M. Fedai, A.Y. Pandya, A.L. Kwansa, Y.G. Yingling
North Carolina State University,
United States
Keywords: biomolecule adsorption, molecular dynamics, carbonic anhydrase, immobilization, graphene, graphene oxide, surface interaction descriptors
Summary:
Designing biomolecule and surface agnostic interaction descriptors using molecular dynamics simulations requires benchmark systems that are both chemically tunable and mechanistically well characterized. We selected graphene-based materials as surface and carbonic anhydrase enzyme as biomolecule models. Graphene (GRA) based materials are attractive controllable platforms where oxidation systematically tunes surface chemistry and properties, while carbonic anhydrase (CA) is a widely studied enzyme with central roles in physiology and strong relevance to immobilized biocatalysis for carbon capture efforts. Yet predicting adsorption is difficult because oxidation produces chemically heterogeneous interfaces while the enzyme presents distinct patches whose engagement depends strongly on orientation and functional relevance. Here, we present a simulation data-driven framework that integrates three coordinated MD efforts to explain CA immobilization and extract transferable descriptors for a surface- and biomolecule-agnostic interaction predictor. First, we simulated CA across varying pH conditions to quantify pH-dependent structure, dynamics, and intrinsic stability, establishing a baseline set of CA-specific stability metrics that can be separated from surface effects. Second, we generated GRA and graphene oxide (GO) sheets (20 × 20 nm²) spanning 0–68% oxidation using a reproducible GO construction workflow and performed fully solvated and water-droplet simulations to map oxidation-dependent wettability and interfacial transport descriptors. Finally, we simulated CA adsorption on GRA/GO across four distinct initial orientations and multiple oxidation levels to identify which surface chemistries and interfacial properties drive adsorption modes and protein perturbations, enabling links between adsorption outcomes and transferable surface descriptors. By unifying pH-dependent CA stability fingerprints with oxidation-dependent surface and interfacial-water descriptors and linking both to adsorption outcomes across orientations and oxidation levels, we define set of descriptors designed to generalize beyond CA to other biomolecules and beyond GRA and GO to broader material classes. This work establishes oxidation as a quantitative design variable and advances a principled route toward predictive, biomolecule- and surface-agnostic models for interfacial binding and stability in catalysis and carbon-capture applications.