Assembly reflects evolution of protein complexes

Abstract

A homomer is formed by self-interacting copies of a protein unit. This is functionally important1,2, as in allostery3-5, and structurally crucial because mis-assembly of homomers is implicated in disease6,7. Homomers are widespread, with 50-70% of proteins with a known quaternary state assembling into such structures8,9. Despite their prevalence, their role in the evolution of cellular machinery10,11 and the potential for their use in the design of new molecular machines12,13, little is known about the mechanisms that drive formation of homomers at the level of evolution and assembly in the cell9,14. Here we present an analysis of over 5,000 unique atomic structures and show that the quaternary structure of homomers is conserved in over 70% of protein pairs sharing as little as 30% sequence identity. Where quaternary structure is not conserved among the members of a protein family, a detailed investigation revealed well-defined evolutionary pathways by which proteins transit between different quaternary structure types. Furthermore, we show by perturbing subunit interfaces within complexes and by mass spectrometry analysis15, that the (dis)assembly pathway mimics the evolutionary pathway. These data represent a molecular analogy to Haeckel's evolutionary paradigm of embryonic development, where an intermediate in the assembly of a complex represents a form that appeared in its own evolutionary history. Our model of self-assembly allows reliable prediction of evolution and assembly of a complex solely from its crystal structure.Although homomers are central to biology, only anecdotal knowledge exists on their principles of evolution and assembly, and no unifying theory has been proposed. Large increases in structural data in recent years, however, have enabled us to study quaternary structure or spatial arrangement of subunits on a data set of 5,375 unique structures. This data set is ∼tenfold greater than any studied previously16 (Methods). On the basis of this data set, we quantify how often proteins change their quaternary structure, and identify the evolutionary routes taken to do so. Subsequently, as evolution of a complex can be viewed as assembly over a long timescale, we compare evolutionary routes with (dis)assembly routes probed by mass spectrometry.Homomers can be separated into two main classes of open or closed symmetry. The first class corresponds to open structures that would polymerize to infinity in the absence of limiting factors. Such assemblies (for example, tubulin and actin) are rare in our data set (3%), probably because their innate dynamic character renders them difficult to crystallize. In contrast, closed symmetries are finite in space, and most homomers adopt either cyclic or (Fig. 1a), with only a small fraction (1%) having cubic symmetry (not shown). Throughout we denote Cn as a cyclic complex containing n subunits, and Dn as a dihedral complex containing 2n subunits.It has long been observed that smaller complexes are more abundant than larger ones, and even numbers of sub...

The Levinthal paradox of the interactome

“…Supporting evidence for this conclusion is provided by a recent mass-spectroscopy study of the conservation and formation of the quaternary structure of protein homomers. 37 This study confirmed that structure alone is sufficient to infer both the evolutionary and physical path of subunit assembly, an example of ''ontogeny recapitulates phylogeny'' at the cellular level.…”

IgG Fab Fragments Forming Bivalent Complexes by a Conformational Mechanism That Is Reversible by Osmolytes

“…Any favored mechanism must take into account the fact that all four Fabs tested in the present study displayed the propensity to form these complexes. It has been reported that 50 -70% of proteins display some positive level of homodimerization (57), which brings up the possibility that the observations in the current work may reflect a more universal tendency among proteins. The phenomena of "protein breathing" and "folding funnels" (58,59) suggest that proteins can vacillate between a number of different conformations that represent entropically favorable free energy states.…”

Asymmetric perturbations of signalling oligomers

“…Advances in electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) has made mass spectroscopy (MS) a powerful tool to assess the architecture, connectivity, evolution, asymmetry of even large multidomain complexes (Bich and Zenobi, 2009;Levy et al, 2008;Kirshenbaum et al, 2010;Sharon, 2013). No requirement for crystals, low sample need (pmol) and short measurement time (min) allowing high-throughput processing are considered to be the main strengths of MS. As it has been shown recently, nanoflow ESI-MS studies can distinguish coexisting protein populations with different number of bound ligands (nucleotides for ATPases) and determine the rank order of binding affinities and the role of transient asymmetries of higher-order ring systems in the function of chaperonins and transcription activators (Dyachenko et al, 2013;Zhang et al, 2014).…”

“…In summary, most dimeric proteins including the signalling ones discussed above have closed (face-to-face) C2 symmetries (Levy et al, 2008). Ligand binding to one subunit can trigger conformational changes of the dimer affecting asymmetrically the binding affinity of the two subunits.…”

“…In fact, it is the least abundant among symmetric proteins (Levy et al, 2008). Still, this symmetry is overrepresented among physiologically and pharmacologically important signalling proteins including the superfamily of pentameric ligand-gated ion channels (pLGICs) with a characteristic Cys-loop.…”