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International Journal of Computational Bioinformatics and In Silico Modeling
2013: Volume-2 Issue-2
ISSN: 2320-0634

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ABSTRACT   REFERENCES  
International Journal of Computational Bioinformatics and In Silico Modeling 2(2) 2013: 94-103

3D structure prediction and protein-DNA interaction of CCCH-type zinc finger transcription factor gene in Rice (Oryza sativa L.)


Dev Mani Pandey* and Ashutosh Kumar

Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand-835215, India.

* Corresponding Author

ABSTRACT

OsCCCH-Zn-1 (LOC_Os05g45020) is differentially expressed under abiotic stresses as well as developmentally regulated. The aim of present study was to find out the conserved domain and its involvement in gene regulation by interacting with core GCC box motif. For this analysis 1K promoter region of OsCCCH-Zn-1 gene was retrieved from TIGR (v6.1) and core GCC box (GCCGCC) was identified in antisense strand using PLACE database. Presence of conserved domain in OsCCCH-Zn-1 protein was identified by InterProScan. 3D structure prediction of OsCCCH-Zn-1 protein was performed by I-TASSER. Stereochemical quality and accuracy was evaluated by Ramachandran plot analysis. DNA model of 25nt long promoter sequence having core GCCGCC motif was generated by 3D-DART. Interaction of OsCCCH-Zn-1 and GCCGCC motif was studied by HADDOCK server. Zinc finger, CCCH type domain was identified by InterProScan in OsCCCH-Zn-1 protein. While best template used for 3D structure prediction of OsCCCH-Zn-1 protein was lipase protein (PDB Id 1TIC). Ramachandran Plot of OsCCCH-Zn-1 protein shows that cumulatively 94.9% residues are in the allowed region, while 5.1% residues in disallowed region. While in the case of protein-DNA docked model of OsCCCH-Zn-1 lowest HADDOCK score of -41.0 +/- 9.6 and Z-score of -1.6 was observed when interacting with linear DNA segment.

Copyright © 2013 | AIZEON publishers | All rights reserved

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Citation: Pandey DM and Kumar A. (2013). 3D structure prediction and protein-DNA interaction of CCCH-type zinc finger transcription factor gene in Rice (Oryza sativa L.). Int J Comput Bioinfo In Silico Model 2(2): 94-103

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