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Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels

Nature Chemistry volume 10, pages 813–820 (2018)Cite this article

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Abstract

The seeming contradiction that K+ channels conduct K+ ions at maximal throughput rates while not permeating slightly smaller Na+ ions has perplexed scientists for decades. Although numerous models have addressed selective permeation in K+ channels, the combination of conduction efficiency and ion selectivity has not yet been linked through a unified functional model. Here, we investigate the mechanism of ion selectivity through atomistic simulations totalling more than 400 μs in length, which include over 7,000 permeation events. Together with free-energy calculations, our simulations show that both rapid permeation of K+ and ion selectivity are ultimately based on a single principle: the direct knock-on of completely desolvated ions in the channels’ selectivity filter. Herein, the strong interactions between multiple ‘naked’ ions in the four filter binding sites give rise to a natural exclusion of any competing ions. Our results are in excellent agreement with experimental selectivity data, measured ion interaction energies and recent two-dimensional infrared spectra of filter ion configurations.

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Fig. 1: Ion selectivity of KcsA.
Fig. 2: Relationship between conduction efficiency, ion selectivity and water co-permeation.
Fig. 3: Calculated 2D IR spectrum for occupancy states characteristic of the direct Coulomb knock-on conduction mechanism.
Fig. 4: Schematic of the mechanisms of K+ ion selective and non-selective channel permeation.

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Acknowledgements

We thank H. Grubmüller, S. Bernèche, F. Heer and S. Llabrés for helpful discussions. This work was supported by the German Research Foundation through FOR 2518 ‘DynIon’, Project P5 (to W.K. and B.L.d.G), the Scottish Universities’ Physics Alliance (to U.Z.) and BBSRC training grant BB/J013072/1 (to O.N.V. and U.Z.). All data and analysis scripts are archived at the Max Planck Institute for Biophysical Chemistry archives and are available upon request.

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Authors and Affiliations

  1. Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

    Wojciech Kopec, David A. Köpfer & Bert L. de Groot

  2. Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK

    Owen N. Vickery & Ulrich Zachariae

  3. Physics, School of Science and Engineering, University of Dundee, Dundee, UK

    Owen N. Vickery & Ulrich Zachariae

  4. University of Groningen, Zernike Institute for Advanced Materials, Groningen, The Netherlands

    Anna S. Bondarenko & Thomas L. C. Jansen

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  1. Wojciech Kopec
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Contributions

U.Z. and B.L.d.G. conceived and supervised the project. W.K. performed and analysed the ion channel simulations under ion gradients and voltage, free-energy simulations, and infrared spectral calculations. D.A.K performed and analysed the KcsA and initial MthK simulations. O.N.V. performed and analysed additional ion channel simulations under voltage. A.S.B. assisted with the infrared spectral calculations. T.L.C.J. designed and supervised the spectral infrared calculations. W.K., D.A.K., O.N.V. and U.Z. prepared the figures. U.Z., B.L.d.G. and W.K. wrote the manuscript with comments from all authors.

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Correspondence to Bert L. de Groot or Ulrich Zachariae.

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Supplementary Methods, Supplementary simulation data, Supplementary Figures 1–14 and Supplementary Tables 1–11

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Kopec, W., Köpfer, D.A., Vickery, O.N. et al. Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. Nature Chem 10, 813–820 (2018). https://doi.org/10.1038/s41557-018-0105-9

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