Three-Dimensional Continuum Simulations of Ion Transport Through Biological Ion Channels: Effect of Charge Distribution in the Constriction Region of Porin

Drift-diffusion models are useful for studying ion transport in open protein channel systems over time scales that cannot be resolved practically by detailed molecular dynamics or quantum approaches. Water is treated as a uniform background medium with a specific dielectric constant and macroscopic current flow is resolved by assigning an appropriate mobility and diffusivity to each ionic species. The solution of Poisson's equation over the entire domain provides a simple way to include external boundary conditions and image force effects at dielectric discontinuities. Here we present a 3-D drift-diffusion model of ion (K⁺ and Cl⁻) permeation through the porin channel ompF, and its mutant G119D, implemented using the computational platform PROPHET.