Absorption spectra of photoactive yellow protein chromophores in vacuum

Biophysical Journal

Volumn 89, Issue 4, 2005, Pages 2597-2604

  Nielsen, I B ^a   Boye Pronne S ^b   El Ghazaly, M O A ^a   Kristensen, M B ^a   Nielsen, S Brøndsted ^a   Andersen, L H ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PARA COUMARIC ACID; PHENOL; PHOTOACTIVE YELLOW PROTEIN; THIOESTER; WATER;

ABSORPTION SPECTROSCOPY; AQUEOUS SOLUTION; ARTICLE; CHEMICAL STRUCTURE; CHROMATOPHORE; ENZYME LINKED IMMUNOSORBENT ASSAY; HALORHODOSPIRA HALOPHILA; MATHEMATICAL ANALYSIS; NONHUMAN; PROTEIN ANALYSIS;

EID: 25844451692     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.061192     Document Type: Article

References (44)

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. van der Horst, M. A., and K. J. Hellingwerf. 2004. Photoreceptor proteins, "Star actors of modern times": a review of the functional dynamics in the structure of representative members of six different photoreceptor families. Acc. Chem. Res. 37:13-20.
3. Meyer, T. E. 1985. Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila. Biochim. Biophys. Acta. 806:175-183.
4. Hoff, W. D., P. Düx, K. Hård, B. Devreese, I. M. Nugteren-Roodzant, W. Crielaard, R. Boelens, R. Kaptein, J. van Beeumen, and K. J. Hellingwerf. 1994. Thiol ester-linked p-coumaric acid as a new photoactive prosthetic group in a protein with rhodopsin-like photochemistry. Biochemistry. 33:13959-13962.
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. 33:14370-14377.
6. 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.
7. Hoff, W. D., I. H. 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.
8. Kort, R., H. Vonk, X. Xu, W. D. Hoff, W. Crielaard, and K. J. Hellingwerf. 1996. Evidence for trans-cis isomerization of the p-coumaric acid chromophore as the photochemical basis of the photocycle of photoactive yellow protein. FEBS Lett. 382:73-78.
9. Xie, A., W. D. Hoff, A. R. Kroon, and K. J. Hellingwerf. 1996. Glu46 donates a proton to the 4-hydroxycinnamate anion chromophore during the photocycle of photoactive yellow protein. Biochemistry. 35:14671-14678.
10. Genick, U. K., G. E. O. Borgstahl, K. Ng, Z. Ren, C. Pradervand, P. M. Burke, V. Srajer, T.-Y. Teng, W. Schildkamp, D. E. McRee, K. Moffat, and E. D. Getzoff. 1997. Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Science. 275:1471-1475.
11. van Brederode, M. E., W. D. Hoff, I. H. M. van Stokkum, M. L. Groot, and K. J. Hellingwerf. 1996. Protein folding thermodynamics applied to the photocycle of the photoactive yellow protein. Biophys. J. 71:365-380.
12. Genick, U. K., S. M. Soltis, P. Kuhn, I. L. Canestrelli, and E. D. Getzoff. 1998. Structure at 0.85 Å resolution of an early protein photocycle intermediate. Nature. 392:206-209.
13. Perman, B., V. Šrajer, Z. Ren, T. Teng, C. Pradervand, T. Ursby, D. Bourgeois, F. Schotte, M. Wulff, R. Kort, K. Hellingwerf, and K. Moffat. 1998. Energy transduction on the nanosecond time scale: Early structural events in a xanthopsin photocycle. Science. 279:1946-1950.
14. Borgstahl, G. E. O., D. R. Williams, and E. D. Getzoff. 1995. 1.4 Å structure of photoactive yellow protein, a cytosolic photoreceptor: Unusual fold, active site, and chromophore. Biochemistry. 34:6278-6287.
15. Changenet-Barret, P., P. Plaza, and M. M. Martin. 2001. Primary events in the photoactive yellow protein chromophore in solution. Chem. Phys. Lett. 336:439-444.
16. Changenet-Barret, P., A. Espagne, N. Katsonis, S. Charier, J.-B. Baudin, L. Jullien, P. Plaza, and M. M. Martin. 2002. Excited-state relaxation dynamics of a pyp chromophore model in solution: influence of the thioester group. Chem. Phys. Lett. 365:285-291.
17. Larsen, D. S., M. Vengris, I. H. M. van Stokkum, M. A. van der Horst, R. A. Cordfunke, K. J. Hellingwerf, and R. van Grondelle. 2003. Initial photo-induced dynamics of the photoactive yellow protein chromophore in solution. Chem. Phys. Lett. 369:563-569.
18. Larsen, D. S., M. Vengris, I. H. M. van Stokkum, M. A. van der Horst, F. L. de Weerd, K. J. Hellingwerf, and R. van Grondelle. 2004. Photoisomerization and photoionization of the photoactive yellow protein chromophore in solution. Biophys. J. 86:2538-2550.
19. Ryan, W. L., D. J. Gordon, and D. H. Levy. 2002. Gas-phase photochemistry of the photoactive yellow protein chromophore trans-p-coumaric acid. J. Am. Chem. Soc. 124:6194-6201.
20. Genick, U. K., S. Devanathan, T. E. Meyer, I. L. Canestrelli, E. Williams, M. A. Cusanovich, G. Tollin, and E. D. Getzoff. 1997b. Active site mutants implicate key residues for control of color and light cycle kinetics of photoactive yellow protein. Biochemistry. 36:8-14.
21. Mihara, K., O. Hisatomi, Y. Imamoto, M. Kataoka, and F. Tokunaga. 1997. Functional expression and site-directed mutagenesis of photoactive yellow protein. J. Biochem. (Tokyo). 121:876-880.
22. Devanathan, S., R. Brudler, B. Hessling, T. T. Woo, K. Gerwert, E. D. Getzoff, M. A. Cusanovich, and G. Tollin. 1999. Dual photoactive species in Glu46Asp and Glu46Ala mutants of photoactive yellow protein: A pH-driven color transition. Biochemistry. 38:13766-13772.
23. Brudler, R., T. E. Meyer, U. K. Genick, S. Devanathan, T. T. Woo, D. P. Millar, K. Gerwert, M. A. Cusanovich, G. Tollin, and E. D. Getzoff. 2000. Coupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein. Biochemistry. 39:13478-13486.
24. Imamoto, Y., H. Koshimizu, K. Mihara, O. Hisatomi, T. Mizukami, K. Tsujimoto, M. Kataoka, and F. Tokunaga. 2001. Roles of amino acid residues near the chromophore of photoactive yellow protein. Biochemistry. 40:4679-4685.
25. Meyer, T. E., S. Devanathan, T. Woo, E. D. Getzoff, G. Tollin, and M. A. Cusanovich. 2003. Site-specific mutations provide new insights into the origin of pH effects and alternative spectral forms in the photoactive yellow protein from Halorhodospira halophila. Biochemistry. 42:3319-3325.
26. He, Z., C. H. Martin, R. Birge, and K. F. Freed. 2000. Theoretical studies on excited states of a phenolate anion in the environment of photoactive yellow protein. J. Phys. Chem. A. 104:2939-2952.
27. Molina, V., and M. Merchán. 2001. On the absorbance changes in the photocycle of the photoactive yellow protein: a quantum chemical analysis. Proc. Natl. Acad. Sci. USA. 98:4299-4304.
28. Sergi, A., M. Grüning, M. Ferrario, and F. Buda. 2001. Density functional study of the photoactive yellow protein's chromophore. J. Phys. Chem. B. 105:4386-4391.
29. Groenhof, G., M. F. Lensink, H. J. C. Berendsen, J. G. Snijders, and A. E. Mark. 2002. Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore. Proteins. 48:202-211.
30. Yoda, M., H. Houjou, Y. Inoue, and M. Sakurai. 2001. Spectral tuning of photoactive yellow protein. Theoretical and experimental analysis of medium effects on the absorption spectrum of the chromophore. J. Phys. Chem. B. 105:9887-9895.
31. Møller, S. P. 1997. Elisa, an electrostatic storage ring for atomic physics. Nucl. Instrum. Meth. Phys. Res. A. 394:281-286.
32. Andersen, L. H., O. Heber, and D. Zajfman. 2004. Physics with electrostatic rings and traps. J. Phys. B. 37:R57-R88.
33. Andersen, J. U., E. Bonderup, and K. Hansen. 2001. On the concept of temperature for a small isolated system. J. Chem. Phys. 114:6518-6525.
34. Andersen, L. H., H. Bluhme, S. Boyé, T. J. D. Jørgensen, H. Krogh, I. B. Nielsen, S. B. Nielsen, and A. Svendsen. 2004. Experimental studies of the photophysics of gas-phase fluorescent protein chromophores. Phys. Chem. Chem. Phys. 6:2617-2627.
35. Andersen, J. U., P. Hvelplund, S. B. Nielsen, S. Tomita, H. Wahlgreen, S. P. Møller, U. V. Pedersen, J. S. Forster, and T. J. D. Jørgensen. 2002. The combination of an electrospray ion source and an electrostatic storage ring for lifetime and spectroscopy experiments on biomolecules. Rev. Sci. Instrum. 73:1284-1287.
36. Kroon, A. R., W. D. Hoff, H. P. M. Fennema, J. Gijzen, G.-J. Koomen, J. W. Verhoeven, W. Crielaard, and K. J. Hellingwerf. 1996. Spectral tuning, fluorescence, and photoactivity in hybrids of photoactive yellow protein, reconstituted with native or modified chromophores. J. Biol. Chem. 271:31949-31956.
37. Nielsen, S. B., A. Lapierre, J. U. Andersen, U. V. Pedersen, S. Tomita, and L. H. Andersen. 2001. Absorption spectrum of the green fluorescent protein chromophore anion in vacuo. Phys. Rev. Lett. 87:228102.
38. Andersen, L. H., A. Lapierre, S. B. Nielsen, I. B. Nielsen, S. U. Pedersen, U. V. Pedersen, and S. Tomita. 2002. Chromophores of the green fluorescent protein studied in the gas phase. Eur. Phys. J. D. 20:597-600.
39. Boyé, S., I. B. Nielsen, S. B. Nielsen, H. Krogh, A. Lapierre, H. B. Pedersen, S. U. Pedersen, U. V. Pedersen, and L. H. Andersen. 2003. Gas-phase absorption properties of a green fluorescent protein-mutant chromophore: The w7 clone. J. Chem. Phys. 119:338-345.
40. Boyé, S., S. B. Nielsen, H. Krogh, I. B. Nielsen, U. V. Pedersen, A. F. Bell, X. He, P. J. Tonge, and L. H. Andersen. 2003. Gas-phase absorption properties of dsred model chromophores. Phys. Chem. Chem. Phys. 5:3021-3026.
41. Boyé, S., H. Krogh, I. B. Nielsen, S. B. Nielsen, S. U. Pedersen, U. V. Pedersen, L. H. Andersen, A. F. Bell, X. He, and P. J. Tonge. 2003. Vibrationally resolved photoabsorption spectroscopy of red fluorescent protein chromophore anions. Phys. Rev. Lett. 90:118103.
42. Ormö, M., A. B. Cubitt, K. Kallio, L. A. Gross, R. Y. Tsien, and S. J. Remington. 1996. Crystal structure of the Aequorea victoria green fluorescent protein. Science. 273:1392-1395.
43. Yang, F., L. G. Moss, and G. N. Phillips, Jr. 1996. The molecular structure of green fluorescent protein. Nat. Biotechnol. 14:1246-1251.
44. Wall, M. A., M. Socolich, and R. Ranganathan. 2000. The structural basis for red fluorescence in the tetrameric gfp homolog dsred. Nat. Struct. Biol. 7:1133-1138.