Molecular Dynamics Simulation of Graphene and Graphene Oxide Clusters in Solution and at the Surface of Bacterial Intracellular Polymers

   Aim is to identify the features of the dynamic behavior of hexagonal graphene and graphene oxide nanoparticles in solution and at the surface of deoxyribonucleic acid (DNA) complexes with the DNA-binding protein Dps.

   Methodology. Based on quantum chemical calculations, the structures, partial charges, and other parameters of molecular dynamics force fields for hexagonal graphene nanoparticles with varying numbers of oxygen-containing groups were determined. Using the all-atom approximation, molecular dynamics simulations were performed to obtain the dynamics of graphene nanoparticles in solution and at the surface of bacterial biopolymers.

   Results. Graphene and graphene oxide nanoparticles have been shown to form clusters in solution and at the surface of proteins and DNA. Graphene nanoparticles can influence the dynamics of DNA and the DNA-binding protein Dps, leading to changes in the structure of DNA-protein complexes.

   Research implications. The obtained data are of practical interest to researchers studying the structure of biological molecules and their complexes exposed to graphene nanoparticles (graphene, graphene oxide, and reduced graphene oxide). These data can also be used to create nanomaterials with tailored properties that combine nano-biointerfaces.

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