Journal of Integrative Natural Science (통합자연과학논문집)

The Basic Science Institute Chosun University (조선대학교 기초과학연구원)
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Structure Prediction of KiSS1-derived Peptide Receptor Using Comparative Modelling

  • Received : 2016.05.30
  • Accepted : 2016.06.25
  • Published : 2016.06.30
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Abstract

KiSS1-derived peptide receptor, a GPCR protein, binds with the hormone kiss peptin. They are important in the neuroendocrine regulation of reproduction and in the secretion of gonadotrophin-releasing hormone. Thus, analysing the structural features of the receptor becomes important. However, the three dimensional structure of the protein is unavailable. Hence in this study, we have performed the homology modelling of KiSS1-derived peptide receptor with 5 different templates. 30 models were constructed using two platforms - Easymodeller and ITasser. The optimal models were chosen based on the model validation. Two models were selected after validation. The developed models could provide useful for analysing the structural features of KiSS1-derived peptide receptor and their pathophysiological role in various disorders related to them.

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References

  1. A. I. Muir, L. Chamberlain, N. A. Elshourbagy, D. Michalovich, D. J. Moore, A. Calamari, P. G. Szekeres, H. M. Sarau, J. K. Chambers, P. Murdock, K. Steplewski, U. Shabon, J. E. Miller, S. E. Middleton, J. G. Darker, C. G. Larminie, S. Wilson, D. J. Bergsma, P. Emson, R. Faull, K. L. Philpott, and D. C. Harrison, "AXOR12, a novel human G protein-coupled receptor, activated by the peptide KiSS-1", J. Biol. Chem., Vol. 276, pp. 28969-28975. 2001. https://doi.org/10.1074/jbc.M102743200
  2. T. Ohtaki, Y. Shintani, S. Honda, H. Matsumoto, A. Hori, K. Kanehashi, Y. Terao, S. Kumano, Y. Takatsu, Y. Masuda, Y. Ishibashi, T. Watanabe, M. Asada, T. Yamada, M. Suenaga, C. Kitada, S. Usuki, T. Kurokawa, H. Onda, O. Nishimura, and M. Fujino, "Metastasis suppressor gene KiSS-1 encodes peptide ligand of a G-protein-coupled receptor", Nature, Vol. 411, pp. 613-617, 2001. https://doi.org/10.1038/35079135
  3. M. Kotani, M. Detheux, A. Vandenbogaerde, D. Communi, J. M. Vanderwinden, E. L. Poul, S. Brezillon, R. Tyldesley, N. Suarez-Huerta, F. Vandeput, C. Blanpain, S. N. Schiffmann, G. Vassart, and M. Parmentier, "The metastasis suppressor gene KiSS-1 encodes kisspeptins, the natural ligands of the orphan G protein-coupled receptor GPR54", J. Biol. Chem., Vol. 276, pp. 34631-34636, 2001. https://doi.org/10.1074/jbc.M104847200
  4. J. H. Lee, M. E. Miele, D. J. Hicks, K. K. Phillips, J. M. Trent, B. E. Weissman, and D. R. Welch, "KiSS-1, a novel human malignant melanoma metastasis-suppressor gene", JNCI-J. Natl. Cancer I., Vol. 88, pp. 1731-1737, 1996. https://doi.org/10.1093/jnci/88.23.1731
  5. S. M. Popa, D. K. Clifton, and R. A. Steiner, "The role of kisspeptins and GPR54 in the neuroendocrine regulation of reproduction", Annu. Rev. Physiol., Vol. 70, pp. 213-238, 2008. https://doi.org/10.1146/annurev.physiol.70.113006.100540
  6. T. M. Plant, S. Ramaswamy, and M. J. Dipietro, "Repetitive activation of hypothalamic G protein-coupled receptor 54 with intravenous pulses of kisspeptin in the juvenile monkey (Macaca mulatta) elicits a sustained train of gonadotropin-releasing hormone discharges", Endocrinology, Vol. 147, pp. 1007-1013, 2006. https://doi.org/10.1210/en.2005-1261
  7. M. Shahab, C. Mastronardi, S. B. Seminara, W. F. Crowley, S. R. Ojeda, and T. M. Plant, "Increased hypothalamic GPR54 signaling: a potential mechanism for initiation of puberty in primates", P. Natl Acad. Sci. U.S.A., Vol. 102, pp. 2129-2134, 2005. https://doi.org/10.1073/pnas.0409822102
  8. S. B. Seminara, S. Messager, E. E. Chatzidaki, R. R. Thresher, J. S. Jr. Acierno, J. K. Shagoury, Y. Bo-Abbas, W. Kuohung, K. M. Schwinof, A. G. Hendrick, D. Zahn, J. Dixon, U. B. Kaiser, S. A. Slaugenhaupt, J. F. Gusella, S. O'Rahilly, M. B. Carlton, W. F. Jr. Crowley, S. A. Aparicio, and W. H. Colledge, "The GPR54 gene as a regulator of puberty", New Engl. J. Med., Vol. 349, pp. 1614-1627, 2003. https://doi.org/10.1056/NEJMoa035322
  9. S. Funes, J. A. Hedrick, G. Vassileva, L. Markowitz, S. Abbondanzo, A. Golovko, S. Yang, F. J. Monsma, and E. L. Gustafson, "The KiSS-1 receptor GPR54 is essential for the development of the murine reproductive system", Biochem. Bioph. Res. Co., Vol. 312, pp. 1357-1363, 2003. https://doi.org/10.1016/j.bbrc.2003.11.066
  10. Y. Horikoshi, H. Matsumoto, Y. Takatsu, T. Ohtaki, C. Kitada, S. Usuki, and M. Fujino, "Dramatic elevation of plasma metastin concentrations in human pregnancy: metastin as a novel placenta-derived hormone in humans". J. Clin. Endocrinol. Metab., Vol. 88, pp. 914-919, 2003. https://doi.org/10.1210/jc.2002-021235
  11. E. J. Mead, J. J. Maguire, R. E. Kuc, and A. P. Davenport, "Kisspeptins are novel potent vasoconstrictors in humans, with a discrete localization of their receptor, G protein-coupled receptor 54, to atherosclerosis-prone vessels", Endocrinology, Vol. 148, pp. 140-147, 2007. https://doi.org/10.1210/en.2006-0818
  12. A. C. Arai, Y. F. Xia, E. Suzuki, M. Kessler, O. Civelli, and H. P. Nothacker, "Cancer metastasis-suppressing peptide metastin upregulates excitatory synaptic transmission in hippocampal dentate granule cells", J. Neurophysiol., Vol. 94, pp. 3648-3652, 2005. https://doi.org/10.1152/jn.00590.2005
  13. A. C. Hauge-Evans, C. C. Richardson, H. M. Milne, M. R. Christie, S. J. Persaud, and P. M. Jones, "A role for kisspeptin in islet function", Diabetologia, Vol. 49, pp. 2131-2135, 2006. https://doi.org/10.1007/s00125-006-0343-z
  14. G. C. Baker, J. J.Smith, and D. A. Cowan, "Review and re-analysis of domain-specific 16S primers", J. Microbiol. Meth., Vol. 55, pp. 541-555, 2003. https://doi.org/10.1016/j.mimet.2003.08.009
  15. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, "Basic local alignment search tool", J. Mol. Biol., Vol. 215, pp. 403-410, 1990. https://doi.org/10.1016/S0022-2836(05)80360-2
  16. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, "The protein data bank", Nucleic Acids Res., Vol. 28, pp. 235-242, 2000. https://doi.org/10.1093/nar/28.1.235
  17. M. Shalini and T. Madhavan, "Homology Modeling of CCR 4: Novel therapeutic target and preferential maker for Th2 cells", J. Chosun Natural Sci., Vol. 7, pp. 234-240, 2014. https://doi.org/10.13160/ricns.2014.7.4.234
  18. B. Sathya and T. Madhavan, "Homology modeling of cysteinyl leukotriene1 receptor", J. Chosun Natural Sci., Vol. 8, pp. 13-18, 2015. https://doi.org/10.13160/ricns.2015.8.1.13
  19. S. K. Nagarajan and T. Madhavan, "3D Structure prediction of thromboxane A2 receptor by homology modeling", J. Chosun Natural Sci., Vol. 8, pp. 75-79, 2015. https://doi.org/10.13160/ricns.2015.8.1.75
  20. B. K. Kuntal, P. Aparoy, and P. Reddanna, "Easy-Modeller: A graphical interface to MODELLER", BMC Research Notes, Vol. 3, pp. 226, 2010. https://doi.org/10.1186/1756-0500-3-226
  21. A. Roy, A. Kucukural, and Y. Zhang, "I-TASSER: a unified platform for automated protein structure and function prediction", Nat. Protoc., Vol. 5, pp. 725-738, 2010. https://doi.org/10.1038/nprot.2010.5
  22. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, and A. Sali, "UNIT 5.6 Comparative Protein Structure Modeling with MODELLER", Current Protocols in Bioinformatics, suppl. 15, New York: John Wiley & Sons, Inc., pp. 1-30, 2006.
  23. J. Yang, R. Yan, A. Roy, D. Xu, J. Poisson, and Y. Zhang, "The I-TASSER Suite: Protein structure and function prediction", Nat. Methods, Vol. 12, pp. 7-8, 2015. https://doi.org/10.1038/nmeth.3213
  24. S. C. Lovell, I. W. Davis, W. B. Arendall III, P. I. W. de Bakker, J. M. Word, M. G. Prisant, J. S. Richardson, and D. C. Richardson, "Structure validation by $C{\alpha}$ geometry: $\phi$, $\psi$ and $C{\beta}$ deviation", Proteins, Vol. 50, pp. 437-450, 2002.
  25. J. U. Bowie, R. Luthy, and D. Eisenberg, "A method to identify protein sequences that fold into a known three-dimensional structure", Science, Vol. 253, pp. 164-170, 1991. https://doi.org/10.1126/science.1853201
  26. C. Colovos and Y. O. Yeates, "Verification of protein structures: patterns of nonbonded atomic interactions", Protein Sci., Vol. 2, pp. 1511-1519, 1993. https://doi.org/10.1002/pro.5560020916
  27. J. D. Thompson, D. G. Higgins, and T. J. Gibson, "CLUSTAL W: improving the sensitivity of progressive sequence weighting, position-specific gap penalties and weight matrix choice", Nucleic Acids Res., Vol. 22, pp. 4673-4680, 1994. https://doi.org/10.1093/nar/22.22.4673

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