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European Biophysics Journal

, Volume 31, Issue 3, pp 198–206 | Cite as

Free energy of a potassium ion in a model of the channel formed by an amphipathic leucine-serine peptide

  • Graham R. Smith
  • Mark S. Sansom
Article

Abstract.

We use molecular dynamics simulations to investigate the position-dependent free energy of a potassium ion in a model of an ion channel formed by the synthetic amphipathic leucine-serine peptide, LS3. The channel model is a parallel bundle of six LS3 helices around which are packed 146 methane-like spheres in order to mimic a membrane. At either end of and within the channel are 1051 water molecules, plus four ions (two potassium and two chloride). The free energy of a potassium ion in the channel was estimated using the weighted histogram analysis (WHAM) method. This is the first time to our knowledge that such a calculation has been carried out as a function of the position of an ion in three dimensions within a channel. The results indicate that for this channel, which is lined by hydrophilic serine sidechains, there is a relatively weak dependence of the free energy on the axial/off-axial position of the ion. There are some off-axis local minima, especially in the C-terminal half of the channel. Using the free energy results, a single channel current-voltage curve was estimated using a one-dimensional Nernst-Planck equation. Although reasonable agreement with experiment is achieved for K+ ions flowing from the N-terminal to the C-terminal mouth, in the opposite direction the current is underestimated. This underestimation may be a consequence of under-sampling of the conformational dynamics of the channel. We suggest that our simulations may have captured, for example, a sub-conductance level (i.e. an incompletely open state) of the LS3 channel.

Leucine-serine peptide Ion channels Potassium ion Molecular dynamics Simulations 

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Copyright information

© EBSA 2002

Authors and Affiliations

  • Graham R. Smith
    • 1
  • Mark S. Sansom
    • 1
  1. 1.Laboratory of Molecular Biophysics, Department of Biochemistry, Rex Richards Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK

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