Molecular docking of HSPs (heat shock proteins) from rice seed

Abstract

The expression of heat shock proteins (HSPs) is an essential part of the heat shock response in plants where HSPs act as chaperones that help in protein folding and unfolding mechanism. This project focuses on determining the docking mechanism and conformation stability of HSPs from rice seed at several simulated temperatures. HSP20 was selected from previously isolated rice seed proteins and the sequence was used for homology modelling. The suitable model of this sequence was then selected to undergo molecular dynamics simulation and docking procedure with the targeted proteins. The simulated environmental temperature was set as 37oC and 100oC during the simulation process. Model for the selected HSP20 protein was generated successfully via I-Tasser server. The results of 50ns simulation at 310K and 373K for selected model were plotted in the graphs of RMSD, RMSF, hydrogen bonding number and radius of gyration. The RMSD result showed that HSP20 model was more stable at simulated temperature of 37oC as compared to 100oC. Whereas for the RMSF graph visualization, two significant loops of this model were found in the same position of its 3D structure as corresponded in both 37oC and 100oC results. For the results of hydrogen bonding number and radius of gyration, the mean numbers were around 102 and 1.6 respectively for 37oC and 100oC simulations. These findings indicated the responsible stability and flexibility of the model’s 3D structure in terms of its secondary structure, folding pattern and loops location. Molecular docking of this HSP20 model with the selected proteins: TPR and SGT1 was carried out successfully with ZDock server. The docked structures generated were used to understand the docking mechanism and protein-protein interactions between these proteins. Further study of these protein models is required for understanding on the roles of binding conformation between them as well as possible protein-protein interaction of HSP20 with other co-chaperones.