Molecular Dynamics Simulation of Protein-Polyphenol Interactions in Nigerian Legume-Based Fermented Foods

Protein-polyphenol interactions in fermented legume foods such as iru, dawadawa, and ogiri profoundly influence bioavailability of both nutrients, as polyphenol-protein complexes can reduce protein digestibility and polyphenol bioaccessibility simultaneously. Understanding these interactions at the molecular level is fundamental to designing processing interventions that optimise nutritional quality. This study applies molecular dynamics simulation to characterise the interactions between the major storage proteins of African locust bean, Parkia biglobosa legumin and vicilin, and the dominant polyphenols of the fermented product including gallic acid, chlorogenic acid, and epicatechin. The theoretical contribution is a multiscale molecular simulation framework that bridges quantum chemical energy calculations, all-atom molecular dynamics simulation, and coarse-grained models of protein aggregate formation in the presence of polyphenols. Ab initio density functional theory calculations first characterise the binding energies of each polyphenol with protein binding site models. All-atom GROMACS molecular dynamics simulations are run for 500 nanoseconds for each protein-polyphenol pair, calculating binding free energies by the molecular mechanics-generalised Born surface area method. Coarse-grained simulations extend the system size to include multiple protein molecules to model aggregate formation kinetics. Simulation predictions of binding constants and aggregate stoichiometry are validated by isothermal titration calorimetry and dynamic light scattering measurements on iru extracted from Oyo State. Simulations identify that epicatechin has the highest binding affinity for vicilin and that intermolecular hydrogen bonding and hydrophobic interactions are the dominant binding mechanisms. The study contributes original computational and experimental insights into protein-polyphenol interactions in fermented African legume foods. Keywords: molecular dynamics, protein-polyphenol, fermented legumes, iru, bioavailability