Hydrophobicity-driven unfolding of Trp-cage encapsulated between graphene sheets

Understanding the interaction between proteins and graphene not only helps elucidate the behaviors of proteins in confined geometries, but is also imperative to the development of a plethora of graphene-based biotechnologies, such as the graphene liquid cell transmission electron microscopy. To discuss the overall geometrical-thermal effects on proteins, we performed molecular dynamics simulations of hydrated Trp-cage miniprotein sandwiched between two graphene sheets and in the bulk environment at the temperatures below and above its unfolding temperature. The structural fluctuations of Trp-cage were characterized using the backbone root mean square displacement and the radius of gyration, from which the free energy landscape of Trp-cage was further constructed. We observed that at both temperatures the confined protein became adsorbed to the graphene surfaces and exhibited unfolded structures. Residue-specific analyses clearly showed the preference for the graphene to interact with the hydrophobic regions of Trp-cage. These results suggested that the conformation space accessible to the protein results from the competition between the thermodynamic driving forces and the geometrical restraints. While confinement usually tends to restrict the conformation of proteins by volume exclusion, it may also induce the unfolding of proteins by hydrophobic interactions.