Figure 8.

Energies calculated with the MCCE implicit solvent method plotted against the distance between Fe²⁺ and the quinone carbonyl O4 atom along the SMD unbinding trajectories. Vertical dashed lines depict the suggested transition-state region where few SQ^– headgroups are found (Figure 5A). (A) Binding free energy for UQ and SQ^–. The color of each point indicates the SMD time point of the structure used for the calculation: orange (2000 ps), green (4800 ps), magenta (5800 ps), blue (6400 ps), and red (8000 ps) (Figure 4). (B) Relative binding energy of SQ^– with respect to UQ (ΔG_bind,SQ– – ΔG_bind,UQ) in structures obtained from both the UQ and SQ^– unbinding paths. Positive values indicate that SQ^– is less stable than UQ in the regions of the protein away from the Q_A site. (C and D) SQ^– total protein interaction (green) and implicit solvation energy (red). These energies are calculated along the UQ (C) and SQ^– (D) exit pathways. The thick black lines plot the median energy at ≈2 Å intervals as a guide to the eye. The inset in (C) magnifies the transition-state region where SQ^– loses stabilizing interactions with the protein.