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Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies

Figure 2

The relationships between superfamily ages, secondary structure and length.

Figure A gives a percentile plot of the age distributions of 5 SCOP classes. For ease of interpretation, plots of multi-domain and membrane proteins have been omitted. Each line represents the distribution of ages generated using a different phylogenetic tree. Noticeably, superfamilies' age distributions rise quicker than those of the other classes. Moreover, superfamilies classified as small under SCOP are significantly younger than the other classes. Figure B gives a boxplot of the length distributions for these SCOP classes. Roughly speaking, the ordering of the classes by length corresponds to their ordering by age. superfamilies are longer and small proteins are shorter than the other classes. Figure C gives a percentile plot of the age distributions of superfamilies with different average domain lengths. Multi-domain superfamilies were omitted from this analysis. Ancient superfamilies are significantly longer than their new-born counterparts. Figure D gives a percentile plot of the age distributions of two populations of superfamilies: those containing a majority parallel strand direction and those with more antiparallel strands. The parallel population is significantly older than the antiparallel superfamilies.

doi: https://doi.org/10.1371/journal.pcbi.1003325.g002