Molecular Interactions Between Bacteriorhodopsin Protein Embedded Within Purple Membrane and the Surfaces of Polyvinyl Alcohol ( PVA ) and Graphene

Bacteriorhodopsin (bR), the light-driven proton pump of Halobacterium salinarum, is a promising candidate for bioelectronic and optoelectronic applications. Its utility in hybrid systems depends on how surrounding materials influence structural stability and photocycle dynamics. In this work, all-atom molecular dynamics simulations are conducted under isothermal-isobaric conditions to evaluate bR in three environments: its native purple membrane, adsorption onto graphene sheets, and incorporation within a polyvinyl alcohol (PVA) matrix. Across all systems, bR displayed preferential adsorption on the extracellular side of the membrane. Graphene promoted strong and stable interactions, preserving native electrostatic contacts, enhancing Van der Waals forces, and allowing conformational flexibility essential for photocycle transitions. In contrast, PVA generated weaker stabilization, a water-rich interface, and disruption of key electrostatic interactions, which constrained protein adaptability. These findings identify graphene as a favorable surface for maintaining both structural integrity and functional dynamics of bR, supporting its integration within PVA based scaffolds toward the development of bio-nano interfaces.