The Role of Calcium on the Active Site of Snake Venom Phospholipase A2: Molecular Dynamics Simulations
Computational Biology and Bioinformatics
Volume 4, Issue 1, February 2016, Pages: 10-14
Received: Jan. 18, 2016; Accepted: Jan. 28, 2016; Published: Feb. 17, 2016
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Authors
Akubugwo Emmanuel I., Department of Biochemistry, Abia State University, Uturu, Nigeria
Okafor Irene N., Department of Biochemistry, Faculty of Natural Sciences, Chukwuemeka Odumegwu Ojukwu University, Uli, Anambra State, Nigeria
Ezebuo Fortunatus C., Department of Biochemistry, Faculty of Natural Sciences, Chukwuemeka Odumegwu Ojukwu University, Uli, Anambra State, Nigeria
Lukong Colin B., Department of Biochemistry, Faculty of Natural Sciences, Chukwuemeka Odumegwu Ojukwu University, Uli, Anambra State, Nigeria
Ifemeje Jonathan C., Department of Biochemistry, Faculty of Natural Sciences, Chukwuemeka Odumegwu Ojukwu University, Uli, Anambra State, Nigeria
Nwaka Andrew C., Department of Biochemistry, Faculty of Natural Sciences, Chukwuemeka Odumegwu Ojukwu University, Uli, Anambra State, Nigeria
Chilaka Ferdinand C., Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria
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Abstract
Snake venoms are rich in phospholipase A2 (PLA2) and their hydrolysis of cell membrane phospholipids explains the role of the enzyme in venom toxicity. Calcium is known to plays important role at the active site of PLA2 during catalysis. In this study, molecular dynamics simulations of free PLA2 and calcium bound PLA2 were carried out using GROMACS 4.5.5 to evaluate the role of calcium in PLA2 catalysis. The results showed that calcium induced formation of helical structures between Arg62 - Lys66, Asn107 - Tyr111 and Asp114 - Cys119 in PLA2 which with time disappeared through the formation and opening of loops. Calcium induced atomistic movements and conformational changes in snake venom PLA2 which led to the formation of a widened cleft at the active site of calcium bound PLA2 when compared with free PLA2. This could lead to a better binding and accommodation of substrate, thus enhancing catalysis. This study confirms the role of calcium towards the action of PLA2 in snake venom toxicity and could provide useful information for the design of small molecules that can function as PLA2 inhibitors.
Keywords
Snake Venoms, Phospholipase A2, Calcium, Catalytic Site, Inhibitors of PLA2, Loop
To cite this article
Akubugwo Emmanuel I., Okafor Irene N., Ezebuo Fortunatus C., Lukong Colin B., Ifemeje Jonathan C., Nwaka Andrew C., Chilaka Ferdinand C., The Role of Calcium on the Active Site of Snake Venom Phospholipase A2: Molecular Dynamics Simulations, Computational Biology and Bioinformatics. Vol. 4, No. 1, 2016, pp. 10-14. doi: 10.11648/j.cbb.20160401.12
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Copyright © 2016 Authors retain the copyright of this article.
This article is an open access article distributed under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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