Fig. 2
From: Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations
Computational predictions and experimental validations of binding affinities and kinetics of PMI–Mdm2. a, b Maximum likelihood estimates of the binding free energy and residence time, respectively, as a function of the amount of data used. Diamonds mark maximum likelihood estimates, error bars indicate 95% confidence intervals. x% of total data means that x% of all biased data and x% of all unbiased data were used. c, d Estimates of binding free energy and residence time as a function of data composition. The fraction of biased simulation data is varied between 0 and 100% of all biased data while keeping the sum of the amount of biased and the amount of unbiased data constant at 502 μs. e Validation of the simulation model: binding free energy differences (ΔΔG) of PMI–Mdm2 upon alanine mutations of the PMI peptide, compared between the present simulations and experiments59. Only biased simulation data was used and analyzed with MBAR62. Error bars mark standard deviations (simulation error computed using bootstrap, see Supplementary Note 3.3). f Cyan: average and standard deviations of anisotropy time traces from three repeats of a binding competition experiment, Mdm2 (10 nM), pre-incubated with labeled PMI (10 nM), was mixed with unlabeled PMI (10 μM). A mono-exponential function (black) was fitted to the average time trace. Gray: control without unlabeled PMI
