Figure 3.

Soft partitioning of the chaperonin complex into stochastically coherent clusters. A total of 35 clusters are identified at reduced level 4, each shown by a different color in (A). Owing to the seven-fold cylindrical symmetry, five distinct types of clusters are observed: clusters (I) 1–7 centered on the GroES monomers, (II) 8–14 centered on A–I domains of the cis ring subunits, (III) 15–21 around the E-domain of cis ring subunits, (IV) 22–28 near the E–I domains of trans ring subunits and (V) 29–35 near A–I domains of trans ring subunits. (B) displays The soft participation of residues in two example clusters encircled in panel A, clusters 11 (top) and 32 (bottom) respectively, by ribbon diagrams, color-coded red–orange–yellow–green–cyan in the order of decreasing probabilistic participation. Results are valid for all cylindrically related seven subunits along the heptameric rings, but for illustration we focus on chains D (yellow) and E (magenta) on cis ring, J (pink) and K (green) on trans ring and R (blue) on GroES, in (C). (D) shows ownership distributions (curves in color) for representative clusters of different types, numbered 1–7, 11, 18, 25 and 32, with the associated clusters shown in color on the ribbon diagrams to the right. The labels on the abscissa indicate the chain identities: A–G on cis ring, H–N on trans ring and O–U on GroES cap. The gray curve in each panel shows the maximal responsibility curve deduced from the maxima of all ownership curves. The portions of the ownership curves, which overlap with the maximal responsibility curve, define the hard clusters displayed in panel A.