A First Passage Time Analysis of Atomic-Resolution Simulations of the Ionic Transport in a Bacterial Porin

TL;DR

This study uses molecular dynamics simulations to analyze ionic transport in a bacterial porin, revealing that ion dynamics vary across the channel and can be modeled with region-specific diffusion and force parameters, impacting simplified channel models.

Contribution

It introduces a region-specific first passage time analysis of ion transport in a bacterial porin, challenging the assumption of uniform diffusion in simplified models.

Findings

Ion dynamics vary significantly across different channel regions.

A constant diffusion coefficient is insufficient to describe ion movement throughout the entire channel.

Region-specific diffusion and force parameters improve the modeling accuracy.

Abstract

We have studied the dynamics of chloride and potassium ions in the interior of the OmpF porin under the influence of an external electric field. From the results of extensive all-atom molecular dynamics simulations of the system we computed several first passage time (FPT) quantities to characterize the dynamics of the ions in the interior of the channel. Such FPT quantities obtained from MD simulations demonstrate that it is not possible to describe the dynamics of chloride and potassium ions inside the whole channel with a single constant diffusion coefficient. However, we showed that a valid, statistically rigorous, description in terms of a constant diffusion coefficient D and an effective deterministic force Feff can be obtained after appropriate subdivison of the channel in different regions suggested by the X-ray structure. These results have important implications for popular simplified descriptions of channels based on the 1D Poisson-Nernst-Planck (PNP) equations. Also, the effect of entropic barriers on the diffusion of the ions is identified and briefly discussed.