Homology Modelling of Shaggy-like Kinase α in Arabidopsis thaliana (ASKα) release_xb2thx3vxndipac35spiziepye

by Michaela Ukowitz

Released as a article-journal .

2019  

Abstract

Plants are often exposed to stress. On the one hand, there is biotic stress caused by bacteria, viruses, fungi or insects. On the other hand, abiotic stress is caused by changing environmental conditions such as drought, heat, frost or high salinity of the soil. These stress factors lead to enormous annual yield losses, which is why research into the mechanisms triggered by stress in plants is of high interest. Therefore, there is interest to develop new methods to improve stress tolerance in plants, which would bring both, economic benefits and ensure sufficient food supply to the population. Several studies attribute the kinase ASKα an important role in stress modulation. The activated kinase increases stress tolerance of plants, which is why it is important to find out more about this protein. A three-dimensional structure of this kinase, which has not yet been determined experimentally, is important. The aim of this work is to model the 3D structure of ASKα and to examine it for possible binding pockets for small molecules. First, a good template was needed, which was identified as GSK3β due to the high sequence identity. The PDB was searched for the most suitable structure of GSK3β. With this template, homology models were calculated with the software Modeller. The calculated models were filtered by different validation criteria (molpdf, DOPE-score). For the most appropriate ones, Ramachandran plots were generated with Procheck. The plots were analysed in detail until a final model could be selected. For the first time, we can provide a 3D structure of ASKα in form of a thoroughly validated homology model. This model allows us to gain deeper insights into ASKα's function and allows further predictions about potential ligand bindings. Therefore, the model was examined with Fpocket for promising binding pockets.
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