Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
권호 표지
DOI QR코드

DOI QR Code

Exploring Fine Structures of Photoactive Yellow Protein in Solution Using Wide-Angle X-ray Scattering

  • Kim, Tae-Kyu (Department of Chemistry and School of Molecular Science (BK21), KAIST) ;
  • Zuo, Xiaobing (Chemistry Division, Argonne National Laboratory) ;
  • Tiede, David M. (Chemistry Division, Argonne National Laboratory) ;
  • Ihee, Hyot-Cherl (Department of Chemistry and School of Molecular Science (BK21), KAIST)
  • Published : 2004.11.20
Download PDF
⟨ Previous Next ⟩

Abstract

We demonstrate that wide-angle X-ray scattering pattern from photoactive yellow protein (PYP) in solution using a high flux third generation synchrotron X-ray source reflects not only the overall structure, but also fine structures of the protein. X-ray scattering data from PYP in solution have been collected in q ranges from 0.02 ${\AA}^{-1}$ to 2.8 ${\AA}^{-1}$. These data are sensitive to the protein structure and consistent with the calculation based on known crystallographic atomic coordinates. Theoretical scattering patterns were also calculated for the intermediates during the photocycle of PYP to estimate the feasibility of time-resolved wide-angle X-ray scattering experiments on such proteins. These results demonstrate the possibility of using the wide-angle solution X-ray scattering as a quantitative monitor of photo-induced structural changes in PYP.

Keywords

References

  1. Edwards, A. M.; Arrowsmith, C. H.; Christendat, D.; Dharamsi, A.; Friesen, J. D.; Greenblatt, J. F.; Vedadi, M. Nat. Struct. Biol. 2000, 7, 970. https://doi.org/10.1038/80751
  2. Kim, S.; Jin, G.; Lim, M. Bull. Korean Chem. Soc. 2003, 24, 1470. https://doi.org/10.5012/bkcs.2003.24.10.1470
  3. Lim, M. Bull. Korean Chem. Soc. 2002, 23, 865. https://doi.org/10.5012/bkcs.2002.23.6.865
  4. Wulff, M.; Plech, A.; Eybert, L.; Randler, R.; Schotte, F.; Anfinrud, P. Faraday Discussions 2003, 122, 13. https://doi.org/10.1039/b202740m
  5. Schotte, F.; Lim, M. H.; Jackson, T. A.; Smirnov, A. V.; Soman, J.; Olson, J. S.; Phillips, G. N.; Wulff, M.; Anfinrud, P. A. Science 2003, 300, 1944. https://doi.org/10.1126/science.1078797
  6. Techert, S.; Schotte, F.; Wulff, M. Phys. Rev. Lett. 2001, 86, 2030. https://doi.org/10.1103/PhysRevLett.86.2030
  7. Bratos, S.; Mirloup, F.; Vuilleumier, R.; Wulff, M. J. Chem. Phys. 2002, 116, 10615. https://doi.org/10.1063/1.1477923
  8. Guinier, A. Fournet, G. Small-Angle Scattering of X-rays; John Wiley & Sons; New York, 1995.
  9. Svergun, D.; Barberato, C.; Koch, M. H. J. J. Appl. Cryst. 1995, 28, 768. https://doi.org/10.1107/S0021889895007047
  10. Chacon, P.; Moran, F.; Diaz, J. F.; Pantos, E.; ANdreu, J. M. Biophys. J. 1998, 74, 2760. https://doi.org/10.1016/S0006-3495(98)77984-6
  11. Svergun, D. Biophys. J. 1999, 76, 2879. https://doi.org/10.1016/S0006-3495(99)77443-6
  12. Fischetti, R. F.; Rodi, D. J.; Mirza, A.; Irving, T. C.; Kondrashkina, E.; Makowski, L. J. Synchrotron Rad. 2003, 10, 398. https://doi.org/10.1107/S0909049503016583
  13. Hirai, M.; Iwase, H.; Hayakawa, T.; Miura, K.; Inoue, K. J. Synchrotron Rad. 2002, 9, 202. https://doi.org/10.1107/S0909049502006593
  14. Tiede, D. M.; Zhang, R.; Seifert, S. Biochemistry 2002, 41, 6605. https://doi.org/10.1021/bi015931h
  15. Zhang, R.; Thiyagarajan, P.; Tiede, D. M. J. Appl. Cryst. 2000, 33, 565. https://doi.org/10.1107/S0021889800001345
  16. Meyer, T. E. Biochem. Biophys. Acta 1985, 806, 175. https://doi.org/10.1016/0005-2728(85)90094-5
  17. Sprenger, W. W.; Hoff, W. D.; Armitage, J. P.; Hellingwerf, K. J. J. Bacteriol. 1993, 175, 3096.
  18. Imamoto, Y.; Mihara, K.; Tokunaga, F.; Kataoka, M. Biochemistry 2001, 40, 14336. https://doi.org/10.1021/bi010468u
  19. Baca, M.; Borgstahl, G. E. O.; Boissinot, M.; Burke, P. M.; Williams, D. R.; Slater, K. A.; Getzoff, E. D. Biochemistry 1994, 33, 14369. https://doi.org/10.1021/bi00252a001
  20. Borgstahl, G. E. O.; Williams, D. R.; Getzoff, E. D. Biochemistry 1995, 34, 6278. https://doi.org/10.1021/bi00019a004
  21. Dux, P.; Rubinstenn, G.; Vuister, G. W.; Boelens, R.; Mulder, F. A.; Hard, K.; Hoff, W. D.; Kroon, A. R.; Crielaard, W.; Hellingwerf, K. J.; Kaptein, R. Biochemistry 1998, 37, 12689. https://doi.org/10.1021/bi9806652
  22. Kort, M.; Vonk, H.; Xu, X.; Hoff, W. D.; Crielaard, W.; Hellingwerf, K. J. FEBS Lett 1996, 382, 73. https://doi.org/10.1016/0014-5793(96)00149-4
  23. Imamoto, Y.; Kataoka, M.; Tokunaga, F.; Asahi, T.; Masuhara, H. Biochemistry 2001, 40, 6047. https://doi.org/10.1021/bi002437p
  24. Ujj, L.; Devanathan, S.; Meyer, T. E.; Cusanovich, M. A.; Tollin, G.; Atkinson, G. H. Biophys. J. 1998, 75, 406. https://doi.org/10.1016/S0006-3495(98)77525-3
  25. Hoff, W. D.; Xie, A.; Van Stokkum, I. H. M.; Tang, X.; Gural, J.; Kroon, A. R.; Hellingwerf, K. J. Biochemistry 1999, 38, 1009. https://doi.org/10.1021/bi980504y
  26. Genick, U. K.; Soltis, S. M.; Kuhn, P.; Canestrelli, I. L.; Getzoff, E. D. Nature 1998, 392, 206. https://doi.org/10.1038/32462
  27. Imamoto, Y.; Ito, T.; Kataoka, M.; Tokunaga, F. FEBS Lett. 1995, 374, 157. https://doi.org/10.1016/0014-5793(95)01096-W
  28. Beno, M. A.; Jennings, G.; Engbretson, M.; Knapp, G. S.; Kurtz, C.; Zabransky, B.; Linton, J.; Seifert, S.; Wiley, C.; Montano, P. A. Nucl. Instrum. Meth. A 2001, 467, 690. https://doi.org/10.1016/S0168-9002(01)00455-7
  29. Warren, B. E. X-ray Diffraction; Dover Publication, Inc.: New York, 1990.
  30. Fraser, R. D. B.; MacRae, T. P.; Suzuki, E. J. Appl. Cryst. 1978, 11, 693. https://doi.org/10.1107/S0021889878014296
  31. Hirai, M.; Iwase, H.; Hayakawa, T. J. Phys. Chem. B 1999, 103, 10136. https://doi.org/10.1021/jp991330c
  32. Ducruix, A.; Guilloteau, J. P.; Ries-Kautt, M.; Tardieu, A. J. Cryst. Growth 1996, 168, 28. https://doi.org/10.1016/0022-0248(96)00359-4
  33. 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.; Moffat, K.; Getzoff, E. D. Science 1997, 275, 1471. https://doi.org/10.1126/science.275.5305.1471
  34. Zhang, R.; Marone, P. A.; Thiyagarajan, P.; Tiede, D. M. Langmuir 1999, 15, 7510. https://doi.org/10.1021/la990076c
  35. Tiede, D. M.; Zhang, R.; Chen, L. X.; Yu, L.; Lindsey, J. S. J. Am. Chem. Soc. 2004, 126, 14054. https://doi.org/10.1021/ja048209q

Cited by

  1. Measurements of complex refractive index change of photoactive yellow protein over a wide wavelength range using hyperspectral quantitative phase imaging vol.8, pp.1, 2018, https://doi.org/10.1038/s41598-018-21403-z
  2. X-ray scattering combined with coordinate-based analyses for applications in natural and artificial photosynthesis vol.102, pp.2-3, 2009, https://doi.org/10.1007/s11120-009-9475-6
  3. Physical Chemistry Research Articles Published in the Bulletin of the Korean Chemical Society: 2003-2007 vol.29, pp.2, 2008, https://doi.org/10.5012/bkcs.2008.29.2.450