Secondary water pore formation for proton transport in a ClC exchanger revealed by an atomistic molecular dynamics simulation

Several prokaryotic ClC proteins have been demonstrated to function as exchangers that transport both chloride ions and protons simultaneously in opposite directions. However, the path of the proton through the ClC exchanger and how the protein brings about the coupled movement of both ions are still unknown. In the present work, we demonstrate that a previously unknown secondary water pore is formed inside a ClC exchanger by using an atomistic molecular dynamics (MD) simulation. From the systematic simulations, it was determined that the glutamate residue exposed to the intracellular solution, E203, plays an important role as a trigger for the formation of the secondary water pore. Based on our simulation results, we conclude that protons in the ClC exchanger are conducted via a water network through the secondary water pore and we propose a new mechanism for the coupled transport of chloride ions and protons.