Figure 3. Orientations of NCBD Cα₁ and Cα₃ with respect to Cα₂ in the unbound state.

All conformations sampled at 305 K during the last 60 ns of the control REX simulation were first aligned using the backbone atoms of Cα₂, and then reoriented such that Cα₂ was aligned with −z axis. The orientations as observed in three distinct folds of NCBD, represented by PDB 1kbh, 1zoq, and 1jj (also see Figure 1), are marked with “+”, “×”, and “★”, respectively. Note that different colors for the same symbol may be used in different panels for clarity. In panels c) and d), ϕ and θ are the inclination and azimuth angles of the spherical coordinate system. Note that the PMFs were computed using sin(θ) instead of θ itself as an order parameter to remove the Jacobian entropy contribution. The range shown corresponds to θ = 0 (top) to π (bottom). Contours are drawn at every kT up to 7 kT, with k being the Boltzmann factor.