Figure 4. Angle-projected energy landscapes of apo-AdK.

A: The free energy surface (θ_NMP, θ_LID) is shown as a function of the NMP–CORE angle θ_NMP and the LID–CORE angle θ_LID. The closed state structure 1AKE is taken as the reference with (1AKE) = 0. A few typical DIMS transition paths are also shown (closed→open; - - - open→closed). Crystal structures are drawn in the same positions as in Figure 3. Errors as estimated from the standard deviation of a block average are typically smaller than 1 kcal/mol. B: Potential energy landscape ΔE(θ_NMP, θ_LID) = E(θ_NMP, θ_LID) −E(1AKE). The closed state is taken as the reference so that ΔE(1AKE) = 0. The average energy of a conformation, E(θ_NMP, θ_LID), in bins of size Δθ = 5° is calculated from the umbrella sampling simulations as the statistical mechanical average of the potential energy less the umbrella biasing contribution, $E({\theta }_{\text{NMP}},{\theta }_{\text{LID}})=\langle U({\theta }_{\text{NMP}}^{\prime }(t),{\theta }_{\text{LID}}^{\prime }(t)-u_{\text{umbrella}}({\theta }_{\text{NMP}}^{\prime },{\theta }_{\text{LID}}^{\prime })$. The standard deviation on ΔE is typically on the order of 200 kcal/mol (not shown).