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Conformational free-energy difference of a miniprotein from nonequilibrium simulations

Martin Spichty, Marco Cecchini, and Martin Karplus (2010)

The Journal of Physical Chemistry Letters, 1(13):1922–1926.

Conformational free-energy differences are essential thermodynamic quantities for understanding the function of many biomolecules. They are accessible from computer simulations, but their accurate calculation is a challenging task. Here nonequilibrium 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 molecular 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 determined by use of the differential fluctuation theorem. The results are in excellent agreement with reference calculations from a long molecular dynamics simulation and from the confinement method. The nonequilibrium approach is a computationally efficient method for the calculation of conformational free-energy differences for biological systems.

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