Elucidating hydrogenase surfaces and tracing the intramolecular tunnels for hydrogenase inhibition in microalgal species

Intramolecular tunnels are majorly attracting attention as possible pathways for entry of inhibitors like oxygen and carbon monoxide to the active sites of the enzymes, hydrogenases. The results of homology modeling of the HydSL protein, a NiFe-hydrogenase from Chlamydomonas reinhardtii and Chlorella vulgaris are presented in this work. Here we identify and describe molecular tunnels observed in HydSL hydrogenase enzyme systems. The possible determinant of the oxygen stability of already studied hydrogenases could be the lack of several intramolecular tunnels. The possible tunnels were traced out using MOLE 2 software, which showed several intramolecular pathways that may be connecting the active sites of the enzyme. The RMSD value showed a great deal of significance in the enzyme homology. This is the first report of its kind in which mapping of the intramolecular tunnels in the four-hydrogenase enzymes disclosed potential variations between designed models and acknowledged structures. We are seeking out the explanations for oxygen sensitivity of studied hydrogenases within the structure of intramolecular tunnels. Local and Global RMSD (Root mean square deviation) was calculated for models and templates, which showed value of 1.284 indicating a successful homology model. The tunnel tracing study by Mole 2 indicated two tunnels joined into one in C. reinhardtii model whereas C. vulgaris model showed one tunnel almost like two tunnels. Templates of both the A. vinosum and D. vulgaris hydrogenase consisted of six tunnels. For HydSL from Chlamydomonas and Chlorella Species the maximal potential was set to 250 kcal/mol (1,046 kJ/mol) and the positive potential areas were marked. Electrostatic studies define electrostatic potential (ESP) that help shuttle protons to the active site.