Conformational changes in the N-terminal region of photoactive yellow protein: A time-resolved diffusion study

Biophysical Journal

Volumn 94, Issue 6, 2008, Pages 2187-2193

  Hoshihara, Yuji ^a   Imamoto, Yasushi ^a   Kataoka, Mikio ^b   Tokunaga, Fumio ^c   Terazima, Masahide ^a  

^a KYOTO UNIVERSITY   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^c OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PHOTOACTIVE YELLOW PROTEIN, BACTERIA; VISUAL PROTEINS AND PIGMENTS;

ARTICLE; BIOPHYSICS; CHEMISTRY; CONFORMATION; DIFFUSION; HYDROGEN BOND; KINETICS; LASER; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SIGNAL TRANSDUCTION; STATISTICAL MODEL; TIME;

BACTERIAL PROTEINS; BIOPHYSICS; DIFFUSION; HYDROGEN BONDING; KINETICS; LASERS; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PHOTORECEPTORS, MICROBIAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SIGNAL TRANSDUCTION; TIME FACTORS;

EID: 44049104501     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.115253     Document Type: Article

References (38)

1. Sprenger, W. W., W. D. Hoff, J. P. Armitage, and K. J. Hellingwerf. 1993. The eubacterium Ectothiorhodospira halophila is negatively phototactic, with a wavelength dependence that fits the absorption spectrum of the photoactive yellow protein. J. Bacteriol. 175:3096-3104.
2. Meyer, T. E., E. Yakali, M. A. Cusanovich, and G. Tollin. 1987. Properties of a water-soluble, yellow protein isolated from a halophilic phototrophic bacterium that has photochemical activity analogous to sensory rhodopsin. Biochemistry. 26:418-423.
3. Hoff, W. D., P. Düx, K. Hard, B. Devreese, I. M. Nugteren-Roodzant, W. Crielaard, R. Boelens, R. Kaptein, J. van Beeumen, and K. J. Hellingwerf. 1994. Thioester-linked p-coumaric acid as a new photo-active prosthetic group in a protein with rhodopsin-like photochemistry. Biochemistry. 33:13959-13962.
4. Hellingwerf, K. J., J. Hendriks, and T. Gensch. 2003. Photoactive yellow protein, a new type of photoreceptor protein: will this ''yellow lab'' bring us where we want to go? J. Phys. Chem. A. 107:1082-1094.
5. Baca, M., G. E. O. Borgstahl, M. Boissinot, P. M. Burke, D. R. Williams, K. A. Slater, and E. D. Getzoff. 1994. Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry. Biochemistry. 33:14369-14377.
6. Meyer, T. E., G. Tollin, J. H. Hazzard, and M. A. Cusanovich. 1989. Photoactive yellow protein from the purple phototrophic bacterium, Ectothiorhodospira halophila. Quantum yield of photobleaching and effects of temperature, alcohols, glycerol, and sucrose on kinetics of photobleaching and recovery. Biophys. J. 56:559-564.
7. Meyer, T. E., G. Tollin, T. P. Causgrove, P. Cheng, and R. E. Blankenship. 1991. Picosecond decay kinetics and quantum yield of fluorescence of the photoactive yellow protein from the halophilic purple phototrophic bacterium, Ectothiorhodospira halophila. Biophys. J. 59:988-991.
8. Kim, M., R. A. Mathies, W. D. Hoff, and K. J. Hellingwerf. 1995. Resonance Raman evidence that the thioester-linked 4-hydroxycinnamyl chromophore of photoactive yellow protein is deprotonated. Biochemistry. 34:12669-12672.
9. Hoff, W. D., I. H. M. van Stokkum, H. J. van Ramesdonk, M. E. van Brederode, A. M. Brouwer, J. C. Fitch, T. E. Meyer, R. van Grondelle, and K. J. Hellingwerf. 1994. Measurement and global analysis of the absorbance changes in the photocycle of the photoactive yellow protein from Ectothiorhodospira halophila. Biophys. J. 67:1691-1705.
10. Takeshita, K., Y. Imamoto, M. Kataoka, K. Mihara, F. Tokunaga, and M. Terazima. 2002. Structural change of site-directed mutants of PYP: new dynamics during pR state. Biophys. J. 83:1567-1577.
11. Cusanovich, M. A., and T. E. Meyer. 2003. Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism. Biochemistry. 42:4759-4770.
12. 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.
13. Harigai, M., Y. Imamoto, H. Kamikubo, Y. Yamazaki, and M. Kataoka. 2003. Role of an N-terminal loop in the secondary structural change of photoactive yellow protein. Biochemistry. 42:13893-13900.
14. Hendriks, J., T. Gensch, L. Hviid, M. A. vanderHorst, K. J. Hellingwerf, and J. J. van Thor. 2002. Transient exposure of hydrophobic surface in the photoactive yellow protein monitored with Nile red. Biophys. J. 82: 1632-1643.
15. Hoff, W. D., A. Xie, I. H. M. van Stokkum, X.-J. Tang, J. Gural, A. R. Kroon, and K. J. Hellingwerf. 1999. Global conformational changes upon receptor stimulation in photoactive yellow protein. Biochemistry. 38:1009-1017.
16. Craven, C. J., N. M. Derix, J. Hendriks, R. Boelens, K. J. Hellingwerf, and R. Kaptein. 2000. Probing the nature of the blue-shifted intermediate of photoactive yellow protein in solution by NMR: hydrogen-deuterium exchange data and pH studies. Biochemistry. 39:14392-14399.
17. Van der Horst, M. A., I. H. Stokkum, W. Crielaard, and K. J. Hellingwerf. 2001. The role of the N-terminal domain of photoactive yellow protein in the transient partial unfolding during signaling state formation. FEBS Lett. 497:26-30.
18. Bernard, C., K. Houben, N. M. Derix, D. Marks, M. A. van der Horst, K. J. Hellingwerf, R. Boelens, R. Kaptein, and N. A. J. van Nuland. 2005. The solution structure of a transient photoreceptor intermediate: δ25 photoactive yellow protein. Structure. 13:953-962.
19. Khan, J. S., Y. Imamoto, Y. Yamazaki, M. Kataoka, F. Tokunaga, and M. Terazima. 2005. A biosensor in the time domain based on the diffusion coefficient measurement: intermolecular interaction of an intermediate of photoactive yellow protein. Anal. Chem. 77:6625-6629.
20. Khan, J. S., Y. Imamoto, M. Harigai, M. Kataoka, and M. Terazima. 2006. Conformational changes of PYP monitored by diffusion coefficient: effect of N-terminal α-helices. Biophys. J. 90:3686-3693.
21. Takeshita, K., Y. Imamoto, M. Kataoka, F. Tokunaga, and M. Terazima. 2002. Thermodynamic and transport properties of intermediate states of the photocyclic reaction of photoactive yellow protein. Biochemistry. 41:3037-3048.
22. Imamoto, Y., H. Kamikubo, M. Harigai, N. Shimizu, and M. Kataoka. 2002. Light-induced global conformational change of photoactive yellow protein in solution. Biochemistry. 41:13595-13601.
23. Chen, E., T. Gensch, A. B. Gross, J. Hendriks, K. J. Hellingwerf, and D. S. Kliger. 2003. Dynamics of protein and chromophore structural changes in the photocycle of photoactive yellow protein monitored by time-resolved optical rotatory dispersion. Biochemistry. 42: 2062-2071.
24. Xie, A., L. Kelemen, J. Hendriks, B. J. White, K. J. Hellingwerf, and W. D. Hoff. 2001. Formation of a new buried charge drives a large- amplitude protein quake in photoreceptor activation. Biochemistry. 40: 1510-1517.
25. Nada, T., and M. Terazima. 2003. A novel method for study of protein folding kinetics by monitoring diffusion coefficient in time domain. Biophys. J. 85:1876-1881.
26. 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.
27. Nakasone, Y., T. Eitoku, D. Matsuoka, S. Tokutomi, and M. Terazima. 2006. Kinetic measurement of transient dimerization and dissociation reaction of Arabidopsis phototropin 1 LOV2 domain. Biophys. J. 91: 645-653.
28. Nakasone, Y., T. Eitoku, D. Matsuoka, S. Tokutomi, and M. Terazima. 2007.Dynamics of conformational changes of Arabidopsis phototropin 1 LOV2 with the linker domain. J. Mol. Biol. 367:432-442.
29. Nishida, S., T. Nada, and M. Terazima. 2004. Kinetics of intermolec- ular interaction during protein folding of reduced cytochrome c. Biophys. J. 87:2663-2675.
30. Nishida, S., T. Nada, and M. Terazima. 2005. Hydrogen bonding dynamics during protein folding of reduced cytochrome c: temperature and denaturant concentration dependence. Biophys. J. 89:2004-2010.
31. Hirota, S., Y. Fujimoto, J. Choi, N. Baden, N. Katagiri, M. Akiyama, R. Hulsker, M. Ubbink, T. Okajima, T. Takabe, N. Funasaki, Y. Watanabe, and M. Terazima. 2006. Conformational changes during apoplastocyanin folding observed by photocleavable modification and transient grating. J. Am. Chem. Soc. 128:7551-7558.
32. Terazima, M. 2006. Diffusion coefficients as a monitor of reaction kinetics of biological molecules. Phys. Chem. Chem. Phys. 8:545-557.
33. Terazima, M. 1998. Photothermal studies of photophysical and photochemical processes by the transient grating method. In Advanced Photochemistry. John-Wiley & Sons, New York
34. Terazima, M., and N. Hirota. 1993. Translational diffusion ofa transient radical studied by the transient grating method, pyrazinyl radical in 2-propanol. J. Chem. Phys. 98:6257-6262.
35. Takeshita, K., N. Hirota, Y. Imamoto, M. Kataoka, F. Tokunaga, and M. Terazima. 2000. Temperature-dependent volume change of the initial step of the photoreaction of photoactive yellow protein (PYP) studied by transient grating. J. Am. Chem. Soc. 122:8524-8528.
36. Imamoto, Y., M. Harigai, and M. Kataoka. 2004. Direct observation of the pH-dependent equilibrium between L-like and M intermediates of photoactive yellow protein. FEBS Lett. 577:75-80.
37. Shimizu, N., Y. Imamoto, M. Harigai, H. Kamikubo, Y. Yamazaki, and M. Kataoka. 2006. pH-dependent equilibrium between long lived near- UV intermediates of photoactive yellow protein. J. Biol. Chem. 281: 4318-4325.
38. Harigai, M., M. Kataoka, and Y. Imamoto. 2006. A single CH/π weak hydrogen bond governs stability and the photocycle of the photoactive yellow protein. J. Am. Chem. Soc. 128:10646-10647.