Conformational Free-​Energy Difference of a Miniprotein from Nonequilibrium Simulations

Conformational free-​energy differences are essential thermodn. quantities for understanding the function of many biomols. They are accessible from computer simulations, but their accurate calcn. is a challenging task. Here nonequil. computer simulations and the differential fluctuation theorem are used to evaluate the free-​energy difference between two conformational states of a structured miniprotein, the β-​hairpin of protein G, with an implicit treatment of the solvent. A mol. dynamics-​based protocol is employed for the simulation of rapid switches between the conformational states in both the forward and the reverse direction. From the work performed on the system in the individual switches, the conformational free-​energy difference is detd. by use of the differential fluctuation theorem. The results are in excellent agreement with ref. calcns. from a long mol. dynamics simulation and from the confinement method. The nonequil. approach is a computationally efficient method for the calcn. of conformational free-​energy differences for biol. systems.