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Article Number - 573BB7D52788


Vol.7(1), pp. 1-7 , May 2015
DOI: 10.5897/JCBBR2013.082
ISSN: 2141-2227



Full Length Research Paper

Computational sequence analysis and in silico modeling of a stripe rust resistance protein encoded by wheat TaHSC70 gene



Zarrin Basharat
  • Zarrin Basharat
  • Microbiology and Biotechnology Research Lab, Department of Environmental Sciences, Fatima Jinnah Women University, 46000, Pakistan.
  • Google Scholar







 Accepted: 27 April 2015  Published: 30 May 2015

Copyright © 2015 Author(s) retain the copyright of this article.
This article is published under the terms of the Creative Commons Attribution License 4.0


TaHSC70 gene of Triticum sp. is an associate of the heat shock protein family and plays a significant role in stress-related and defense responses educed by contagion with stripe rust fungus through a Jasmonic acid dependent signal transduction pathway. Hence, understanding molecular structure and function of the protein coded by this gene is of paramount importance for plant biologists working on stripe rust. The present study was aimed at sequence and in silico structural analysis of Hsp70 protein coded by this gene, through comparative modeling approach. Validation of the overall folds and structure, errors over localized regions and stereo chemical parameters was carried out using PDBSum server. Structure was a monomer with seven sheets, 1 β-α-βunit, 12 hairpins, 13β-bulges, 29 strands, 21 helices, 16 helix-helix interacs, 44 β-turns and 1 ϒ-turn.  Two major domains were detected belonging to Hsp70 family while neural network analysis revealed protein to be highly phosphorylated at serine and threonine residues.
 
Key words: TaHSC70, Hsp70, Stripe rust, homology modelling, wheat.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic local alignment search tool. J. Mol. Biol. 215 (3):403-410.
Crossref
 
Alvim FC (2001). Enhanced accumulation of BiP in transgenic plants confers tolerance to water stress. Plant Physiol. 126:1042-1054.
Crossref
 
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000). The Protein Data Bank. Nucleic Acids Res. 28 (1):235-242.
Crossref
 
Bhadula SK, Elthon TE, Habben JE, Helentjaris TG, Jiao S, Ristic Z (2001). Heat-stress induced synthesis of chloroplast protein synthesis elongation factor (EF-Tu) in a heat-tolerant maize line. Planta 212(3):359-366.
Crossref
 
Blom N, Gammeltoft S, Brunak S (1999). Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J. Mo. Biol. 294(5):1351-1362.
Crossref
 
Colovos C, Yeates TO (1993). Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 2(9):1511-1519.
Crossref
 
Daugaard M, Rohde M, Jäättelä M (2007). The heat shock protein 70 family: Highly homologous proteins with overlapping and distinct functions. FEBS Lett. 581(19):3702-3710.
Crossref
 
Duan YH, Guo J, Ding K, Wang SJ, Zhang H, Dai XW, Chen YY, Govers F, Huang LL, Kang ZS (2011). Characterization of a wheat HSP70 gene and its expression in response to stripe rust infection and abiotic stresses. Mol. Biol. Rep. 38(1):301-307.
Crossref
 
Efeoğlu B, Ekmekci Y, Cicek N (2009). Physiological responses of three maize cultivars to drought stress and recovery. S. Afr. J. Bot. 75(1):34-42.
Crossref
 
Eswar N, Eramian D, Webb B, Shen M, Sali A (2008). Protein structure modelling with MODELLER. Methods. J Mol Biol. 426:145-159.
 
Feng PM, Chen W, Lin H, Chou KC. (2013). iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition. Anal. Biochem. 442(1):118-125.
Crossref
 
Fiser A, Sali A (2003). Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 374:461-491.
Crossref
 
Guex N, Peitsch MC (1997). SWISS‐MODEL and the Swiss‐Pdb Viewer: an environment for comparative protein modeling. Electrophoresis 18(15):2714-2723.
Crossref
 
Guo M, Zhai YF, Lu JP, Chai L, Chai WG, Gong ZH, Lu MH. (2014). Characterization of CaHsp70-1, a Pepper Heat-Shock Protein Gene in Response to Heat Stress and Some Regulation Exogenous Substances in Capsicum annuum L. Int. J. Mol. Sci. 15(11):19741-19759.
Crossref
 
Guy CL, Li QB (1998). The organization and evolution of thenspinach stress 70 molecular chaperone gene family. Plant Cell. 10:539-556.
Crossref
 
Jego G, Hazoumé A, Seigneuric R, Garrido C. (2013). Targeting heat shock proteins in cancer. Cancer Lett. 332(2): 275-285.
Crossref
 
Kumar RR, Rai RD (2014). Can Wheat Beat the Heat: Understanding the Mechanism of Thermotolerance in Wheat (Triticum aestivum L.). Cereal Res. Commun. 42(1):1-18.
Crossref
 
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993). PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:283-291.
Crossref
 
Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Šali A (2000). Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29(1): 291-325.
Crossref
 
May T, Soll J (2000). 14-3-3 proteins form a guidance complex with chloroplast precursor proteins in plants. Plant Cell Online 12(1):53-63.
Crossref
 
Morris AL, MacArthur MW, Hutchinson EG, Thornton JM (1992). Stereochemical quality of protein structure coordinates. Proteins 12 (4): 345-364.
Crossref
 
Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963). Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7:95-99.
Crossref
 
Safdar W, Majeed H, Ali B, Naveed I (2012). Molecular evolution and diversity of small heat shock proteins genes in plants. Pak. J. Bot. 44:211-218.
 
Sali A, Blundell TL (1993). Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234 (3): 779–815.
Crossref
 
Sarkar NK, Kundnani P, Grover A (2013). Functional analysis of Hsp70 superfamily proteins of rice (Oryza sativa). Cell Stress Chaperones 18(4):427-437.
Crossref
 
Usman MG, Rafii MY, Ismail MR, Malek MA, Latif MA, Oladosu Y (2014). Heat Shock Proteins: Functions And Response Against Heat Stress In Plants. Int. J. Sci. Technol. Res. 3(11):204-218.
 
Wang X, Gou M, Bu H, Zhang S, Wang G (2014). Proteomic analysis of Arabidopsis constitutive expresser of pathogenesis-related gene1 (Cpr30/cpr1-2) mutant. Plant Omics J. 7(3): 142-151.

 


APA Basharat, Z. (2015). Computational sequence analysis and in silico modeling of a stripe rust resistance protein encoded by wheat TaHSC70 gene. Journal of Computational Biology and Bioinformatics Research, 7(1), 1-7.
Chicago Zarrin Basharat. "Computational sequence analysis and in silico modeling of a stripe rust resistance protein encoded by wheat TaHSC70 gene." Journal of Computational Biology and Bioinformatics Research 7, no. 1 (2015): 1-7.
MLA Zarrin Basharat. "Computational sequence analysis and in silico modeling of a stripe rust resistance protein encoded by wheat TaHSC70 gene." Journal of Computational Biology and Bioinformatics Research 7.1 (2015): 1-7.
   
DOI 10.5897/JCBBR2013.082
URL http://academicjournals.org/journal/JCBBR/article-abstract/573BB7D52788

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