Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model

TL;DR

This study compares detailed all-atom and simplified reduced models of a rectifying mutant ion channel, revealing that the reduced model captures rectification behavior while the all-atom model does not, due to noise effects.

Contribution

The paper demonstrates that a simplified reduced model can reproduce rectification in a mutant ion channel, unlike the all-atom model, highlighting the importance of key degrees of freedom.

Findings

Reduced model exhibits rectification consistent with experiments.

All-atom model fails to produce rectification due to noise.

Rectification mechanism differs from semiconductor diodes.

Abstract

We study a rectifying mutant of the OmpF porin ion channel using both all-atom and reduced models. The mutant was created by Miedema et al. [Nano Lett., 2007, 7, 2886] on the basis of the N-P semiconductor diode, in which an N-P junction is formed. The mutant contains a pore region with positive amino acids on the left-hand side and negative amino acids on the right-hand side. Experiments show that this mutant rectifies. Although we do not know the structure of this mutant, we can build an all-atom model for it on the basis of the structure of the wild type channel. Interestingly, molecular dynamics simulations for this all-atom model do not produce rectification. A reduced model that contains only the important degrees of freedom (the positive and negative amino acids and free ions in an implicit solvent), on the other hand, exhibits rectification. Our calculations for the reduced model (using the Nernst-Planck equation coupled to Local Equilibrium Monte Carlo simulations) reveal a rectification mechanism that is different from that seen for semiconductor diodes. The basic reason is that the ions are different in nature from electrons and holes (they do not recombine). We provide explanations for the failure of the all-atom model including the effect of all the other atoms in the system as a noise that inhibits the response of ions (that would be necessary for rectification) to the polarizing external field.