Skip to main content
SpringerLink
Log in

Small-angle X-Ray analysis of macromolecular structure: the structure of protein NS2 (NEP) in solution

  • Structure of Macromolecular Compounds
  • Published:
Crystallography Reports Aims and scope Submit manuscript

Abstract

A complex structural analysis of nuclear export protein NS2 (NEP) of influenza virus A has been performed using bioinformatics predictive methods and small-angle X-ray scattering data. The behavior of NEP molecules in a solution (their aggregation, oligomerization, and dissociation, depending on the buffer composition) has been investigated. It was shown that stable associates are formed even in a conventional aqueous salt solution at physiological рН value. For the first time we have managed to get NEP dimers in solution, to analyze their structure, and to compare the models obtained using the method of the molecular tectonics with the spatial protein structure predicted by us using the bioinformatics methods. The results of the study provide a new insight into the structural features of nuclear export protein NS2 (NEP) of the influenza virus A, which is very important for viral infection development.

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. N. H. Acheson, Fundamentals of Molecular Virology (Wiley, New York, 2006).

    Google Scholar 

  2. K. Das, J. Aramini, and L-C. Ma, Nat. Struct. Mol. Biol. 17, 530 (2010).

    Article  Google Scholar 

  3. B. Mänz, M. Schwemmle, and L. Brunotte, J. Virol. 87, 7200 (2013).

    Article  Google Scholar 

  4. Y. Zhang, BMC Bioinformatics 9, 40 (2008).

    Article  Google Scholar 

  5. V. Darapaneni, V. K. Prabhaker, and A. Kukol, J. Gen. Virol. 90, 2124 (2009).

    Article  Google Scholar 

  6. H. Akarsu, W. Burmeister, and C. Petosa, EMBO J. 22, 4646 (2003).

    Article  Google Scholar 

  7. D. Paterson and E. Fodor, PLoS Pathog. 8, 1 (2012).

    Article  Google Scholar 

  8. B. Mänz, L. Brunotte, P. Reuther, et al., Nat. Commun. 3, 802 (2012).

    Article  Google Scholar 

  9. P. Reuther, S. Giese, and V. Götz, J. Virol. 88, 263 (2014).

    Article  Google Scholar 

  10. E. C. Hutchinson, E. M. Denham, and B. Thomas, PLoS Pathog. 8, 1 (2012).

    Article  Google Scholar 

  11. T. Gorai, H. Goto, and T. Noda, Proc. Natl. Acad. Sci. USA 109, 4615 (2012).

    Article  ADS  Google Scholar 

  12. S. Huang, J. Chen, and Q. Chen, J. Virol. 87, 767 (2013).

    Article  Google Scholar 

  13. J. Yasuda, S. Nakada, A. Kato, et al., Virol. J. 196, 249 (1993).

    Article  Google Scholar 

  14. S. Boulo, H. Akarsu, R. Ruigrok, et al., Virus Res. J. 124, 12 (2007).

    Article  Google Scholar 

  15. L. Brunotte, J. Flies, and H. Bolte, J. Biol Chem. 289, 20067 (2014).

    Article  Google Scholar 

  16. T. Shimizu, N. Takizawa, and K. Watanabe, FEBS Lett. 585, 41 (2011).

    Article  Google Scholar 

  17. K. Watanabe, T. Shimizu, S. Noda, et al., FEBS Open Bio. 4, 683 (2014).

    Article  Google Scholar 

  18. A. O. Golovko, O. N. Koroleva, and V. L. Drutsa, Proc. XXIX Winter School of Young Scientists “Promising Directions in Physicochemical Biology and Biotechnology”, Moscow, February 7–10, 2017.

    Google Scholar 

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

    Article  ADS  Google Scholar 

  20. A. L. Ksenofontov, V. S. Kozlovskii, and L. V. Kordyukova, Mol. Biol. 40, 172 (2006).

    Article  Google Scholar 

  21. G. P. S. Raghava, Proc. Conf. CASP5, California, December 1–5, 2000, p. 132.

    Google Scholar 

  22. A. Drozdetskiy, C. Cole, J. Procter, et al., Nucl. Acids Res. 43, 389 (2015).

    Article  Google Scholar 

  23. J. Cuff and G. J. Barton, Proteins 40, 502 (1999).

    Article  Google Scholar 

  24. D. W. A. Buchan, F. Minneci, T. C. O. Nugent, et al., Nucl. Acids Res. 41, 340 (2013).

    Article  Google Scholar 

  25. R. Adamczak, A. Porollo, and J. Meller, Proteins: Struct., Funct., Bioinf. 56, 753 (2004).

    Article  Google Scholar 

  26. R. Adamczak, A. Porollo, and J. Meller, Proteins: Struct., Funct., Bioinf. 59, 467 (2005).

    Article  Google Scholar 

  27. M. Wagner, R. Adamczak, A. Porollo, et al., J. Comput. Biol. 12, 355 (2005).

    Article  Google Scholar 

  28. A. Porollo, R. Adamczak, M. Wagner, et al., Proc. Conf. CIRAS, Singapore, December 15–18, 2003, p. 1.

    Google Scholar 

  29. M. Källberg, H. Wang, S. Wang, et al., Nat. Protoc. 7, 1511 (2012).

    Article  Google Scholar 

  30. L. A. Kelley, S. Mezulis, C. M. Yates, et al., Nat. Protoc. 10, 845 (2015).

    Article  Google Scholar 

  31. J. Haas, S. Roth, K. Arnold, et al., Database (Oxford), Bat031, 1 (2013).

    Google Scholar 

  32. M. Kallerg, H. Wang, J. Peng, et al., Nat. Protoc. 7, 1511 (2012).

    Article  Google Scholar 

  33. Z. Dosztányi, V. Csizmók, P. Tompa, et al., J. Mol. Biol. 347, 827 (2005).

    Article  Google Scholar 

  34. Z. Dosztányi, V. Csizmók, P. Tompa, et al., Bioinformatics 21, 3433 (2005).

    Article  Google Scholar 

  35. R. Linding, L. J. Jensen, F. Diella, et al., Structure 11, 453 (2003).

    Article  Google Scholar 

  36. O. V. Galzitskaya, S. O. Garbuzynskiy, and M. Yu. Lobanov, Bioinformatics 22, 2948 (2006).

    Article  Google Scholar 

  37. O. V. Galzitskaya, S. O. Garbuzynskiy, and M. Yu. Lobanov, Mol. Biol. 40, 341 (2006).

    Google Scholar 

  38. O. V. Galzitskaya, S. O. Garbuzynskiy, and M. Yu. Lobanov, PLoS Comput. Biol. 2, e177 (2006).

    Article  ADS  Google Scholar 

  39. O. V. Galzitskaya, S. O. Garbuzynskiy, and M. Yu. Lobanov, Protein Sci. 13, 2871 (2004).

    Google Scholar 

  40. L. J. McGuffin, Bioinformatics 24, 1798 (2008).

    Article  Google Scholar 

  41. C. E. Blanchet, A. Spilotros, F. Schwemmer, et al., J. Appl. Crystallogr. 48, 431 (2015).

    Article  Google Scholar 

  42. P. V. Konarev, V. V. Volkov, A. V. Sokolova, et al., Appl. Crystallogr. 36, 1277 (2003).

    Article  Google Scholar 

  43. A. Guinier, Ann. Phys. 12, 161 (1939).

    Article  Google Scholar 

  44. G. Porod, Small-Angle X-Ray Scattering (Academic, London, 1982), p. 17.

    Google Scholar 

  45. C. E. Blanchet and D. I. Svergun, Annu. Rev. Phys. Chem. 64, 37 (2013).

    Article  ADS  Google Scholar 

  46. D. I. Svergun, J. Appl. Crystallogr. 25, 495 (1992).

    Article  Google Scholar 

  47. D. I. Svergun, Biophys. J. 76 (6), 2879 (1999).

    Article  ADS  Google Scholar 

  48. V. V. Volkov and D. I. Svergun, J. Appl. Crystallogr. 36, 860 (2003).

    Article  Google Scholar 

  49. M. V. Petoukhov and D. I. Svergun, Biophys. J. 89 (2), 1237 (2005).

    Article  Google Scholar 

  50. D. I. Svergun, C. Barberato, and M. H. J. Koch, J. Appl. Crystallogr. 28, 768 (1995).

    Article  Google Scholar 

  51. D. Franke, A. G. Kikhney, and D. I. Svergun, Nucl. Instrum. Methods Phys. Res., Sect. A 689, 52 (2012).

    Article  ADS  Google Scholar 

  52. J. Cheng, A. Z. Randall, M. J. Sweredoski, et al., Nucl. Acids Res. 33, 2 (2005).

    Article  Google Scholar 

  53. E. V. Shtykova, L. A. Baratova, N. V. Fedorova, et al., PloS one 8, 1 (2013).

    Article  Google Scholar 

  54. J. Zhang, V. Frey, M. Corcoran, et al., Mol. Pharmaceutics 13, 3362 (2016).

    Article  Google Scholar 

  55. K. Shiraki, M. Kudou, S. Nishikori, et al., Eur. J. Biochem. 271, 3242 (2004).

    Article  Google Scholar 

  56. E. R. Castellanos, C. Ciferri, and W. Phung, Protein Expr. Purif. 124, 10 (2016).

    Article  Google Scholar 

  57. A. J. Dingley, J. R. Mackay, and B. E. Chapman, J. Biomol. NMR 6, 321 (1995).

    Article  Google Scholar 

  58. E. V. Shtykova, Ross. Nanotekhnol. 10, 60 (2015).

    Google Scholar 

  59. X. H. Guo, N. M. Zhao, S. H. Chen, et al., Biopolymers 29, 335 (1990).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,”, Russian Academy of Sciences, Moscow, 119333, Russia

    E. V. Shtykova & L. A. Dadinova

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

    E. V. Shtykova & E. N. Bogacheva

  3. EMBL, Hamburg Outstation, c/o DESY, Hamburg, Germany

    C. M. Jeffries

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

    N. V. Fedorova & L. A. Baratova

  5. Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia

    A. O. Golovko

  6. Frumkin Institute of Electrochemistry, Russian Academy of Sciences, Moscow, 119071, Russia

    O. V. Batishchev

Authors
  1. E. V. Shtykova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. E. N. Bogacheva
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. L. A. Dadinova
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. C. M. Jeffries
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. N. V. Fedorova
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. A. O. Golovko
    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

  8. O. V. Batishchev
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to E. V. Shtykova.

Additional information

Original Russian Text © E.V. Shtykova, E.N. Bogacheva, L.A. Dadinova, C.M. Jeffries, N.V. Fedorova, A.O. Golovko, L.A. Baratova, O.V. Batishchev, 2017, published in Kristallografiya, 2017, Vol. 62, No. 6, pp. 907–916.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shtykova, E.V., Bogacheva, E.N., Dadinova, L.A. et al. Small-angle X-Ray analysis of macromolecular structure: the structure of protein NS2 (NEP) in solution. Crystallogr. Rep. 62, 894–902 (2017). https://doi.org/10.1134/S1063774517060220

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1063774517060220

Search

Navigation