Skip to main content

Mathematical simulation of interactions of protein molecules and prediction of their reactivity

Abstract

A physical model of interactions of protein molecules has been developed. The regularities of their reactivity have been studied using electrostatics methods for two histone dimers H2A–H2B and H3–H4 assembled from monomers. The formation of histone dimers from different monomers has been simulated and their ability to the formation of stable compounds has been investigated by analyzing the potential energy matrix using the condition number. The results of a simulation of the electrostatic interaction in the formation of dimers from complete amino acid sequences of selected proteins and their truncated analogs have been considered. The calculations have been performed taking into account the screening of the electrostatic charge of charged amino acids for different concentrations of the monovalent salt using the Gouy–Chapman theory.

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

References

  1. K. G. Kulikov and T. V. Koshlan, Tech. Phys. 60, 639 (2015).

    Article  Google Scholar 

  2. Q. Hong, Biophys. J. 95, 10 (2008).

    Article  Google Scholar 

  3. D. William, et al., Anal. Chem. 80, 3270 (2008).

    Article  Google Scholar 

  4. A. Bar-Even, et al., Biochemistry 50, 4402 (2011).

    Article  Google Scholar 

  5. J. C. Biro, Theor. Biol. Med. Modell. 3 15, (2006).

    Article  Google Scholar 

  6. N. Bernardes, Nuovo Cimento 11, 628 (1959).

    MathSciNet  Article  Google Scholar 

  7. S. Tanaka and H. A. Scheraga, Macromolecules 9, 945 (1976).

    ADS  Article  Google Scholar 

  8. S. Tanaka and H. A. Scheraga, Macromolecules 9, 945 (1976).

    ADS  Article  Google Scholar 

  9. S. Miyazawa and R. L. Jernigan, Macromolecules 18, 534 (1985).

    ADS  Article  Google Scholar 

  10. S. Miyazawa and R. L. Jernigan, J. Mol. Biol. 256, 623 (1996).

    Article  Google Scholar 

  11. S. Miyazawa and R. L. Jernigan, J. Chem. Phys. 122, 024901-1 (2005).

    ADS  Article  Google Scholar 

  12. R. Dias and B. Lindman, DNA Interactions with Polymers and Surfactans (Wiley, Hoboken, 2008).

    Book  Google Scholar 

  13. J. Mazurkiewicz, F. J. Kepert, and K. Rippe, J. Biol. Chem. 281, 16462 (2006).

    Article  Google Scholar 

  14. A. T. Fenley, D. A. Adams, and A. V. Onufriev, Biophys. J. 99, 1577 (2010).

    ADS  Article  Google Scholar 

  15. C. L. White, et al., EMBO J. 20, 5207 (2001).

    Article  Google Scholar 

  16. S. I. Grashchenkov, Tech. Phys. 56, 914 (2011).

    Article  Google Scholar 

  17. M. H. Davis, Q. J. Mech. Appl. Math. 17, 499 (1964).

  18. M. H. Davis, Two charged spherical conductors in a uniform electric field: Forces and field strength, Rand. Corp. Memorandum RM-3860-PR (1964).

    Google Scholar 

  19. V. A. Saranin, Phys. Usp. 42, 385 (1999).

    ADS  Article  Google Scholar 

  20. V. A. Saranin, Phys. Usp. 45, 1287 (2002).

    ADS  Article  Google Scholar 

  21. W. R. Smythe, Static and Dynamic Electricity (McGraw-Hill, New York, 1950: Inostrannaya Literatura, Moscow, 1954).

    MATH  Google Scholar 

  22. S. S. Dukhin, Dielectrical Phenomena and Double Layer in Disperse Systems and Polyelectrolytes (Naukova Dumka, Kiev, 1972).

    Google Scholar 

  23. K. B. Oldham, J. Electroanal. Chem. 613, 131 (2008).

    Article  Google Scholar 

  24. J. H. Masliyah and S. Bhattacharjee, Electrokinetic and Colloid Transport Phenomena (Wiley, New York, 2006).

    Book  Google Scholar 

  25. M. Gerstein and F. M. Richards, Protein Geometry: Volumes, Areas, and Distances (Chapman and Hall, London, 1977).

    Google Scholar 

  26. D. B. Douglas and L. M. Gloss, Biochemistry 42, 6827 (2003).

    Article  Google Scholar 

  27. J. P. Brandon and L. M. Gloss, Biochemistry 41, 14960 (2002).

    Article  Google Scholar 

  28. M. Lisa, et al., Biochemistry 41, 14951 (2002).

    Article  Google Scholar 

  29. V. I. Karantza, et al., Biochemistry 35, 2037 (1996).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to K. G. Kulikov.

Additional information

Original Russian Text © K.G. Kulikov, T.V. Koshlan, 2016, published in Zhurnal Tekhnicheskoi Fiziki, 2016, Vol. 86, No. 10, pp. 131–138.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Kulikov, K.G., Koshlan, T.V. Mathematical simulation of interactions of protein molecules and prediction of their reactivity. Tech. Phys. 61, 1572–1579 (2016). https://doi.org/10.1134/S1063784216100194

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1063784216100194