Molecular mechanics investigation of the transport mechanisms in the CIC-ec1 H+/CI⁻ exchanger and P-glycoprotein/Sav1866 ABC transporter

Although channels and transporters were thought to display completely different transport mechanisms, new findings have revealed that the boundaries between them might be more blurred. ABC family, which includes thousands of transporters, holds a channel member, CFTR (cystic fibrosis transmembrane conductance regulator). ClC-ec1, which was considered as a chloride ion channel as other members of the ClC family, was found to function as a Cl-/H+ exchanger. Since the proteins within the family have similar sequences and structures, it suggests that some small structural difference is enough to underlie the very different functions of channels and transporters. In order to identify this small but important difference and further understand mechanisms of channels and transporters, members from these two families were investigated by molecular dynamic simulations, P-glycoprotein/Sav1866 from ABC family and ClC-ec1 from ClC family.
In the investigation of P-glycoprotein/Sav1866 systems, unambiguous conformational changes in trans-membrane domains were demonstrated for the first time, which involve rotation of helices that potentially contributes to allocrites transport. Nucleotide-binding domains experience small changes in which the two domains never completely dissociate. Asymmetric nucleotide occupancy states were accompanied by an opening of the trans-membrane domain, while no cavity was seen in symmetric nucleotide occupancy states. Q-loop and X-loop were identified to be two essential motifs in the coupling between trans-membrane domains and nucleotide binding domains.
In ClC-ec1, an open intracellular gate was demonstrated for the first time and identified to be essential for ion permeation. It was further found that the interaction between Y445 and I402 at helix O, controlled by the conformation of helix O, is related to the opening of the intracellular gate. Furthermore, conformational changes of F357 were identified to be also essential for chloride ion permeation. Two conformations of F357 are correlated with inward facing and outward facing conformations of ClC-ec1, which constitute the alternating mechanism of chloride ion transport. The conformation of F357 is correlated to ion occupancy in the pore as well as the conformation of E148. The transport of ClC-ec1 was proposed to take a modified alternating mechanism, in which the protein transports chloride ions by alternating between the outward facing and inward facing conformations, while the binding of chloride ion in the pore triggers proton transport.