Fig. 3: Agreement between simulations and SAXS data for multidomain proteins.
From: Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution
Mean radii of gyration (Rg) calculated from simulations plotted against Rg determined from Guinier fits to SAXS data for (a) simulations with unmodified Martini 3, (b) simulations with protein-water interactions in Martini 3 rescaled by λPW = 1.10, and (c) simulations with protein-protein interactions in Martini 3 rescaled by λPP = 0.88. Error bars on the experimental Rg-values were determined using Atsas AUTORG and represent a fitting error from the Guinier fit plus a standard deviation over possible selections of the Guinier region. The diagonal is shown as a dashed line and a linear fit with intercept 0 weighted by experimental errors is shown as a solid line. Pearson correlation coefficients (rP) with standard error of the mean from bootstrapping with 9999 resamples are shown on the plots. d Reduced χ2 to experimental SAXS intensities given by SAXS intensities calculated from unmodified Martini 3 simulations (blue) and Martini 3 simulations with protein-water interactions rescaled by λPW = 1.10 (orange) or protein-protein interactions rescaled by λPP = 0.88 (green). Mean and standard error of the mean over all 15 proteins are shown on the plot. Note the logarithmic scale for \({\chi }_{r}^{2}\). e Representative conformation of TIA1 with an Rg corresponding to the average Rg in (blue) simulations with unmodified Martini 3, (orange) simulations with protein-water interactions in Martini 3 rescaled by λPW = 1.10, and (green) simulations with protein-protein interactions in Martini 3 rescaled by λPP = 0.88. Simulations of hnRNPA1, hisSUMO-hnRNPA1 and TIA1 with λPW = 1.10 were taken from Thomasen et al.7. Source data are provided as a Source Data file.
