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Copyright © 2013 | AIZEON publishers | All rights reserved

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International Journal of Computational Bioinformatics and In Silico Modeling
2013: Volume-2 Issue-4
ISSN: 2320-0634

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ABSTRACT   REFERENCES  
International Journal of Computational Bioinformatics and In Silico Modeling 2(4) 2013: 141-146

Unraveling the sequence similarities, conserve domain and 3D structure of cocoonase to gain insights into their functional integrity


Smita Lata1, Dev Mani Pandey1* and Jay Prakash Pandey2

1 Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.
2 Silkworm Physiology Laboratory, Central Tasar Research & Training Institute, Piska Nagari, Ranchi, Jharkhand, India.

* Corresponding Author

ABSTRACT

Cocoonase is proteolytic enzyme having capacity to hydrolyze sericin of the cocoons. It is secreted by emerging silk moth during pupal-adult development which allows the exit of moth from the cocoon. Cocoonase hydrolyses the interstitial matrix of cocoon that is composed of fibroin and sericin protein and acts on sericin without affecting the fibroin. However, as a ruling practice, softening of tasar cocoon is generally performed in alkaline solution by using soap, soda, H2O2, and alkali etc. which adversely affects the natural color and softness of tasar silk. Seeking the importance of this enzyme in cocoon softening we aim to see the presence of cocoonase in other sericigenous insects and do the phylogenetic analysis and conserved domain prediction. For this analysis nucleotide and protein sequences of this enzyme were retrieved from NCBI. Phylogenetic analysis was performed using MEGA 5.1Beta4 software. Presence of conserved domain in all retrieved protein sequences was identified by the online SMART software. Further, presence of conserved domain in Antheraea pernyi cocoonase protein sequence was identified by InterProScan and the 3D structure prediction was performed by I-TASSER. Total fourteen nucleotide and fourteen protein sequences of cocoonase were retrieved from NCBI. Phylogenetic analysis revealed that Bombyx mori and B. mandarina cocoonase mRNA sequences are closely related while A. pernyi cocoonase mRNA sequence showed little variation. It is evident that, although both (Bombyx and Antheraea) are sericigenous insects but divergence in mRNA sequences were observed. Moreover, on the other hand, all the cocoonase mRNA sequences have common conserved region of trypsin like serine protease and Peptidase S1 domain was identified by InterProScan in A. pernyi. 3D structure prediction of A. pernyi cocoonase protein was carried out using 2ANY (plasma kallikrein protein) as template.


Copyright © 2013 | AIZEON publishers | All rights reserved

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Citation: Smita Lata et al. (2013). Unraveling the sequence similarities, conserve domain and 3D structure of cocoonase to gain insights into their functional integrity. Int J Comput Bioinfo In Silico Model 2(4): 141-146

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