Translational diffusion of fluorescent proteins by molecular fourier imaging correlation spectroscopy

Biophysical Journal

Volumn 91, Issue 9, 2006, Pages 3482-3498

  Fink, Michael C ^a   Adair, Kenneth V ^a   Guenza, Marina G ^a   Marcus, Andrew H ^a,b  

^a UNIVERSITY OF OREGON   (United States)

^b Oregon Center for Applied Science   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCEIN DERIVATIVE;

ARTICLE; CORRELATION ANALYSIS; DIFFUSION; FOURIER ANALYSIS; IMAGING SYSTEM; LIGHT SCATTERING; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; NOISE MEASUREMENT; SPECTROSCOPY;

EID: 33751239776     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.085712     Document Type: Article

References (54)

1. Alberts, B., A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. 2002. Molecular Biology of the Cell, 4th Ed. Garland Science, New York.
2. Alberts, B. 1998. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell. 92:291-294.
3. Luby-Phelps, K. 1994. Physical properties of the cytoplasm. Curr. Opin. Cell Biol. 6:3-9.
4. Luby-Phelps, K. 2000. Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area. Int. Rev. Cytol. 192:189-221.
5. Ritchie, K., R. Iino, T. Fujiwara, K. Murase, and A. Kusumi. 2003. The fence and picket structure of the plasma membrane of live cells as revealed by single molecule techniques. Mol. Membr. Biol. 20:13-18.
6. Douglass, A. D., and R. D. Vale. 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.
7. Yu, J., J. Xiao, X. Ren, K. Lao, and X. S. Xie. 2006. Probing gene expression in live cells, one protein molecule at a time. Science. 311:1600-1603.
8. Iino, R., I. Koyama, and A. Kusumi. 2001. Single molecule imaging of green fluorescent proteins in living cells: E-Cadherin forms oligomers on the free cell surface. Biophys. J. 80:2667-2677.
9. Lommerse, P. H. M., B. E. Snaar-Jagalska, H. P. Spaink, and T. Schmidt. 2005. Single-molecule diffusion measurements of H-Ras at the plasma membrane of live cells reveal microdomain localization upon activation. J. Cell Sci. 118:1799-1809.
10. Lawson, J. L., and G. E. Uhlenbeck. 1950. Threshold Signals. McGraw Hill, New York.
11. Baird, G. S., D. A. Zacharias, and R. Y. Tsien. 2000. Biochemistry, mutagenesis, and oligomerization of DsRed, a red fluorescent protein from coral. Proc. Natl. Acad. Sci. USA. 97:11984-11989.
12. Gross, L. A., G. S. Baird, R. C. Hoffman, K. K. Baldridge, and R. Y. Tsien. 2000. The structure of the chromophore within DsRed, a red fluorescent protein from coral. Proc. Natl. Acad. Sci. USA. 97:11990-11995.
13. Yarbrough, D., R. M. Wachter, K. Kallio, M. V. Matz, and S. J. Remington. 2001. Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0 Å resolution. Proc. Natl. Acad. Sci. USA. 98:462-467.
14. Shaner, N. C., R. E. Campbell, P. A. Steinbach, B. N. G. Giepmans, A. E. Palmer, and R. Y. Tsien. 2004. Improved monomeric red, orange, and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22:1567-1572.
15. Margineantu, D., R. A. Capaldi, and A. H. Marcus. 2000. Dynamics of the mitochondrial reticulum in live cells using Fourier imaging correlation spectroscopy and digital video microscopy. Biophys. J. 79:1833-1849.
16. Grassman, T. J., M. K. Knowles, and A. H. Marcus. 2000. Structure and dynamics of fluorescently labeled complex fluids by Fourier imaging correlation spectroscopy. Phys. Rev. E. 62:8245-8257.
17. Knowles, M. K., T. J. Grassman, and A. H. Marcus. 2000. Measurement of the dynamic structure function of fluorescently labeled complex fluids by Fourier imaging correlation spectroscopy. Phys. Rev. Lett. 85:2837-2840.
18. Knowles, M. K., D. Margineantu, R. A. Capaldi, and A. H. Marcus. 2002. Translational dynamics of fluorescently labeled species by Fourier imaging correlation spectroscopy. In Liquid Dynamics: Experiment, Simulation and Theory. J. T. Fourkas, Editor. American Chemical Society, Washington, DC.
19. Knowles, M. K., A. R. Honerkamp-Smith, and A. H. Marcus.2005. Direct measurement of relative and collective diffusion in a dilute binary colloidal suspension. J. Chem. Phys. 122:234909-1-234909-13.
20. Lounis, B., J. Deich, F. I. Rosell, S. G. Boxer, and W. E. Moerner. 2001. Photophysics of DsRed, a red fluorescent protein, from the ensemble to the single-molecule level. J. Phys. Chem. B. 105:5048-5054.
21. Heikal, A. A., S. T. Hess, G. S. Baird, R. Y. Tsien, and W. W. Webb. 2000. Molecular spectroscopy and dynamics of intrinsically fluorescent proteins: coral red (DsRed) and yellow (Citrine). Proc. Natl. Acad. Sci. USA. 97:11996-12001.
22. Malvezzi-Campeggi, F., M. Jahnz, K. G. Heinze, P. Dittrich, and P. Schwille. 2001. Light-induced flickering of DsRed provides evidence for distinct and interconvertible fluorescent states. Biophys. J. 81:1776-1785.
23. Mazo, R. M. 2002. Brownian motion: fluctuations, dynamics and applications. In International Series of Monographs on Physics, Vol. 112, 1st Ed. Oxford Science Publications, Oxford, UK.
24. Hansen, J.-P., and I. R. McDonald. 1986. Theory of Simple Liquids. Academic Press, San Diego.
25. Berne, B. J., and R. Pecora. 1976. Dynamic Light Scattering. Krieger, Malabar, FL.
26. Pusey, P. N., and R. J. A. Tough. 1985. Particle interactions. In Dynamic Light Scattering: Applications of Photon Correlation Spectroscopy. R. Pecora, Editor. Plenum Press, New York.
27. Ediger, M. D., C. A. Angell, and S. R. Nagel. 1996. Supercooled liquids and glasses. J. Phys. Chem. 100:13200-13212.
28. Pusey, P. N., H. M. Fijnaut, and A. Vrij. 1982. Mode amplitudes in dynamic light scattering by concentrated liquid suspensions of polydisperse hard spheres. J. Chem. Phys. 77:4270-4281.
29. Brown, J. C., P. N. Pusey, and R. Dietz. 1975. Photon correlation study of polydisperse samples of polystyrene in cyclohexane. J. Chem. Phys. 62:1136-1144.
30. Koppel, D. E. 1972. Analysis of macromolecular polydispersity in intensity correlation spectroscopy: the method of cumulants. J. Chem. Phys. 57:4814-4820.
31. Davoust, J., P. F. Devaux, and L. Leger. 1982. Fringe pattern photo-bleaching, a new method for the measurement of transport coefficients of biological macromolecules. EMBO J. 1:1233-1238.
32. Fink, M. C. 2006. Molecular Fourier imaging correlation spectroscopy to studies of molecular diffusion. In Chemistry. University of Oregon, Eugene, OR.
33. Bowen, B., and N. Woodbury. 2003. Single-molecule fluorescence lifetime and anisotropy measurements of the red fluorescent protein, DsRed, in solution. Photochem. Photobiol. 77:362-369.
34. Aragon, S. R., and R. Pecora. 1976. Fluorescence correlation spectroscopy as a probe of molecular dynamics. J. Chem. Phys. 64:1791-1803.
35. Aragon, S. R., and R. Pecora. 1975. Fluorescence correlation spectroscopy and Brownian rotational diffusion. Biopolymers. 14:119-138.
36. Axelrod, D. 1989. Fluorescence polarization microscopy. Methods Cell Biol. 30:333-352.
37. Axelrod, D. 1979. Carbocyanine dye orientation in red cell membrane studied bymicroscopic fluorescence polarization. Biophys. J. 26:557-574.
38. Lakowicz, J. R. 1983. Principles of Fluorescence Spectroscopy. Plenum Press, New York.
39. Horowitz, P., and W. Hill. 1986. The Art of Electronics. Cambridge University Press, New York.
40. Schwille, P., S. Kummer, A. A. Heikal, W. E. Moerner, and W. W. Webb. 2000. Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins. Proc. Natl. Acad. Sci. USA. 97:151-156.
41. Bonsma, S., J. Gallus, F. Konz, R. Purchase, and S. Volker. 2004. Light-induced conformational changes and energy transfer in red fluorescent protein. J. Luminesc. 107:203-212.
42. Creemers, T. M. H., A. J. Lock, V. Subramaniam, T. M. Jovin, and S. Volker. 2000. Photophysics and optical switching in green fluorescent protein mutants. Proc. Natl. Acad. Sci. USA. 97:2974-2978.
43. Creemers, T. M. H., A. J. Lock, V. Subramaniam, T. M. Jovin, and S. Volker. 2002. Red-shifted mutants of green fluorescent protein: reversible photoconversions studied by hole-burning and high-resolution spectroscopy. Chem. Phys. 275:109-121.
44. Konz, F., R. Purchase, S. Bonsma, J. Gallus, and S. Volker. 2004. Optical dephasing in red fluorescent protein. J. Luminesc. 108:153-157.
45. Schwille, P., S. Kummer, A. A. Heikal, W. E. Moerner, and W. W. Webb. 2000. Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescence proteins. Proc. Natl. Acad. Sci. USA. 97:151-156.
46. Cantor, C. R., and P. R. Schimmel. 1980. Biophysical Chemistry: Techniques for the Study of Biological Structure and Function, Vol. II. W. H. Freeman, New York.
47. Weast, R. C. 1983. CRC Handbook of Chemistry and Physics. CRC Press, Boca Raton, FL.
48. Phillies, G. D. J. 2005. Interpretation of light-scattering spectra in terms of particle displacements. J. Chem. Phys. 122:224905-1-224905-8.
49. Glotzer, S. C. 2000. Spatially heterogeneous dynamics in liquids: insights from simulation. J. Non-Cryst. Sol. 274:342-355.
50. Richert, R. 2002. Heterogeneous dynamics in liquids: fluctuations in space and time. J. Phys. Condens. Matter. 14:R703-R738.
51. Deschenes, L. A., and D. A. Vanden Bout. 2001. Single-molecule studies of heterogeneous dynamics in polymer melts near the glass transition. Science. 292:255-258.
52. Behrends, R., K. Fuchs, U. Kaatze, Y. Hayashi, and Y. Feldman. 2006. Dielectric properties of glycerol/water mixtures at temperatures between 10 and 50°C. J. Chem. Phys. 124:144512-1-144512-8.
53. Sudo, S., M. Shimomura, N. Shinyashiki, and S. Yagihara. 2002. Broadband dielectric study of α-β separation for supercooled glycerol-water mixtures. J. Non-Cryst. Sol. 307-310:356-363.
54. Boon, J. P., and S. Yip. 1980. Molecular Hydrodynamics. Dover Publications, New York.