(A) The 2D folding free energy landscape of DPO4 projected onto the fractions of total () and interdomain () native contacts for the default SBM parameter at the folding temperature . There are six folding states identified on the free energy landscape, which are denoted by , , , , , and , with corresponding typical DPO4 structures shown. The all-atom representations of DPO4 were reconstructed based on the structures from the simulations (Rotkiewicz and Skolnick, 2008). Domains of DPO4 are labeled with different colors: the finger domain (F, blue, residues 11–77), the palm domain (P, red, residues 1–10 and 78–166), the thumb domain (T, green, residues 167–229), the little finger domain (LF, purple, residues 245–341), and the flexible linker (gray, residues 230–244), which connects the T and LF domains. (B) The 1D folding free energy landscape of DPO4 projected onto for different values of the ratio of interdomain to intradomain native contact strength, denoted by ρ and ranging from 0.5 to 1.5 (indicated by different colors). It is worth noting that the and states cannot be distinguished by . The black line corresponds to the free energy landscape for the default SBM parameter . We set the zeros of the free energies at the lowest detected from the simulations. (C) Change in stability of each folding state for ρ relative to that for at the corresponding folding temperature according to the expression , where represents the folding state (, , , or ) and is the stability of the folding state at ρ. is calculated as the free energy difference between the folding state and the unfolded state , where is the free energy obtained from (B).