Time-resolved detection of conformational changes in oat phytochrome A: Time-dependent diffusion

Biophysical Journal

Volumn 91, Issue 10, 2006, Pages 3797-3804

  Eitoku, Takeshi ^a   Zarate, Xristo ^b   Kozhukh, Gennady V ^b   Kim, Jeong Il ^b,c,d   Song, Pill Soon ^b,d,e   Terazima, Masahide ^a  

^a KYOTO UNIVERSITY   (Japan)

^b Kumho Life and Environmental Science Laboratory   (South Korea)

^c Chonnam National University   (South Korea)

^d Gyeongsang National University   (South Korea)

^e Jeju National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

PHYTOCHROME; PHYTOCHROME A; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DIFFUSION COEFFICIENT; DYNAMICS; EXCITATION; MOLECULAR INTERACTION; NONHUMAN; OAT; PHOTOREACTIVITY; REACTION TIME;

EID: 33751216180     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.092882     Document Type: Article

References (41)

1. Briggs, W. R., and H. V. Rice. 1972. Phytochrome: chemical and physical properties and mechanism of action. Annu. Rev. Plant Physiol. 23:293-334.
2. Furuya, M. 1987. Phytochrome and Photoregulation in Plants. Academic Press, New York.
3. Sineshchekov, V. A. 1995. Photobiophysics and photobiochemistry of the heterogeneous phytochrome system. Biochim. Biophys. Acta. 1228:125-164.
4. Song, P.-S. 1988. The molecular topography of phytochrome: chromophore and apoprotein. J. Photochem. Photobiol. B. 2:43-57.
5. Jordan, E. T., J. R. Cherry, J. M. Walker, and R. D. Viestra. 1996. The amino-terminus of phytochrome A contains two distinct functional domains. Plant J. 9:243-257.
6. Matsushita, T., N. Mochizuki, and A. Nagatani. 2003. Dimers of the N-terminal domain of phytochrome B are functional in the nucleus. Nature. 424:571-574.
7. Sarkar, H. K., D. K. Moon, P.-S. Song, T. Chang, and H. Yu. 1984. Tertiary structure of phytochrome probed by quasi-elastic light scattering and rotational relaxation time measurements. Biochemistry. 23: 1882-1888.
8. Jones, A. M., and H. P. Erickson. 1989. Domain structure of 124-kiloDalton phytochrome from Avena sativa visualized by electron micrography. Photochem. Photobiol. 49:479-483.
9. Tokutomi, S., M. Nakasako, J. Sakai, M. Kataoka, K. T. Yamamoto, M. Wada, F. Tokunaga, and M. Furuya. 1989. A model for the dimeric molecular structure of phytochrome based on small-angle x-ray scattering. FEBS Lett. 247:139-142.
10. Nakasako, M., M. Wada, S. Tokutomi, K. T. Yamamoto, J. Sakai, M. Kataoka, F. Tokunaga, and M. Furuya. 1990. Quaternary structure of pea phytochrome I dimer studied with small-angle x-ray scattering and rotary-shadowing electron microscopy. Photochem. Photobiol. 52:3-12.
11. Lagarias, J. C., and F. M. Mercurio. 1985. Structure function studies on phytochrome. J. Biol. Chem. 260:2415-2423.
12. Hunt, R. E., and L. H. Pratt. 1981. Physicochemical difference between the red- and the far-red-absorbing forms of phytochrome. Biochemistry. 20:941-945.
13. Deforce, L., S. Tokutomi, and P.-S. Song. 1994. Phototransformation of pea phytochrome A induces an increase in α-helical folding of the apoprotein: comparison with a Monocot phytochrome A and CD analysis by different methods. Biochemistry. 33:4918-4922.
14. Chai, Y. G., P.-S. Song, M. M. Cordonnier, and L. H. Pratt. 1987. A photoreversible circular dichroism spectral change in oat phytochrome is suppressed by a monoclonal antibody that binds near its N-terminus and by chromophore modification. Biochemistry. 26:4947-4952.
15. Tokutomi, S., M. Kataoka, J. Sakai, M. Nakasako, F. Tokunaga, M. Tasumi, and M. Furuya. 1988. Small-angle x-ray scattering studies on the macromolecular structure of the red-light-absorbing form of 121 kDa pea phytochrome and its 114 kDa chromopeptide. Biochim. Biophys. Acta. 953:297-305.
16. Nakasako, M., T. Iwata, K. Inoue, and S. Tokutomi. 2005. Light-induced global structural changes in phytochrome A regulating photomorphogenesis in plants. FEBS J. 272:603-612.
17. Eilfeld, P., P. Eilfeld, J. Vogel, and R. Maurer. 1987. Evidence for a sequential pathway from Pr to Pfr of the phototransformation of 124-kDa oat phytochrome. Photochem. Photobiol. 45:825-830.
18. Zhang, C. F., D. L. Farrens, S. C. Bjorling, P.-S. Song, and D. S. Kliger. 1992. Time-resolved absorption studies of native etiolated oat phytochrome. J. Am. Chem. Soc. 114:4569-4580.
19. Losi, A., and S. E. Braslavsky. 2003. The time-resolved thermodynamics of the chromophore-protein interactions in biological photosensors as derived from photothermal measurements. Phys. Chem. Chem. Phys. 5:2739-2750.
20. Chen, E. F., W. Parker, J. W. Lewis, P.-S. Song, and D. S. Kliger. 1993. Time-resolved UV circular dichroism of phytochrome A: folding of the N-terminal region. J. Am. Chem. Soc. 115:9854-9855.
21. Chen, E. F., V. N. Lapko, P.-S. Song, and D. S. Kliger. 1997. Dynamics of the N-terminal α-helix unfolding in the photoreversion reaction of phytochrome A. Biochemistry. 36:4903-4908.
22. Cussler, E. L., 1984. Diffusion, Mass Transfer in Fluid Systems. Cambridge University Press, Cambridge, MA.
23. Tyrrell, H. J. V., and K. R. Harris. 1984. Diffusion in Liquids: A Theoretical and Experimental Study. Butterworth, London, UK.
24. Nishida, S., T. Nada, and M. Terazima. 2004. Kinetics of intermolecular interaction during protein folding of reduced cytochrome c. Biophys. J. 87:2663-2675.
25. Eitoku, T., Y. Nakasone, D. Matsuoka, S. Tokutomi, and M. Terazima. 2005. Conformational dynamics of phototropin 2 LOV2 domain with the linker upon photoexcitation. J. Am. Chem. Soc. 127:13238-13244.
26. Terazima, M., and N. Hirota. 1993. Translational diffusion of a transient radical studied by the transient grating method, pyrazinyl radical in 2-propanol. J. Chem. Phys. 98:6257-6262.
27. Terazima, M., K. Okamoto, and N. Hirota. 1995. Translational diffusion of transient radicals created by the photoinduced hydrogen abstraction reaction in solution - anomalous size dependence in the radical diffusion. J. Chem. Phys. 102:2506-2515.
28. Terazima, M. 2000. Is the translational diffusion of organic radicals different from that of closed-shell molecules? Acc. Chem. Res. 33:687-694.
29. Nada, T., and M. Terazima. 2003. A novel methods for study of protein folding kinetics by monitoring diffusion coefficient in time domain. Biophys. J. 85:1876-1881.
30. Lapko, V. N., and P.-S. Song. 1995. A simple and improved method of isolation and purification for native oat phytochrome. Photochem. Photobiol. 62:194-198.
31. Lagarias, J. C., and F. M. Mercurio. 1985. Structure function studies on phytochrome. J. Biol. Chem. 260:2415-2423.
32. Michler, I., and S. E. Braslavsky. 2001. Time-resolved thermodynamic analysis of the oat phytochrome A phototransformation. A photothermal beam deflection study. Photochem. Photobiol. 74:624-635.
33. Hem, L. H., and B. Niemeyer. 2003. A novel correlation for protein diffusion coefficients based on molecular weight and radius of gyration. Biotechnol. Prog. 19:544-548.
34. Hazra, P., K. Inoue, W. Laan, J. Hellingwerf, and M. Terazima. 2006. Tetramer formation kinetics in the signaling state of AppA monitored by the time-resolved diffusion. Biophys. J. 91:654-661.
35. Nakasone, Y., T. Eitoku, D. Matsuoka, S. Tokutomi, and M. Terazima. 2006. Kinetic measurement of transient dimerization and dissociation reactions of Arabidopsis phototropin 1 LOV2 domain. Biophys. J. 91:645-653.
36. Inoue, K., N. Baden, and M. Terazima. 2005. Diffusion coefficient and the secondary structure of poly-L-glutamic acid in aqueous solution. J. Phys. Chem. B. 109:22623-22628.
37. Choi, J. H., H. Kim, and S. Lee. 1998. Correlation dimension as a measure of surface roughness of protein molecules. J. Chem. Phys. 109:7001-7004.
38. Kircher, S., L. Kozma-Bognar, L. Kim, E. Adam, K. Harter, E. Schafer, and F. Nagy. 1999. Light quality-dependent nuclear import of the plant photoreceptors phytochrome A and B. Plant Cell. 11:1445-1456.
39. Sakamoto, K., and A. Nagatani. 1996. Nuclear localization activity of phytochrome B. Plant J. 10:859-868.
40. Quail, P. H., M. T. Boylan, B. M. Parks, T. W. Short, Y. Xu, and D. Wagner. 1995. Phytochromes - photosensory perception and signal-transduction. Science. 268:675-680.
41. Spiegel, D. R., A. H. Marshall, N. T. Jukam, H. S. Park, and T. Chang. 1998. Measurement of mass diffusion coefficients using nonexponential forced Rayleigh scattering signals. J. Chem. Phys. 109:267-274.