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


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.


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



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.


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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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