New Proteins for New Sensing Methodologies: The Case of the Protein-Binding Family

The solute transport systems in prokaryotes are based on two types depending on the energetic requirement of the transport system: (i) the secondary transporters where proton or sodium motive force drives the transport and (ii) the ATP-binding cassette (ABC) primary transporters that use the hydrolysis of ATP as fuel. Highaffinity binding protein-dependent ABC transporters were originally discovered in Gram-negative bacteria. These transport proteins play an important physiological role in the transport of different molecules through biological membranes. Bacterial ABC transporters predominantly import essential nutrients that are delivered to them by specific binding proteins. A typical ABC is composed of five domains or subunits, two of which are hydrophobic and are predicted to span the membrane multiple times in an α-helical conformation, and two of which bind nucleotide and are exposed to the cytoplasm. The fifth component is the periplasmic soluble binding protein, a high-affinity receptor, that interacts with the substrate to be transported. The soluble ligand-bound binding protein interacts with the transporters proteins, stimulates the ATPase activity and initiates the transport process. These periplasmic binding proteins have two globular domains attached by a flexible hinge and in the ligand-bound structures the ligand is buried deep within the cleft between the two domains. Solute-binding proteins for a variety of ligands have been identified, including carbohydrates, amino acids, anions, metal ions, dipeptides and oligopeptides. Conformational changes involving the hinge are thought to be necessary for ligands to get in and out of the protein-binding site. Differences in the structures of the ligand-bound and ligand-free proteins are essential for their proper recognition by the membrane components