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An aqueous H+ permeation pathway in the voltage-gated proton channel Hv1

Abstract

Hv1 voltage-gated proton channels mediate rapid and selective transmembrane H+ flux and are gated by both voltage and pH gradients. Selective H+ transfer in membrane proteins is commonly achieved by Grotthuss proton 'hopping' in chains of ionizable amino acid side chains and intraprotein water molecules. To identify whether ionizable residues are required for proton permeation in Hv1, we neutralized candidate residues and measured expressed voltage-gated H+ currents. Unexpectedly, charge neutralization was insufficient to abrogate either the Hv1 conductance or coupling of pH gradient and voltage-dependent activation. Molecular dynamics simulations revealed water molecules in the central crevice of Hv1 model structures but not in homologous voltage-sensor domain (VSD) structures. Our results indicate that Hv1 most likely forms an internal water wire for selective proton transfer and that interactions between water molecules and S4 arginines may underlie coupling between voltage- and pH-gradient sensing.

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Figure 1: Charge-neutralizing mutations in Hv1 conduct H+ current.
Figure 2: Voltage- and pH-gradient sensitivity of Hv1 mutations.
Figure 3: An aqueous crevice in the molecular dynamics–equilibrated Hv1 open-state homology model.
Figure 4: Water density in molecular dynamics simulations of Hv1 and other VS domains.
Figure 5: H+ permeation in Hv1 channels.

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References

  1. Bezanilla, F. How membrane proteins sense voltage. Nat. Rev. Mol. Cell Biol. 9, 323–332 (2008).

    Article  CAS  Google Scholar 

  2. Long, S.B., Campbell, E.B. & Mackinnon, R. Voltage sensor of Kv1.2: structural basis of electromechanical coupling. Science 309, 903–908 (2005).

    Article  CAS  Google Scholar 

  3. Swartz, K.J. Sensing voltage across lipid membranes. Nature 456, 891 (2008).

    Article  CAS  Google Scholar 

  4. Ramsey, I.S., Moran, M.M., Chong, J.H.A. & Clapham, D.E. A voltage-gated proton-selective channel lacking the pore domain. Nature 440, 1213–1216 (2006).

    Article  CAS  Google Scholar 

  5. Sasaki, M., Takagi, M. & Okamura, Y. A voltage sensor-domain protein is a voltage-gated proton channel. Science 312, 589–592 (2006).

    Article  CAS  Google Scholar 

  6. DeCoursey, T.E. Voltage-gated proton channels. Cell. Mol. Life Sci. 65, 2554–2573 (2008).

    Article  CAS  Google Scholar 

  7. Musset, B. et al. Detailed comparison of expressed and native voltage-gated proton channel currents. J. Physiol. (Lond.) 586, 2477 (2008).

    Article  CAS  Google Scholar 

  8. Tombola, F., Ulbrich, M.H. & Isacoff, E.Y. The voltage-gated proton channel Hv1 has two pores, each controlled by one voltage sensor. Neuron 58, 546–556 (2008).

    Article  CAS  Google Scholar 

  9. Koch, H.P. et al. Multimeric nature of voltage-gated proton channels. Proc. Natl. Acad. Sci. USA 105, 9111–9116 (2008).

    Article  CAS  Google Scholar 

  10. Swanson, J.M. et al. Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. J. Phys. Chem. B 111, 4300–4314 (2007).

    Article  CAS  Google Scholar 

  11. Buch-Pedersen, M.J., Pedersen, B.P., Veierskov, B., Nissen, P. & Palmgren, M.G. Protons and how they are transported by proton pumps. Pflugers Arch. 457, 573 (2009).

    Article  CAS  Google Scholar 

  12. Cukierman, S. The transfer of protons in water wires inside proteins. Front. Biosci. 8, s1118–s1139 (2003).

    Article  CAS  Google Scholar 

  13. Cherny, V.V., Markin, V.S. & DeCoursey, T.E. The voltage-activated hydrogen ion conductance in rat alveolar epithelial cells is determined by the pH gradient. J. Gen. Physiol. 105, 861–896 (1995).

    Article  CAS  Google Scholar 

  14. Starace, D.M. & Bezanilla, F. A proton pore in a potassium channel voltage sensor reveals a focused electric field. Nature 427, 548 (2004).

    Article  CAS  Google Scholar 

  15. Tombola, F., Ulbrich, M., Kohout, S. & Isacoff, E. The opening of the two pores of the Hv1 voltage-gated proton channel is tuned by cooperativity. Nat. Struct. Mol. Biol. 17, 44–50 (2010).

    Article  CAS  Google Scholar 

  16. Sakata, S. et al. Functionality of the voltage-gated proton channel truncated in S4. Proc. Natl. Acad. Sci. USA 107, 2313–2318 (2010).

    Article  CAS  Google Scholar 

  17. Jiang, Y. et al. X-ray structure of a voltage-dependent K+ channel. Nature 423, 33–41 (2003).

    Article  CAS  Google Scholar 

  18. Long, S.B., Tao, X., Campbell, E.B. & MacKinnon, R. Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature 450, 376–382 (2007).

    Article  CAS  Google Scholar 

  19. Scott, K.A. et al. Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure 16, 621–630 (2008).

    Article  CAS  Google Scholar 

  20. Wolf, S., Bockmann, M., Howeler, U., Schlitter, J. & Gerwert, K. Simulations of a G protein-coupled receptor homology model predict dynamic features and a ligand binding site. FEBS Lett. 582, 3335–3342 (2008).

    Article  CAS  Google Scholar 

  21. Musset, B. et al. Zinc inhibition of monomeric and dimeric proton channels suggests cooperative gating. J. Physiol. 588, 1435–1449 (2010).

    Article  CAS  Google Scholar 

  22. Gonzalez, C., Koch, H., Drum, B. & Larsson, H.P. Strong cooperativity between subunits in voltage-gated proton channels. Nat. Struct. Mol. Biol. 17, 51–56 (2010).

    Article  CAS  Google Scholar 

  23. Freites, J.A., Tobias, D.J. & White, S.H. A voltage-sensor water pore. Biophys. J. 91, L90–L92 (2006).

    Article  CAS  Google Scholar 

  24. Wang, D. & Voth, G.A. Proton transport pathway in the ClC Cl/H+ antiporter. Biophys. J. 97, 121–131 (2009).

    Article  CAS  Google Scholar 

  25. Chen, H., Wu, Y. & Voth, G. Origins of proton transport behavior from selectivity domain mutations of the aquaporin-1 channel. Biophys. J. 90, L73 (2006).

    Article  CAS  Google Scholar 

  26. Garczarek, F. & Gerwert, K. Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 439, 109–112 (2006).

    Article  CAS  Google Scholar 

  27. Tiwari-Woodruff, S.K., Lin, M.A., Schulteis, C.T. & Papazian, D.M. Voltage-dependent structural interactions in the Shaker K+ channel. J. Gen. Physiol. 115, 123–138 (2000).

    Article  CAS  Google Scholar 

  28. Decoursey, T.E. Voltage-gated proton channels and other proton transfer pathways. Physiol. Rev. 83, 475–579 (2003).

    Article  CAS  Google Scholar 

  29. Alabi, A.A., Bahamonde, M.I., Jung, H.J., Kim, J.I. & Swartz, K.J. Portability of paddle motif function and pharmacology in voltage sensors. Nature 450, 370–375 (2007).

    Article  CAS  Google Scholar 

  30. Blanchet, J., Pilote, S. & Chahine, M. Acidic residues on the voltage-sensor domain determine the activation of the NaChBac sodium channel. Biophys. J. 92, 3513–3523 (2007).

    Article  CAS  Google Scholar 

  31. Tao, X. et al. A gating charge transfer center in voltage sensors. Science 328, 67–73 (2010).

    Article  CAS  Google Scholar 

  32. Markovitch, O. et al. Special pair dance and partner selection: elementary steps in proton transport in liquid water. J. Phys. Chem. B 112, 9456–9466 (2008).

    Article  CAS  Google Scholar 

  33. DeCoursey, T.E. & Cherny, V.V. Deuterium isotope effects on permeation and gating of proton channels in rat alveolar epithelium. J. Gen. Physiol. 109, 415–434 (1997).

    Article  CAS  Google Scholar 

  34. Kuno, M. et al. Temperature dependence of proton permeation through a voltage-gated proton channel. J. Gen. Physiol. 134, 191–205 (2009).

    Article  CAS  Google Scholar 

  35. Chen, H. et al. Charge delocalization in proton channels, I: the aquaporin channels and proton blockage. Biophys. J. 92, 46–60 (2007).

    Article  CAS  Google Scholar 

  36. DeCoursey, T.E. & Cherny, V.V. Voltage-activated proton currents in membrane patches of rat alveolar epithelial cells. J. Physiol. (Lond.) 489, 299–307 (1995).

    Article  CAS  Google Scholar 

  37. Sansom, M.S., Kerr, I.D., Smith, G.R. & Son, H.S. The influenza A virus M2 channel: a molecular modeling and simulation study. Virology 233, 163–173 (1997).

    Article  CAS  Google Scholar 

  38. Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

    Article  CAS  Google Scholar 

  39. Henikoff, S. & Henikoff, J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915–10919 (1992).

    Article  CAS  Google Scholar 

  40. Shi, J., Blundell, T.L. & Mizuguchi, K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310, 243–257 (2001).

    Article  CAS  Google Scholar 

  41. Bond, P.J., Holyoake, J., Ivetac, A., Khalid, S. & Sansom, M.S.P. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J. Struct. Biol. 157, 593–605 (2007).

    Article  CAS  Google Scholar 

  42. Marrink, S.J., de Vries, A.H. & Mark, A.E. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B 108, 750–760 (2004).

    Article  CAS  Google Scholar 

  43. Shelley, J.C., Shelley, M.Y., Reeder, R.C., Bandyopadhyay, S. & Klein, M.L. A coarse grain model for phospholipid simulations. J. Phys. Chem. B 105, 4464–4470 (2001).

    Article  CAS  Google Scholar 

  44. Bond, P.J. & Sansom, M.S.P. Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 128, 2697–2704 (2006).

    Article  CAS  Google Scholar 

  45. Bond, P.J., Wee, C.L. & Sansom, M.S. Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. Biochemistry 47, 11321–11331 (2008).

    Article  CAS  Google Scholar 

  46. Berendsen, H.J.C., van der Spoel, D. & van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 91, 43–56 (1995).

    Article  CAS  Google Scholar 

  47. Clayton, G.M. et al. Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel. Proc. Natl. Acad. Sci. USA 105, 1511–1515 (2008).

    Article  CAS  Google Scholar 

  48. Atilgan, A.R. et al. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80, 505–515 (2001).

    Article  CAS  Google Scholar 

  49. Keskin, O., Jernigan, R.L. & Bahar, I. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys. J. 78, 2093–2106 (2000).

    Article  CAS  Google Scholar 

  50. Sands, Z.A. & Sansom, M.S. How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain. Structure 15, 235–244 (2007).

    Article  CAS  Google Scholar 

  51. Berger, O., Edholm, O. & Jahnig, F. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidycholine at full hydration, constant pressure and constant temperature. Biophys. J. 72, 2002–2013 (1997).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  53. van Gunsteren, W.F. et al. in Biomolecular Simulation: The GROMOS96 Manual and User Guide (Biomos & Hochschulverlag AG an der ETH Zurich, Groningen & Zurich, 1996).

  54. Darden, T., York, D. & Pedersen, L. Particle mesh Ewald - an N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993).

    Article  CAS  Google Scholar 

  55. Nose, S. & Klein, M.L. Constant pressure molecular-dynamics for molecular-systems. Mol. Phys. 50, 1055–1076 (1983).

    Article  CAS  Google Scholar 

  56. Parrinello, M. & Rahman, A. Polymorphic transitions in single-crystals - a new molecular-dynamics method. J. Appl. Phys. 52, 7182–7190 (1981).

    Article  CAS  Google Scholar 

  57. Hess, B., Bekker, H., Berendsen, H.J.C. & Fraaije, J.G.E.M. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472 (1997).

    Article  CAS  Google Scholar 

  58. Humphrey, W., Dalke, A. & Schulten, K. VMD—visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).

    Article  CAS  Google Scholar 

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Acknowledgements

We are grateful to J.W. Klingelhoefer for writing MATLAB script to calculate the water-count profiles, M.M. Moran and J.A. Chong for their invaluable support and critical insight and E. Ruchti for superb technical assistance. The Mental Retardation/Developmental Disabilities Research Center Molecular Genetics Core Facility at Children's Hospital is supported by US National Institutes of Health Grant P30-HD18655. Work in the Sansom laboratory is supported by grants from the UK Biotechnology and Biological Sciences Research Council and the Wellcome Trust.

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I.S.R. and I.C. designed experiments, created Hv1 point mutations and performed electrophysiological experiments; Y.M. and Z.A.S. created Hv1 models and performed molecular dynamics simulations; D.E.C. and M.S.P.S. directed research activities; I.S.R., Y.M., Z.A.S., M.S.P.S. and D.E.C. wrote the paper.

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Correspondence to I Scott Ramsey.

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Ramsey, I., Mokrab, Y., Carvacho, I. et al. An aqueous H+ permeation pathway in the voltage-gated proton channel Hv1. Nat Struct Mol Biol 17, 869–875 (2010). https://doi.org/10.1038/nsmb.1826

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