Identification of RNA-binding sites in artemin based on docking energy landscapes and molecular dynamics simulation

There are questions concerning the functions of artemin, an abundant stress protein found in Artemia during embryo development. It has been reported that artemin binds RNA at high temperatures in vitro, suggesting an RNA protective role. In this study, we investigated the possibility of the presence of RNA-binding sites and their structural properties in artemin, using docking energy landscapes and molecular dynamics simulation. Analysis of docking energy landscapes revealed sites in artemin with the potential of binding RNAs. We found a good agreement between RNA-binding sites of artemin and RNA-interacting sites of a specific group of RNA-binding proteins called PUF, as regards to the type of their interactions with RNA molecules. Furthermore, the results from molecular dynamics simulation showed that firstly, the presence of RNA molecule and its interaction with artemin cause significant decrease in the secondary structure content of artemin; secondly, RNA-binding sites are mostly located in the low flexible regions. Finally, it seems that these binding sites are distributed in such a way that leads RNA molecule into the interior of the protein, strengthening the previous suggestion for RNA-protecting role of artemin.