Calculation of configurational entropy change on ligand binding with DNA minor groove
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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References
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2. Suckling C.J. Molecular recognition and physico–chemical properties in the discovery of selective antibac-terial minor groove binders // J. Phys. Org. Chem. – 2008. – V.21. – P. 575–583.
3. Wang L., Bailly C., Kumar A., Ding D., Bajic M., Boykin D.W., Wilson W.D. Specific molecular recognition of mixed nucleic acid sequences: an aromatic dication that binds in the DNA minor groove as a dimer // Proc. Natl. Acad. Sci. USA – 2000. – V.97. – P. 12–16.
4. Anthony N.G., Fox K.R., Johnston B.F., Khalaf A.I., Mackay S.P., McGroarty I.S., Parkinson J.A., Skellern G.G., Suckling C.J., Waigh R.D. DNA binding of short lexitropsins // Bioorg. Med. Chem. Lett. – 2004. – V.14. – P. 1353–1356.
5. Tanious F.A., Hamelberg D., Baily C., Czarny A., Boykin D.W., Wilson W.D. DNA sequence dependent monomer–dimer binding modulation of asymmetric benzimidazole derivatives // J. Am. Chem. Soc. – 2004. – V.126. – P. 143–153.
6. Haq I. Thermodynamics of drug–DNA interactions // Arch. Biochem. Biophys. – 2002. – V.403. – P.1–15.
7. Shaikh S.A., Ahmed S.R., Jayaram B. A molecular thermodynamic view of DNA–drug interactions: a case study of 25 minor–groove binders // Arch. Biochem. Biophys. – 2004. – V.429. – P. 81–99.
8. Treesuwan W., Wittayanarakul K., Anthony N.G., Huchet G., Alniss H., Hannongbua S., Khalaf A.I., Suck-ling C.J., Parkinson J.A., Mackay S.P. A detailed binding free energy study of 2:1 ligand–DNA complex forma-tion by experiment and simulation // Phys. Chem. Chem. Phys. – 2009. – V.11. – P. 10682–10693.
9. Zhou H.–X., Gilson M.K. Theory of free energy and entropy in noncovalent binding // Chem. Rev. – 2009. – V.109. – P. 4092–4107.
10. Harris S.A., Gavathiotis E., Searle M.S., Orozco M., Laughton C.A. Cooperativity in Drug–DNA recognition: a molecular dynamics study // J. Am. Chem. Soc. – 2001. – V.123. – P. 12658–12663.
11. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I. N., Bourne P.E. The protein data bank // Nucleic Acids Res. – 2000. – V. 28. – P. 235–242.
12. Brunger A.T. X–PLOR. A system for X–ray crystallography and NMR. – Yale: Univ. Press, 1992. – 382 p.
13. Cornell W.D., Cieplak P.,. Bayly C.I, Gould I.R., Merz K.M.J., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules // J. Am. Chem. Soc. – 1995. – Vol. 117. – P. 5179–5197.
14. Gaussian, Inc., 2004. Gaussian 03. Gaussian, Wallingford, CT.
15. Костюков В.В., Хомутова Н.М., Евстигнеев М.П. Вклад изменения трансляционных, ротационных и вибрационных степеней свободы в энергию комплексообразования ароматических лигандов с ДНК // Биофизика. - 2009. – Т. 54. - С. 606–615.
16. Carlsson J., Aquist J. Calculations of solute and solvent entropies from molecular dynamics simulations // Phys. Chem. Chem. Phys. – 2006. – V.8. – P. 5385–5395.
17. DuBay K.H., Geissler P. Calculation of proteins’ total side–chain torsional entropy and its influence on pro-tein–ligand interactions // J. Mol. Biol. – 2009. – V.391. – P. 484–497.
18. Dolenc J., Baron R., Oostenbrink C., Koller J., van Gunsteren W.F. Configurational entropy change of ne-tropsin and distamycin upon DNA minor–groove binding // Biophys. J. – 2006. – V.91. – P. 1460–1470.
19. Wang H., Laughton C.A. Molecular modelling methods for prediction of sequence–selectivity in DNA rec-ognition // Methods. – 2007. – V.42. – P.196–203.
20. Spackova N., Cheatham III T.E., Ryjacek F., Lankas F., van Meervelt L., Hobza P., Sponer J. Molecular dynamics simulations and thermodynamics analysis of DNA–drug complexes. Minor groove binding between 4’,6–diamidino–2–phenylindole and DNA duplexes in solution // J. Am. Chem. Soc. – 2003. – V.125. – P. 1759–1769.
21. Tidor B., Karplus M. The contribution of vibrational entropy to molecular association // J. Mol. Biol. – 1994. – V.238. – P. 405–414.
22. Chang C.A., Chen W., Gilson M.K. Ligand configurational entropy and protein binding // Proc. Natl. Acad. Sci. USA. – 2007. – V.104. – P.1534–1539.
23. Yu Y.B., Privalov P.L., Hodges R.S. Contribution of translational and rotational motions to molecular asso-ciations in aqueous solution // Biophys. J. – 2001. – V.81. – P. 1632–1642.
24. Gilson M.K., Given J.A., Bush B.L., McCammon J.A. The statistical–thermodynamic basis for computation of binding affinities: a critical review // Biophys. J. – 1997. – V.72. – P.1047–1069.
25. Baginski M., Fogolari F., Briggs J.M. Electrostatic and non–electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA // J. Mol. Biol. – 1997. – V.274. – 253–267.
26. Finkelstein A.V., Janin J. The price of lost freedom: entropy of bimolecular complex formation // Protein Eng. – 1989. – V.3. – P. 1–3.
27. Searle M.S., Williams D.H., Gerhard U. Partitioning of free energy contributions in the estimation of binding constants: residual motions and consequences for amide–amide hydrogen bond strengths // J. Am. Chem. Soc. – 1992. – V.114. – P. 10697–10704.
28. Kostjukov V.V., Khomytova N.M., Evstigneev M.P. Partition of thermodynamic energies of drug–DNA complexation // Biopolymers. – 2009. – V.91. – P. 773–790.
29. Костюков В.В., Твердохліб Н.М., Євстигнєєв М.П. Енергетичний аналіз комплексоутворення арома-тичних молекул у водному розчині // Укр. фізичн. журн. – 2011. – Т.56. – С.38-49.
30. Gilson M.K., Zhou H.–X. Calculation of protein–ligand binding affinities // Annu. Rev. Biophys. Biomol. Struct. – 2007. – V.36. – P. 21–42.
31. Noskov S.Yu., Lim C. Free energy decomposition of protein–protein interactions // Biophys. J. – 2001. – V.81. – P. 737–750.
32. Ayala P.Y., Schlegel H.B. Identification and treatment of internal rotation in normal mode vibrational anal-ysis // J. Chem. Phys. – 1998. – V.108. – P. 2314–2325.
Cited
How to Cite
Kostjukov, V. V., & Evstigneev, M. P. (1). Calculation of configurational entropy change on ligand binding with DNA minor groove. Biophysical Bulletin, 2(25). Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/2719
Section
Molecular biophysics
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