Fig. 5: Structural evolutionary analysis of ORF2p.
From: Structures, functions and adaptations of the human LINE-1 ORF2 protein
a, Structural Shannon entropy (‘structural entropy’) in ORF2p, measured from 57 L1 sequences from diverse vertebrates and plants and smoothed by averaging a 130-residue (approximately 10% of protein length) sliding window was lowest in the ancestral palm domain and highest in the C-terminal domain. b, Structural entropy correlates strongly with retrotransposition (retroT, ****P < 10−15, two-tailed t-test), comparing with retroT measurements from 417 consecutive scanning trialanine mutants of ORF2p38. c, Mapping retroT and structural entropy onto the structure of ORF2p highlighted the overall concordance, as well as a notable discordance in the helix clamp around residue Y823 (inset). d, Structural perplexity, an information-theoretic measurement of the structural distance between two proteins, relative to ORF2p RT of a curated set of 50 proteins calculated using Plexy (Supplementary Methods). e, Normalized structural perplexity between full-length ORF2p and all proteins in the curated set, represented using multidimensional scaling such that the relative pairwise Euclidean distances were preserved (Supplementary Methods). For RT and RT-like proteins, the polypeptide with polymerase activity is used; for other proteins, the entire biological assembly is used. Dashed red lines represent the first and second standard deviations of the two-dimensional distance from full-length ORF2p. 2D, two-dimensional.
