On the variation of structural divergence among residues in enzyme evolution

Structural divergence varies among protein residues. Unlike the classic problem of substitution rate variation, this structural divergence variation has been largely ignored. Here we show that in families of functionally conserved homologous enzymes, structural divergence increases with both residue flexibility and distance from the active site. Although these factors are correlated, we demonstrate through modelling that the pattern arises from two independent types of evolutionary constraints, non-functional and functional. Their relative importance varies across enzyme families: as functional constraints increase from 4% to 85%, non-functional constraints decrease from 96% to 15%, reshaping the divergence pattern. This analysis revises two accepted views in protein evolution: First, evolutionary variation has been thought to mirror protein dynamics generally, but we show this similarity exists only when non-functional constraints dominate. Second, active site structural conservation has been attributed to functional constraints alone, but we show it stems largely from their location in rigid regions where non-functional constraints are high.