Molecular dynamics: Molecular docking simulation of substrates and inhibitors of beta-N-acetylhexosaminidase of Aspergillus Oryzae
Natallia Kulik1, Peter Palenčár1, Michal Kutý1, Vladimír Křen2, Karel Bezouška2,3 and Rüdiger Ettrich1
1Laboratory of High Performance Computing, Institute of Systems Biology and Ecology ASCR and Institute of Physical Biology USB, Zamek 136, 37333 Nové Hrady, Czech Republic.
2Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
3Department of Biochemistry, Faculty of Science, Charles University, Albertov 2030, CZ-12840 Prague 2, Czech Republic
Fungal beta-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into monosaccharides. It plays an important role in life cycle of the fungus for formation septa, germ tubes and fruit bodies. The interesting features of the enzyme from Aspergillus Orizae are its high catalytic activity and good relationship with a wide range of modified substrates . Recently was examined the tolerance of beta-N-acetylhexosaminidase to C4- and C6 -modified carbohydrates . Our main interest is to examine possible substrates and inhibitors of the mentioned enzyme.
Models of modified ligands were prepared in Yasara – p-nitrophenol-2-acetamino-2 deoxy-6-sulfo-beta-D-glucopyranoside (normal and reduced at sulfo-group) and p-nitrophenol-2-acetamino-2 deoxy-beta-D-glucopyranoside. Partial charges and force field parameters were calculated in Gaussian for the YAMBER2 force field. The substrates were docked into the active site of the enzyme and data were collected for 5 ns of molecular dynamics simulation. The temperature was adjusted to 298K. The experiment was carried out in TIP3 water, periodic boundary conditions were applied and pressure was kept constant to account for the changes of the structure in solution.
To predict the stability of the complex “substrate-enzyme” and to examine the possible inhibition ability of certain substrates we calculate internal and binding energies over time and analyze displacement of critical amino acids.
One of the predicted structures shows a similar binding energy as the natural substrate, with a similar small contribution of estimated solvation contribution to the binding energy. A structural analysis gives clear theoretical evidence that the substrate might work as a competitive inhibitor. These results will be used by organic chemists to synthesize this substrate and to verify our results.
The support by grants from the Ministry of Education of Czech Republic (MSM6007665808, MSM0021620835, LC06010), the Institutional Research Concept of the Academy of Science of the Czech Republic (No. AVOZ60870520) and the Grant Agency of Czech Republic (203/05/0172) is acknowledged.
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