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. Author manuscript; available in PMC: 2016 May 1.
Published in final edited form as: Biochem Biophys Res Commun. 2015 Mar 18;460(2):434–438. doi: 10.1016/j.bbrc.2015.03.051

Figure 3. Force-protocols to explore the free energy landscape of a tandem protein using Brownian dynamics.

Figure 3

A) Free energies and E-curves depicting the trajectory of a single unfolding-refolding-unfolding Brownian Dynamics simulation. Movement along a single free energy may result in folding or unfolding while diffusion along an E-curve changes the end-to-end length of the protein without folding events. B) Traces obtained from Brownian dynamics simulations for two different cycles (cycle 1 and 2). The first cycle considers the total unfolding at 30 pN from a to b, followed by a quench of 7 pN causing diffusion along the E8 curve to c, and a final refolding of five domains from c to d. For the second cycle, the refolding force is reduced to 18 pN instead of 7 pN, causing the shortening of the polyprotein from b to c’ without refolding any domains.