Thermodynamics of type IVb Pili protein adsorption and aggregation on graphene interface via molecular dynamics...

Biocorrosion, driven by microbial activity such as that of sulfate-reducing bacteria (SRB), poses a significant challenge in various industries. Yet, the molecular mechanisms driving early-stage biofilm adhesion on advanced materials remain insufficiently understood. Pilin systems, particularly Type IV pili, are crucial in biofilm formation, a process central to microbial corrosion, with the flp component being the initial attachment protein. A critical knowledge gap exists in understanding how Type IVb pilin proteins, the initial adhesion factors in SRB biofilms, interact with two-dimensional surfaces like graphene. Using Oleidesulfovibrio alaskensis G20 as the model organism, this study investigates the interaction between the tad flp pilus component and pristine graphene (PG) surfaces via molecular dynamics simulations. Our findings reveal the molecular origins of pilin component adsorption onto graphene and its conformational changes, shedding light on molecular-level interactions at the biofilm-surface interface. By employing enhanced free energy sampling methods, we have predicted protein adsorption and assembly affinities on 2D surfaces. The adsorption process was driven by physisorption, characterized by multiple van der Waals interactions, resulting in a binding free energy of -34.68 kcal/mol at a center-of-mass distance of 8.5 Å from the graphene surface. The initial RMSD of the pilin protein was 1.378 Å, which increased to 3.5 Å as the α2 helix bent towards the PG surface and the α1 helix bent away. This resulted in partial unfolding of the protein upon adsorption. The average RMSD stabilized at 2.61 Å, with the secondary structure largely intact. Additionally, the study explores the aggregation behavior of pilin proteins. In bulk water, the dimerization of pilin proteins exhibited RMSDs of 4 Å and 3.5 Å for the two proteins over 180 ns. On the PG surface, protein aggregation was slightly reduced, with the RMSDs stabilizing around 4.6 Å and 3.8 Å, respectively. The contact surface area (CSA) of protein aggregation was approximately 500 Ų on graphene, compared to 350 Ų in bulk water, indicating that the presence of graphene enhances protein aggregation due to its large van der Waals surface area. Further thermodynamic analysis revealed that the binding internal energy for protein adsorption was -40.372 kcal/mol, with a binding entropy contribution (TΔS) of -5.700 kcal/mol, while protein-protein aggregation in bulk water showed an internal energy change of -27.764 kcal/mol and an aggregation entropy contribution of -2.458 kcal/mol. While the graphene surface structure minimally impacts adsorption properties, it significantly influences protein aggregation patterns. This work addresses the gap in molecular-level insights into protein-graphene interactions, elucidating how pilin protein adsorption and aggregation contribute to biofilm adhesion on two-dimensional materials. These findings provide a mechanistic foundation for developing graphene-based coatings to mitigate microbial colonization and biocorrosion.