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

Z. Ható, D. Boda, D. Gillespie, J. Vrabec, G. Rutkai, T. Kristóf

Research output: Contribution to journalArticle

8 Citations (Scopus)

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, inwhichanN-Pjunctionisformed.Themutantcontainsaporeregionwithpositiveaminoacidsontheleft-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.

Original languageEnglish
Article number13802
JournalCondensed Matter Physics
Volume19
Issue number1
DOIs
Publication statusPublished - 2016

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rectification
semiconductor diodes
simulation
atoms
amino acids
ions
degrees of freedom
molecular dynamics
electrons

Keywords

  • Ion channel
  • Monte carlo
  • Primitive model electrolytes
  • Selectivity

ASJC Scopus subject areas

  • Physics and Astronomy (miscellaneous)
  • Condensed Matter Physics

Cite this

Simulation study of a rectifying bipolar ion channel : Detailed model versus reduced model. / Ható, Z.; Boda, D.; Gillespie, D.; Vrabec, J.; Rutkai, G.; Kristóf, T.

In: Condensed Matter Physics, Vol. 19, No. 1, 13802, 2016.

Research output: Contribution to journalArticle

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