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International Journal of Computational Bioinformatics and In Silico Modeling
2013: Volume-2 Issue-5
ISSN: 2320-0634

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ABSTRACT   REFERENCES  
International Journal of Computational Bioinformatics and In Silico Modeling 2(5) 2013: 249-256

Computational study of SnRK2 in Arabidopsis thaliana: An in silico approach for homology modeling and functional characterization of SRK2G/SnRK2.1


Mst. Saleha Sultana*, Ravi Kant Ojha, Mohammad Majharul Islam, Md. Anik Ashfaq Khan, Kaniz Fatema and Pijush Sutradhar

Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet-3114, Bangladesh .

* Corresponding Author

ABSTRACT

Sucrose non-fermenting1-related protein kinase 2 (SnRK2) is a serine/threonine protein kinase. The protein is of utmost importance because it has been found in all plants analyzed to date and is thought to play a significant role in stress and metabolic responses. Arabidopsis thaliana, a model plant, encodes ten members from three subclasses of SnRK2 family, but the least is known about 3D structure and physiological role. Comparative analysis among five different proteins of SnRK2 subclass I and subclass III was performed using bioinformatics tools. Members of subclass I and III were found to be highly similar regarding physicochemical properties, presence of antigenic determinant sites and structural behavior. The tertiary structure of one of the proteins of subclass I, namely SnRK2.1 was constructed based on homology modeling approach. Predicted structure was verified by Ramachandran plot and verify3D and was evaluated by superimposing on its three templates. The functional analysis of this protein revealed nucleotide binding activity, ATP-binding activity, transferase, catalytic activity as well as other cellular activities with high confidence level. This study may play role in revelation of crystallographic structure of SnRK2.1 protein based on this predicted three-dimensional conformation as well as in further laboratory studies to find out functional role of SnRK2 subclass I kinases in plant metabolic pathway.


Copyright © 2013 | AIZEON publishers | All rights reserved

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Citation: Saleha Sultana et. al. (2013). Computational study of SnRK2 in Arabidopsis thaliana: An in silico approach for homology modeling and functional characterization of SRK2G/SnRK2.1 Int J Comput Bioinfo In Silico Model 2(5): 249-256

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