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Journal of Mathematical Chemistry

, Volume 51, Issue 8, pp 2020–2032 | Cite as

Modelling interaction between ammonia and nitric oxide molecules and aquaporins

  • Hakim Al Garalleh
  • Ngamta Thamwattana
  • Barry J. Cox
  • James M. Hill
Original Paper

Abstract

Aquaporin is a family of small membrane-proteins that are capable of transporting nano-sized materials. In the present paper, we investigate the structure of these channels and provide information about the mechanism of individual molecules being encapsulated into aquaglyceroporin (GlpF) and aquaporin-1 (AQP1) channels by calculating the potential energy. In particular, we presents a mathematical model to determine the total potential energy for the interaction of the ammonia and nitric oxide molecules and different aquaporin channels which we assume to have a symmetrical cylindrical structure. We propose to describe these interactions in two steps. Firstly, we model the nitrogen atom as a discrete point and secondly, we model the three hydrogen atoms on the surface of a sphere of a certain radius. Then, we find the total potential energy by summing these interactions. Next, by considering the nitric oxide molecule as two discrete atoms uniformly distributed interacting with GlpF and AQP1 channels then gathering all pairs of interaction to determine the potential energy. Our results show that the ammonia and nitric oxide molecules can be encapsulated into both GlpF and AQP1 channels.

Keywords

Aquaporins (AQPs) Aquaporin-1 (AQP1) Aquaglyceroporin (GlpF) Ammonia molecule (NH\(_3\)Nitric oxide (NO) Lennard-Jones potential  van der Waals interaction 

Notes

Acknowledgments

The authors are grateful to the Australian Research Council for support through the Discovery project scheme and for the provision of an APD for BJC. They are also grateful to the provision of an UPA for HA.

References

  1. 1.
    A.S. Verkman, K.A. Mitra, Structure and function of aquaporin water channels. Am. J. Physiol. Renal Physiol. 278, 13–28 (2000)Google Scholar
  2. 2.
    K. Murata, K. Mitsouka, T. Hirai, T. Walz, P. Agre, J.B. Heymann, A. Engel, Y. Fujiyoshi, Structural determinants of water permeation through aquaporin-1. Nature 407, 599–605 (2000)CrossRefGoogle Scholar
  3. 3.
    G. Ren, V.S. Reddy, A. Cheng, P. Mylnek, A.K. Mitra, Three-dimensional fold of the human aqp1 water channel determined at 4Å resolution by electron crystallography of two-dimensional crystals embedded in ice. J. Mol. Biol. 301, 369–387 (2000)Google Scholar
  4. 4.
    D. Fu, A. Libson, L.J.W. Miercke, C. Weitzman, P. Nollert, J. Krucinski, R.M. Stroud, Structure of a glycerol-conducting channel and the basis for its selectivity. Science 290, 481–486 (2000)CrossRefGoogle Scholar
  5. 5.
    G.M. Preston, T.P. Carrol, W.B. Guggino, P. Agre, Appearance of water channels in xenopus oocytes expressing red cell CHIP28 water channel. Science 256, 385–387 (1992)CrossRefGoogle Scholar
  6. 6.
    S. Phongphanphanee, N. Yoshida, F. Hirata, Molecular selectivity in aquaporin channels studied by the 3D-RISM theory. J. Phys. Chem. B 114, 7967–7973 (2010)CrossRefGoogle Scholar
  7. 7.
    M.O. Jensen, S. Park, K. Schulten, E. Tajkhorshid, and ed. by L.D. Donald, Energetics of glycerol conduction through aquaglyceroporin GlpF. Proc. Natl. Acad. Sci. 99, 6731–6736 (2002)Google Scholar
  8. 8.
    J.M. Verbavats, D. Brown, I. Sabolic, G. Valenti, D.A. Siello, A.N. Van Hoek, T. Ma, A.S. Verkman, Tetrameric assembly of CHIP28 water channels in liposomes and cell membranes: a freeze-fracture study. Cell Biology 123, 605–618 (1993)CrossRefGoogle Scholar
  9. 9.
    J.S. Jung, G.M. Preston, B.L. Smith, W.B. Guggino, P. Agre, Molecular structure of the water channel through aquaporin CHIP. The hourglass model. J. Biol. Chem. 269, 14648–14654 (1994)Google Scholar
  10. 10.
    G.M. Pao, L.F. Wu, K.D. Johnson, H. Hofte, M.J. Crispeels, G. Sweet, N.N. Sandal, M. Sauer, Evolution of the mip family of integral membrane transport proteins. Mol. Microbiol. 5, 33–37 (1991)CrossRefGoogle Scholar
  11. 11.
    G.J. Wistow, M.M. Pisano, A.B. Chepelinsky, Tandem sequence repeats in transmembrane channel proteins. Trend Biol. Sci. 16, 170–171 (1991)CrossRefGoogle Scholar
  12. 12.
    G.M. Preston, J.S. Jung, W.B. Guggino, P. Agre, Membrane topology of aquaporin chip. Analysis of functional epitope-scanning mutants by vectorial proteolysis. J. Biol. Chem. 269, 1668–1673 (1994)Google Scholar
  13. 13.
    B.L. Smith, P. Agre, Erythrocyte mr 28,000 transmembrane protein exists as a multisubunit oligomer similar to channel proteins. J. Biol. Chem. 266, 6407–6415 (1991)Google Scholar
  14. 14.
    K.B. Heller, E.C. Lin, T.H. Wilson, Substrate specificity and transport properties of the glycerol facilitator of escherichia coli. Bacteriol 144, 274–278 (1980)Google Scholar
  15. 15.
    G. Ren, V.S. Reddy, A. Cheng, A.K. Mitra, Visualization of a water-selective pore by electron crystallography in vitreous ice. Proc. Natl. Acad. Sci. 98, 1398–1403 (2001)CrossRefGoogle Scholar
  16. 16.
    J.S. Hub, L.B. de Groot, Comment on “molecular selectivity in aquaporin channels studied by the 3D-RISM theory”. J. Phys. Chem. B 115, 8364–8366 (2011)CrossRefGoogle Scholar
  17. 17.
    E. Kruse, N. Uehlein, R. Kaldenhoff, The aquaporins. Genome Biol. J. 7(2), 206–211 (2006)CrossRefGoogle Scholar
  18. 18.
    J.S. Hub, L.B. de Groot, Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc. Natl. Acad. Sci. USA 105, 1198–1203 (2008)CrossRefGoogle Scholar
  19. 19.
    Y.C. Hou, A. Janczuk, P.G. Wang, Current trends in the development of nitric oxide donors. Current Pharm. Des. 5(6), 417–441 (1999)Google Scholar
  20. 20.
    A.S. Verkman, Does aquaporin-1 pass gas? An opposing view. J. Physiol. 542, 31 (2002)CrossRefGoogle Scholar
  21. 21.
    M. Herrera, N.J. Hong, J.L. Garvin, Aquaporin-1 transports NO across cell membranes. Hypertension 48, 157–164 (2006)CrossRefGoogle Scholar
  22. 22.
    N.L. Nakhoul, K.S. Hering-Smith, S.M. Abdulnour-Nakhoul, L.L. Hamm, Transport of NH\(_3\)/NH in oocytes expressing aquaporin-1. Am. J. Physiol.-Renal Fluid Electrol. Physiol. 281, 255–263 (2001)Google Scholar
  23. 23.
    N.M. Holbrook, M.A. Zwieniecki, Plant biology: water gate. Nature 425, 361 (2003)CrossRefGoogle Scholar
  24. 24.
    D.F. Savage, P.F. Egea, C.Y. Robles, J.D. O’Conell III, and R.M. Stroud, Architecture and selectivity in aquaporins 2.5 Å x-ray structure of aquaporin Z. Public Libr. Sci. Biol. 1, 334–340 (2003)Google Scholar
  25. 25.
    J.O. Hirschfelder, C.F. Curtiss, R.B. Byron, The molecular theory of gases and liquids. Society For Industrial and Applied Mathematics, NewYork, University of Winsconsin, Madison, 1964Google Scholar
  26. 26.
    L.T. Cottrell, The Strengths of Chemical Bonds (Butterworths, London, 1954)Google Scholar
  27. 27.
    L. Pauling, The Nature of the Chemical Bonds (Cornell University Press, Ithaca, NY, 1960)Google Scholar
  28. 28.
    L.A. Girifalco, M. Hodak, R.S. Lee, Carbon nanotube, buckyballs, ropes and a universal graphitic potential. Phys. Rev. Lett. 62, 104–110 (2000)Google Scholar
  29. 29.
    H. Al Garalleh, N. Thamwattana, B.J. Cox, J.M. Hill, Modelling van der waals interaction between water molecules and biological channels. J. Comput. Theor. Nanosci. 10, 1–10 (2013)Google Scholar
  30. 30.
    B.J. Cox, N. Thamwattana, J.M. Hill, Mechanics of atoms and fullerenes in single-walled carbon nanotubes, in Proceedings of The Royal Society A, vol. 463 (The Royal Society, 2006), pp. 461–476Google Scholar
  31. 31.
    L.E. Sutton, Table of interatomic distances and configuration in molecules and ions. (Chemical Society, London, 1965)Google Scholar
  32. 32.
    A.K. Rappi, C.J. Casewit, K.S. Colwell, W.M. Skid, UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 114, 10024–10035 (1992)CrossRefGoogle Scholar
  33. 33.
    Y. Wang, J. Cohen, W.F. Boron, K. Schulten, E. Tajkhorshid, Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics. J. Struct. Biol. 157, 534 –544 (2007)Google Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Hakim Al Garalleh
    • 1
  • Ngamta Thamwattana
    • 1
  • Barry J. Cox
    • 2
  • James M. Hill
    • 2
  1. 1.Nanomechanics Group, School of Mathematics and Applied Statistics University of WollongongWollongongAustralia
  2. 2.Nanomechanics Group, School of Mathematical SciencesUniversity of Adelaide AdelaideAustralia

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