A transport equation for confined structures applied to the OprP, Gramicidin A, and KcsA channels

Amirreza Khodadadian, Clemens Heitzinger

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

A transport equation for confined structures is used to calculate the ionic currents through various transmembrane proteins. The transport equation is a diffusion-type equation where the concentration of the particles depends on the one-dimensional position in the confined structure and on the local energy. The computational significance of this continuum model is that the (6 + 1)-dimensional Boltzmann equation is reduced to a (2 + 1)-dimensional diffusion-type equation that can be solved with small computational effort so that ionic currents through confined structures can be calculated quickly. The applications here are three channels, namely OprP, Gramicidin A, and KcsA. In each case, the confinement potential is estimated from the known molecular structure of the channel. Then the confinement potentials are used to calculate ionic currents and to study the effect of parameters such as the potential of mean force, the ionic bath concentration, and the applied voltage. The simulated currents are compared with measurements, and very good agreement is found in each case. Finally, virtual potassium channels with selectivity filters of varying length are simulated in order to discuss the optimality of the filter.

Original languageEnglish (US)
Article number680
Pages (from-to)524-532
Number of pages9
JournalJournal of Computational Electronics
Volume14
Issue number2
DOIs
StatePublished - Mar 7 2015

Fingerprint

Gramicidin
Transport Equation
Boltzmann equation
Potassium Channels
Molecular structure
Potassium
Filter
Proteins
Calculate
Continuum Model
Electric potential
filters
Selectivity
Boltzmann Equation
Optimality
Voltage
baths
Protein
molecular structure
selectivity

Keywords

  • Boltzmann equation
  • Confined structures
  • Ionic transport

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Atomic and Molecular Physics, and Optics
  • Electronic, Optical and Magnetic Materials
  • Modeling and Simulation

Cite this

A transport equation for confined structures applied to the OprP, Gramicidin A, and KcsA channels. / Khodadadian, Amirreza; Heitzinger, Clemens.

In: Journal of Computational Electronics, Vol. 14, No. 2, 680, 07.03.2015, p. 524-532.

Research output: Contribution to journalArticle

Khodadadian, Amirreza ; Heitzinger, Clemens. / A transport equation for confined structures applied to the OprP, Gramicidin A, and KcsA channels. In: Journal of Computational Electronics. 2015 ; Vol. 14, No. 2. pp. 524-532.
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