Research Article | Volume: 2, Issue: 4, July-Aug, 2014

Homology Modelling and Molecular Docking Study of Voltage Gated Ion Channels for their Role in Plant Abiotic Stress

Ravi Ranjan Kr. Niraj Nikita Singh Sween and Ajit Kumar   

Open Access   

Published:  Aug 27, 2014

DOI: 10.7324/JABB.2014.2402

Voltage-gated ion channels (VGICs) are responsible for generation of electrical signals in cell membranes. They exist mainly in three major forms namely, VGKC (Voltage-gated potassium channel), VGCC (Voltage-gated calcium channel), and VGSC (Voltage-gated sodium channel). VGICs have been studied extensively in animal system, especially for their role in electrical signalling during nerve conduction. Their existence in plant system has been related from very early period of evolution but their role in plant system has not been studied intensively and is a less explored area. Therefore, the present study was undertaken to investigate the role of VGICs in plant stress response, abiotic stress in particular, using in-silico tool of docking simulation. No solved crystal structure of plant VGICs were available at Protein Databank for the purpose of docking studies. Therefore, 3D-structures of three different VGICs (VGCC, VGKC and VGSC) were constructed using homology modelling tool of SWISS-MODEL and were selected after structure evaluation. These structures were subjected to docking simulation against major soil salts and fertilizers. While conducting molecular docking simulation studies, it was observed that VGICs seems to have negligible role in simple salts physiology like NaCl or KCl, while VGKC showed good binding pattern with ammonium nitrate and ammonium sulfate, reflecting its significant role in ammonium -ion physiology. Also, phosphoric acid binding was found significant towards VGKC. Superphosphate ions and Calcium nitrate showed a good binding pattern towards VGCC while VGSC showed good affinity for nitrate, phosphate, sodium and ammonium–ions. Also, during simulated annealing docking, it was observed that binding of phosphoric acid (or phosphate ion) increased at both extreme temperature ends (lower and higher). The study has provided a good platform for further investigation to establish the role of VGICs in plant stress response and correlated to other living systems like animals, fungi, etc.

Keyword:     DockingHomology modellingSalt stress Thermal stress.


Ravi Ranjan Kr. Niraj, Nikita Singh, Sween, Ajit Kumar. Homology Modelling and Molecular Docking Study of Voltage Gated Ion Channels for their Role in Plant Abiotic Stress. J App Biol Biotech, 2014; 2 (04): 007-015. DOI: 10.7324/JABB.2014.2402

Copyright: Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

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1. Armstrong CM, Hille B. Voltage-Gated Ion Channels and Electrical Excitability. Neuron. 1998; 20: 371–380.

2. Noda M, Shimuzu S, Tanabe T, Takai T, KayanoT, Ikeda T, Takahashi H, Nakayama H, Kanaoka Y, Minamino N, Kengawa K, Matsuo H, Raftery M, Hirose T, Inayama S, Hayashida H, Miyata T, Numa S. Primary structure of Electrophorus electricus sodium channel deduced from cDNA sequence. Nature.1984; 312: 121-127.

3. Noda M, Ikeda T, Kayano T,Suzuki H, Takeshima H, Kurasaki, Takahashi H, Numa S. Existence of distinct sodium channel messenger RNAs in rat brain. Nature. 1986; 320: 188- 192.

4. Tempel TM, Papazian DM, Schwarz TL, Jan YN, Jan LY. Sequence of a probable potassium channel component encoded at Shaker locus in drosophila. Science. 1987; 237: 770–775.

5. Amtmann A, Armengaud P, Volkov V. Potassium nutrition and salt stress. In: Blatt MR (ed) Membrane transport in plants. Blackwell Oxford; 2004, p. 293–339.

6. Serrano R, Mulet JM, Rios G, Marquez JA, de Larrinoa IF, Leube MP, Mendizabal I, Pascual-Ahuir A, Proft M, Ros R, Montesinos C. A glimpse of the mechanisms of ion homeostasis during salt stress. J Exp Bot. 1999; 50:1023–1036.

7. Wyn Jones RJ, Pollard A. Proteins, enzymes and inorganic ions. Encyclopedia of Plant Physiology, Springer. 1983; 126: 528–562.

8. Hepler PK, Wayne RO. Calcium and plant development. Annu. Rev. Plant Physiol. 1985; 36: 397-439.

9. Leonard RT, Hepler PK. Eds. Calcium in Plant Growth and Development. Rockville, MD: American Society of Plant Physiologists; 1990.

10. Thuleau P, Ward JM, Ranjeva R, Schroeder JI. Voltage dependent calcium-permeable channels in the plasma membrane of a higher plant cell. EMBO J. 1994; 13: 2970-2975.

11. Huang JW, Grunes DL, Kochian LV. Voltage dependent Ca2+ influx into right-side-out plasma membrane vesicles from wheat roots: Characterization of a putative Ca 2+ channel. Proc. Natl. Acad. Sci. USA. 1994; 91: 3473-3477.

12. Marshall J, Corzo A, Lelgh RA, Sanders D. Membrane potential dependent calcium transport in right-side-out plasma membrane vesicles from Zea mays L. roots. Plant J. 1994; 5: 683-694.

13. Piήeros M, Tester M. Characterization of a voltage dependent Ca2+-selective channel from wheat roots. Planta. 1995; 195: 478-488.

14. Ward JM, Maser P, Schroeder JI. Plant Ion Channels: Gene Families, Physiology and Functional Genomics Analyses. Annual review of physiology. 2009; 71: 59–82.

15. McAinsh MR, Brownlee C, Hetherington AM. Calcium ions as second messengers in guard cell signal transduction. Physiologia Plantarum. 1997; 100: 16-29.

16. Grabov A, Blatt MR. Membrane voltage initiates Ca2+waves and potentiates Ca2+ increases with abscisic acid in stomatal guard cells. Proceedings of the National Academy of Sciences, USA. 1998; 95: 4778-4783.

17. White PJ. Calcium channels in the plasma membrane of root cells. Annals of Botany. 1998; 81: 173-183.

18. White PJ, Biskup B, Elzenga JTM, Homann U, Thiel G, Wissing F, Maathuis FJM. Advanced patch-clamp techniques and single-channel analysis. Journal of Experimental Botany. 1999; 50:1037-1054.

19. Ji-Ping Gao, Dai-Yin Chao, Hong-Xuan Lin. Understanding Abiotic Stress Tolerance Mechanisms: Recent Studies on Stress Response in Rice. Journal of Integrative Plant Biology. 2007; 49(6): 742−750.

20. NCBI: https://www.ncbi.nlm.nih/gov


22. Hekkelman ML, Beek TA, Pettifer SR, Thorne D, Attwood, Virend G. WIWS: a protein structure bioinformatics Web service collection. Nuc. Ac. Res. 2010; 38: W719-723.

23. UCSF-Chimera:

24. Chemsketch:

25. Open Babel: https://www.

26. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. Autodock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Computational Chemistry. 2009; 16: 2785-91.

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