Imperfect symmetry facilitated the evolution of specificity and high-order stoichiometry in vertebrate hemoglobin

ABSTRACT

Many proteins form paralogous multimers – molecular complexes in which evolutionarily related proteins are arranged into specific quaternary structures. Little is known about the mechanisms by which they acquired their stoichiometry (the number of total subunits in the complex) and heterospecificity (the preference of subunits for their paralogs rather than other copies of the same protein). Here we use ancestral protein reconstruction and biochemical experiments to study historical increases in stoichiometry and specificity during the evolution of vertebrate hemoglobin (Hb), a α _2β2 heterotetramer that evolved from a homodimeric ancestor after a gene duplication. We show that the mechanisms for this evolutionary transition was simple. One hydrophobic substitution in subunit β after the gene duplication was sufficient to cause the ancestral dimer to homotetramerize with high affinity across a new interface. During this same interval, a single-residue deletion in subunit α at the older interface conferred specificity for the heterotetrameric form and the trans -orientation of subunits within it. These sudden transitions in stoichiometry and specificity were possible because the interfaces in Hb are isologous – involving the same surface patch on interacting subunits, rotated 180° relative to each other – but the symmetry is slightly imperfect. This architecture amplifies the impacts of individual mutations on stoichiometry and specificity, especially in higher-order complexes, and allows single substitutions to differentially affect heteromeric vs homomeric interactions. Many multimers are isologous, and symmetry in proteins is always imperfect; our findings therefore suggest that elaborate and specific molecular complexes may often evolve via simple genetic and physical mechanisms.

Significance statement

Many molecular complexes are made up of proteins related by gene duplication, but how these assemblies evolve is poorly understood. Using ancestral protein reconstruction and biochemical experiments, we dissected how vertebrate hemoglobin, which comprises two copies each of two related proteins, acquired this architecture from a homodimeric ancestor. Each aspect of this transition – from dimer to tetramer and homomer to heteromer – had a simple genetic basis: a single-site mutation in each protein drove the changes in size and specificity. These rapid transitions were possible because hemoglobin’s architecture is symmetric, which amplified the effect of small biochemical changes on the assembly of the complex. Many protein complexes are symmetrical, suggesting that they too may have evolved via simple genetic mechanisms.