Fig. 5: Protein self-association in solution.
From: Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution
a Fraction bound calculated from MD simulations of two copies of the folded proteins ubiquitin and villin HP36, and two copies of the IDPs α-synuclein, p15PAF, hTau40, and FUS LCD, with unmodified Martini 3 (blue), Martini 3 with protein-water interactions rescaled by λPW = 1.10 (orange) (taken from Thomasen et al.7), and Martini 3 with protein-protein interactions rescaled by λPP = 0.88 (green). Box plots show the results of 10 replica simulations. The bound fraction in agreement with Kd = 4.9 mM for ubiquitin self-association is shown as a dashed line37. The bound fraction in agreement with Kd > 1.5 mM for villin HP36 self-association is shown as a shaded gray area38. α-synuclein, p15PAF, and hTau40 should not self-associate under the given conditions based on PRE34,35 or SEC-MALLS39 data, while FUS LCD should transiently self-associate based on PRE data33. Boxplots show the first quartile, median, and third quartile; whiskers extend from the box to the farthest data point lying within 1.5 times the inter-quartile range from the box, and points outside the whiskers are shown individually. b Interchain PREs calculated from the simulations of two copies of FUS LCD from panel a and comparison with experimental PREs (black)33. PREs are shown for the three spin-label sites at residues 16, 86, and 142 marked with dashed black lines. The rotational correlation time, τc, was selected individually for each λ to minimize \({\chi }_{r}^{2}\). Error bars represent the standard error of the mean over 10 replica simulations. c \({\chi }_{r}^{2}\) between calculated and experimental PRE data for two copies of FUS LCD shown in panel (b). Source data are provided as a Source Data file.
