(515d) Thermodynamics of Type IVb Pili Proteins on Graphene-Cu(111) and Defective Graphene-Cu(111) Interfaces Via Molecular Simulation

Despite their prevalence in natural and engineered systems, the exact molecular mechanisms and forces controlling biofilm formation and adhesion are relatively unknown. Recent work has hypothesized that biofilm formation and adhesion may be related to the adsorption of key, early protein molecules (such as type IV (T4P) pilus 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.[1], [2]

Our previous study postulated that T4P was the culprit for adhesion to abiotic surfaces and, as such, their size necessitated coarse-grained (CG) modelling. But now, recent literature indicates that tight adherence (tad) flp/fap pilus component (pdb Dde_2357), a subunit of type IVb pilus (T4bP) has been identified to promote initial surface attachment and auto-aggregation of Oleidesulfovibrio alaskensis G20 biofilms on surfaces.[3]–[5] While T4b pilins are larger (an average of 180 to 200 residues), flp pilins are significantly smaller, containing only 50 to 80 residues. The smaller size of these proteins allows for more detailed all-atom molecular modeling studies.

Therefore, to obtain greater agreement with recent experimental efforts, in this study we perform all-atom molecular dynamics simulations to investigate the dynamic process of adsorption of the tad flp/fap pilin component of T4bP 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 explicit water as solvent to deduce the effect of solvation on the adsorption behavior. To highlight and explore the difference between CG and all-atom models, coarse-grained MD simulations have also been performed for our system.

Specifically, molecular dynamics simulations are conducted using the LAMMPS molecular dynamics simulation software package. 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. Assisted Model Building with Energy Refinement (AMBER) potential was used to model the tad flp/fap protein. For coarse-grained model, MARTINI3 force field was used to capture the structural and thermodynamic properties of the key early conditioning film biomolecules (peptides and proteins) including T4bP. 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.[6]–[10]

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.

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[3] M. Tomich, D. H. Fine, and D. H. Figurski, “The TadV Protein of Actinobacillus actinomycetemcomitans Is a Novel Aspartic Acid Prepilin Peptidase Required for Maturation of the Flp1 Pilin and TadE and TadF Pseudopilins,” J Bacteriol, vol. 188, no. 19, p. 6899, Oct. 2006, doi: 10.1128/JB.00690-06.

[4] M. Pu and D. A. Rowe-Magnus, “A Tad pilus promotes the establishment and resistance of Vibrio vulnificus biofilms to mechanical clearance,” npj Biofilms and Microbiomes 2018 4:1, vol. 4, no. 1, pp. 1–8, Apr. 2018, doi: 10.1038/s41522-018-0052-7.

[5] C. L. Giltner, Y. Nguyen, and L. L. Burrows, “Type IV pilin proteins: versatile molecular modules,” Microbiol Mol Biol Rev, vol. 76, no. 4, pp. 740–772, Dec. 2012, doi: 10.1128/MMBR.00035-12.

[6] S. Plimpton, “Short-Range Molecular Dynamics,” J Comput Phys, vol. 117, no. 6, pp. 1–42, 1997, [Online]. Available: http://www.cs.sandia.gov/∼sjplimp/main.html

[7] S. J. Stuart, A. B. Tutein, and J. A. Harrison, “A reactive potential for hydrocarbons with intermolecular interactions,” Journal of Chemical Physics, vol. 112, no. 14, pp. 6472–6486, 2000, doi: 10.1063/1.481208.

[8] C. Tian et al., “Ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution,” J Chem Theory Comput, vol. 16, no. 1, pp. 528–552, Jan. 2020, doi: 10.1021/ACS.JCTC.9B00591/SUPPL_FILE/CT9B00591_SI_002.ZIP.

[9] H. Grubmller, “Predicting slow structural transitions in macromolecular systems: Conformational flooding,” Phys Rev E, vol. 52, no. 3, p. 2893, Sep. 1995, doi: 10.1103/PhysRevE.52.2893.

[10] P. C. T. Souza et al., “Martini 3: a general purpose force field for coarse-grained molecular dynamics,” Nature Methods 2021 18:4, vol. 18, no. 4, pp. 382–388, Mar. 2021, doi: 10.1038/s41592-021-01098-3.