Protein nanopores are present in cell membranes and act as biological gateways. This means that they can also be used for the detection of specific bioactive molecular chains, like sugar chains, such as molecules from the glycosaminoglycan family. The latter are responsible for key interactions at the cellular level. They typically mediate interactions with cell surfaces or with proteins, resulting in the activiation of physiological and pathological effects in embryonic development, cell growth and differentiation, inflammatory response, tumour growth and microbial infection. The use of such nanopores as biosensors requires to fully understand the intricate mechanisms occurring as sugar chains pass through them.