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. Author manuscript; available in PMC: 2016 Mar 23.
Published in final edited form as: J Mol Biol. 2005 Sep 16;352(2):370–381. doi: 10.1016/j.jmb.2005.07.036

Figure 3.

Figure 3

Free energy landscapes of DPDP from REMD simulations at 346K representing about 130,000 structures. Data is much better converged than that obtained from standard MD, as seen from the similarity of the landscapes from simulations starting from different structures. (a) and (b) show QTotal vs. RG for simulations starting from collapsed and linear structures respectively. There are at least three major minima in these landscapes, showing that DPDP is a non-two-state system. (c) and (d) show QH1 vs. QH2 for simulations starting from collapsed and linear structures respectively. These landscapes indicate DPDP behaves more like a four-state system, with minima corresponding to (clockwise from top-right) fully formed β-sheet, only hairpin 1 folded, unfolded, and only hairpin 2 folded. Both (c) and (d) show that hairpin 2 alone is about 1.0 kcal mol−1 more stable than hairpin 1 alone.