Molecular docking of nanosized titanium dioxide material to the extracellular part of GABAB-receptor
2016
A. M. Naumenko | A. Yu. Nyporko | O. V. Tsymbalyuk | N. Ye. Nuryshchenko | I. S. Voiteshenko | T. L. Davidovska
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 GABAB1а 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 GABAB1а receptor subunit of GABAB 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 GABAB1а receptor subunit of GABAB with 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 GABAB1а receptor subunit of GABAB, was analyzed in accordance to their amino acid composition.
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