Functional determinants of protein assembly into homomeric complexes

Abstract

Approximately half of proteins with experimentally determined structures can interact with other copies of themselves and assemble into homomeric complexes, the overwhelming majority of which (>96%) are symmetric. Although homomerisation is often assumed to a functionally beneficial result of evolutionary selection, there has been little systematic analysis of the relationship between homomer structure and function. Here, utilizing the large numbers of structures and functional annotations now available, we have investigated how proteins that assemble into different types of homomers are associated with different biological functions. We observe that homomers from different symmetry groups are significantly enriched in distinct functions, and can often provide simple physical and geometrical explanations for these associations in regards to substrate recognition or physical environment. One of the strongest associations is the tendency for metabolic enzymes to form dihedral complexes, which we suggest is closely related to allosteric regulation. We provide a physical explanation for why allostery is related to dihedral complexes: it allows for efficient propagation of conformational changes across isologous (i.e. symmetric) interfaces. Overall we demonstrate a clear relationship between protein function and homomer symmetry that has important implications for understanding protein evolution, as well as for predicting protein function and quaternary structure.

Figure 1

The top five most significant positively enriched non-redundant GO terms within each symmetry group in the sequence filtered set of proteins are tabulated with their associated P-value from Fisher’s Exact Test. The equivalent enrichment and P-values in the more stringent, domain-filtered, set is also shown for comparison. (a) Twofold symmetric homomers are associated with annotated functions that involve small and/or twofold symmetric binding partners. Cartoon of a symmetric dimer illustrating the twofold rotation element and isologous interface (blue) with the DNA-binding domain of a heat-shock transcription factor serving as an example. (b) Higher-order cyclic protein complexes are required for specialist architectures and are enriched in functional terms involving membrane structures. A C₄ symmetric complex with the fourfold rotation element and heterologous interfaces (red) highlighted. These interfaces are formed by a head-to-tail orientation of the protein subunits (orange). An inositol-1,4,5-triphosphate activated trans-membrane Ca²⁺ ion channel illustrates an example. (c) Protein complexes with dihedral symmetries have a mixture of both isologous and heterologous interfaces and are enriched in metabolic processes. Dihedral complexes in group D_N constitutes either N symmetric dimers or two symmetric N-mers. A D₃ dehydrogenase illustrates an example of a dimer-of-trimers with heterologous (red) interfaces in the head-to-tail trimers that form a dimer with isologous (blue) interfaces. (d) Monomers preferentially act together with large substrates. A β-amylase monomer from B. cereus illustrates an example (yellow).

Figure 2

Enrichment of allostery in homomers from different symmetry groups. (a) Enrichment by complexes with closed symmetry in the subset of allosteric proteins. (b) A similar enrichment profile is seen when controlling for metabolic enzymes. The enrichment is calculated as the difference between the fraction of complexes in the specific set compared to the whole set of homomers. The enrichment is presented as the odds ratio, plotted on a logarithmic axis. P-values are calculated with Fisher’s exact test and error bars represent 68% melded binomial confidence intervals.

Figure 3

Allostery is associated with the present of isologous intersubunit interfaces. (a) Cartoon representation of the intersubunit interactions D₂ and D₃ complexes. D₂ complexes have two perpendicular twofold symmetry axes and therefore have only isologous interfaces, whereas D₃ complexes can have either all isologous interfaces or a mixture of isologous and heterologous interfaces. (b) Comparison of the enrichment in allostery between dihedral tetramers (D₂) vs. dihedral homomers with six or more subunits (D_n(n > 2)). P-values are calculated with Fisher’s exact test and error bars represent 68% melded binomial confidence intervals. (c) Density plot illustrating the distribution of isologous interfaces in the allosteric (orange) and non-allosteric (light blue) sets of dihedral complexes with more than four subunits. The P-value is from the two-sample Wilcoxon test.