Abstract
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.
Highlights
The genetic potential of improved crop cultivars to perform better in field conditions is often constrained by a wide spectrum of biotic and abiotic stresses
Homology Modelling of OsMAPKKs and OsMAPKs In order to understand the molecular interaction properties of a protein, it is a prerequisite to have the information about its 3D structure
3D structures of eleven mitogenactivated protein kinase (MAPK) and five mitogen activated protein kinase kinase (MAPKK) were predicted by homology modelling
Summary
The genetic potential of improved crop cultivars to perform better in field conditions is often constrained by a wide spectrum of biotic and abiotic stresses. These factors directly and indirectly affect the growth and development of plants and result in lower production of food grains. Protein kinases are crucial players, in regulating various stress responses and in growth and development. The highly conserved mitogenactivated protein kinase (MAPK) pathways in eukaryotes play pivotal role in basic cellular process, development, hormone biosynthesis/signalling, senescence, plant immunity as well as in producing responses to several stress conditions [1,2,3]. Much of our knowledge comes from the model plant Arabidopsis thaliana while in the case of most of the crop plants the knowledge about these facets is still in its nascent stage
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