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A molecular dynamics simulation of structure self-organization in model biomimetic polymers

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Abstract

The folding of macromolecules into three-dimensional structures has been investigated using the methods of molecular dynamics. A freely jointed polymer chain with rigid covalent bonds and van der Waals forces acting between the chain elements has been considered. Conditions for the formation of various spatial structures that mimic α-helices, β-strands, and double helices that occur in biomolecular systems have been defined.

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Abbreviations

LD:

Lennard-Jones potential

References

  1. A. Fersht, Enzyme Structure and Mechanism, 2nd ed. (Freeman, New York, 1985).

    Google Scholar 

  2. D. S. Chernavskii and N. M. Chernavskaya, Protein Machine: Biological Macromolecular Constructions (Moscow State Univ., Moscow, 1999) [in Russian].

    Google Scholar 

  3. H. Frauenfelder, G. A. Petsko, and D. Tsernoglou, Nature 280, 558 (1979).

    Article  ADS  Google Scholar 

  4. K. V. Shaitan, Biofizika 39, 949 (1994).

    Google Scholar 

  5. A. B. Rubin, S. K. Chamorovskii, A. A. Kononenko, and K. V. Shaitan, Mol. Biol. (Moscow) 24, 417 (1990).

    Google Scholar 

  6. O. B. Ptitsyn and A. V. Finkelstein, Biopolymers 22, 15 (1983).

    Article  Google Scholar 

  7. A. G. Murzin and A. V. Finkelstein, J. Mol. Biol. 204, 749 (1988).

    Article  Google Scholar 

  8. Y. Levy, J. Jortner, and O. M. Becker, Proc. Natl. Acad. Sci. U. S. A. 98 (5), 2188 (2001).

    Article  ADS  Google Scholar 

  9. J. Rumbley, L. Hoang, L. Mayne, and S. W. Englander, Proc. Natl. Acad. Sci. U. S. A. 98 (1), 105 (2001).

    Article  ADS  Google Scholar 

  10. P. G. Khalatur, V. V. Novikov, and A. R. Khokhlov, Phys. Rev. E. 67, 051901 (2003).

    Article  Google Scholar 

  11. V. A. Ivanov, A. V. Cherovich, A. A. Lazutin, et al., Macromol. Symp. 146, 259 (1999).

    Article  Google Scholar 

  12. A. V. Cherovich, V. A. Ivanov, B. G. Zavin, and A. R. Khokhlov, Macromol. Theory Simul. 11, 751 (2002).

    Article  Google Scholar 

  13. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon Press, Oxford, 1990).

    Google Scholar 

  14. K. V. Shaitan, N. K. Balabaev, A. S. Lemak, et al., Biofizika 42 (1), 47 (1997).

    Google Scholar 

  15. M. Levitt and R. Sharon, Proc. Natl. Acad. Sci. USA. 85, 7557 (1988).

    Article  ADS  Google Scholar 

  16. F. Parak, H. Hartmann, M. Schmidt, et al., Eur. Biophys. J. 21, 313 (1992).

    Google Scholar 

  17. P. J. Steinbach and B. R. Brooks, Proc. Natl. Acad. Sci. USA. 90, 9135 (1993).

    Article  ADS  Google Scholar 

  18. K. V. Shaitan, M. D. Ermolaeva, N. K. Balabaev, et al., Biofizika 42 (3), 558 (1997).L

    Google Scholar 

  19. A. S. Lemak and N. K. Balabaev, Mol. Simulation 13, 177 (1994).

    Article  Google Scholar 

  20. C. H. Andersen, Chem. Phys. J. 72, 2384 (1980).

    Article  ADS  Google Scholar 

  21. V. L. Golo and K. V. Shaitan, Biophysics (Moscow) 47 (4), 567 (2002).

    Google Scholar 

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Authors and Affiliations

  1. Department of Biology, Moscow State University, Moscow, 119991, Russia

    K. V. Shaitan & I. V. Fedik

Authors
  1. K. V. Shaitan
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  2. I. V. Fedik
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Correspondence to K. V. Shaitan.

Additional information

Original Russian Text © K.V. Shaitan, I.V. Fedik, 2015, published in Biofizika, 2015, Vol. 60, No. 3, pp. 421–427.

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Shaitan, K.V., Fedik, I.V. A molecular dynamics simulation of structure self-organization in model biomimetic polymers. BIOPHYSICS 60, 335–340 (2015). https://doi.org/10.1134/S0006350915030161

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  • DOI: https://doi.org/10.1134/S0006350915030161

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