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

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Abstract

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.

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Acknowledgments

We thank Dr. Saree Phongphanphanee (Department of Materials Science, Faculty of Science, Kasetsart University) for helpful discussions. Financial support was provided by the Kasetsart University Research and Development Institute (KURDI) [JW], the Faculty of Science at Kasetsart University [JW], the Graduate School at Kasetsart University [JW] and the Asia Research Center (ARC) at Chulalongkorn University [JW]. Computational resources were provided by SHARCNET (www.sharcnet.ca), Compute Canada and the Department of Physics, Faculty of Science, Kasetsart University.

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  1. Department of Physics, Faculty of Science, Kasetsart University, 50 Phahon Yothin Rd, Chatuchak, Bangkok, Thailand, 10900

    Jirasak Wong-ekkabut

  2. Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1

    Mikko Karttunen

  3. Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, MetaForum, 5600 MB, Eindhoven, The Netherlands

    Mikko Karttunen

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  1. Jirasak Wong-ekkabut
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Wong-ekkabut, J., Karttunen, M. Molecular dynamics simulation of water permeation through the alpha-hemolysin channel. J Biol Phys 42, 133–146 (2016). https://doi.org/10.1007/s10867-015-9396-x

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