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Comparative Homology Modeling and Physicochemical Characterization of Cyprinus carpio Hsp70 Protein

DOI: 10.18805/IJAR.B-4215    | Article Id: B-4215 | Page : 1018-1026
Citation :- Comparative Homology Modeling and Physicochemical Characterization of Cyprinus carpio Hsp70 Protein.Indian Journal of Animal Research.2021.(55):1018-1026
Pravas Ranjan Sahoo, Santosini Sahu, Geetanjali Das, Gyanaranjan Sahoo, Prakash Chandra Behera pravasvet86@gmail.com
Address : Department of Veterinary Biochemistry, College of Veterinary Science and Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar-7510 03, Odisha, India.
Submitted Date : 11-06-2020
Accepted Date : 28-09-2020

Abstract

Background: Expression of the heat shock proteins (Hsp) is responsible for the protection from adverse climatic changes particularly heat stress in Common carp (Cyprinus carpio). Although, with advancement of molecular techniques, Hsp70 protein has been isolated but this protein needs to be characterized by both physicochemically and structurally for the functional annotation of fish genome. So this current study was undertaken with aim of generation of various protein models and also for thorough physiochemical characterization of this protein.
Methods: In this study, Hsp70 protein of common carp was characterized by both physiochemical and structurally through insilco platform and as the crystal structure of this protein is not available, protein models were created though homology modelling upon Modeller version 9.21, Phyre2 and Swiss-model and then the generated predicted models were evaluated through Rampage, Errat, Verify 3D, ProQ and ProSA analysis.
Result: Our investigation showed that this protein is very stable, hydrophilic with no disulphide bonds and the protein models which were generated from this study, are of good quality with z value of - 9.58, -9.48 and -10.93 and quality factor of 82.56, 59.43 and 95.27 respectively. So this study was concluded that the generated Hsp70 protein models would provide an avenue for the other researchers for development of high-throughput gene function assignment in fish.

Keywords

Cyprinus carpio Homology Modeling Hsp70 Physicochemical characteristics

References

  1. Altschul, S.F, Gish, W., Miller, W., Myers, E.W., Lipman, D.J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3):403-10.
  2. Basyuni, M., Wati, R., Sulistiyono, N., et al. (2018). Protein modelling of triterpene synthase genes from mangrove plants using Phyre2 and Swiss-model. Journal of Physics: Conference Series. 978(1): 012095.
  3. Bischof, J.C., He, X. (2005). Thermal stability of proteins. Annals of the New York Academy of Sciences. 1066: 12-33.
  4. Chakrabarti, P., Pal, D. (2001). The interrelationships of side-chain and main-chain conformations in proteins. Progress in Biophysics and Molecular Biology. 76: 1-102. 
  5. Cheeseman, M.D., Westwood I.M., Barbeau, O., et al. (2016). Exploiting Protein Conformational Change to Optimize Adenosine-Derived Inhibitors of HSP70. Journal of Medicinal Chemistry. 59(10):4625 4636
  6. Colovos, C., Yeates, T.O. (1993). Verification of protein structures: patterns of non bonded atomic interactions. Protein Science. 2(9): 1511-1519. doi:10.1002/pro.5560020916.
  7. De Maio, A. (1999). Heat shock proteins: facts, thoughts, and dreams. Shock, 11 (1): 1-12. doi:10.1097/00024382-199901000-00001. 
  8. DeLano, W.L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography. 40: 82-92.
  9. Deller, M.C., Kong, L., Rupp, B. (2016). Protein stability: a crystallo grapher’s perspective. Acta Crystallographica Section F: Structural Biology Communications. 72: 72-95.
  10. Eisenberg, D., et al. (1997). VERIFY3D: assessment of protein models with three-dimensional profiles. Methods in Enzymology. 277: 396-404.
  11. Fishery and Aquaculture Country Profiles: India. Food and Agriculture Organization of the United Nations. 2011.
  12. Fujiwara, K., Toda, H., Ikeguchi, M. (2012). Dependence of á-helical and â-sheet amino acid propensities on the overall protein fold type. BMC Structural Biology. 12: 8-16. 
  13. Garnier, J., Gibrat, J.F., Robson, B. (1996). GOR secondary structure prediction method version IV. Methods in Enzymolology. 266: 540-553.
  14. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R, Appel, R.D., Bairoch, A. (2005). Protein Identification and Analysis Tools on the ExPASy Server. (In) John M. Walker (ed): The Proteomics Protocols Handbook, John M. Walker (ed): Humana Press. pp. 571-607.
  15. Gupta, S., Deepti, A., Deegan, S., Lisbona, F., Hetz, C., Samali, A. (2010). Kelly JW (ed.). HSP72 protects cells from ER stress-induced apoptosis via enhancement of IRE1alpha- XBP1 signaling through a physical interaction. PLoS Biology. 8 (7): e1000410. 
  16. Jiang, J., Prasad, K., Lafer, E.M., Sousa, R. (2005). Structural basis of interdomain communication in the Hsc70 chaperone. Molecular Cell. 20(4): 513 524. 
  17. Kelley, L.A. et al. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols. 10: 845-858. 
  18. Kozlowski, L.P. (2017). Proteome-pI: proteome isoelectric point database. Nucleic Acids Research. 45(D1): D1112-D1116. https://doi.org/10.1093/nar/gkw978.
  19. Kufareva, I., Abagyan, R. (2012). Methods of protein structure comparison A.J.W. Orry (Ed.), Homology Modeling, Humana Press, New York. pp. 231-257.
  20. Kyte, J., Doolittle, R.F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology. 157 (1): 105-32
  21. Michiaki, Y., Takeshi, Y., Nobuhiko, O. (2010). Stress protein HSP70 in fish. Aqua-Bio Science Monographs. 3: 111-141. 10.5047/absm.2010.00304.0111.
  22. Olejniczak, M., Storz, G. (2017). ProQ/FinO-domain proteins: another ubiquitous family of RNA matchmakers? Molecular Microbiology. 104: 905-915.
  23. Padmini, E., Usha, R.M. (2008). Impact of seasonal variation on HSP70 expression quantitated in stressed fish hepatocytes. Comparative Biochemistry and Physiology - Part B: Biochemistry and Molecular Biology. 151(3): 278-85.
  24. Portz, D., Woodley, C., Cech, J. (2006). Stress-associated impacts of short-term holding on fishes. Reviews in Fish Biology and Fisheries. 16: 125-170. 10.1007/s11160-006-9012-z.
  25. Pradhan, P., Rasal, K.D., Swain, D., Swain, P., Sundaray, J.K, Jayasankar, P. (2017). Impact analysis of missense variants on heat shock protein offarmed carp rohu, Labeo rohita (Hamilton, 1822). Indian Journal of Animal Research. 51: 44-51.
  26. Radivojac, P., Clark, W.T., Oron, T.R, Schnoes, A.M, Wittkop, T., Sokolov, A. et al. (2013). A large-scale evaluation of computational protein function prediction. Nature Methods. 10(3): 221-7.
  27. Ramp, U., Mahotka, C., Heikaus, S., Shibata, T., Grimm, M.O., Willers, R., Gabbert, H.E (2007). Expression of heat shock protein 70 in renal cell carcinoma and its relation to tumor progression and prognosis. Histology and Histopathology. 22 (10): 1099-107. 
  28. Rath, S.N., Ray, M., Pattnaik, A., Pradhan, S.K. (2016). Drug Target Identification and Elucidation of Natural Inhibitors for Bordetella petrii: An In Silico Study. Genomics & informatics 14(4): 241–254. https://doi.org/10.5808/GI.2016.14.4.241.
  29. Roy, K. (2017). Technicalities to be considered for culture fisheries development in Indian inland waters: seed and feed policy review. Environment, Development and Sustainability. 21: 281-302. doi: 10.1007/s10668-017-0037
  30. Sahoo, P.R., Mishra, S., Mohapatra, S., Sahu, S., Sahoo, G., Behera, P. (2019). In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals. Indian Journal of Animal Research. 10.18805/ijar.B-3712.
  31. Sampuda, K.M., Riley, M., Boyd, L. (2017). Stress induced nuclear granules form in response to accumulation of misfolded proteins in Caenorhabditis elegans. BMC Cell Biology. 18 (1): 18-25.
  32. Schwede, T., et al. (2003). SWISS-MODEL: an automated protein homology-modeling server, Nucleic Acids Research. 31: 3381-3385.
  33. Shennan, L., et al. (2020), CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Research. 48 (D1): 265-8.
  34. Sigrist, C.J.A., de Castro, E., Cerutti, L., Cuche, B.A, Hulo, N., Bridge, A., Bougueleret, L., Xenarios, I. (2012). New and continuing developments at PROSITE. Nucleic Acids Research. doi: 10.1093/nar/gks1067.
  35. Sung, Y., Roberts, R., Bossier, P. (2012). Enhancement of Hsp70 synthesis protects common carp, Cyprinus carpio L., against lethal ammonia toxicity. Journal of Fish Diseases. 35: 563-568.
  36. Wang, P., Zeng, S., Xu, P., Zhou, L., Zeng, L., Lu, X. et al. (2014). Identification and expression analysis of two HSP70 isoforms in mandarin fish Siniperca chuatsi. Fisheries science. 80 (4): 803-17.
  37. Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research. 46 (W1), W296-W303.
  38. Webb, B., Sali, A. (2016). Comparative Protein Structure Modeling Using MODELLER. Current Protocols in Bioinformatics. 54: 5.6.1 5.6.37
  39. Wiederstein, M., Sippl, M.J. (2007). ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research. 35: W407-W41.
  40. Xi, E., et al. (2017). Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context. Proceedings of the National Academy of Sciences of the United States of America. 114 (51):13345-13350.
  41. Zhang, C., Xing, W., Jiang, N., Li, T., Ma, Z., Luo, L. (2011). Submitted to the EMBL/GenBank/ DDBJ databases. 
  42. Zhou, J.F., Wu, Q.J., Ye, Y.Z., Tong, J.G. (2003). Genetic divergence between Cyprinus carpio carpio and Cyprinus carpio haematopterus as assessed by mitochondrial DNA analysis, with emphasis on origin of European domestic carp. Genetica. 119: 93-97.

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