(181j) Coarse-Grained Molecular Dynamics Investigation of Adsorption of Type IV Pili Proteins Onto Graphene-Cu(111) and Defective Graphene-Cu(111) Interfaces | AIChE

(181j) Coarse-Grained Molecular Dynamics Investigation of Adsorption of Type IV Pili Proteins Onto Graphene-Cu(111) and Defective Graphene-Cu(111) Interfaces


Davidson, M., South Dakota School of Mines & Technology
Benjamin, K., South Dakota School of Mines & Technology
Despite their prevalence in natural and engineered systems, the exact molecular mechanisms and forces controlling biofilm formation and adhesion are relatively unknown. While most modeling studies to date have focused more on continuum or macroscopic film behavior, investigations at the molecular level are needed, too. Moreover, surface engineering of systems to prevent microbial adhesion and biofilm formation has become a key challenge for both biomedical and materials/corrosion communities.

Recent work has hypothesized that biofilm formation and adhesion may be related to the adsorption of key, early protein molecules (such as type IV pili proteins) and exopolysaccharides (EPS) included in conditioning films (CFs) to metal surfaces preceding the attachment of microbes. Reducing this early biofilm layer attachment to abiotic surfaces has shown great promise in mitigating biofilm formation, and in turn reducing microbial induced corrosion of metal surfaces. Graphene and graphene derivatives are potential candidates to be used as biofilm inhibiting coatings for metal surfaces due to their potential antibacterial properties.

In this study, we use coarse-grained molecular dynamics simulation to investigate the dynamic process of adsorption of Type IV pili (T4P) onto graphene and graphene-modified Copper slab (moire’ superlattice Gr-Cu{111}) and its conformation change after adsorption on the surface(s), as a key step towards understanding the fundamental molecular level interactions that occur at the biofilm-surface interface. All the simulations were conducted in vacuum and in the presence of coarse-grained water as solvent to deduce the effect of solvation on the adsorption behavior.

Specifically, the molecular dynamics simulations are conducted using the LAMMPS molecular dynamics simulation software package. The coarse-grained MARTINI force field was used to capture the structural and thermodynamic properties of the key early conditioning film biomolecules (peptides and proteins) including Type IV pili. Graphene, it’s derivatives (defective/pristine/multi-layer graphene) and Gr-Cu{111} substrate were modelled using a combination of the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential to describe the C-C interactions, Embedded Atom Method (EAM) potential to describe Cu-Cu atoms interactions, and Lennard-Jones 6–12 potential to describe only nonbonded Cu-C interactions. The adsorption energies and the binding free energies of proteins on graphene-coated-Cu{111} and pristine/multi-layer/defective graphene modified surfaces are evaluated to study the adsorption phenomena. The binding free energies are computed using the metadynamics technique.

The results of this molecular-level study should aid in developing a larger, fundamental understanding of the interaction, adsorption, and adhesion of proteins and microbes to two-dimensional surfaces (with and without defects) and metal substrates, such as found in industrial and biomedical applications.