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Conformation of Thermus thermophilus ribosomal protein S1 in solution at different ionic strengths

  • Molecular Biophysics
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Abstract

Small-angle x-ray and neutron scattering were used to study the structure of the ribosomal protein S1 (61 kDa) from Thermus thermophilus in solution at low and moderate ionic strength (0 and 100 mM NaCl). The protein was found to be globular in both cases. Modeling of the S1 structure comprising six homologous domains on the basis of the NMR data for one domain showed that the best fit to scattering data was provided by compact domain packing. The calculated gyration radius was 28–29 Å, as typical of globular proteins about 60 kDa. The protein was prone to self-association, forming mainly dimers and trimers at moderate ionic strength and higher compact associates at low ionic strength. Neutron scattering assays in heavy water at 100 mM NaCl revealed markedly elongated associates. The translational diffusion coefficient calculated for S1 at 100 mM NaCl from dynamic light scattering was markedly lower than the one expected for its globular monomer (D 20,w = (2.7 ± 0.1)·10−7 versus (5.8–6.0)·10−7 cm2 s−1), confirming protein association under equilibrium conditions.

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Abbreviations

SAXS:

small-angle x-ray scattering

SANS:

small-angle neutron scattering

References

  1. M. Laughrea and P. B. Moore, J. Mol. Biol. 112, 399 (1977).

    Article  Google Scholar 

  2. A. R. Subramanian, Prog. Nucleic Acid Res. Mol. Biol. 28, 101 (1983).

    Article  Google Scholar 

  3. M. Gribskov, Gene (Amst.) 119, 107 (1992).

    Google Scholar 

  4. M. Bycroft, T. J. P. Hubbrard, M. Proctor, et al., Cell 88, 235 (1997).

    Article  Google Scholar 

  5. P. Regnier, M. GrunbergManago, and C. Portier, J. Biol. Chem. 262, 63 (1987).

    Google Scholar 

  6. R. S. Cormack, J. L. Genereaux, and G. A. Mackie, Proc. Natl. Acad. Sci. USA 90, 9006 (1993).

    Article  ADS  Google Scholar 

  7. A. J. Wahba, M. J. Miller, A. Niveleau, et al., J. Biol. Chem. 249, 3314 (1974).

    Google Scholar 

  8. R. Kamen, M. Kondo, W. Rommer, and C. Weissmann, Eur. J. Biochem. 31, 44 (1972).

    Article  Google Scholar 

  9. J. Ruckman, S. Ringquist, E. Brody, and L. Gold, J. Biol. Chem. 269, 26655 (1994).

    Google Scholar 

  10. Y. Feng, H. Huang, J. Liao, and S. N. Cohen, J. Biol. Chem. 276, 31651 (2001).

    Article  Google Scholar 

  11. L. Giri and A. P. Subramanian, FEBS Lett. 81, 199 (1977).

    Article  Google Scholar 

  12. T. Yokota, K. Arai, and Y. Kaziro, J. Biochem. 86, 1725 (1979).

    Google Scholar 

  13. H. Labischinski and A. P. Subramanian, Eur. J. Biochem. 95, 359 (1979).

    Article  Google Scholar 

  14. Y. Sillers and P. B. Moore, J. Mol. Biol. 153, 761 (1981).

    Article  Google Scholar 

  15. B. T. Wimberly, D. E. Brodersen, W. M. Clemons, et al., Nature 407, 327 (2000).

    Article  ADS  Google Scholar 

  16. J. Sengupta, R. K. Arawal, and J. Frank, Proc. Natl. Acad. Sci. USA 98, 11991 (2001).

    Article  ADS  Google Scholar 

  17. N. V. Berestovskaya, V. D. Vasiliev, A. A. Volkov, and Chetverin A.B., FEBS Lett. 228, 263 (1988).

    Article  Google Scholar 

  18. V. M. Shiryaev, O. M. Selivanova, T. Hartsch, et al., FEBS Lett. 525, 88 (2002).

    Article  Google Scholar 

  19. O. M. Selivanova, V. M. Shiryaev, E. I. Tiktopulo, et al., J. Biol. Chem. 278, 36311 (2003).

    Google Scholar 

  20. U. K. Laemmli, Nature 227, 680 (1970).

    Article  ADS  Google Scholar 

  21. M. M. Bradford, Anal. Biochem. 72, 248 (1976).

    Article  Google Scholar 

  22. Y. Amemiya, K. Wakabayashi, T. Hamanaka, et al., Nucl. Instr Methods 208, 471 (1983).

    Article  Google Scholar 

  23. A. A. Timchenko, B. S. Melnik, H. Kihara, et al., FEBS Lett. 471, 211 (2000).

    Article  Google Scholar 

  24. M. Yu. Pavlov, and B. A. Fedorov, Biopolymers 22, 1507 (1983).

    Article  Google Scholar 

  25. O. Glatter, and O. Kratky, Small Angle X-ray Scattering (Academic Press, London, 1982).

    Google Scholar 

  26. A. V. Semenyuk, and D. I. Svergun, J. Appl. Crystallog. 24, 537 (1991).

    Article  Google Scholar 

  27. J. Zhao, and H. B. Stuhrmann, J. de Physique 3, 233 (1993).

    Google Scholar 

  28. A. A. Timchenko, N. B. Griko, and I. N. Serdyuk, Optika Spektrosk. 64, 343 (1988).

    Google Scholar 

  29. R. D. Danovich, and I. N. Serdyuk, in Photon Correlation Techniques in Fluid Mechanics, Ed. by E.O. Shulz-De-Bois (Berlin, 1983), Vol. 38, pp. 315–321.

  30. G.V. Semisotnov, H. Kihara, N. V. Kotova, et al., J. Mol. Biol. 262, 559 (1996).

    Article  Google Scholar 

  31. C. Dirix, F. Meersman, C. E. MacPhee, et al., J. Mol. Biol. 347, 903 (2005).

    Article  Google Scholar 

  32. I. K. Wower, C. W. Zwieb, S. A. Guven, and J. Wower, EMBO J. 19, 6612 (2000).

    Article  Google Scholar 

  33. McGinness K. E., and R. Sauer, Proc. Natl. Acad. Sci. USA 101, 13454 (2004).

    Google Scholar 

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Authors and Affiliations

  1. Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia

    A. A. Timchenko, V. M. Shiryaev, Yu. Yu. Fedorova & O. M. Selivanova

  2. Physics Laboratory, Kansai Medical University, Hirokata, 573-1136, Osaka, Japan

    H. Kihara

  3. Department of Biochemistry, Dokkyo University, Mibu, Tochigu, 321-02, Japan

    K. Kimura

  4. GRSS Research Center, Geeshacht, Germany

    R. Willumeit & V. M. Garamus

Authors
  1. A. A. Timchenko
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  2. V. M. Shiryaev
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  3. Yu. Yu. Fedorova
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  4. H. Kihara
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  5. K. Kimura
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  6. R. Willumeit
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  7. V. M. Garamus
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  8. O. M. Selivanova
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Additional information

Original Russian Text © A.A. Timchenko, V.M. Shiryaev, Yu.Yu. Fedorova, H. Kihara, K. Kimura, R. Willumeit, V.M. Garamus, O.M. Selivanova, 2007, published in Biofizika, 2007, Vol. 52, No. 2, pp. 216–222.

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Timchenko, A.A., Shiryaev, V.M., Fedorova, Y.Y. et al. Conformation of Thermus thermophilus ribosomal protein S1 in solution at different ionic strengths. BIOPHYSICS 52, 162–167 (2007). https://doi.org/10.1134/S0006350907020030

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  • DOI: https://doi.org/10.1134/S0006350907020030

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