The Binding Mechanism of Epolactaene to Hsp60 Unveiled by in Silico Modelling

Abstract

Molecular Dynamics (MD) simulations and DFT/MM calculations were performed in order to rationalize available experimental results and to provide structural details on the binding mechanism of Epolactaene (EPO) to the 60 KDa Heat Shock Protein (Hsp60). The available crystal structure of Hsp60 represents the last step of the chaperone folding cycle, while the Hsp60-EPO complex was obtained by using a homology model of Hsp60, in order to simulate a state related to the beginning of the folding cycle (Rs1). The results of MD simulations point out that EPO shows the highest binding affinity for the empty ATP binding site. The presence of ATP opens a channel that allows the entrance of both EPO diastereoisomers. However, only (15S)-EPO possesses a suitable orientation to bind its target, Cys442. A DFT/MM study was performed to investigate the structure of EPO attached through a CS covalent bond and to estimate the binding free energy of such reaction. Interestingly, the MD simulation of Hsp60-EPO shows that the covalent bond between EPO and Cys442 hinders the conformational change leading to the R-open structure, which is involved in the formation of the Hsp60/Hsp10 complex, essential for the known chaperone activity of Hsp60.