ArticleJournal of molecular evolution2026
Hierarchical Organization of Evolutionary Constraint in Duplicated EF-Hand Motifs.
Article in Journal of molecular evolution, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Calmodulin is a conserved [Formula: see text]-binding protein composed of four EF-hand motifs that retain structural symmetry despite functional differences. How evolutionary constraint is organized across these repeated EF-hands remains unclear. Here, we analyzed calmodulin using a protein language model (PLM) to determine whether divergence is distributed uniformly across the motifs or concentrated at residues in the [Formula: see text]-binding loops. In native embedding space, EF-hands showed greater similarity between duplicated pairs than between same-lobe pairs. Position-specific differences were strongest at loop positions, including both canonical coordinating and non-coordinating positions. These results support a hierarchical organization in which the duplicated structure remains conserved while divergence emerges through localized specialization. Our findings show that the PLM captures sequence-context information that is not fully explained by alignment-based conservation.
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