In this work, molecular dynamics approach was used to study of thermal denaturation mechanism of spinach plastocyanin protein and related molecular dynamics advantages are presented. The only significant change in Cα RMSD and Rg plot was seen at 453K temperature. At this temperature, less stability for Met92 with respect to the other residues was found. More flexible region was found for residues 40-56 at all temperatures. In our simulation, three steady states including native, intermediate and denatured states and two transition states ensembles have been found at 453K temperature. Secondary structure analysis have shown that the structure of first transition state is more similar to the native state while the second transition state is more like to denatured state.

Keywords