Fig. 4: Unique conformational remodeling of macromolecular complexes is specifically associated with different stimuli.

Correlation comparison for a functional clusters presented in Fig. 3, b interacting proteins, and c, d proteins annotated with gene ontology terms associated with macromolecular complexes. The pairwise correlation strength was calculated for all comparison proteins then binned according to whether one (outside) or both (inside) proteins identified with the feature of interest. The mean for each protein in both bins was then calculated and the resultant inside and outside values were compared according to a two-tailed t-test. *p < 0.05, **p < 0.01, ***p < 0.001. Terms related to the proteasome are highlighted in bold text. e–g Human 26 S proteasome ribbon structure adapted from PDB: 6MSB, consisting of the core 20 S proteasome (dark gray) and a single 19 S regulatory particle (light gray). Variations of the structure are presented for e MG132, f VER155008, and g novobiocin, whereby individual cysteine-containing peptides are colored according to their increase (red) or decrease (blue) in reactivity. The corresponding protein subunits are labeled with an equivalent color scheme. In a–d, individual points are overlayed on boxplots displayed as follows: center line corresponds to the median; box limits display upper and lower quartiles; and where shown, whiskers extend to the last or first data point that is within 1.5× the interquartile range of the box limits in the upper and lower directions respectively. Source data are provided as a Source Data file.