Molecular dynamics simulation of water permeation through the alpha-hemolysin channel

Jirasak Wong-ekkabut, M.E.J. Karttunen

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The alpha-hemolysin (AHL) nanochannel is a non-selective channel that allows for uncontrolled transport of small molecules across membranes leading to cell death. Although it is a bacterial toxin, it has promising applications, ranging from drug delivery systems to nano-sensing devices. This study focuses on the transport of water molecules through an AHL nanochannel using molecular dynamics (MD) simulations. Our results show that AHL can quickly transport water across membranes. The first-passage time approach was used to estimate the diffusion coefficient and the mean exit time. To study the energetics of transport, the potential of mean force (PMF) of a water molecule along the AHL nanochannel was calculated. The results show that the energy barriers of water permeation across a nanopore are always positive along the channel and the values are close to thermal energy (kBT). These findings suggest that the observed quick permeation of water is due to small energy barriers and a hydrophobic inner channel surface resulting in smaller friction. We speculate that these physical mechanisms are important in how AHL causes cell death. Keywords: Alpha hemolysin Molecular dynamics simulations Water permeation Biological membrane Lipid bilayer
Original languageEnglish
Pages (from-to)133-146
Number of pages14
JournalJournal of Biological Physics
Issue number1
Publication statusPublished - 1 Jan 2016


  • Alpha hemolysin
  • Biological membrane
  • Lipid bilayer
  • Molecular dynamics simulations
  • Water permeation


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