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.
Similar content being viewed by others
References
Jackson, S. E. (1998) Fold. Des., 3, R81–R91.
Finkelstein, A. V., and Badretdinov, A. Ya. (1997) Fold. Des., 2, 115–121.
Thirumalai, D. (1995) J. Phys. Orsay Fr., 5, 1457–1467.
Gutin, A. M., Abkevich, V. I., and Shakhnovich, E. I. (1996) Phys. Rev. Lett., 77, 5433–5436.
Koga, N., and Takada, S. (2001) J. Mol. Biol., 313, 171–180.
Finkelstein, A. V., and Galzitskaya, O. V. (2004) Phys. Life Rev., 1, 23–56.
Galzitskaya, O. V., Ivankov, D. N., and Finkelstein, A. V. (2001) FEBS Lett., 489, 113–118.
Galzitskaya, O. V., Garbuzynskiy, S. O., Ivankov, D. N., and Finkelstein, A. V. (2003) Proteins, 51, 162–166.
Fersht, A. R. (1997) Curr. Opin. Struct. Biol., 7, 3–9.
Plaxco, K. W., Simons, K. W., and Baker, D. (1998) J. Mol. Biol., 277, 985–994.
Guijarro, J. I., Morton, C. J., Plaxco, K. W., Campbell, I. D., and Dobson, C. M. (1998) J. Mol. Biol., 276, 657–667.
Plaxco, K. W., Guijarro, J. I., Morton, C. J., Pitkeathly, M., Campbell, I. D., and Dobson, C. M. (1998) Biochemistry, 37, 2529–2537.
Perl, D., Welker, Ch., Schindler, Th., Schroder, K., Marahiel, M. A., Jaenicke, R., and Schmid, F. X. (1998) Nature Struct. Biol., 5, 229–235.
Van Nuland, N. A. J., Chiti, F., Taddei, N., Raugei, G., Ramponi, G., and Dobson, C. M. (1998) J. Mol. Biol., 283, 883–891.
Zerovnik, E., Virden, R., Jerala, R., Turk, V., and Waltho, J. P. (1998) Proteins, 32, 296–303.
Ivankov, D. N., Garbuzynskiy, S. O., Alm, E., Plaxco, K. W., Baker, D., and Finkelstein, A. V. (2003) Protein Sci., 12, 2057–2062.
Galzitskaya, O. V., Bogatyreva, N. S., and Ivankov, D. N. (2008) J. Bioinform. Comput. Biol., 6, 667–680.
Galzitskaya, O. V., Reifsnyder, D. C., Bogatyreva, N. S., Ivankov, D. N., and Garbuzynskiy, S. O. (2008) Proteins, 70, 329–332.
Ivankov, D. N., Bogatyreva, N. S., Lobanov, M. Yu., and Galzitskaya, O. V. (2009) PLoS ONE, 4, e6476.
Punta, M., and Rost, B. (2005) J. Mol. Biol., 348, 507–512.
Ivankov, D. N., and Finkelstein, A. V. (2004) Proc. Natl. Acad. Sci. USA, 101, 8942–8944.
Zhou, H., and Zhou, Y. (2002) Biophys. J., 82, 458–463.
Gong, H., Isom, D. G., Srinivasan, R., and Rose, G. D. (2003) J. Mol. Biol., 327, 1149–1154.
Capriotti, E., and Casadio, R. (2007) Bioinformatics, 23, 385–386.
Gromiha, M. M., Thangakani, A. M., and Selvaraj, S. (2006) Nucleic Acids Res., 34, W70–W74.
Gromiha, M. M., and Selvaraj, S. (2001) J. Mol. Biol., 310, 27–32.
Ma, B. G., Chen, L. L., and Zhang, H. Y. (2007) J. Mol. Biol., 370, 439–448.
Gromiha, M. M. (2005) J. Chem. Inf. Model, 45, 494–501.
Lobkovsky, A. E., Wolf, Yu. I., and Koonin, E. V. (2010) Proc. Natl. Acad. Sci. USA, 107, 2983–2988.
Povolotskaya, I. S., and Kondrashov, F. A. (2010) Nature, 465, 922–927.
Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) J. Mol. Biol., 247, 536–540.
Winstanley, H. F., Abeln, S., and Deane, C. M. (2005) Bioinformatics, 21, i449–i458.
Bogatyreva, N. S., Finkelstein, A. V., and Galzitskaya, O. V. (2005) J. Bioinform. Comput. Biol., 4, 597–608.
Widmann, M., and Christen, P. (2000) J. Biol. Chem., 275, 18619–18622.
Spirin, A. S. (2010) Molecular Biology: Ribosome Structure and Protein Biosynthesis (in press).
Chang, H. C., Kaiser, C. M., Hartl, F. U., and Barral, J. M. (2005) J. Mol. Biol., 353, 397–409.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © O. V. Galzitskaya, N. S. Bogatyreva, A. V. Glyakina, 2011, published in Biokhimiya, 2011, Vol. 76, No. 2, pp. 274–286.
Rights and permissions
About this article
Cite this article
Galzitskaya, O.V., Bogatyreva, N.S. & Glyakina, A.V. Bacterial proteins fold faster than eukaryotic proteins with simple folding kinetics. Biochemistry Moscow 76, 225–235 (2011). https://doi.org/10.1134/S000629791102009X
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S000629791102009X