Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein

Structure

Volumn 12, Issue 6, 2004, Pages 1039-1045

  Anderson, Spencer ^a,c   Srajer, Vukica ^a,c   Pahl, Reinhard ^c   Rajagopal, Sudarshan ^a   Schotte, Friedrich ^d   Anfinrud, Philip ^d   Wulff, Michael ^e   Moffat, Keith ^a,b,c  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

^e EUROPEAN SYNCHROTRON RADIATION FACILITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MUTANT PROTEIN; PHOTOACTIVE YELLOW PROTEIN;

ARTICLE; CHROMATOPHORE; CONFORMATIONAL TRANSITION; CRYSTALLOGRAPHY; HYDROGEN BOND; INFORMATION PROCESSING; PHOTOACTIVATION; PHOTORECEPTOR; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; STRUCTURE ANALYSIS;

BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DATABASES; ELECTRONS; LIGHT; MODELS, MOLECULAR; MUTATION; PHOTORECEPTORS, MICROBIAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SPECTROPHOTOMETRY; TEMPERATURE; TIME FACTORS;

BACTERIA (MICROORGANISMS);

EID: 2942533032     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.04.008     Document Type: Article

References (36)

1. Anderson S., Crosson S., Moffat K. Short hydrogen bonds in photoactive yellow protein. Acta Crystallogr. D Biol. Crystallogr. 60:2004;1008-1016
2. Borgstahl G.E., Williams D.R., Getzoff E.D. 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor. unusual fold, active site, and chromophore Biochemistry. 34:1995;6278-6287
3. Brudler R., Meyer T.E., Genick U.K., Devanathan S., Woo T.T., Millar D.P., Gerwert K., Cusanovich M.A., Tollin G., Getzoff E.D. Coupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein. Biochemistry. 39:2000;13478-13486
4. Brudler R., Rammelsberg R., Woo T.T., Getzoff E.D., Gerwert K. Structure of the I1 early intermediate of photoactive yellow protein by FTIR spectroscopy. Nat. Struct. Biol. 8:2001;265-270
5. Crosson S., Moffat K. Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch. Plant Cell. 14:2002;1067-1075
6. Crosson S., Rajagopal S., Moffat K. The LOV domain family. photoresponsive signaling modules coupled to diverse output domains Biochemistry. 42:2003;2-10
7. Cusanovich M.A., Meyer T.E. Photoactive Yellow protein. a prototypic PAS domain sensory protein and development of a common signaling mechanism Biochemistry. 42:2003;965-970
8. Englander S. Protein folding intermediates and pathways studied by hydrogen exchange. Annu. Rev. Biophys. Biomol. Struct. 29:2000;213-238
9. Genick U.K., Borgstahl G.E., Ng K., Ren Z., Pradervand C., Burke P.M., Srajer V., Teng T.Y., Schildkamp W., McRee D.E., et al. Structure of a protein photocycle intermediate by millisecond time-resolved crystallography. Science. 275:1997;1471-1475. a
10. Genick U.K., Devanathan S., Meyer T.E., Canestrelli I.L., Williams E., Cusanovich M.A., Tollin G., Getzoff E.D. Active site mutants implicate key residues for control of color and light cycle kinetics of photoactive yellow protein. Biochemistry. 36:1997;8-14. b
11. Harper S., Neil L., Gardner K. Structural basis of a phototropin light switch. Science. 301:2003;1541-1544
12. Hellingwerf K.J., Hendriks J., Gensch T. Photoactive yellow protein, a new type of photoreceptor protein. will this "yellow lab" bring us where we want to go? J. Phys. Chem. A. 107:2003;1082-1094
13. Hendriks J., Gensch T., Hviid L., van der Horst M.A., Hellingwerf K.J., van Thor J.J. Transient exposure of hydrophobic surface in the photoactive yellow protein monitored with Nile red. Biophys. J. 82:2002;1632-1643
14. Hoff W.D., van Stokkum I.H., van Ramesdonk H.J., van Brederode M.E., Brouwer A.M., Fitch J.C., Meyer T.E., van Grondelle R., Hellingwerf K.J. Measurement and global analysis of the absorbance changes in the photocycle of the photoactive yellow protein from Ectothiorhodospira halophila. Biophys. J. 67:1994;1691-1705
15. Imamoto Y., Koshimizu H., Mihara K., Hisatomi O., Mizukami T., Tsujimoto K., Kataoka M., Tokunaga F. Roles of amino acid residues near the chromophore of photoactive yellow protein. Biochemistry. 40:2001;4679-4685. a
16. Imamoto Y., Mihara K., Tokunaga F., Kataoka M. Spectroscopic characterization of the photocycle intermediates of photoactive yellow protein. Biochemistry. 40:2001;14336-14343. b
17. Lee B.C., Croonquist P.A., Sosnick T.R., Hoff W.D. PAS domain receptor photoactive yellow protein is converted to a molten globule state upon activation. J. Biol. Chem. 276:2001;20821-20823
18. McRee D.E. XtalView Xfit. a versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125:1999;156-165
19. Meyer T.E. Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira-Halophila. Biochim. Biophys. Acta. 806:1985;175-183
20. 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. 26:1987;418-423
21. Mihara K., Hisatomi O., Imamoto Y., Kataoka M., Tokunaga F. Functional expression and site-directed mutagenesis of photoactive yellow protein. J. Biochem. (Tokyo). 121:1997;876-880
22. Perman B., Srajer V., Ren Z., Teng T., Pradervand C., Ursby T., Bourgeois D., Schotte F., Wulff M., Kort R., et al. Energy transduction on the nanosecond time scale. early structural events in a xanthopsin photocycle Science. 279:1998;1946-1950
23. Ren Z., Moffat K. Quantitative-analysis of synchrotron Laue diffraction patterns in macromolecular crystallography. J. Appl. Crystallogr. 28:1995;461-481
24. Ren Z., Perman B., Srajer V., Teng T.Y., Pradervand C., Bourgeois D., Schotte F., Ursby T., Kort R., Wulff M., Moffat K. A molecular movie at 1.8 A resolution displays the photocycle of photoactive yellow protein, a eubacterial blue-light receptor, from nanoseconds to seconds. Biochemistry. 40:2001;13788-13801
25. Rubinstenn G., Vuister G.W., Mulder F.A.A., Dux P.E., Boelens R., Hellingwerf K.J., Kaptein R. Structural and dynamic changes of photoactive yellow protein during its photocycle in solution. Nat. Struct. Biol. 5:1998;568-570
26. Rubinstenn G., Vuister G.W., Zwanenburg N., Hellingwerf K.J., Boelens R., Kaptein R. NMR experiments for the study of photointermediates. application to the photoactive yellow protein J. Magn. Reson. 137:1999;443-447
27. Schmidt M., Rajagopal S., Ren Z., Moffat K. Application of singular value decomposition to the analysis of time-resolved macromolecular X-ray data. Biophys. J. 84:2003;2112-2129
28. Schmidt M., Pahl R., Srajer V., Anderson S., Ren Z., Ihee H., Rajagopal S., Moffat K. Protein kinetics. structure of intermediates and reaction mechanism from time-resolved X-ray data Proc. Natl. Acad. Sci. USA. in press:2004
29. Sheldrick, G. (1997). SHELXL97 (Göttingen, Germany: University of Göttingen).
30. 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. 175:1993;3096-3104
31. Srajer V., Teng T.Y., Ursby T., Pradervand C., Ren Z., Adachi S., Schildkamp W., Bourgeois D., Wulff M., Moffat K. Photolysis of the carbon monoxide complex of myoglobin. nanosecond time-resolved crystallography Science. 274:1996;1726-1729
32. Terwilliger T.C., Berendzen J. Difference refinement. obtaining differences between 2 related structures Acta Crystallogr D Biol. Crystallogr. 51:1995;609-618
33. Ujj L., Devanathan S., Meyer T.E., Cusanovich M.A., Tollin G., Atkinson G.H. New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila. picosecond transient absorption spectroscopy Biophys. J. 75:1998;406-412
34. Ursby T., Bourgeois D. Improved estimation of structure-factor difference amplitudes from poorly accurate data. Acta Crystallogr. A. 53:1997;564-575
35. Xie A., Kelemen L., Hendriks J., White B.J., Hellingwerf K.J., Hoff W.D. Formation of a new buried charge drives a large-amplitude protein quake in photoreceptor activation. Biochemistry. 40:2001;1510-1517
36. Zhou Y., Ujj L., Meyer T.E., Cusanovich M.A., Atkinson G.H. Photocycle dynamics and vibrational spectroscopy of the E46Q mutant of photoactive yellow protein. J. Phys. Chem. A. 105:2001;5719-5726