Ionic partition and transport in multi-ionic channels: A Molecular Dynamics Simulation study of the OmpF bacterial porin

TL;DR

This study uses molecular dynamics simulations to analyze how mutations in bacterial OmpF channels affect ion partitioning and conductance, revealing charge-based exclusion effects and inhomogeneous ion distributions.

Contribution

It provides new insights into how specific mutations alter ionic selectivity and flow in bacterial porins through detailed atomistic simulations.

Findings

Mutations reduce cation flow by excluding them from the constriction zone.

Ion distribution inside mutants is highly inhomogeneous, with regions of excess cations or anions.

Overall, mutants maintain a higher number of cations than anions, similar to wild type, due to charge balance.

Abstract

We performed all-atom molecular dynamics simulations studying the partition of ions and the ionic current through the bacterial porin OmpF and two selected mutants. The study is motivated by new interesting experimental findings concerning their selectivity and conductance behaviour at neutral pH. The mutations considered here are designed to study the effect of removal of negative charges present in the constriction zone of the wild type OmpF channel (which contains on one side a cluster with three positive residues and on the other side two negatively charged residues). Our results show that these mutations induce an exclusion of cations from the constriction zone of the channel, substantially reducing the flow of cations. In fact, the partition of ions inside the mutant channels is strongly inhomogeneous, with regions containing excess of cations and regions containing excess of anions. Interestingly, the overall number of cations inside the channel is larger than the number of anions in the two mutants, as in the OmpF wild type channel. We found that the differences in ionic charge inside these channels are justified by the differences in electric charge between the wild type OmpF and the mutants, following an electroneutral balance.