Bead-like passage of chloride ions through ClC chloride channels

Influences of mutations on the electrostatic binding free energies of chloride ions in Escherichia coli ClC

Mutations in ClC channel proteins may cause serious functional changes and even diseases. The function of ClC proteins mainly manifests as Cl(-) transport, which is related to the binding free energies of chloride ions. Therefore, the influence of a mutation on ClC function can be studied by investigating the mutational effect on the binding free energies of chloride ions. The present study provides quantitative and systematic investigations on the influences of residue mutations on the electrostatic binding free energies in Escherichia coli ClC (EcClC) proteins, using all-atom molecular dynamics simulations. It was found that the change of the electrostatic binding free energy decreases linearly with the increase of the residue-chloride ion distance for a mutation. This work reveals how changes in the charge of a mutated residue and in the distance between the mutated residue and the binding site govern the variations in the electrostatic binding free energies and therefore influence the transport of chloride ions and conduction in EcClC. This work would facilitate our understanding of the mutational effects on transport of chloride ions and functions of ClC proteins and provide a guideline to estimate which residue mutations will have great influences on ClC functions.

A three-state multi-ion kinetic model for conduction properties of ClC-0 chloride channel

A three-state, multiion kinetic model was proposed to enable the conduction properties of the mammalian channel ClC-0 to be well characterized. Using this rate-theory based model, the current-voltage and conductance-concentration relations were obtained. The five parameters needed were determined by fitting the data of conduction experiments of the wild-type ClC-0 and its K519C mutant. The model was then tested against available calculation and simulation data, and the energy differences between distinct chloride-occupancy states computed agreed with an independent calculation on the binding free energies solved by using the Poisson-Boltzmann equation. The average ion number of conduction and the ion passing duration calculated closely resembled the values obtained from Brownian dynamics simulations. According to the model, the decrease of conductance caused by mutating residue K519 to C519 can be attributed to the effect of K519C mutation on translocation rate constants. Our study sets up a theoretical model for ion permeation and conductance in ClC-0. It provides a starting point for experimentalists to test the three-state model, and would help in understanding the conduction mechanism of ClC-0.

Proton pathways and H+/Cl- stoichiometry in bacterial chloride transporters

H+/Cl- antiport behavior has recently been observed in bacterial chloride channel homologs and eukaryotic CLC-family proteins. The detailed molecular-level mechanism driving the stoichiometric exchange is unknown. In the bacterial structure, experiments and modeling studies have identified two acidic residues, E148 and E203, as key sites along the proton pathway. The E148 residue is a major component of the fast gate, and it occupies a site crucial for both H+ and Cl- transport. E203 is located on the intracellular side of the protein; it is vital for H+, but not Cl-, transport. This suggests two independent ion transit pathways for H+ and Cl- on the intracellular side of the transporter. Previously, we utilized a new pore-searching algorithm, TransPath, to predict Cl- and H+ ion pathways in the bacterial ClC channel homolog, focusing on proton access from the extracellular solution. Here we employ the TransPath method and molecular dynamics simulations to explore H+ pathways linking E148 and E203 in the presence of Cl- ions located at the experimentally observed binding sites in the pore. A conclusion is that Cl- ions are required at both the intracellular (S(int)) and central (S(cen)) binding sites in order to create an electrostatically favorable H+ pathway linking E148 and E203; this electrostatic coupling is likely related to the observed 1H+/2Cl- stoichiometry of the antiporter. In addition, we suggest that a tyrosine residue side chain (Y445), located near the Cl- ion binding site at S(cen), is involved in proton transport between E148 and E203.

Ion permeation dynamics in carbon nanotubes

Molecular dynamics simulations are carried out to investigate the permeation of ions and water in a membrane consisting of single wall carbon nanotubes possessing no surface charges connecting two reservoirs. Our simulations reveal that there are changes in the first hydration shell of the ions upon confinement in tubes of 0.82 or 0.90 nm effective internal diameter. Although the first minimum in the g(r) is barely changed in the nanotube compared to in the bulk solution, the hydration number of Na(+) ion is reduced by 1.0 (from 4.5 in bulk to 3.5 in the 0.90 nm tube) and the hydration number is reduced further in the 0.82 nm tube. The changes in the hydration shell of Cl(-) ion are negligible, within statistical errors. The water molecules of the first hydration shell of both ions exchange less frequently inside the tube than in the bulk solution. We compare ion trajectories for ions in the same tube under identical reservoir conditions but with different numbers of ions in the tubes. This permits investigation of changes in structure and dynamics which arise from multiple ion occupancy in a carbon nanotube possessing no surface charges. We also investigated the effects of tube flexibility. Ions enter the tubes so as to form a train of ion pairs. We find that the radial distribution profiles of Na(+) ions broaden significantly systematically with increasing number of ion pairs in the tube. The radial distribution profiles of Cl(-) ions change only slightly with increasing number of ions in the tube. Trajectories reveal that Na(+) ions do not pass each other in 0.90 nm tubes, while Cl(-) ions pass each other, as do ions of opposite charge. An ion entering the tube causes the like-charged ions preceding it in the tube to be displaced along the tube axis and positive or negative ions will exit the tube only when one or two other ions of the same charge are present in the tube. Thus, the permeation mechanism involves multiple ions and Coulomb repulsion among the ions plays an essential role.