Calculation of configurational entropy change on ligand binding with DNA minor groove

Authors

  • V. V. Kostjukov Sevastopol National Technical University image/svg+xml Author
  • M. P. Evstigneev Sevastopol National Technical University image/svg+xml Author

Keywords:

minor groove, degrees of freedom, internal rotation, configurational entropy

Abstract

Calculation of change of energetic equivalents of translational, rotational, vibrational degrees of freedom
and internal rotation (rotamery) for 10 ligands on their complexation with minor groove of doublestranded DNA was performed by molecular modeling methods. It is shown that the loss of translational,
rotational and high-frequency vibrational (vibrations of chemical bonds) degrees of freedom is
considerably energetically unfavorable. At the same time, the residual low-frequency vibrations in the
complex considerably stabilize it. The contribution of conformational entropy due to rotamery is
insignificant and does not exceed 2 kcal/mol.

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Author Biographies

  • V. V. Kostjukov, Sevastopol National Technical University

    Universitetskaya str., 33, Sevastopol, 99053, Ukraine

  • M. P. Evstigneev, Sevastopol National Technical University

    Universitetskaya str., 33, Sevastopol, 99053, Ukraine

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Issue

Vol. 2 No. 25 (2010): Біофізичний вісник

Section

Molecular biophysics

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How to Cite

Calculation of configurational entropy change on ligand binding with DNA minor groove. (2015). Biophysical Bulletin, 2(25). https://periodicals.karazin.ua/biophysvisnyk/article/view/2719

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