232.
6. Lachmanovich E., et al. Co-localization analysis of complex formation among membrane proteins by computerized fluorescence microscopy: application to immunofluorescence co-patching studies. J. Microsc. 2003, 212(Pt 2):122-131.
7. Costes S.V., et al. Automatic and quantitative measurement of protein-protein colocalization in live cells. Biophys. J. 2004, 86(6):3993-4003.
8. Kolin D.L., Wiseman P.W. Advances in image correlation spectroscopy: measuring number densities, aggregation states, and dynamics of fluorescently labeled macromolecules in cells. Cell Biochem. Biophys. 2007, 49(3):141-164.
9. Costantino S., et al. Accuracy and dynamic range of spatial image correlation and cross-correlation spectroscopy. Biophys. J. 2005, 89(2):1251-1260.
10. Comeau J.W., Costantino S., Wiseman P.W. A guide to accurate fluorescence microscopy colocalization measurements. Biophys. J. 2006, 91(12):4611-4622.
11. Kenworthy A.K. Imaging protein-protein interactions using fluorescence resonance energy transfer microscopy. Methods 2001, 24(3):289-296.
12. Zal T., Zal M.A., Gascoigne N.R. Inhibition of T cell receptor-coreceptor interactions by antagonist ligands visualized by live FRET imaging of the T-hybridoma immunological synapse. Immunity 2002, 16(4):521-534.
13. Loura L.M., Prieto M., Fernandes F. Quantification of protein-lipid selectivity using FRET. Eur. Biophys. J. 2010, 39(4):565-578.
14. Maurel D., et al. Cell-surface protein-protein interaction analysis with time-resolved FRET and snap-tag technologies: application to GPCR oligomerization. Nat. Methods 2008, 5(6):561-567.
15. Hink M.A., Bisselin T., Visser A.J. Imaging protein-protein interactions in living cells. Plant Mol. Biol. 2002, 50(6):871-883.
16. Sengupta P., Holowka D., Baird B. Fluorescence resonance energy transfer between lipid probes detects nanoscopic heterogeneity in the plasma membrane of live cells. Biophys. J. 2007, 92(10):3564-3574.
17. Stryer L., Haugland R.P. Energy transfer: a spectroscopic ruler. Proc. Natl. Acad. Sci. USA 1967, 58(2):719-726.
18. Stryer L. Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 1978, 47:819-846.
19. Zal T., Gascoigne N.R. Photobleaching-corrected FRET efficiency imaging of live cells. Biophys. J. 2004, 86(6):3923-3939.
20. Kenworthy A.K., Edidin M. Distribution of a glycosylphosphatidylinositol-anchored protein at the apical surface of MDCK cells examined at a resolution of <100Å using imaging fluorescence resonance energy transfer. J. Cell Biol. 1998, 142(1):69-84.
21. Bacia K., Schwille P. Practical guidelines for dual-color fluorescence cross-correlation spectroscopy. Nat. Protoc. 2007, 2(11):2842-2856.
22. Thews E., et al. Cross talk free fluorescence cross correlation spectroscopy in live cells. Biophys. J. 2005, 89(3):2069-2076.
23. Leutenegger M., et al. Dual-color total internal reflection fluorescence cross-correlation spectroscopy. J. Biomed. Opt. 2006, 11(4):040502.
24. Ries J., et al. Modular scanning FCS quantifies receptor-ligand interactions in living multicellular organisms. Nat. Methods 2009, 6(9):643-645.
25. Morrison I.E., et al. Detecting and quantifying colocalization of cell surface molecules by single particle fluorescence imaging. Biophys. J. 2003, 85(6):4110-4121.
26. Trabesinger W., et al. Statistical analysis of single-molecule colocalization assays. Anal. Chem. 2001, 73(6):1100-1105.
27. Schutz G.J., Trabesinger W., Schmidt T. Direct observation of ligand colocalization on individual receptor molecules. Biophys. J. 1998, 74(5):2223-2226.
28. James J.R., et al. Single-molecule level analysis of the subunit composition of the T cell receptor on live T cells. Proc. Natl. Acad. Sci. USA 2007, 104(45):17662-17667.
29. Koyama-Honda I., et al. Fluorescence imaging for monitoring the colocalization of two single molecules in living cells. Biophys. J. 2005, 88(3):2126-2136.
30. Dunne P.D., et al. DySCo: quantitating associations of membrane proteins using two-color single-molecule tracking. Biophys. J. 2009, 97(4):L5-L7.
31. Ruprecht V., Brameshuber M., Schütz G.J. Two-color single molecule tracking combined with photobleaching for the detection of rare molecular interactions in fluid biomembranes. Soft Matter 2010, 6(3):568-581.
32. Hern J.A., et al. Formation and dissociation of M1 muscarinic receptor dimers seen by total internal reflection fluorescence imaging of single molecules. Proc. Natl. Acad. Sci. USA 2010, 107(6):2693-2698.
33. Suzuki K.G., et al. GPI-anchored receptor clusters transiently recruit Lyn and G alpha for temporary cluster immobilization and Lyn activation: single-molecule tracking study 1. J. Cell Biol. 2007, 177(4):717-730.
34. 2+ signaling: single-molecule tracking study 2. J. Cell Biol. 2007, 177(4):731-742.
35. Douglass A.D., Vale R.D. Single-molecule microscopy reveals plasma membrane microdomains created by protein-protein networks that exclude or trap signaling molecules in T cells. Cell 2005, 121(6):937-950.
36. Cai D., et al. Single molecule imaging reveals differences in microtubule track selection between Kinesin motors. PLoS Biol. 2009, 7(10):e1000216.
37. Subach F.V., et al. Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cells. J. Am. Chem. Soc. 2010, 132(18):6481-6491.
38. Dahan M., et al. Diffusion dynamics of glycine receptors revealed by single-quantum dot tracking. Science 2003, 302(5644):442-445.
39. Serge A., et al. Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes. Nat. Methods 2008, 5(8):687-694.
40. Agrawal A., et al. Nanometer-scale mapping and single-molecule detection with color-coded nanoparticle probes. Proc. Natl. Acad. Sci. USA 2008, 105(9):3298-3303.
41. Pinaud F., et al. Probing cellular events, one quantum dot at a time. Nat. Methods 2010, 7(4):275-285.
42. Pons T., Mattoussi H. Investigating biological processes at the single molecule level using luminescent quantum dots. Ann. Biomed. Eng. 2009, 37(10):1934-1959.
43. Drbal K., et al. Single-molecule microscopy reveals heterogeneous dynamics of lipid raft components upon TCR engagement. Int. Immunol. 2007, 19(5):675-684.
44. Rabeau J.R., et al. Single nitrogen vacancy centers in chemical vapor deposited diamond nanocrystals. Nano Lett. 2007, 7(11):3433-3437.
45. Schütz G.J., et al. Properties of lipid microdomains in a muscle cell membrane visualized by single molecule microscopy. EMBO J. 2000, 19(5):892-901.
46. Lommerse P.H., et al. Single-molecule diffusion reveals similar mobility for the Lck, H-ras, and K-ras membrane anchors. Biophys. J. 2006, 91(3):1090-1097.
47. Sako Y., Minoghchi S., Yanagida T. Single-molecule imaging of EGFR signalling on the surface of living cells. Nat. Cell Biol. 2000, 2(3):168-172.
48. Harms G.S., et al. Single-molecule imaging of l-type Ca(2+) channels in live cells. Biophys. J. 2001, 81(5):2639-2646.
49. Seisenberger G., et al. Real-time single-molecule imaging of the infection pathway of an adeno-associated virus. Science 2001, 294(5548):1929-1932.
50. Jacquier V., et al. Visualizing odorant receptor trafficking in living cells down to the single-molecule level. Proc. Natl. Acad. Sci. USA 2006, 103(39):14325-14330.
51. Füreder-Kitzmüller E., et al. Non-exponential bleaching of single bioconjugated Cy5 molecules. Chem. Phys. Lett. 2005, 404:13-18.
52. Moertelmaier M.A., et al. Single molecule microscopy in living cells: subtraction of autofluorescence based on two color recording. Single Mol. 2002, 3(4):225-231.
53. Nadrigny F., et al. Systematic colocalization errors between acridine orange and EGFP in astrocyte vesicular organelles. Biophys. J. 2007, 93(3):969-980.
54. Saxton M.J., Jacobson K. Single-particle tracking: applications to membrane dynamics. Annu. Rev. Biophys. Biomol. Struct. 1997, 26:373-399.
55. Wieser S., Schutz G.J. Tracking single molecules in the live cell plasma membrane-Do's and Don't's. Methods 2008, 46(2):131-140.
56. Schmidt T., et al. Imaging of single molecule diffusion. Proc. Natl. Acad. Sci. USA 1996, 93(7):2926-2929.
57. Mashanov G.I., Molloy J.E. Automatic detection of single fluorophores in live cells. Biophys. J. 2007, 92(6):2199-2211.
58. Thompson R.E., Larson D.R., Webb W.W. Precise nanometer localization analysis for individual fluorescent probes. Biophys. J. 2002, 82(5):2775-2783.
59. Hesse J., et al. RNA expression profiling at the single molecule level. Genome Res. 2006, 16(8):1041-1045.
60. Tvarusko W., et al. Time-resolved analysis and visualization of dynamic processes in living cells. Proc. Natl. Acad. Sci. USA 1999, 96(14):7950-7955.
61. Yoon J.W., et al. Bayesian inference for improved single molecule fluorescence tracking. Biophys. J. 2008.
62. Mortensen K.I., et al. Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nat. Methods 2010, 7(5):377-381.
63. Smith C.S., et al. Fast, single-molecule localization that achieves theoretically minimum uncertainty. Nat. Methods 2010, 7(5):373-375.
64. Bobroff N. Position measurement with a resolution and noise-limited instrument. Rev. Sci. Instrum. 1986, 57(6):1152-1157.
65. Claytor K., et al. Accurately determining single molecule trajectories of molecular motion on surfaces. J. Chem. Phys. 2009, 130(16):164710.
66. Kural C., et al. Kinesin and dynein move a peroxisome in vivo: a tug-of-war or coordinated movement?. Science 2005, 308(5727):1469-1472.
67. Wieser S., et al. (Un)confined diffusion of CD59 in the plasma membrane determined by high-resolution single molecule microscopy. Biophys. J. 2007, 92(10):3719-3728.
68. Churchman L.S., et al. Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. Proc. Natl. Acad. Sci. USA 2005, 102(5):1419-1423.
69. Karakikes I., et al. Co-localization of cell surface receptors at high spatial resolution by single-particle fluorescence imaging. Biochem. Soc. Trans. 2003, 31(Pt 6):1453-1455.
70. Pinaud F., et al. Dynamic partitioning of a glycosyl-phosphatidylinositol-anchored protein in glycosphingolipid-rich microdomains imaged by single-quantum dot tracking. Traffic 2009, 10(6):691-712.
71. Zacharias D.A., et al. Partitioning of lipid-modified monomeric GFPs into membrane microdomains of live cells. Science 2002, 296(5569):913-916.
72. Eggeling C., et al. Direct observation of the nanoscale dynamics of membrane lipids in a living cell. Nature 2009, 457(7233):1159-1162.
73. Sieber J.J., et al. Anatomy and dynamics of a supramolecular membrane protein cluster. Science 2007, 317(5841):1072-1076.
74. Willig K.I., et al. STED microscopy reveals that synaptotagmin remains clustered after synaptic vesicle exocytosis. Nature 2006, 440(7086):935-939.
75. Hess S.T., et al. Dynamic clustered distribution of hemagglutinin resolved at 40nm in living cell membranes discriminates between raft theories. Proc. Natl. Acad. Sci. USA 2007, 104(44):17370-17375.
76. Churchman L.S., Flyvbjerg H., Spudich J.A. A non-Gaussian distribution quantifies distances measured with fluorescence localization techniques. Biophys. J. 2006, 90(2):668-671.
77. Trabesinger W., et al. Detection of individual oligonucleotide pairing by single-molecule microscopy. Anal. Chem. 1999, 71(1):279-283.