Duplication accelerates the evolution of structural complexity in protein quaternary structure

Abstract

Gene duplication, from single genes to whole genomes, has been observed in organisms across all taxa. Despite its prevalence, the evolutionary benefits of this mechanism are the subject of ongoing debate. Gene duplication can significantly alter the self-assembly of protein quaternary structures, impacting the dosage or interaction proclivity. Here we use a lattice model of self-assembly as a coarse-grained representation of protein complex assembly, and show that it can be used to examine potential evolutionary advantages of duplication. Duplication provides a unique mechanism for increasing the evolvability of protein complexes by enabling the transformation of symmetric homomeric interactions into heteromeric ones. This transformation is extensively observed in in silico evolutionary simulations of the lattice model, with duplication events significantly accelerating the rate at which structural complexity increases. These coarse-grained simulation results are corroborated with a large-scale analysis of complexes from the Protein Data Bank.