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 Artemiaduring 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-bindingsites and their structural properties in artemin, using docking energy landscapes and molecular dynamicssimulation. Analysis of docking energy landscapes revealed sites in artemin with the potential of bindingRNAs. We found a good agreement between RNA binding sites of artemin and RNA-interacting sites of aspecific 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 presenceof RNA molecule and its interaction with artemin cause significant decrease in the secondary structure contentof artemin; secondly, RNA-binding sites are mostly located in the low flexible regions. Finally, it seems thatthese 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.