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Study on protein allosteric processes attracts most interest in the fields of biology,biotechnology and medicine.Understanding the mechanisms of the processes can be helpful to design artificial protein switches that can be applied to biological imaging,biosensors and therapeutic agents.A number of experimental studies have provided sufficient evidences for protein allosteric switch,but are difficult to address micro dynamic processes in detail.In recent work,the targeted molecular dynamics(TMD)simulation and the potential of mean force(PMF)were employed to explore the free energy potential of the allosteric processes for butane and the villin subdomain protein unfolding.PMF was calculated by using umbrella-sampling MD simulations with different reaction coordinates from the initial structure to a target structure.Taking the small molecular butane as an example,the corresponding PMF calculations with the reaction coordinates of dihedral angle from-180°to 180°and the root-mean-square deviation(RMSD)were performed and are shown in Figure 1(a).The results show that the two free energy profiles for the butane allostery resemble each other.The villin subdomain protein unfolding process has been investigated through TMD simulation(see Figure 1(b)),which will be applied to its PMF calculation.