MOLECULAR DOCKING OF NANOSIZED TITANIUM DIOXIDE MATERIAL TO THE EXTRACELLULAR PART OF GABA B -RECEPTOR

A. M. Naumenko; A. Zu. Nyporko; O. V. Tsymbalyuk; N. Ye. Nuryshchenko; I. S. Voiteshenko; T. L. Davidovska

doi:10.30970/sbi.1003.506

MOLECULAR DOCKING OF NANOSIZED TITANIUM DIOXIDE MATERIAL TO THE EXTRACELLULAR PART OF GABA_B-RECEPTOR

A. M. Naumenko, A. Zu. Nyporko, O. V. Tsymbalyuk, N. Ye. Nuryshchenko, I. S. Voiteshenko, T. L. Davidovska

DOI: http://dx.doi.org/10.30970/sbi.1003.506

Abstract

A spatial model of nanosized titanium dioxide material was created using Discovery Studio Visualizer software, versions 2.0 and 2.5. A search for and analysis of possible sites of its docking to the extracellular part of GABA_B1а receptor subunit were performed using the algorythm for molecular docking PatchDock. The dimensions of the obtained ТіО₂ nanoparticle surface were (18.925 × 3.785 × 19.028) Å. Four potentially possible sites of ТіО₂ docking to the extracellular part of GABA_B1а receptor subunit of GABA_B were identified. The ТіО₂ nanoparticle demonstrated high affinity of docking to one of the receptor sites with the geometric shape complementarity score of 12562, taking the following values in other sites: 10746; 10370; 10204. The approximate interface area of complex of the extracellular part of GABA_B1а receptor subunit of GABA_Bwith ТіО₂ for the site with the highest geometric shape complementarity score was 1949.80 Å, and for others – 1273.20 Å, 1261.10 Å and 1170.30 Å, respectively. The evaluation of аtomic contact energy demonstrated the following values for the sites of ТіО₂ nanoparticle docking: 362.92; 173.93; 340.63 and 224.61. The nature of connections, stabilizing the sites of ТіО₂ docking to the extracellular part of GABA_B1а receptor subunit of GABA_B, was analyzed in accordance to their amino acid composition.

Keywords

ТіО2 nanoparticles, GABAB receptor, molecular docking, PatchDock

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References

1. Bettler B., Kaupmann K., Mosbacher J., Gassmann M. Molecular structure and physiological functions of GABA(B) receptors. Physiological Reviews, 2004; 84(3): 835-867. https://doi.org/10.1152/physrev.00036.2003 PMid:15269338

2. Bormann J. The "ABC" of GABA receptors. Trends in Pharmacological Sciences, 2000; 21(1): 16-19. https://doi.org/10.1016/S0165-6147(99)01413-3

3. Chukin G.D., Khrustalev S.V. Hydrate cover and the active centers of the titanium dioxide surface. Journal of Physical Chemistry, 1973; 40(8): 2055-2058. (In Russian)

4. Davydov A.A. The titanium dioxide surface condition according to IR spectroscopy. The Adsorption of Adsorbents, 1977; 5: 83-89. (In Russian)

5. Dolmatov Y.D., Rogachevskaya T.L. Determination of chemically bound OH-groups in the hydrated titanium dioxide. Journal of Applied Chemistry, 1973; 46(5): 964-967. (In Russian)

6. Duhovny D., Nussinov R., Wolfson H.J. Efficient unbound docking of rigid molecules. Proceedings of the Fourth International Workshop on Algorithms in Bioinformatics, 2002; 2452: 185-200. https://doi.org/10.1007/3-540-45784-4_14

7. Fahmi A., Minot C., Silvi B., Cause M. Theoretical analysis of the structure of titanium dioxide crystals. Physical Review B, 1993; 47(18): 11717-11724. https://doi.org/10.1103/PhysRevB.47.11717 PMid:10005339

8. Geng Y., Bush M., Mosyak L. et al. Structural mechanism of ligand activation in human GABAB receptor. Nature, 2013; 504(7479): 254-259. https://doi.org/10.1038/nature12725 PMid:24305054 PMCid:PMC3865065

9. Geng Y., Xiong D., Mosyak L. et al. Structure and functional interaction of the extracellular domain of human GABA(B) receptor GBR2. Nature Neuroscience, 2012; 15(7): 970-978. https://doi.org/10.1038/nn.3133 PMid:22660477 PMCid:PMC3374333

10. Goroshchenko Y.G. Chemistry of Titanium. Kyiv: Scientific Thought, 1970. 416 p. (In Russian)

11. Hill D.R., Dolphin A.C. Modulation of adenylate cyclase activity by GABAB receptors. Neuropharmacology, 1984; 23(7B): 829-830. https://doi.org/10.1016/0028-3908(84)90268-5

12. Jacimovic J., Vaju C., Gaal R. et al. High-pressure study of anatase TiO2. Materials, 2010; 3: 1509-1514. https://doi.org/10.3390/ma3031509 PMCid:PMC5445885

13. Jackson M. Molecular and cellular biophysics. Moscov: Binomial, 1990. 551 p. (In Russian)

14. Kostrikin A.V., Kuznetsova R.V., Kosenkova O.V.et al. IR spectrum of hydrated titanium dioxide. Questions of Modern Science and Practice, 2007; 8(2): 181-186. (In Russian)

15. Langel W., Menken L. Simulation of the interface between titanium oxide and amino acids in solution by first principles MD. Surface Science, 2003; 538(1-2): 1-9. https://doi.org/10.1016/S0039-6028(03)00723-4

16. Qazi Mohd S.J. Elucidation of Mechanism of Carcinogenesis by Environmental Carcinogens and their Prevention by Nanoparticles: an In Silico study. Lucknow, India: Integral University, 2014. 190 p.

17. Mezhevoy I.N., Badelin V.G. Dissolution and solvation enthalpies of L-serine in aqueous-alcoholic solutions at 298.15 K. Journal of Physical Chemistry, 2008; 82(4): 789-791. (In Russian)

18. Mudunkotuwa I.A., Grassian V.H. Histidine adsorption on TiO2 nanoparticles: an integrated spectroscopic, thermodynamic, and molecular-based approach toward understanding nano−bio interactions. Langmuir, 2014; 30(29): 8751-8760. https://doi.org/10.1021/la500722n PMid:24978817

19. Nyporko A.Yu., Naumenko A.M., Golius A. et al. 3D reconstruction of a full-size GABAB receptor. Neurophysiology, 2015; 47(5): 364-375. https://doi.org/10.1007/s11062-016-9544-3

20. O'Neil K.T., DeGrado W.F. A thermodynamic scale for the heliх - forming tendencies of the commonly occurring amino acids. Science,1990; 250: 646-651. https://doi.org/10.1126/science.2237415 PMid:2237415

21. Pele L.C., Thoree V., Bruggbaber S.F.A. et al. Pharmaceutical/food grade titanium dioxide particles are absorbed into the bloodstream of human volunteers. Part Fibre Toxicology, 2015; 12: 26-32. https://doi.org/10.1186/s12989-015-0101-9 PMid:26330118 PMCid:PMC4557898

22. Pin J.P., Kniazeff J., Binet V. et al. Activation mechanism of the heterodimeric GABA(B) receptor. Biochemical Pharmacology, 2004; 68(8): 1565-1572. https://doi.org/10.1016/j.bcp.2004.06.035 PMid:15451400

23. Radchenko N.V., Shapoval L.M., Davidovska T.L., Prilutsky Yu.I. Mathematical modeling of the effects of GABA injection into medullary NO-synthesizing rat cardiovascular neurons. Bulletin of V.N. Karazin Kharkiv National University, 2007; 18(1): 69-73. (In Ukrainian)

24. Radchenko N.V., Shapoval L.M., Davidovska T.L. et al. GABAergic control features of blood circulation function by rats medulla oblongata neurons. Neurophysiology, 2013; 45(5-6): 407-416. (In Ukrainian) https://doi.org/10.1007/s11062-013-9386-1

25. Schneidman-Duhovny D., Inbar Y., Nussinov R., Wolfson H.J. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Research, 2005; 33 (Web Server issue): W363-367. https://doi.org/10.1093/nar/gki481 PMid:15980490 PMCid:PMC1160241

26. Shapoval L.M., Sahach V.F., Pobihaylo L.S., Stepanenko L.G., Yermolinska N.V. The role of nitric oxide in the effects implementation of intrabulbar introduced γ-aminobutyric acid on the blood circulation system. Physiological Journal, 2005; 51(1): 43-50. (In Ukrainian)

27. Zakharova N.V., Sychev M.M., Korsakov V.G., Myakin S.V. Ferroelectric surface donor-acceptor centers evolution upon dispersing. Condensed Matter and Status, 2011; 13(1): 56-62. (In Russian)

28. Zhang C., Vasmatzis G., Cornette J.L., DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. Journal of Molecular Biology, 1997; 267: 707-726. https://doi.org/10.1006/jmbi.1996.0859 PMid:9126848

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Biologichni Studii / Studia Biologica

MOLECULAR DOCKING OF NANOSIZED TITANIUM DIOXIDE MATERIAL TO THE EXTRACELLULAR PART OF GABAB-RECEPTOR