Energetics of multi-ion conduction pathways in potassium ion channels

Philip W. Fowler, Enrique Abad, Oliver Beckstein, Mark S P Sansom

Research output: Contribution to journalArticle

24 Scopus citations

Abstract

Potassium ion channels form pores in cell membranes, allowing potassium ions through while preventing the passage of sodium ions. Despite numerous high-resolution structures, it is not yet possible to relate their structure to their single molecule function other than at a qualitative level. Over the past decade, there has been a concerted effort using molecular dynamics to capture the thermodynamics and kinetics of conduction by calculating potentials of mean force (PMF). These can be used, in conjunction with the electro-diffusion theory, to predict the conductance of a specific ion channel. Here, we calculate seven independent PMFs, thereby studying the differences between two potassium ion channels, the effect of the CHARMM CMAP forcefield correction, and the sensitivity and reproducibility of the method. Thermodynamically stable ion-water configurations of the selectivity filter can be identified from all the free energy landscapes, but the heights of the kinetic barriers for potassium ions to move through the selectivity filter are, in nearly all cases, too high to predict conductances in line with experiment. This implies it is not currently feasible to predict the conductance of potassium ion channels, but other simpler channels may be more tractable.

Original languageEnglish (US)
Pages (from-to)5176-5189
Number of pages14
JournalJournal of Chemical Theory and Computation
Volume9
Issue number11
DOIs
Publication statusPublished - Nov 12 2013

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ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications

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