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Rice mitogen activated protein kinase kinase and mitogen activated protein kinase interaction network revealed by in-silico docking and yeast two-hybrid approaches

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Title Rice mitogen activated protein kinase kinase and mitogen activated protein kinase interaction network revealed by in-silico docking and yeast two-hybrid approaches
 
Creator Wankhede, Dhammaprakash Pandhari
Misra, Mohit
Singh, Pallavi
Sinha, Alok Krishna
 
Subject Rice
MAPKK
MAPK
Oryza sativa
 
Description Accepted date: April 23, 2013
Protein-protein interaction is one of the crucial ways to decipher the functions of proteins and to understand their role in complex pathways at cellular level. Such a protein-protein interaction network in many crop plants remains poorly defined owing largely to the involvement of high costs, requirement for state of the art laboratory, time and labour intensive techniques. Here, we employed computational docking using ZDOCK and RDOCK programmes to identify interaction network between members of Oryza sativa mitogen activated protein kinase kinase (MAPKK) and mitogen activated protein kinase (MAPK). The 3-dimentional (3-D) structures of five MAPKKs and eleven MAPKs were determined by homology modelling and were further used as input for docking studies. With the help of the results obtained from ZDOCK and RDOCK programmes, top six possible interacting MAPK proteins were predicted for each MAPKK. In order to assess the reliability of the computational prediction, yeast two-hybrid (Y2H) analyses were performed using rice MAPKKs and MAPKs. A direct comparison of Y2H assay and computational prediction of protein interaction was made. With the exception of one, all the other MAPKK-MAPK pairs identified by Y2H screens were among the top predictions by computational dockings. Although, not all the predicted interacting partners could show interaction in Y2H, yet, the harmony between the two approaches suggests that the computational predictions in the present work are reliable. Moreover, the present Y2H analyses per se provide interaction network among MAPKKs and MAPKs which would shed more light on MAPK signalling network in rice.
Authors thank Accelrys India for providing a trial version of the Discovery
Studio Software. Dr. Shaveta Kanoria, NIPGR is acknowledged for
critically reading and editing the manuscript.
 
Date 2015-11-26T06:46:30Z
2015-11-26T06:46:30Z
2013
 
Type Article
 
Identifier PLoS One, 8(5): e65011
1932-6203
http://172.16.0.77:8080/jspui/handle/123456789/385
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065011
10.1371/journal.pone.0065011
 
Language en_US
 
Publisher PLOS