Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation

Nature Structural Biology

Volumn 10, Issue 8, 2003, Pages 663-668

  Getzoff, Elizabeth D ^a   Gutwin, Karl N ^b   Genick, Ulrich K ^a,b  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b BRANDEIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOTOACTIVE YELLOW PROTEIN;

ABSORPTION; ACCURACY; ANISOTROPY; ARTICLE; CHROMATOPHORE; CRYSTAL STRUCTURE; FLUORESCENCE; GEOMETRY; ISOMERISM; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PHOTOCHEMISTRY; PHOTORECEPTOR; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; X RAY DIFFRACTION;

BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ELECTROSTATICS; FLUORESCENCE POLARIZATION; ISOMERISM; LIGHT; MODELS, MOLECULAR; PHOTORECEPTORS, MICROBIAL; PROTEIN CONFORMATION;

BACTERIA (MICROORGANISMS);

EID: 0043125483     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb958     Document Type: Article

References (28)

1. Sprenger, W.W., Hoff, W.D., Armitage, J.P. & Hellingwerf, K.J. 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 (1993).
2. Jiang, Z. et al. Bacterial photoreceptor with similarity to photoactive yellow protein and plant phytochromes. Science 285, 406-409 (1999).
3. Devanathan, S. et al. Femtosecond spectroscopic observations of initial intermediates in the photocycle of the photoactive yellow protein from Ectothiorhodospira halophila. Biophys. J. 77, 1017-1023 (1999).
4. Imamoto, Y., Mihara, K., Tokunaga, F. & Kataoka, M. Spectroscopic characterization of the photocycle intermediates of photoactive yellow protein. Biochemistry 40, 14336-14343 (2001).
5. Borgstahl, G.E., Williams, D.R. & Getzoff, E.D. 1.4 Å structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. Biochemistry 34, 6278-6287 (1995).
6. Genick, U.K. et al. Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Science 275, 1471-1475 (1997).
7. Genick, U.K., Soltis, S.M., Kuhn, P., Canestrelli, I.L. & Getzoff, E.D. Structure at 0.85 Å resolution of an early protein photocycle intermediate. Nature 392, 206-209 (1998).
8. Craven, C.J. et al. 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 (2000).
9. Ren, Z. et al. A molecular movie at 1.8 Å resolution displays the photocycle of photoactive yellow protein, a eubacterial blue-light receptor from nanoseconds to seconds. Biochemistry 40, 13788-13801 (2001).
10. Unno, M., Kumauchi, M., Sasaki, J., Tokunaga, F. & Yamauchi, S. Resonance Raman spectroscopy and quantum chemical calculations reveal structural changes in the active site of photoactive yellow protein. Biochemistry 41, 5668-5674 (2002).
11. Thompson, M.J., Bashford, D., Noodleman, L. & Getzoff, E.D. Photoisomerization and proton transfer in photoactive yellow protein. J. Am. Chem. Soc. 125, 8186-8194 (2003).
12. Baca, M. et al. Complete chemical structure of photoactive yellow protein: novel thioester-linked 4-hydroxycinnamyl chromophore and photocycle chemistry. Biochemistry 33, 14369-14377 (1994).
13. van Brederode, M.E., Gensch, T., Hoff, W.D., Hellingwerf, K.J. & Braslavsky, S.E. Photoinduced volume change and energy storage associated with the early transformations of the photoactive yellow protein from Ectothiorhodospira halophila. Biophys. J. 68, 1101-1109 (1995).
14. Meyer, T.E., Yakali, E., Cusanovich, M.A. & Tollin, G. 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 (1987).
15. Kim, M., Mathies, R.A., Hoff, W.D. & Hellingwerf, K.J. Resonance Raman evidence that the thioester-linked 4-hydroxycinnamyl chromophore of photoactive yellow protein is deprotonated. Biochemistry 34, 12669-12672 (1995).
16. Brudler, R. et al. Coupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein. Biochemistry 39, 13478-13486 (2000).
17. Demchuk, E., Genick, U.K., Woo, T.T., Getzoff, E.D. & Bashford, D. Protonation states and pH titration in the photocycle of photoactive yellow protein. Biochemistry 39, 1100-1113 (2000).
18. Word, J.M. et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J. Mol. Biol. 285, 1711-1733 (1999).
19. Ben-Nun, M. & Martinez, T.J. Ab initio molecular dynamics study of cis-trans photoisomerization in ethylene. Chem. Phys. Lett. 298, 57-65 (1998).
20. Kobayashi, T., Saito, T. & Ohtani, H. Real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization. Nature 414, 531-534 (2001).
21. Takeshita, K., Imamoto, Y., Kataoka, M., Tokunaga, F. & Terazima, M. Themodynamic and transport properties of intermediate states of the photocyclic reaction of photoactive yellow protein. Biochemistry 41, 3037-3048 (2002).
22. Alber, T., Gilber, W.A., Ponzi, B.R. & Petzko, G.A. The role of mobility in the substrate binding and catalytic machinery of enzymes. Ciba Found. Symp. 93, 4-24 (1983).
23. Agarwal, P.K., Billeter, S.R., Rajagopalan, P.T., Benkovic, S.J. & Hammes-Schiffer, S. Network of coupled promoting motions in enzyme catalysis. Proc. Natl. Acad. Sci. USA 99, 2794-2799 (2002).
24. Caratzoulas, S., Mincer, J.S. & Schwartz, S.D. Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase. J. Am. Chem. Soc. 124, 3270-3276 (2002).
25. McRee, D.E. XtalView/XFIT - a versatile program for manipulation of atomic coordinates and electron density. J. Struct. Biol. 125, 156-165 (1999).
26. Sheldrick, G.M. & Schneider, T.R. SHELXL: high resolution refinement. Methods Enzymol. 277, 319-343 (1997).
27. Press, W., Teukolsky, S.A., Vetterling, W.T. & Flannery, B.P. Numerical Recipes in C: The Art of Scientific Computing edn. 2 (Cambridge Univ. Press, Cambridge, UK, 1995).
28. Merritt, E.A. & Bacon, D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505-524 (1997).