To explore the binding mechanism of CTPR8Y 16 -C 60 A in more detail, the distance between the centre of mass of CTPR8Y 16 and the centre of mass of each of the eight C 60 A molecules along the MD trajectory was monitored (Fig. ). As shown in Fig. and, all fullerenes are recognised by CTPR8Y 16 in less than 100 ns of MD simulation time, reaching the final binding site after 300 ns, where C 60 A remain for the rest of the simulation. Six out of the eight fullerene molecules bind hot spots located more than 25 Å far away from the CTPR8Y 16 centre of mass, indicating that C 60 A prefer to interact with the CTPR modules located at the N-and C-terminal domains of CTPR8Y 16 . Close examination of molecular interactions showed predominantly - interactions between C 60 A and some of the introduced tyrosine residues (Fig. ). Thus, the introduced tyrosine residues enhance supramolecular interactions with the aromatic surface of the fullerene, fixing the fullerene molecule in a particular binding site. In some hot spots, the fullerene is stabilised by -stacking interactions with a total of six tyrosine residues, i.e. Tyr209, Tyr213, Tyr216, Tyr240, Tyr243, and Tyr247 (A in Fig. ), located at the extreme of the CTPR8 unit. These interactions are able to retain the C 60 A molecule in the hot spot for the rest of the simulation time. Additional binding sites are located at the inner hydrophobic cavity and display a broader range of interactions (B in Fig. ). The simulations reveal that Arg203 establishes cation••• interactions with C 60 A, the introduced Tyr138 on helix A displays OH••• interactions with the fullerene, while Lys81 and Lys115 stabilise the carboxylate groups of C 60 A by salt bridge interactions. Such strong interactions are not observed in the simulations where pristine C 60 is used, with the fullerene more delocalised all over the protein surface. To gain a deeper insight into the recognition and binding processes, five replicas of 500 ns of MD simulations with 24 C 60 A molecules were performed for CTPR8Y . Increasing the number of fullerenes led to their aggregation in groups of 6-8 molecules mediated by sodium cations. Interestingly, fullerene aggregates accumulate at the same binding sites observed previously with a smaller number of C 60 A (Fig. ).