Protein-protein interactions (PPIs) underlie the molecular mechanisms of most biological processes. Mitogen-activated protein kinases (MAPKs) can be dephosphorylated by MAPK-specific phosphatases such as PP2C, which are critical to transduce extracellular signals into adaptive and programmed responses. However, the experimental approaches for identifying PPIs are expensive, time-consuming, laborious and challenging. In response, many computational methods have been developed to predict PPIs. Yet, these methods have inherent disadvantages such as high false positive and negative results. Thus, it is crucial to develop in silico approaches for predicting PPIs efficiently and accurately.
Recently, a research team led by Dr Zhaoqing Chu from Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science (CAS), Shanghai Chenshan Botanical Garden, has constructed a PPIs network of MAPK and PP2C gene family and uncovered a novel docking site variants in B. distachyon.
In this study, we identified PPIs among 16 BdMAPKs and 86 BdPP2Cs in B. distachyon using a novel docking approach. Further, we systematically investigated the docking site (D-site) of BdPP2C which plays a vital role for recognition and docking of BdMAPKs. D-site analysis revealed that there were 96 pairs of PPIs including all BdMAPKs and most BdPP2Cs, which indicated that BdPP2C may play roles in other signaling networks. Moreover, most BdPP2Cs have a D-site for BdMAPKs in our prediction results, which suggested that our method can effectively predict PPIs, as confirmed by their 3D structure. In addition, we validated this methodology with known Arabidopsis and yeast phosphatase-MAPK interactions from the STRING database. The results obtained provide a vital research resource for exploring an accurate network of PPIs between BdMAPKs and BdPP2Cs.
This work entitled “In silico-prediction of protein–protein interactions network about MAPKs and PP2Cs reveals novel docking site variants in Brachypodium distachyon”, has been published online in Scientific Reports on Oct 10, 2018.
The study was funded by the Grant from Chinese Academy of Sciences strategic resource service network planning of plant germplasm resources innovation project ZSZC-013 and Grant from Shanghai Landscaping Administrative Bureau (Grant Nos.G162406 and G162407).
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