Fig 4. Relative thermodynamic stability of the lateral bond in the double-PF system.

(A), Thermodynamic cycle demonstrating the idea behind estimating the effect of unequal PF conformations on the association free energy between the PFs. While simulating the horizontal transitions (PF association) is computationally more expensive, the free energy changes linked to the vertical transitions (PF compaction) have already been obtained (Figs 2 and 3). (B) and (C), Distributions of the relative stability of the double-PF systems with respect to their equilibrium conformations marked with orange and cyan circles for GTP- and GDP-state, respectively, as a function of dimer rise and nucleotide state. White circles denote conformations with the strongest observed dimer rise mismatch. Free energy color coding is adjusted such that red (blue) areas correspond to conformations of the double-PF system in which the lateral bond is destabilized (stabilized) relative to equilibrium. White areas correspond to no change in the lateral bond stability.