(515d) Thermodynamics of Type IVb Pili Proteins on Graphene-Cu(111) and Defective Graphene-Cu(111) Interfaces Via Molecular Simulation
AIChE Annual Meeting
2023
2023 AIChE Annual Meeting
Engineering Sciences and Fundamentals
Thermodynamics of Biomolecular Folding and Assembly
Tuesday, November 7, 2023 - 4:18pm to 4:34pm
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]â[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 (moireâ 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, itâs 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 6â12 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]â[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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