통합자연과학논문집 (Journal of Integrative Natural Science)

조선대학교 기초과학연구원 (The Basic Science Institute Chosun University)
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P2X Receptor 3D Structure Prediction Using Homology Modelling

  • Sruthy Sathish (Computational Biology Laboratory, Department of Genetic Engineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology) ;
  • Thirumurthy Madhavan (Computational Biology Laboratory, Department of Genetic Engineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology)
  • 투고 : 2023.02.28
  • 심사 : 2023.03.21
  • 발행 : 2023.04.10
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초록

P2X receptors are ATP-activated ion channels in the plasma membrane. P2X receptors have a role in a diverse range of disorders, making them a valuable therapeutic target. Hence, the present investigation employed homology modelling of the P2X receptor based on the crystal structure of 5SVJ, 6AH4, 5YVE and 5SVL. Twenty models, using both single- and multiple template-based methods, were developed, and the best model was chosen based on the validation result. We observed that a strategy based on multiple templates provided greater accuracy. Future studies involving binding site and docking analysis can make use of the produced structures.

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참고문헌

  1. Abbracchio MP. P1 and P2 receptors in cell growth and differentiation. Drug Dev. Res. 39: 393-406, 1996. https://doi.org/10.1002/(SICI)1098-2299(199611/12)39:3/4<393::AID-DDR21>3.0.CO;2-1
  2. Abbracchio MP and Burnstock G. Purinoceptors: are there families of P2X and P2Y receptors? Pharmacol. Ther. 64: 445-475, 1994. https://doi.org/10.1016/0163-7258(94)00048-4
  3. Abraham EH, Pratt AG, Gerweck L, Seneveratne T, Arceci RJ, Kramer R, Guidotti G and Cantiello HF. Themultidrug resistance (mdr1) gene product, 1993.
  4. North R. A. Molecular physiology of P2X receptors. Physiological reviews, 82(4), 1013-1067, 2002. https://doi.org/10.1152/physrev.00015.2002
  5. Burnstock G. Introduction to purinergic signalling in the brain. Advances in experimental medicine and biology, 986, 1-12, 2013. https://doi.org/10.1007/978-94-007-4719-7_1
  6. Burnstock, G., Fredholm, B. B., North, R. A., & Verkhratsky, A. The birth and postnatal development of purinergic signalling. Acta physiologica (Oxford, England), 199 (2), 93 -147, (2010). https://doi.org/10.1111/j.1748-1716.2010.02114.x
  7. Burnstock, G., & Kennedy, C. P2X receptors in health and disease. Advances in pharmacology (San Diego, Calif.), 61, 333 -372, 2011.
  8. Baker, G. C., Smith, J. J., & Cowan, D. A. Review and re-analysis of domain-specific 16S primers. Journal of microbiological methods, 55 (3), 541-555, 2003. https://doi.org/10.1016/j.mimet.2003.08.009
  9. Santhosh K N & Thirumurthy M. 3D Structure Prediction of Thromboxane A2 Receptor by Homology Modeling. J. Chosun Natural Sci. Vol. 8, No. 1 pp. 75-79, 2015.
  10. Mobarec JC, Sanchez R, Filizola M. Modern homology modeling of G-protein coupled receptors: which structural template to use? J Med Chem. Aug 27;52(16):5207-16, 2009. https://doi.org/10.1021/jm9005252
  11. B. K. Kuntal, P. Aparoy, and P. Reddanna, "EasyModeller: A graphical interface to MODELLER", BMC Research Notes, Vol. 3, pp. 226, 2010.
  12. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, and A. Sali, "Comparativeprotein structure modeling with MODELLER", Current Protocols in Bioinformatics, Vol. 5, pp. 1-5, 2006. https://doi.org/10.1002/0471250953.bi0506s15
  13. S. C. Lovell, I. W. Davis, W. B. Arendall III, P. I. W. Bakker, J. M. Word, M. G. Prisant, J. S. Richardson, and D. C. Richardson, "Structure validation by Cα geometry: φ, ψ and Cβ deviation", Proteins., Vol. 50, pp. 437-450, 2003. https://doi.org/10.1002/prot.10286
  14. C. Colovos and T. O. Yeates, "Verificationof protein structures: patterns of nonbondedatomic interactions", Protein Sci., Vol. 2, pp. 1511-1519, 1993. https://doi.org/10.1002/pro.5560020916