Extended Data Fig. 7: Correlation of E1A linker dimensions with sequence-encoded features.
From: Conformational buffering underlies functional selection in intrinsically disordered protein regions
a, Linker length control titration experiment. End-to-end distance (Re) of natural sequences (colored circles) compared to synthetic sequences of varying length and constant sequence composition matching the HF_HAdV40 linker (yellow squares). Natural sequences: n = 15 independent simulations were run for each sequence, points represent the mean Re value and error bars represent the standard deviation over the population obtained from the total ensemble from 15 simulations. Synthetic sequences: n = 20 random permutations were generated for each length and simulated under equivalent conditions. The mean Re value (yellow square) is a double average over both conformational space and sequence space. Lines within the yellow squares represent the standard error of the mean across all simulations of a given length, shown to confirm that all random permutations have very similar Re values. b, Net-charge per residue (NCPR) as a function of normalized end-to-end distance for the 27 linkers of Fig. 4a. Inset: NCPR as a function of linker length. Sequences used in the grafting experiment are shown as solid circles and the rest as transparent circles. R = Pearson’s correlation coefficient. c, Correlation between distinct sequence parameters and normalized end-to-end distance (upper panels) or linker length (lower panels) (Supplementary Text 1). R = Pearson’s correlation coefficient. Most R values are < 0.3 with several exceptions. d, Hydrodynamic radius (Rh) for motif-linker-motif constructs of five cleaved E1A variants (shown in Extended Data Fig. 1f,g). The length of each construct is indicated above each bar. Rh was determined from size exclusion chromatography run on Superdex 75 (n = 1, striped colored bars) or Superdex 200 (n = 1, cross-hatched colored bars). The height of each bar indicates the estimated Rh value and the error bars represent the standard deviation obtained from interpolation in the –logMW vs Kav calibration curve (see Methods). Rh was also predicted from all-atom simulations (colored bars). The height of each bar represents the mean Rh value from ten independent simulations of each construct (n = 10), while each individual marker is the mean of each independent simulation.
