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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
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.
Keywords: Docking, Homology modelling, Salt stress; Thermal stress.