PMC

A-O₂ free energy landscape obtained from the ILS calculations. Two isosurface contours are shown, with free energy levels at -5 (blue inner contour) and 5 (cyan contour) kJ·mol⁻¹. B- Comparison of the O₂ free energy landscape obtained from the ILS calculations (blue maps) and high-affinity regions from the O₂ explicit MD simulations (red maps). The probability density contours at 0.00015 Å⁻³ are represented as a red isosurface. C- O₂ lowest free energy pathways obtained from the ILS energy landscape. The spheres represent the local free energy minima while the tubes connecting the minima represent the pathways. The size of the spheres representing the local energy minima scales linearly along the displayed free energy range (small spheres indicates high free energy while large spheres indicate low free energy). The diameter of the pathways scales linearly with the free energy and thus with the oxygen affinity (thinner radius represent high free energies and low oxygen affinity). The free energy at the minima and along the pathways follows the same color scale. The channel 1 coincides with the channel inferred from the X-ray data , whereas the channel 2 and channel 3 are alternative routes to reach the BNC.

shows the relation between the association constant, 1/Kd, and the total binding free energy ∆Gtot, the binding free energy of the covalent state ∆Gdc and noncovalent state ∆Gdm. Each binding state and the corresponding free energy term are illustrated on the free energy profile.

(A) The free energy (potential of mean force) changes for the first, second and third methyl transfers from AdoMet to H3-K9, H3-K9me1 and H3-K9me2, respectively, as a function of the reaction coordinate [R = r(C_M…S_δ)−r(C_M…N_ζ)] in the wild-type GLP. The first methyl transfer: blue and solid line with a free energy barrier of 13.4 kcal/mol; the second methyl transfer: red and dashed line with a free energy barrier of 15.8 kcal/mol (or about 2.4 kcal/mol higher than that of the first methyl transfer); the third methyl transfer: green and solid line with a free energy barrier of 22.1 kcal/mol (or about 8.7 kcal/mol higher than that of the first methyl transfer). (B) The free energy changes for the first and second methyl transfers as a function of the reaction coordinate in the F1209Y mutant. The first methyl transfer: blue and solid line with a free energy barrier of 13.8 kcal/mol; the second methyl transfer: red and dashed line with a free energy barrier of 17.4 kcal/mol (or about 3.6 kcal/mol higher than that of the first methyl transfer).

RACER simulation predicted free energy is compared with Mfold minimum free energy as well as unity slope (dashed line). RACER and Mfold have the same correlation free energy predictive capability (R² = 0.93 to experimental free energies, experiment), but RACER has a slope closer to unity (slope = 1.2), while Mfold over-stabilizes the free energy of larger RNAs (slope = 1.5). Error bars present on RACER data come from a Monte Carlo bootstrap error analysis as implemented in WHAM by Alan Grossfield (most errors are within the data point).