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

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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References

  1. 1.

    Zhou, Y., Morais-Cabral, J. H., Kaufman, A. & MacKinnon, R. Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 A resolution. Nature 414, 43–48 (2001).

  2. 2.

    MacKinnon, R. Potassium channels and the atomic basis of selective ion conduction (Nobel Lecture). Angew. Chem. Int. Ed. 43, 4265–4277 (2004).

  3. 3.

    Mullins, L. J. An analysis of conductance changes in squid axon. J. Gen. Physiol. 42, 1013–1035 (1959).

  4. 4.

    Bezanilla, F. & Armstrong, C. M. Negative conductance caused by entry of sodium and cesium ions into the potassium channels of squid axons. J. Gen. Physiol. 60, 588–608 (1972).

  5. 5.

    Hille, B. Potassium channels in myelinated nerve. Selective permeability to small cations. J. Gen. Physiol. 61, 669–686 (1973).

  6. 6.

    Neyton, J. & Miller, C. Discrete Ba2 + block as a probe of ion occupancy and pore structure in the high-conductance Ca2 +-activated K+ channel. J. Gen. Physiol. 92, 569–586 (1988).

  7. 7.

    Nimigean, C. M. & Allen, T. W. Origins of ion selectivity in potassium channels from the perspective of channel block. J. Gen. Physiol. 137, 405–413 (2011).

  8. 8.

    MacKinnon, R., Cohen, S. L., Kuo, A., Lee, A. & Chait, B. T. Structural conservation in prokaryotic and eukaryotic potassium channels. Science 280, 106–109 (1998).

  9. 9.

    Doyle, D. A. et al. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280, 69–77 (1998).

  10. 10.

    Alberts, B. et al. Molecular Biology of the Cell 4th edn (Garland Science, New York, 2002).

  11. 11.

    Steven, A., Baumeister, W., Johnson, L. N. & Perham, R. N. Molecular Biology of Assemblies and Machines (Garland Science, New York, 2016).

  12. 12.

    Zhou, Y. & MacKinnon, R. The occupancy of ions in the K+ selectivity filter: charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates. J. Mol. Biol. 333, 965–975 (2003).

  13. 13.

    Thompson, A. N. et al. Mechanism of potassium-channel selectivity revealed by Na+ and Li+ binding sites within the KcsA pore. Nat. Struct. Mol. Biol. 16, 1317–1324 (2009).

  14. 14.

    Noskov, S. Y., Berneche, S. & Roux, B. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431, 830–834 (2004).

  15. 15.

    Noskov, S. Y. & Roux, B. Ion selectivity in potassium channels. Biophys. Chem. 124, 279–291 (2006).

  16. 16.

    Aqvist, J. & Luzhkov, V. Ion permeation mechanism of the potassium channel. Nature 404, 881–884 (2000).

  17. 17.

    Medovoy, D., Perozo, E. & Roux, B. Multi-ion free energy landscapes underscore the microscopic mechanism of ion selectivity in the KcsA channel. Biochim. Biophys. Acta 1858, 1722–1732 (2016).

  18. 18.

    Bostick, D. L. & Brooks, C. L. 3rd Selectivity in K+ channels is due to topological control of the permeant ion’s coordinated state. Proc. Natl Acad. Sci. USA 104, 9260–9265 (2007).

  19. 19.

    Thomas, M., Jayatilaka, D. & Corry, B. The predominant role of coordination number in potassium channel selectivity. Biophys. J. 93, 2635–2643 (2007).

  20. 20.

    Varma, S. & Rempe, S. B. Tuning ion coordination architectures to enable selective partitioning. Biophys. J. 93, 1093–1099 (2007).

  21. 21.

    Shrivastava, I. H., Tieleman, D. P., Biggin, P. C. & Sansom, M. S. K+ versus Na+ ions in a K channel selectivity filter: a simulation study. Biophys. J. 83, 633–645 (2002).

  22. 22.

    Fowler, P. W., Tai, K. & Sansom, M. S. The selectivity of K+ ion channels: testing the hypotheses. Biophys. J. 95, 5062–5072 (2008).

  23. 23.

    Furini, S. & Domene, C. Selectivity and permeation of alkali metal ions in K+-channels. J. Mol. Biol. 409, 867–878 (2011).

  24. 24.

    Egwolf, B. & Roux, B. Ion selectivity of the KcsA channel: a perspective from multi-ion free energy landscapes. J. Mol. Biol. 401, 831–842 (2010).

  25. 25.

    Kim, I. & Allen, T. W. On the selective ion binding hypothesis for potassium channels. Proc. Natl Acad. Sci. USA 108, 17963–17968 (2011).

  26. 26.

    Jensen, M. O., Jogini, V., Eastwood, M. P. & Shaw, D. E. Atomic-level simulation of current–voltage relationships in single-file ion channels. J. Gen. Physiol. 141, 619–632 (2013).

  27. 27.

    Kopfer, D. A. et al. Ion permeation in K+ channels occurs by direct Coulomb knock-on. Science 346, 352–355 (2014).

  28. 28.

    Furini, S. & Domene, C. Atypical mechanism of conduction in potassium channels. Proc. Natl Acad. Sci. USA 106, 16074–16077 (2009).

  29. 29.

    Berneche, S. & Roux, B. Energetics of ion conduction through the K+ channel. Nature 414, 73–77 (2001).

  30. 30.

    Kratochvil, H. T. et al. Instantaneous ion configurations in the K+ ion channel selectivity filter revealed by 2D IR spectroscopy. Science 353, 1040–1044 (2016).

  31. 31.

    Heer, F. T., Posson, D. J., Wojtas-Niziurski, W., Nimigean, C. M. & Berneche, S. Mechanism of activation at the selectivity filter of the KcsA K+ channel. eLife 6, e25844 (2017).

  32. 32.

    LeMasurier, M., Heginbotham, L. & Miller, C. KcsA: it’s a potassium channel. J. Gen. Physiol. 118, 303–314 (2001).

  33. 33.

    Heginbotham, L., LeMasurier, M., Kolmakova-Partensky, L. & Miller, C. Single Streptomyces lividans K+ channels: functional asymmetries and sidedness of proton activation. J. Gen. Physiol. 114, 551–560 (1999).

  34. 34.

    Nimigean, C. M. & Miller, C. Na+ block and permeation in a K+ channel of known structure. J. Gen. Physiol. 120, 323–335 (2002).

  35. 35.

    Valiyaveetil, F. I., Leonetti, M., Muir, T. W. & Mackinnon, R. Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation. Science 314, 1004–1007 (2006).

  36. 36.

    Domene, C. & Furini, S. Dynamics, energetics, and selectivity of the low-K+ KcsA channel structure. J. Mol. Biol. 389, 637–645 (2009).

  37. 37.

    Shi, N., Ye, S., Alam, A., Chen, L. & Jiang, Y. Atomic structure of a Na+- and K+-conducting channel. Nature 440, 570–574 (2006).

  38. 38.

    Derebe, M. G. et al. Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites. Proc. Natl Acad. Sci. USA 108, 598–602 (2011).

  39. 39.

    Alam, A. & Jiang, Y. High-resolution structure of the open NaK channel. Nat. Struct. Mol. Biol. 16, 30–34 (2009).

  40. 40.

    Alam, A. & Jiang, Y. Structural analysis of ion selectivity in the NaK channel. Nat. Struct. Mol. Biol. 16, 35–41 (2009).

  41. 41.

    Derebe, M. G., Zeng, W., Li, Y., Alam, A. & Jiang, Y. Structural studies of ion permeation and Ca2 + blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore. Proc. Natl Acad. Sci. USA 108, 592–597 (2011).

  42. 42.

    Sauer, D. B., Zeng, W., Canty, J., Lam, Y. & Jiang, Y. Sodium and potassium competition in potassium-selective and non-selective channels. Nat. Commun. 4, 2721 (2013).

  43. 43.

    Thomas, M., Jayatilaka, D. & Corry, B. Mapping the importance of four factors in creating monovalent ion selectivity in biological molecules. Biophys. J. 100, 60–69 (2011).

  44. 44.

    Noskov, S. Y. & Roux, B. Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. J. Gen. Physiol. 129, 135–143 (2007).

  45. 45.

    Shi, C. et al. A single NaK channel conformation is not enough for non-selective ion conduction. Nat. Commun. 9, 717 (2018).

  46. 46.

    Furini, S. & Domene, C. Nonselective conduction in a mutated NaK channel with three cation-binding sites. Biophys. J. 103, 2106–2114 (2012).

  47. 47.

    Lodish, H. et al. Molecular Cell Biology 5th edn (W. H. Freeman, New York, 2003).

  48. 48.

    Zhekova, H. R., Ngo, V., da Silva, M. C., Salahub, D. & Noskov, S. Selective ion binding and transport by membrane proteins—a computational perspective. Coord. Chem. Rev. 345, 108–136 (2017).

  49. 49.

    Payandeh, J., Scheuer, T., Zheng, N. & Catterall, W. A. The crystal structure of a voltage-gated sodium channel. Nature 475, 353–358 (2011).

  50. 50.

    Roux, B. et al. Ion selectivity in channels and transporters. J. Gen. Physiol. 137, 415–426 (2011).

  51. 51.

    Lockless, S. W. Structural and thermodynamic properties of selective ion binding in a K+ channel. PLoS Biol. 5, e121 (2007).

  52. 52.

    Kutzner, C., Grubmuller, H., de Groot, B. L. & Zachariae, U. Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophys. J. 101, 809–817 (2011).

  53. 53.

    Kutzner, C. et al. Insights into the function of ion channels by computational electrophysiology simulations. Biochim. Biophys. Acta 1858, 1741–1752 (2016).

  54. 54.

    Roux, B. The membrane potential and its representation by a constant electric field in computer simulations. Biophys. J. 95, 4205–4216 (2008).

  55. 55.

    Cuello, L. G., Jogini, V., Cortes, D. M. & Perozo, E. Structural mechanism of C-type inactivation in K+ channels. Nature 466, 203–208 (2010).

  56. 56.

    Ye, S., Li, Y. & Jiang, Y. Novel insights into K+ selectivity from high-resolution structures of an open K+ channel pore. Nat. Struct. Mol. Biol. 17, 1019–1023 (2010).

  57. 57.

    Van Der Spoel, D. et al. GROMACS: fast, flexible, and free. J. Comput. Chem. 26, 1701–1718 (2005).

  58. 58.

    Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435–447 (2008).

  59. 59.

    Pronk, S. et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845–854 (2013).

  60. 60.

    Abraham, M. J. et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).

  61. 61.

    Sauer, D. B., Zeng, W., Raghunathan, S. & Jiang, Y. Protein interactions central to stabilizing the K+ channel selectivity filter in a four-sited configuration for selective K+ permeation. Proc. Natl Acad. Sci. USA 108, 16634–16639 (2011).

  62. 62.

    Jansen, T. & Knoester, J. Nonadiabatic effects in the two-dimensional infrared spectra of peptides: application to alanine dipeptide. J. Phys. Chem. B 110, 22910–22916 (2006).

  63. 63.

    Liang, C. & Jansen, T. L. An efficient N3-scaling propagation scheme for simulating two-dimensional infrared and visible spectra. J. Chem. Theory Comput. 8, 1706–1713 (2012).

  64. 64.

    Shirts, M. R. & Chodera, J. D. Statistically optimal analysis of samples from multiple equilibrium states. J. Chem. Phys. 129, 124105 (2008).

  65. 65.

    Klimovich, P. V., Shirts, M. R. & Mobley, D. L. Guidelines for the analysis of free energy calculations. J. Comput. Aided Mol. Des. 29, 397–411 (2015).

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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.

Author information

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.

Competing interests

The authors declare no competing interests.

Correspondence to Bert L. de Groot or Ulrich Zachariae.

Supplementary information

  1. Supplementary Information

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

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Further reading

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.