Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Structural mechanism of plant aquaporin gating

Nature volume 439, pages 688–694 (2006)Cite this article

Abstract

Plants counteract fluctuations in water supply by regulating all aquaporins in the cell plasma membrane. Channel closure results either from the dephosphorylation of two conserved serine residues under conditions of drought stress, or from the protonation of a conserved histidine residue following a drop in cytoplasmic pH due to anoxia during flooding. Here we report the X-ray structure of the spinach plasma membrane aquaporin SoPIP2;1 in its closed conformation at 2.1 Å resolution and in its open conformation at 3.9 Å resolution, and molecular dynamics simulations of the initial events governing gating. In the closed conformation loop D caps the channel from the cytoplasm and thereby occludes the pore. In the open conformation loop D is displaced up to 16 Å and this movement opens a hydrophobic gate blocking the channel entrance from the cytoplasm. These results reveal a molecular gating mechanism which appears conserved throughout all plant plasma membrane aquaporins.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Diagram illustrating the structural mechanism of aquaporin gating in plant plasma membranes.
Figure 2: Structures of the closed and open conformations of SoPIP2;1.
Figure 3: Characterizing the SoPIP2;1 channel.
Figure 4: Results of molecular dynamics simulations of the non-phosphorylated, phosphorylated, and induced open systems.
Figure 5: Electron density at the sites of regulation by phosphorylation and pH for SoPIP2;1 in its closed conformation.
Figure 6: Regulation of the cytoplasmic entrance into the SoPIP2;1 channel.

Similar content being viewed by others

References

  1. Preston, G. M., Carroll, T. P., Guggino, W. B. & Agre, P. Appearance of water channels in Xenopus oocytes expressing red cell CHIP28 protein. Science 256, 385–387 (1992)

    Article  ADS  CAS  Google Scholar 

  2. Johansson, I., Karlsson, M., Johanson, U., Larsson, C. & Kjellbom, P. The role of aquaporins in cellular and whole plant water balance. Biochim. Biophys. Acta 1465, 324–342 (2000)

    Article  CAS  Google Scholar 

  3. Agre, P. & Kozono, D. Aquaporin water channels: molecular mechanisms for human diseases. FEBS Lett. 555, 72–78 (2003)

    Article  CAS  Google Scholar 

  4. King, L. S., Kozono, D. & Agre, P. From structure to disease: the evolving tale of aquaporin biology. Nature Rev. Mol. Cell Biol. 5, 687–698 (2004)

    Article  CAS  Google Scholar 

  5. Tamas, M. J. et al. A short regulatory domain restricts glycerol transport through yeast Fps1p. J. Biol. Chem. 278, 6337–6345 (2003)

    Article  CAS  Google Scholar 

  6. Johanson, U. et al. The complete set of genes encoding major intrinsic proteins in Arabidopsis provides a framework for a new nomenclature for major intrinsic proteins in plants. Plant Physiol. 126, 1358–1369 (2001)

    Article  ADS  CAS  Google Scholar 

  7. Morishita, Y., Sakube, Y., Sasaki, S. & Ishibashi, K. Molecular mechanisms and drug development in aquaporin water channel diseases: aquaporin superfamily (superaquaporins): expansion of aquaporins restricted to multicellular organisms. J. Pharmacol. Sci. 96, 276–279 (2004)

    Article  CAS  Google Scholar 

  8. Borstlap, A. C. Early diversification of plant aquaporins. Trends Plant Sci. 7, 529–530 (2002)

    Article  CAS  Google Scholar 

  9. Johansson, I. et al. Water transport activity of the plasma membrane aquaporin PM28A is regulated by phosphorylation. Plant Cell 10, 451–459 (1998)

    Article  CAS  Google Scholar 

  10. Johansson, I., Larsson, C., Ek, B. & Kjellbom, P. The major integral proteins of spinach leaf plasma membranes are putative aquaporins and are phosphorylated in response to Ca2+ and apoplastic water potential. Plant Cell 8, 1181–1191 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Tournaire-Roux, C. et al. Cytosolic pH regulates root water transport during anoxic stress through gating of aquaporins. Nature 425, 393–397 (2003)

    Article  ADS  CAS  Google Scholar 

  12. Murata, K. et al. Structural determinants of water permeation through aquaporin-1. Nature 407, 599–605 (2000)

    Article  ADS  CAS  Google Scholar 

  13. Sui, H., Han, B. G., Lee, J. K., Walian, P. & Jap, B. K. Structural basis of water-specific transport through the AQP1 water channel. Nature 414, 872–878 (2001)

    Article  ADS  CAS  Google Scholar 

  14. Savage, D. F., Egea, P. F., Robles-Colmenares, Y., O'Connell, J. D. & Stroud, R. M. Architecture and selectivity in aquaporins: 2.5 Å X-ray structure of aquaporin Z. PLoS Biol. 1, E72 (2003)

    Article  Google Scholar 

  15. Gonen, T., Sliz, P., Kistler, J., Cheng, Y. & Walz, T. Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature 429, 193–197 (2004)

    Article  ADS  CAS  Google Scholar 

  16. Harries, W. E., Akhavan, D., Miercke, L. J., Khademi, S. & Stroud, R. M. The channel architecture of aquaporin 0 at a 2.2 Å resolution. Proc. Natl Acad. Sci. USA 101, 14045–14050 (2004)

    Article  ADS  CAS  Google Scholar 

  17. Fu, D. et al. Structure of a glycerol-conducting channel and the basis for its selectivity. Science 290, 481–486 (2000)

    Article  ADS  CAS  Google Scholar 

  18. Tajkhorshid, E. et al. Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 296, 525–530 (2002)

    Article  ADS  CAS  Google Scholar 

  19. de Groot, B. L. & Grubmuller, H. Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF. Science 294, 2353–2357 (2001)

    Article  ADS  CAS  Google Scholar 

  20. Jensen, M. O., Tajkhorshid, E. & Schulten, K. The mechanism of glycerol conduction in aquaglyceroporins. Structure 9, 1083–1093 (2001)

    Article  CAS  Google Scholar 

  21. Jensen, M. O., Park, S., Tajkhorshid, E. & Schulten, K. Energetics of glycerol conduction through aquaglyceroporin GlpF. Proc. Natl Acad. Sci. USA 99, 6731–6736 (2002)

    Article  ADS  CAS  Google Scholar 

  22. Daniels, M. J., Chrispeels, M. J. & Yeager, M. Projection structure of a plant vacuole membrane aquaporin by electron cryo-crystallography. J. Mol. Biol. 294, 1337–1349 (1999)

    Article  CAS  Google Scholar 

  23. Kukulski, W. et al. The 5 Å structure of heterologously expressed plant aquaporin SoPIP2;1. J. Mol. Biol. 350, 611–616 (2005)

    Article  CAS  Google Scholar 

  24. Hedges, S. B., Blair, J. E., Venturi, M. L. & Shoe, J. L. A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol. Biol. 4, 2 (2004)

    Article  Google Scholar 

  25. Jung, J. S., Preston, G. M., Smith, B. L., Guggino, W. B. & Agre, P. Molecular structure of the water channel through aquaporin CHIP. The hourglass model. J. Biol. Chem. 269, 14648–14654 (1994)

    CAS  PubMed  Google Scholar 

  26. Wang, Y., Schulten, K. & Tajkhorshid, E. What makes an aquaporin a glycerol channel: A comparative study of AqpZ and GlpF. Structure 13, 1107–1118 (2005)

    Article  CAS  Google Scholar 

  27. de Groot, B. L., Frigato, T., Helms, V. & Grubmuller, H. The mechanism of proton exclusion in the aquaporin-1 water channel. J. Mol. Biol. 333, 279–293 (2003)

    Article  CAS  Google Scholar 

  28. Jensen, M. O., Tajkhorshid, E. & Schulten, K. Electrostatic tuning of permeation and selectivity in aquaporin water channels. Biophys. J. 85, 2884–2899 (2003)

    Article  ADS  CAS  Google Scholar 

  29. Chakrabarti, N., Tajkhorshid, E., Roux, B. & Pomes, R. Molecular basis of proton blockage in aquaporins. Structure 12, 65–74 (2004)

    Article  CAS  Google Scholar 

  30. Ilan, B., Tajkhorshid, E., Schulten, K. & Voth, G. A. The mechanism of proton exclusion in aquaporin channels. Proteins 55, 223–228 (2004)

    Article  CAS  Google Scholar 

  31. de Groot, B. L. & Grubmüller, H. The dynamics and energetics of water permeation and proton exclusion in aquaporins. Curr. Opin. Struct. Biol. 15, 176–183 (2005)

    Article  CAS  Google Scholar 

  32. Smart, O. S., Goodfellow, J. M. & Wallace, B. A. The pore dimensions of gramicidin A. Biophys. J. 65, 2455–2460 (1993)

    Article  CAS  Google Scholar 

  33. Nemeth-Cahalan, K. L. & Hall, J. E. pH and calcium regulate the water permeability of aquaporin 0. J. Biol. Chem. 275, 6777–6782 (2000)

    Article  CAS  Google Scholar 

  34. Zelenina, M., Bondar, A. A., Zelenin, S. & Aperia, A. Nickel and extracellular acidification inhibit the water permeability of human aquaporin-3 in lung epithelial cells. J. Biol. Chem. 278, 30037–30043 (2003)

    Article  CAS  Google Scholar 

  35. Zelenina, M., Tritto, S., Bondar, A. A., Zelenin, S. & Aperia, A. Copper inhibits the water and glycerol permeability of aquaporin-3. J. Biol. Chem. 279, 51939–51943 (2004)

    Article  CAS  Google Scholar 

  36. Madsen, D. & Kleywegt, G. J. Interactive motif and fold recognition in protein structures. J. Appl. Crystallogr. 35, 137–139 (2001)

    Article  Google Scholar 

  37. Karlsson, M. et al. Reconstitution of water channel function of an aquaporin overexpressed and purified from Pichia pastoris. FEBS Lett. 537, 68–72 (2003)

    Article  CAS  Google Scholar 

  38. Bailey, S. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

    Article  Google Scholar 

  39. Morris, R. J., Perrakis, A. & Lamzin, V. S. ARP/wARP and automatic interpretation of protein electron density maps. Methods Enzymol. 374, 229–244 (2003)

    Article  CAS  Google Scholar 

  40. Brunger, A. T. et al. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    Article  CAS  Google Scholar 

  41. Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R. & Thornton, J. M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477–486 (1996)

    Article  CAS  Google Scholar 

  42. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  43. Kalé, L. et al. NAMD2: Greater scalability for parallel molecular dynamics. J. Comp. Phys. 151, 283–312 (1999)

    Article  ADS  Google Scholar 

  44. MacKerell, A. D. et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586–3616 (1998)

    Article  CAS  Google Scholar 

  45. Schlenkrich, M., Brickmann, J., MacKerell, A. D. & Karplus, M. in Biological Membranes: A Molecular Perspective from Computation and Experiment (eds Merz, K. M. & Roux, B.) 31–81 (Birkhauser, Boston, Massachusetts, 1996)

    Book  Google Scholar 

  46. 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  ADS  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank C. Larsson for useful discussions; the Pittsburgh Supercomputer Center and the National Center for Supercomputing Applications for providing computer time; and the European Synchrotron Radiation Facility and the Swiss Light Source for access to synchrotron radiation. Financial support was provided by Formas, the Research School of Pharmaceutical Sciences (FLÄK), Swegene, the Swedish Research Council (VR), the Swedish Strategic Research Foundation (SSF), the European Commission Integrated Projects EMEP and SPINE, the Chalmers Bioscience Programme and the NIH.

Author information

Authors and Affiliations

  1. Department of Chemistry and Bioscience, Chalmers University of Technology, P O Box 462, SE-40530, Göteborg, Sweden

    Susanna Törnroth-Horsefield, Kristina Hedfalk & Richard Neutze

  2. Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Illinois, 61801, Urbana, USA

    Yi Wang & Emad Tajkhorshid

  3. Department of Plant Biochemistry, Lund University, P O Box 124, SE-22100, Lund, Sweden

    Urban Johanson, Maria Karlsson & Per Kjellbom

Authors
  1. Susanna Törnroth-Horsefield
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yi Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kristina Hedfalk
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Urban Johanson
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Maria Karlsson
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Emad Tajkhorshid
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Richard Neutze
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Per Kjellbom
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Emad Tajkhorshid, Richard Neutze or Per Kjellbom.

Ethics declarations

Competing interests

The coordinates and structure factor amplitudes for the closed and open structures have been deposited in the Protein Data Bank under the accession codes 1Z98 and 2B5F, respectively. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

This file contains the Supplementary Methods, Supplementary Tables and Supplementary Figures 1–8. (DOC 9094 kb)

Supplementary Data 1

A pdb file for the non-phosphorylated molecular dynamics trajectory. (TXT 143 kb)

Supplementary Data 2

A pdb file for the phosphorylated molecular dynamics trajectory. (TXT 143 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Törnroth-Horsefield, S., Wang, Y., Hedfalk, K. et al. Structural mechanism of plant aquaporin gating. Nature 439, 688–694 (2006). https://doi.org/10.1038/nature04316

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature04316

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing