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. 2004 Sep 3;101(37):13460–13465. doi: 10.1073/pnas.0405585101

Fig. 5.

Fig. 5.

Correlation between underwrapping and ancestry of structural superfamilies and their time evolution. (A) Extent of overall wrapping deficiency of yeast domain folds versus the ancestry of the proteins. The overall wrapping deficiency r, defined as number of dehydrons per 100 backbone hydrogen bonds, is inferred from sequence (Methods), except for domains reported in the PDB (e.g., the yeast Hsp90 chaperone, or the yeast cellular prion protein). The ancestry group of a protein is determined by the number of organisms (from a group of four) containing orthologs of the protein, as indicated in main text. The symbol 〈r〉 indicates average over all yeast proteins in a SCOP superfamily. The open squares represent the average 〈r〉 over each ancestry group, whereas the filled squares represent averages over individual SCOP superfamilies represented in an ancestry group. The wrapping deficiency r value dispersions over all proteins in an ancestry group are shown as error bars. Ancestry group 1 comprises 4,913 yeast proteins and 161 SCOP superfamilies; group 2 comprises 1,149 proteins and 41 SCOP superfamilies; group 3 comprises 175 proteins and 6 SCOP superfamilies; and group 4 comprises 57 proteins and 2 SCOP superfamilies. Selected families are plotted for each ancestry group. Listed in decreasing dehydron density, they are as follows: group 4: P loop NTP hydrolases (signal transduction), ARM repeat; group 3: protein kinases (PK), phospholipase C/P1 nucleases, class II aaRS biotin synthetases; group 2: Rossman fold domains, NAD(P) binding, trypsin-like serine proteases, EF-hand; group 1: nucleotidyl transferases. The figure reveals a significant correlation between ancestry and wrapping deficiency, thereby implying a relationship between centrality and age, as wrapping is a structural marker for interactivity (5). (B) Dependence of the average number of wrapping defects on evolutionary time for selected SCOP superfamilies in yeast belonging to ancestry groups 2, 3, and 4. The exponential time dependence is indicative of an autocatalytic rate of accretion of dehydrons or, equivalently, of connectivities (4), supporting the “rich gets richer” scenario of network evolution. The phospholipase C/P1 nucleases from ancestry group 3 have a relatively low intercept, only slightly above the intercept for the Rossman domain, belonging to group 2. This is compatible with the large dispersion in wrapping deficiency within the ancestry families, as shown in A.