Figure 1.
Results summary for predicted change in protein-protein binding affinity for 19 protein-protein interaction targets [13].
Each R2 is the correlation between the predicted change in binding affinity and the experimental change in binding affinity. Three different refinement methods were used, as described in Materials and Methods. Accuracy is an overall measure of the ability to categorize residues as “neutral” or “hot spot” (see Results and Discussion). “Hotspot precision” indicates the ability of the model to select mutations that make binding affinity worse by more than 1 kcal/mol. The experimental standard deviation is computed after removing qualifiers from qualified values (i.e. >2.0 is treated as 2.0) and has units of kcal/mol.
Figure 2.
Plots of observed versus predicted affinity using the “minimization” refinement method, for four targets: 1JCK, 1VFB, 1DFJ, and 3HFM.
The R2 correlation, accuracy, and hotspot precision are shown for each target.
Figure 3.
Mutations in where repacking residues nearby the mutation improves the prediction compared to minimization alone.
In each case the mutant structure refined by minimization is shown in cyan and the mutant structure where a 5A radius was refined by side-chain prediction is shown in brown. The mutation residue is shown in ball-and-stick. Panel A shows the C:Thr170Ala mutation in 1AHW along with nearby residues. Panels B and C show the C:Trp43Ala mutation in 1FCC.
Figure 4.
Comparison of the Accuracy metric for the minimization MM-GBSA refinement method to two different null hypotheses: the null hypothesis that all mutations are neutral, and the null hypothesis that all mutations make binding affinity worse by more than 1 kcal/mol.
Figure 5.
Plots of predicted versus experimental change in protein-protein binding affinity for two additional targets: 1C4Z and 2OM2.
For 2OM2 the results shown are for the minimization refinement method (with only the mutated residue minimized) and for 1C4Z the results shown are for side chain refinement, with a 0 Å radius (i.e. only the mutated residue refined).
Figure 6.
Thermodynamic cycle for calculating the net ΔΔG free energy difference between binding the wild-type protein P and the mutant protein P’.
In the associated equation for ΔΔGbind, E is the calculated energy of each protein or complex after refinement.