Molecular Dynamics Study of Candida rugosa Lipase in Water, Methanol, and Pyridinium Based Ionic Liquids

The structure of Candida rugosa lipase can be affected by solvents used in the enzymatic reactions. Using molecular dynamics simulation as a tool to study the Candida rugosa lipase structure, we studied the effect of various solvent systems, such as water, water-methanol, and water-methanol-ionic liquid. These solvent systems have been chosen because lipase is able to function in both aqueous and non-aqueous medium. In this study, pyridinium (Py)-based ionic liquids were selected as co-solvent. The MD simulation was run for 50 nanoseconds for each solvent system at 328 K. In the case of water-methanol-ionic liquids solvent systems, the total number of the ionic liquids added were varied: 222, 444, and 888 molecules. Water was used as the reference solvent system. The structure of Candida rugosa lipase in water-methanol system significantly changed from the initial structure as indicated by the RMSD value, which was about 6.4 Å after 50 ns simulation. This value was relatively higher compared to the other water-methanol solvent system containing ionic liquid as co-solvent, which were 2.43 Å for 4Py-Br, 2.1 Å for 8Py-Br, 3.37 Å for 4Py-BF4 and 3.49 Å for 8Py-BF4 respectively. Further analysis by calculating the root mean square fluctuation (RMSF) of each lipase residue found that the presence of ionic liquids could reduce changes in the enzyme structure. This happened because the anion component of the ionic liquid interacts relatively more strongly with residues on the surface of the protein as compared to methanol, thereby lowering the possibility of methanol to come into contact with the protein.