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Biochemistry (Moscow)

, Volume 76, Issue 2, pp 225–235 | Cite as

Bacterial proteins fold faster than eukaryotic proteins with simple folding kinetics

  • O. V. GalzitskayaEmail author
  • N. S. Bogatyreva
  • A. V. Glyakina
Article

Abstract

Protein domain frequency and distribution among kingdoms was statistically analyzed using the SCOP structural database. It appeared that among chosen protein domains with the best resolution, eukaryotic proteins more often belong to α-helical and β-structural proteins, while proteins of bacterial origin belong to α/β structural class. Statistical analysis of folding rates of 73 proteins with known experimental data revealed that bacterial proteins with simple kinetics (23 proteins) exhibit a higher folding rate compared to eukaryotic proteins with simple folding kinetics (27 proteins). Analysis of protein domain amino acid composition showed that the frequency of amino acid residues in proteins of eukaryotic and bacterial origin is different for proteins with simple and complex folding kinetics.

Key words

“all-or-none” transition eukaryotic and bacterial proteins folding intermediates folding rate protein folding 

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References

  1. 1.
    Jackson, S. E. (1998) Fold. Des., 3, R81–R91.PubMedCrossRefGoogle Scholar
  2. 2.
    Finkelstein, A. V., and Badretdinov, A. Ya. (1997) Fold. Des., 2, 115–121.PubMedCrossRefGoogle Scholar
  3. 3.
    Thirumalai, D. (1995) J. Phys. Orsay Fr., 5, 1457–1467.CrossRefGoogle Scholar
  4. 4.
    Gutin, A. M., Abkevich, V. I., and Shakhnovich, E. I. (1996) Phys. Rev. Lett., 77, 5433–5436.PubMedCrossRefGoogle Scholar
  5. 5.
    Koga, N., and Takada, S. (2001) J. Mol. Biol., 313, 171–180.PubMedCrossRefGoogle Scholar
  6. 6.
    Finkelstein, A. V., and Galzitskaya, O. V. (2004) Phys. Life Rev., 1, 23–56.CrossRefGoogle Scholar
  7. 7.
    Galzitskaya, O. V., Ivankov, D. N., and Finkelstein, A. V. (2001) FEBS Lett., 489, 113–118.PubMedCrossRefGoogle Scholar
  8. 8.
    Galzitskaya, O. V., Garbuzynskiy, S. O., Ivankov, D. N., and Finkelstein, A. V. (2003) Proteins, 51, 162–166.PubMedCrossRefGoogle Scholar
  9. 9.
    Fersht, A. R. (1997) Curr. Opin. Struct. Biol., 7, 3–9.PubMedCrossRefGoogle Scholar
  10. 10.
    Plaxco, K. W., Simons, K. W., and Baker, D. (1998) J. Mol. Biol., 277, 985–994.PubMedCrossRefGoogle Scholar
  11. 11.
    Guijarro, J. I., Morton, C. J., Plaxco, K. W., Campbell, I. D., and Dobson, C. M. (1998) J. Mol. Biol., 276, 657–667.PubMedCrossRefGoogle Scholar
  12. 12.
    Plaxco, K. W., Guijarro, J. I., Morton, C. J., Pitkeathly, M., Campbell, I. D., and Dobson, C. M. (1998) Biochemistry, 37, 2529–2537.PubMedCrossRefGoogle Scholar
  13. 13.
    Perl, D., Welker, Ch., Schindler, Th., Schroder, K., Marahiel, M. A., Jaenicke, R., and Schmid, F. X. (1998) Nature Struct. Biol., 5, 229–235.PubMedCrossRefGoogle Scholar
  14. 14.
    Van Nuland, N. A. J., Chiti, F., Taddei, N., Raugei, G., Ramponi, G., and Dobson, C. M. (1998) J. Mol. Biol., 283, 883–891.PubMedCrossRefGoogle Scholar
  15. 15.
    Zerovnik, E., Virden, R., Jerala, R., Turk, V., and Waltho, J. P. (1998) Proteins, 32, 296–303.PubMedCrossRefGoogle Scholar
  16. 16.
    Ivankov, D. N., Garbuzynskiy, S. O., Alm, E., Plaxco, K. W., Baker, D., and Finkelstein, A. V. (2003) Protein Sci., 12, 2057–2062.PubMedCrossRefGoogle Scholar
  17. 17.
    Galzitskaya, O. V., Bogatyreva, N. S., and Ivankov, D. N. (2008) J. Bioinform. Comput. Biol., 6, 667–680.PubMedCrossRefGoogle Scholar
  18. 18.
    Galzitskaya, O. V., Reifsnyder, D. C., Bogatyreva, N. S., Ivankov, D. N., and Garbuzynskiy, S. O. (2008) Proteins, 70, 329–332.PubMedCrossRefGoogle Scholar
  19. 19.
    Ivankov, D. N., Bogatyreva, N. S., Lobanov, M. Yu., and Galzitskaya, O. V. (2009) PLoS ONE, 4, e6476.PubMedCrossRefGoogle Scholar
  20. 20.
    Punta, M., and Rost, B. (2005) J. Mol. Biol., 348, 507–512.PubMedCrossRefGoogle Scholar
  21. 21.
    Ivankov, D. N., and Finkelstein, A. V. (2004) Proc. Natl. Acad. Sci. USA, 101, 8942–8944.PubMedCrossRefGoogle Scholar
  22. 22.
    Zhou, H., and Zhou, Y. (2002) Biophys. J., 82, 458–463.PubMedCrossRefGoogle Scholar
  23. 23.
    Gong, H., Isom, D. G., Srinivasan, R., and Rose, G. D. (2003) J. Mol. Biol., 327, 1149–1154.PubMedCrossRefGoogle Scholar
  24. 24.
    Capriotti, E., and Casadio, R. (2007) Bioinformatics, 23, 385–386.PubMedCrossRefGoogle Scholar
  25. 25.
    Gromiha, M. M., Thangakani, A. M., and Selvaraj, S. (2006) Nucleic Acids Res., 34, W70–W74.PubMedCrossRefGoogle Scholar
  26. 26.
    Gromiha, M. M., and Selvaraj, S. (2001) J. Mol. Biol., 310, 27–32.PubMedCrossRefGoogle Scholar
  27. 27.
    Ma, B. G., Chen, L. L., and Zhang, H. Y. (2007) J. Mol. Biol., 370, 439–448.PubMedCrossRefGoogle Scholar
  28. 28.
    Gromiha, M. M. (2005) J. Chem. Inf. Model, 45, 494–501.PubMedCrossRefGoogle Scholar
  29. 29.
    Lobkovsky, A. E., Wolf, Yu. I., and Koonin, E. V. (2010) Proc. Natl. Acad. Sci. USA, 107, 2983–2988.PubMedCrossRefGoogle Scholar
  30. 30.
    Povolotskaya, I. S., and Kondrashov, F. A. (2010) Nature, 465, 922–927.PubMedCrossRefGoogle Scholar
  31. 31.
    Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) J. Mol. Biol., 247, 536–540.PubMedGoogle Scholar
  32. 32.
    Winstanley, H. F., Abeln, S., and Deane, C. M. (2005) Bioinformatics, 21, i449–i458.PubMedCrossRefGoogle Scholar
  33. 33.
    Bogatyreva, N. S., Finkelstein, A. V., and Galzitskaya, O. V. (2005) J. Bioinform. Comput. Biol., 4, 597–608.CrossRefGoogle Scholar
  34. 34.
    Widmann, M., and Christen, P. (2000) J. Biol. Chem., 275, 18619–18622.PubMedCrossRefGoogle Scholar
  35. 35.
    Spirin, A. S. (2010) Molecular Biology: Ribosome Structure and Protein Biosynthesis (in press).Google Scholar
  36. 36.
    Chang, H. C., Kaiser, C. M., Hartl, F. U., and Barral, J. M. (2005) J. Mol. Biol., 353, 397–409.PubMedCrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2011

Authors and Affiliations

  • O. V. Galzitskaya
    • 1
    Email author
  • N. S. Bogatyreva
    • 1
  • A. V. Glyakina
    • 2
  1. 1.Institute of Protein ResearchRussian Academy of SciencesPushchino, Moscow RegionRussia
  2. 2.Institute of Mathematical Problems of BiologyRussian Academy of SciencesPushchino, Moscow RegionRussia

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