A fast in silico simulation of ion flux through the large-pore channel proteins.

The PSST program (see accompanying article) utilizes the detailed structure of a large-pore channel protein as the sole input for selection of trajectories along which negative and positive ions propagate. In the present study we applied this program to reconstruct the ion flux through five large-pore channel proteins (PhoE, OmpF, the WT R. blastica general diffusion porin and two of its mutants). The conducting trajectories, one for positive and one for negative particles, are contorted pathways that run close to arrays of charged residues on the inner surface of the channel. In silico propagation of the charged particles yielded passage time values that are compatible with the measured average passage time of ions. The calculated ionic mobilities are close to those of the electrolyte solution of comparable concentrations. Inspection of the transition probabilities along the channel revealed no region that could impose a rate-limiting step. It is concluded that the ion flux is a function of the whole array of local barriers. Thus, the conductance of the large-pore channel protein is determined by the channel's shape and charge distribution, while the selectivity also reflects the features of the channel's vestibule.