Multi-domain proteins form the majority of proteins in eukaryotes. During their formation by tandem duplication or gene fusion, new interactions between domains may arise as a result of the structurally-forced proximity of domains. The proper function of the formed proteins likely required the molecular adjustment of these stress zones by specific amino acid replacements, which should be detectable by the molecular signature of selection that governed their changes. We used multi-domain globins from three different invertebrate lineages to investigate the selective forces that acted throughout the evolution of these molecules. In the youngest of these molecules [Branchipolynoe scaleworm; original duplication ca. 60 million years (Ma)], we were able to detect some amino acids under positive selection corresponding to the initial duplication event. In older lineages (didomain globin from bivalve mollusks and nematodes), there was no evidence of amino acid positions under positive selection, possibly the result of accumulated non-adaptative mutations since the original duplication event (165 and 245 Ma, respectively). Some amino acids under positive selection were sometimes detected in later branches, either after speciation events, or after the initial duplication event. In Branchipolynoe, the position of the amino acids under positive selection on a 3D model suggests some of them are located at the interface between two domains; while others are locate in the heme pocket.
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