Skip to main content
SpringerLink
Log in

Modeling of protein spatial structure using tritium planigraphy

  • Molecular Biophysics
  • Published:
Biophysics Aims and scope Submit manuscript

Abstract

The results of protein spatial structure modeling using the tritium planigraphy technique are presented. The knowledge of 3D structure of macromolecules is obligatory for understanding the basic mechanisms of interaction in biological systems and complex technological processes. Known limitations of the X-ray analysis (crystal state) and NMR (molecular weight) make it necessary to seek new approaches to modeling the spatial structure of proteins. Semiempirical tritium planigraphy is one of these approaches. The method is based on bombardment of the object with a beam of hot tritium atoms (E at ≥ 0.3 eV) and computer simulation. On the example of proteins of different structural classes, we show that this integrated approach can yield a 3D model well consistent with the X-ray data. An important factor is the sequence of searching for contacts between secondary structure elements: the best fit with the native structure is achieved by assembling the elements from the N- to the C-terminus of the polypeptide chain.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Protein Reviews: Proteomic and Protein-Protein Interactions, Ed. by G. Waksman (2005), Vol. 3.

  2. I. N. Serdyuk, Uspekhi Biol. Nauk 42, 3 (2002).

    Google Scholar 

  3. H. Zhou, S. Pandit, S. Y. Lee, et al., Proteins 69(Suppl. l8), 90 (2007).

    Article  Google Scholar 

  4. I. Cymerman, M. Feder, M. Pawlowski, et al., Nucl. Acids Mol. Biol. 15, 1 (2005).

    Article  Google Scholar 

  5. J. M. Bujnicki, Chembiochem. 7, 19 (2006).

    Article  Google Scholar 

  6. Y. Zhang and J. Scolnick, Proc. Natl. Acad. Sci. USA 102, 1029 (2005).

    Article  ADS  Google Scholar 

  7. C. B. Anfinsen, Science 181, 293 (1973).

    Article  Google Scholar 

  8. C. Levinthal, J. Chem. Phys. 65, 44 (1968).

    Google Scholar 

  9. A. Yu. Grosberg, Uspekhi Biol. Nauk 167(2), 129 (1997).

    Article  Google Scholar 

  10. S. Auer, M. A. Miller, S. V. Krivov, et al., Phys. Rev. Lett. 99, 178104 (2007).

    Article  ADS  Google Scholar 

  11. S. Wallin and E. I. Shakhnovich, J. Phys. Cond. Matt. 20, 283101 (2008).

    Article  Google Scholar 

  12. V. A. Kolb, Mol. Biol. 35, 682 (2001).

    Article  Google Scholar 

  13. B. Hardesty, T. Tsalkova, and G. Kramer, Curr. Opin. Struct. Biol. 9, 111 (1999).

    Article  Google Scholar 

  14. L. A. Baratova, E. N. Bogacheva, V. I. Goldanskii, et al., Tritium Planigraphy of Biological Macromolecules (Nauka, Moscow, 1999) [in Russian].

    Google Scholar 

  15. A. V. Gedrovich, M. M. Yusupov, A. V. Shishkov, V. I. Goldanskii, and A. S. Spirin, Dokl. AN SSSR 267, 1255 (1982).

    Google Scholar 

  16. N. D. Belayev, V. G. Budker, V. A. Dubrovskaya, et al., FEBS Lett. 297, 43 (1992).

    Article  Google Scholar 

  17. V. I. Goldanskii, I. A. Kashirin, A. V. Shishkov, et al., J. Mol. Biol. 201, 567 (1988).

    Article  Google Scholar 

  18. E. N. Dobrov, A. V. Efimov, and L. A. Baratova, Mol. Biol. 38, 945 (2004).

    Article  Google Scholar 

  19. A. V. Shishkov, V. I. Goldanskii, L. A. Baratova, et al., Proc. Natl. Acad. Sci. USA 96, 7827 (1999).

    Article  ADS  Google Scholar 

  20. E. N. Bogacheva, V. I. Goldanskii, A. V. Shishkov, et al., Proc. Natl. Acad. Sci. USA 95, 2790 (1998).

    Article  ADS  Google Scholar 

  21. H. M. Berman, J. Westbrook, Z. Feng, et al., Nucl. Acid. Res. 28, 235 (2000).

    Article  Google Scholar 

  22. E. N. Bogacheva, V. I. Goldanskii и A. V. Shishkov, Khim. Fizika 22(2), 8 (2003).

    Google Scholar 

  23. A. V. Shishkov and E. N. Bogacheva, in Methods in Protein Structure and Stability Analysis: Conformational Stability, Size, Shape and Surface of Protein Molecules, Ed. by V. N. Uversky, E. A. Permyakov (Nova Science Publishers, N.-Y., 2007).

    Google Scholar 

  24. F. E. Cohen, T. J. Richmond, and F. M. Richards, J. Mol. Biol. 132(3), 275 (1979).

    Article  Google Scholar 

  25. A. S. Spirin, Ribosome Structure and Protein Biosynthesis (ONTI NTsBI AN SSSR, Pushchino, 1981) [in Russian].

    Google Scholar 

  26. W. J. Netzer and F. U. Hartl, Trends Biochem. Sci. 23(2), 68 (1998).

    Article  Google Scholar 

  27. R. Zana, Biopolymers 14, 2425 (1975).

    Article  Google Scholar 

  28. F. Avbelj and L. Fele, Proteins 31, 74 (1998).

    Article  Google Scholar 

  29. A. A. Komar, A. Kommer, I. A. Krasheninnikov, and A. S. Spirin, J. Biol. Chem. 272, 10646 (1997).

    Article  Google Scholar 

  30. A. A. Komar, A. Kommer, I. A. Krasheninnikov, and A. S. Spirin, FEBS Lett. 326, 261 (1993).

    Article  Google Scholar 

  31. I. Hamlin and I. Zabin, Proc. Natl. Acad. Sci. USA 69, 412 (1972).

    Article  ADS  Google Scholar 

  32. V. A. Kolb, E. V. Makeev, and A. S. Spirin, EMBO J. 13, 3631 (1994).

    Google Scholar 

  33. S. N. Timasheff and G. Xie, Biophys. Chem. 105, 421 (2003).

    Article  Google Scholar 

  34. K. Kuwajima, FASEB J. 10, 102 (1996).

    Google Scholar 

  35. B. Sha and M. Luo, Nat. Struct. Biol. 4, 239 (1997).

    Article  Google Scholar 

  36. A. Harris, F. Forouhar, S. Qiu, et al., Virology 289, 34 (2001).

    Article  Google Scholar 

  37. S. Artz, F. Baudin, A. Barge, et al., Virology 279, 439 (2001).

    Article  Google Scholar 

  38. http://cubic.bioc.columbia.edu/eva.

  39. A. V. Efimov, Prog. Biophys. Mol. Biol. 60(3), 201 (1993).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia

    E. N. Bogacheva, A. N. Bogachev, I. B. Dmitriev, A. A. Dolgov, A. L. Chulichkov & A. V. Shishkov

  2. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119899, Russia

    L. A. Baratova

Authors
  1. E. N. Bogacheva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. N. Bogachev
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. I. B. Dmitriev
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A. A. Dolgov
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. L. Chulichkov
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. A. V. Shishkov
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. L. A. Baratova
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to E. N. Bogacheva.

Additional information

Original Russian Text © E.N. Bogacheva, A.N. Bogachev, I.B. Dmitriev, A.A. Dolgov, A.L. Chulichkov, A.V. Shishkov, L.A. Baratova, 2011, published in Biofizika, 2011, Vol. 56, No. 6, pp. 1024–1037.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bogacheva, E.N., Bogachev, A.N., Dmitriev, I.B. et al. Modeling of protein spatial structure using tritium planigraphy. BIOPHYSICS 56, 1011–1020 (2011). https://doi.org/10.1134/S0006350911060030

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0006350911060030

Keywords

Search

Navigation