Analysis of Stability of Transcription System in Octane Media by Molecular Dynamics Simulation

Enzymatic catalysis in nonaqueous environments has many advantages over that in aqueous solution. However, structural stability and flexibility of enzymes restrict their applications in nonaqueous environments. It was proposed that nonaqueous media decrease the flexibility of enzymes, resulting in their reduced activity. There is little detailed information to clarify the impact of nonaqueous solvents on the structure and flexibility of enzymes at molecular level. In this work, by using the molecular dynamics simulation technology, we placed an entire transcription system in organic solvent to investigate the effects of nonpolar solvent on an enzyme. A small transcription machine, T7 RNA polymerase (T7 RNAP), was used as model enzyme to conduct this study. We constructed two models with the T7 RNAP complex solvated in organic solvent. The first one is to solvate the T7 RNAP complex in pure octane directly. Our observation shows that T7 RNAP suffers serious structural deterioration in octane, especially in the active site, that the original correct binding of the substrate was completely destroyed. The structural deterioration may seriously affect the activity of T7 RNAP. Another model was built by pulling the transcription system from water into octane. It was observed that a small portion of water with some ions was carried into the organic media and coated on the surface of the complex. The water layer forms a microaqueous solution environment that plays an important role in protecting the internal structure of the transcription system. However, the flexibility of some key residues was reduced in the simulation time. It is deduced that a higher temperature is necessary to improve its activity in nonaqueous solvents. Our results are in good agreement with those reported in the literature. It is expected that our research could provide valuable information for the application of enzymes in nonaqueous environments.