MODELING 3D-STRUCTURE OF HOX-HYDROGENASES FROM PURPLE SULFUR BACTERIUM THIOCAPSA ROSEOPERSICINA BBS
Atomic structure of hydrogenase fragments of two cytoplasmic Hox-complexes (subunits Hox1H, Hox1Y, Hox2H, Hox2Y) from purple sulfur bacterium Thiocapsa roseopersicina was modeled in the work. Two cytoplasmic hydrogenase structures determined earlier by other researchers (hydrogenases from Methanothermococcus thermolithotrophicus and from Hydrogenophilus thermoluteolus) were chosen as templates for homology modeling. Confidence level of the obtained models was calculated on base of discrete optimized protein energy (DOPE) and its z-score. The chosen optimization protocol was shown to provide improved quality of model building (normalized DOPE z-score values below -1 were achieved). The obtained models of large subunits contain nickel atom, iron atom with one CO- and two CN-ligands, and magnesium atom; small subunits contain electron-transferring iron-sulfur cluster. The analysis of intrasubunit and intersubunit interactions (hydrogen bonds, ionic pairs, hydrophobic contacts) was carried out. The preliminary data do not allow making any confident suggestions on types of interactions stabilizing Hox-type hydrogenases and on temperature-related properties of these hydrogenases. Molecular docking analysis showed that cytoplasmic hydrogenases could interact with hydrogenase electrode components used in laboratory practice, such as neutral red oligomers and coronene (the latter was chosen as a model compound simulating graphite surface). Stable tendency of binding Gibbs energy decrease (i.e. affinity enhancement) from monomer to trimer of neutral red was observed. Meanwhile, both hydrogenases bound neutral red trimer stronger than coronene. This allows to suggest that poly-(neutral red) would be an optimal electrode material for experimental examination of enzymatic hydrogen electrodes fabricated on base of the studied hydrogenases. It was supposed that presence of only one iron-sulfur cluster would provide the shortest path from active site to the electrode, which could be the advantage of Hox-hydrogenases over other hydrogenases of this bacterium.