Watching conformational- and photodynamics of single fluorescent proteins in solution

Nature Chemistry

Volumn 2, Issue 3, 2010, Pages 179-186

  Goldsmith, Randall H ^a   Moerner, W E ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOPHYCOCYANIN; IMMOBILIZED PROTEIN; PHOTOPROTEIN; PHYCOCYANIN;

ARTICLE; BLEACHING; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRODE; LIGHT; METABOLISM; MICROFLUIDIC ANALYSIS; OSMOSIS; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; RADIATION EXPOSURE; SOLUTION AND SOLUBILITY; SPECTROFLUOROMETRY; TIME;

ELECTRODES; IMMOBILIZED PROTEINS; LIGHT; LUMINESCENT PROTEINS; MICROFLUIDIC ANALYTICAL TECHNIQUES; MODELS, MOLECULAR; OSMOSIS; PHOTOBLEACHING; PHYCOCYANIN; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; SOLUTIONS; SPECTROMETRY, FLUORESCENCE; TIME FACTORS;

EID: 77649101065     PISSN: 17554330     EISSN: 17554349     Source Type: Journal    
DOI: 10.1038/nchem.545     Document Type: Article

References (50)

1. Moerner, W. E. & Orrit, M. Illuminating single molecules in condensed matter. Science 283, 1670-1676 (1999).
2. Myong, S. et al. Cytosolic viral sensor RIG-I Is a 5'-triphosphate- dependent translocase on double-stranded RNA. Science 323, 1070-1074 (2009).
3. Hofmann, C., Aartsma, T. J., Michel, H. & Kohler, J. Direct observation of tiers in the energy landscape of a chromoprotein: A single-molecule study. Proc. Natl Acad. Sci. USA 100, 15534-15538 (2003).
4. Bopp, M. A., Jia, Y., Li, L., Cogdell, R. J. & Hochstrasser, R. M. Fluorescence and photobleaching dynamics of single light-harvesting complexes. Proc. Natl Acad. Sci. USA 94, 10630-10635 (1997).
5. Hofkens, J. et al. Probing photophysical processes in individual multichromophoric dendrimers by single-molecule spectroscopy. J. Am. Chem. Soc. 122, 9278-9288 (2000).
6. Rothwell, P. J. et al. Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/ template complexes. Proc. Natl Acad. Sci. USA 100, 1655-1660 (2003).
7. Nie, S., Chiu, D. T. & Zare, R. N. Probing individual molecules with confocal fluorescence microscopy. Science 266, 1018-1021 (1994).
8. Shera, E. B., Seitzinger, N. K., Davis, L. M., Keller, R. A. & Soper, S. A. Detection of single fluorescent molecules. Chem. Phys. Lett. 174, 553-557 (1990).
9. Rasnik, I., McKinney, S. A. & Ha, T. Surfaces and orientations: Much to FRET About? Acc. Chem. Res. 38, 542-548 (2005).
10. Rasnik, I., Myong, S., Cheng, W., Lohman, T. M. & Ha, T. DNA-binding orientation and domain conformation of the E-coli Rep helicase monomer bound to a partial duplex junction: Single-molecule studies of fluorescently labeled enzymes. J. Mol. Biol. 336, 395-408 (2004).
11. Okumus, B., Wilson, T. J., Lilley, D. M. J. & Ha, T. Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic. Biophys. J. 87, 2798-2806 (2004).
12. Friedel, M., Baumketner, A. & Shea, J. E. Effects of surface tethering on protein folding mechanisms. Proc. Natl Acad. Sci. USA 103, 8396-8401 (2006).
13. Talaga, D. S. et al. Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy. Proc. Natl Acad. Sci. USA 97, 13021-13026 (2000).
14. Cohen, A. E. & Moerner, W. E. Suppressing Brownian motion of individual biomolecules in solution. Proc. Natl Acad. Sci. USA 103, 4362-4365 (2006).
15. Cohen, A. E. & Moerner, W. E. Controlling Brownian motion of single protein molecules and single fluorophores in aqueous buffer. Opt. Express 16, 6941-6956 (2008).
16. Murakoshi, H. et al. Single-molecule imaging analysis of Ras activation in living cells. Proc. Natl Acad. Sci. USA 101, 7317-7322 (2004).
17. Lee, S. J. R., Escobedo-Lozoya, Y., Szatmari, E. M. & Yasuda, R. Activation of CaMKII in single dendritic spines during long-term potentiation. Nature 458, 299-304 (2009).
18. Berglund, A. J. & Mabuchi, H. Feedback controller design for tracking a single fluorescent molecule. Appl. Phy. B 78, 653-659 (2004).
19. Enderlein, J. Tracking of fluorescent molecules diffusing within membranes. Appl. Phy. B 71, 773-777 (2000).
20. Cohen, A. E. & Moerner, W. E. Principal-components analysis of shape fluctuations of single DNA molecules. Proc. Natl Acad. Sci. USA 104, 12622-12627 (2007).
21. MacColl, R. Allophycocyanin and energy transfer. Biochim. Biophys. Acta 1657, 73-81 (2004).
22. Brejc, K., Ficner, R., Huber, R. & Steinbacher, S. Isolation, crystallization, crystal structure analysis and refinement of allophycocyanin from the cyanobacterium Spirulina platensis at 2.3 A resolution. J. Mol. Biol. 249, 424-440 (1995).
23. Edington, M. D., Riter, R. E. & Beck,W. F. Evidence for coherent energy-transfer in allophycocyanin trimers. J. Phys. Chem. 99, 15699-15704 (1995).
24. Edington, M. D., Riter, R. E. & Beck, W. F. Interexciton-state relaxation and exciton localization in allophycocyanin trimers. J. Phys. Chem. 100, 14206-14217 (1996).
25. Beck, W. F. & Sauer, K. Energy-transfer and exciton-state relaxation processes in allophycocyanin. J. Phys. Chem. 96, 4658-4666 (1992).
26. Loos, D., Cotlet, M., De Schryver, F. C., Habuchi, S. & Hofkens, J. Singlemolecule spectroscopy selectively probes donor and acceptor chromophores in the phycobiliprotein allophycocyanin. Biophys. J. 87, 2598-2608 (2004).
27. Ying, L. & Xie, X. S. Fluorescence spectroscopy, exciton dynamics, and photochemistry of single allophycocyanin trimers. J. Phys. Chem. B 102, 10399-10409 (1998).
28. Watkins, L. P. & Yang, H. Detection of intensity change points in time-resolved single-molecule measurements. J. Phys. Chem. B 109, 617-628 (2005).
29. Vallee, R. A. L. et al. Fluorescence lifetime fluctuations of single molecules probe the local environment of oligomers around the glass transition temperature. J. Chem. Phys. 126 (2007).
30. Vallee, R. A. L., Van Der Auweraer, M., De Schryver, F. C., Beljonne, D. & Orrit, M. A microscopic model for the fluctuations of local field and spontaneous emission of single molecules in disordered media. Chem. Phys. Chem. 6, 81-91 (2005).
31. Lakowicz, J. R. in Principles of Fluorescence Spectroscopy 954 (Springer Science, 2006).
32. McKinney, S. A., Joo, C. & Ha, T. Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophys. J. 91, 1941-1951 (2006).
33. Scheer, H. Biliproteins. Angew. Chem. Int. Ed. 20, 241-261 (1981).
34. Langer, E., Lehner, H., Rudiger, W. & Zickendrahtwendelstadt, B. Circulardichroism of C-phycoerythrin-a conformational analysis. Z. Naturforsch. C 35, 367-375 (1980).
35. Bischoff, M. et al. Excited-state processes in phycocyanobilin studied by femtosecond spectroscopy. J. Phys. Chem. B 104, 1810-1816 (2000).
36. Braslavsky, S. E., Holzwarth, A. R. & Schaffner, K. Solution conformations, photophysics, and photochemistry of bile-pigments-bilirubin and biliverdin dimethyl esters and related linear tetrapyrroles. Angew. Chem. Int. Ed. 22, 656-674 (1983).
37. Su-Ping, Z. et al. Generation and identification of the transient intermediates of allophycocyanin by laser photolytic and pulse radiolytic techniques. Int. J. Radiat. Biol. 77, 637-642 (2001).
38. Beladakere, N. N. et al. Photovoltaic effects and charge transport studies in phycobiliproteins. Mat. Res. Soc. Symp. Proc. 292, 193-198 (1993).
39. Katona, G. et al. Conformational regulation of charge recombination reactions in a photosynthetic bacterial reaction center. Nature Struct. Biol. 12, 630-631 (2005).
40. Belcher, J., Sansone, S., Fernandez, N. F., Haskins, W. E. & Brancaleona, L. Photoinduced unfolding of beta-lactoglobulin mediated by a water-soluble porphyrin. J. Phys. Chem. B 113, 6020-6030 (2009).
41. Nesvadba, P. & Gossauer, A. Synthesis of Bile-Pigments.14. Synthesis of a bilindionostilbenoparacyclophane as a model for stretched bile pigment chromophores of biliproteins. J. Am. Chem. Soc. 109, 6545-6546 (1987).
42. Greene, B. I., Lamola, A. A. & Shank, C. V. Picosecond primary photoprocesses of bilirubin bound to human-serum albumin. Proc. Natl Acad. Sci. USA 78, 2008-2012 (1981).
43. Margineanu, A. et al. Visualization of membrane rafts using a perylenemonoimide derivative and fluorescence lifetime Imaging. Biophys. J. 93, 2877-2891 (2007).
44. Gilson, M. K. & Honig, B. H. The dielectric-constant of a folded protein. Biopolymers 25, 2097-2119 (1986).
45. Kartalov, E., Unger, M. & Quake, S. R. Polyelectrolyte surface interface for single-molecule fluorescence studies of DNA polymerase. BioTechniques 34, 505-510 (2003).
46. Ong, L. J. & Glazer, A. N. Crosslinking of allophycocyanin. Physiol. Veg. 23, 777-787 (1985).
47. Mao, H. B. et al. Effects of glycerol and high temperatures on structure and function of phycobilisomes in Synechocystis sp PCC 6803. FEBS Lett. 553, 68-72 (2003).
48. He, J. A., Hu, Y. Z. & Jiang, L. J. Photodynamic action of phycobiliproteins: In situ generation of reactive oxygen species. Biochim. et Biophys. Acta Bioenerg. 1320, 165-174 (1997).
49. Zander, C. et al. Detection and characterization of single molecules in aqueous solution. Appl. Phy. B 63, 517-523 (1996).
50. Pawitan, Y. in In All Likelihood: Statistical Modeling and Inference Using Likelihood 528 (Clarendon Press, 2001).