Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures

Abstract

Background: Bioremediation is a biotechnology field that uses living organisms to remove contaminants from soil and water; therefore, they could be used to treat oil spills from the environment.

Methods: Herein, we present a new mechanistic approach combining Molecular Docking Simulation and Density Functional Theory to modeling the bioremediation-based nanointeractions of a heterogeneous mixture of oil-derived hydrocarbons by using pristine and oxidized graphene nanostructures and the substrate-specific transport protein (TodX) from Pseudomonas putida.

Results: The theoretical evidences pointing that the binding interactions are mainly based on noncovalent bonds characteristic of physical adsorption mechanism mimicking the "Trojan-horse effect".

Conclusion: These results open new horizons to improve bioremediation strategies in over-saturation conditions against oil-spills and expanding the use of nanotechnologies in the context of environmental modeling health and safety.

Keywords: DFT-simulation; Graphene; Molecular docking; Nanostructures; Petroleum; TodX protein.