Molecular Mechanism of Proline-Mediated Regulation of Graphene–Bacterial Membrane Interactions: A Balance between Dispersion Stabilization and Membrane Disruption

Abstract Graphene nanosheets have attracted considerable attention as antibacterial nanomaterials due to their ability to directly damage bacterial membranes. However, the poor dispersion of graphene in aqueous environments limits its practical applications. Recently, natural amino acids [Mao, T.; et al.Nature2025, 645, 915–921].have been proposed as biocompatible stabilizers for nanomaterials. Nevertheless, how amino acid concentration affects graphene-membrane interactions remains unclear. Here, all-atom molecular dynamics simulations were performed to investigate the regulation of monomeric proline on graphene insertion into bacterial membranes. Three systems containing 0, 1, and 2 M proline were constructed to reveal the influence of proline on graphene transport behavior, membrane perturbation, and molecular interactions. The results show that graphene can spontaneously insert into bacterial membranes under all investigated conditions, indicating that proline cannot completely eliminate graphene-membrane interactions. However, introducing proline significantly delays graphene penetration by enhancing graphene stabilization in the aqueous environment. The average insertion time increases from 22.3 ± 6.8 ns without proline to 95.3 ± 22.4 ns and 102.7 ± 29.1 ns under 2 and 1 M proline conditions, respectively. After insertion, graphene still induces membrane deformation, alters lipid ordering, and changes lipid mobility, suggesting that its membrane-disruptive activity is maintained. Energetic analyses reveal that the regulation mechanism originates from the competition between graphene-proline stabilization and graphene-membrane attraction. Proline strengthens graphene interactions with surrounding solution molecules, while graphene-lipid interactions remain sufficiently strong to drive membrane insertion. These findings provide molecular insights into the balance between graphene stabilization and antibacterial activity and offer guidance for designing amino acid-assisted graphene-based antibacterial materials.