Skip to main content

Modeling of conformational transitions of fibrillogenic peptide, homologous to beta-domain of human alpha-lactalbumin


The behavior of the peptide corresponding to beta domain of human alpha-lactalbumin (GYDTQAIVENNESTEYG, WT) has been simulated by the molecular dynamics method. It is shown that, within the model considered, the monomer of this peptide does not tend to form a stable secondary structure; however, simulation of the behavior of several peptide molecules revealed the occurrence of beta structures due to the formation of intermolecular hydrogen bonds. Since the aforementioned interactions involve the terminal portions of peptides, the influence of the tetrapeptide corresponding to the N-terminal portion of WT, TDYG (R), on the secondary structure has been analyzed. The model calculations show that the interaction of this peptide with WT monomer facilitates formation of beta-structures. It is suggested that peptide R may affect the quaternary structure of WT.

This is a preview of subscription content, access via your institution.


  1. V. V. Egorov, K. V. Solovyov, N. A. Grudinina, et al., Protein Pept. Lett. 14 (5), 471 (2007).

    Article  Google Scholar 

  2. G. Merlini and V. Bellotti, New Engl. J. Med. 349 (6), 583 (2003).

    Article  Google Scholar 

  3. G. Merlini, D. C. Seldin, and M. A. Gertz, J. Clin. Oncol. 29 (14), 1924 (2011).

    Article  Google Scholar 

  4. C. Wasmer, A. Lange, H. Van Melckebeke, et al., Science 319, 1523 (2008).

    Article  ADS  Google Scholar 

  5. V. V. Egorov, Yu. P. Garmai, K. V. Solov’ev, et al., Dokl. Akad. Nauk 414 (6), 828 (2007) Dokl. Phys. 414 (6), (2007).

    Google Scholar 

  6. Schrödinger LLC. The PyMOL Molecular Graphics System, Version 1.3 r1 // Py-MOL, The PyMOL Molecular Graphics System, Version (2010), p. 1.


  8. B. Hess, D. van Der Spoel, and E. Lindahl, Gromacs User Manual Version 4.5.4 (University of Groningen, Netherland, 2010).

    Google Scholar 

  9. S. Pronk, S. Páll, R. Schulz, et al., Bioinformatics 29 (7), 845 (2013).

    Article  Google Scholar 

  10. K. Lindorff-Larsen, S. Piana, K. Palmo, et al., Proteins: Struct., Funct., Bioinf. 78 (8), 1950 (2010).

    Google Scholar 

  11. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, et al., J. Chem. Phys. 79 (2), 926 (1983).

    Article  ADS  Google Scholar 

  12. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98 (12), 10089 (1993).

    Article  ADS  Google Scholar 

  13. W. Kabsch and C. Sander, Biopolymers 22 (12), 2577 (1983).

    Article  Google Scholar 

  14. A. Kuklin, A. Kh. Islamov, and V. I. Gordeliy, Neutron News 16 (3), 16 (2005).

    Article  Google Scholar 

  15. V. V. Egorov, D. V. Lebedev, A. A. Shaldzhyan, et al., Prion (2014). doi 10.4161/19336896.2014.9837

    Google Scholar 

  16. V. Egorov, A. Shaldzhyan, A. Sirotkin, et al., FEBS J. 280 (SI1), 133 (2013).

    Google Scholar 

  17. J. Nguyen, M. A. Baldwin, F. E. Cohen, et al., Biochemistry 34 (13), 4186 (1995).

    Article  Google Scholar 

  18. M. R. Nilsson and C. M. Dobson, Biochemistry 42 (2), 375 (2003).

    Article  Google Scholar 

  19. R. Mishra, K. Sörgjerd, S. Nyström, et al., J. Mol. Biol. 366 (3), 1029 (2007).

    Article  Google Scholar 

  20. P. Debye and A. M. Bueche, J. Appl Phys. 20, 518 (1949).

    Article  ADS  Google Scholar 

Download references

Author information

Authors and Affiliations


Corresponding author

Correspondence to V. V. Kadochnikov.

Additional information

Original Russian Text © V.V. Kadochnikov, V.V. Egorov, A.V. Shvetsov, A.I. Kuklin, V.V. Isaev-Ivanov, D.V. Lebedev, 2016, published in Kristallografiya, 2016, Vol. 61, No. 1, pp. 107–114.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Kadochnikov, V.V., Egorov, V.V., Shvetsov, A.V. et al. Modeling of conformational transitions of fibrillogenic peptide, homologous to beta-domain of human alpha-lactalbumin. Crystallogr. Rep. 61, 98–105 (2016).

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI:


  • Fibril
  • Crystallography Report
  • Conformational Transition
  • Beta Structure
  • Fibril Growth