Large protein complex interfaces have evolved to promote cotranslational assembly

Abstract

Assembly pathways of protein complexes should be precise and efficient to minimise misfolding and unwanted interactions with other proteins in the cell. One way to achieve this is by seeding complex assembly during translation via nascent chain engagement. Here, we considered the possibility that the propensity of subunits to cotranslationally assemble is ingrained within the interface hierarchy of protein complexes. Using a combination of proteome-specific structure data and assembly-onset positions determined by ribosome profiling, we show that larger interfaces are prioritised in the course of cotranslational assembly. We observe that this effect is not exclusive to homomeric complexes, but appears to drive the assembly of heteromeric subunits, to the extent that interface size differences are detectable between N and C-terminal locations, with the former being larger on average. We provide explanations to this phenomenon and discuss its importance in a biological context.

Buffering of genetic dominance by allele-specific protein complex assembly

“…We have previously shown that cotranslationally assembling members of the different symmetry groups tend to have larger interfaces (Badonyi and Marsh 2022), but they also differ in their level of cotranslational assembly, with members of the cyclic group being the least likely to cotranslationally assemble ( Figure S1E ). When we subset AD and AR homomers based upon their symmetry group, we find a relatively large variation in the level of cotranslational assembly ( Figure S1F ).…”

“…The third structural property we investigated is the relative interface location (Badonyi and Marsh 2022). N-terminal regions of proteins are more likely to be involved in cotranslational interactions because of vectorial synthesis on the ribosome, an intuitive assumption supported by experimental observations (Bertolini et al 2021; Kamenova et al 2019; Natan et al 2018; Shiber et al 2018).…”

“…We next assessed the influence of subunit interface area in homomeric subunits, which we have shown to have a strong relationship with cotranslational assembly (Badonyi and Marsh 2022).…”

“…The relative interface location is a value between 0 and 1 indicating the location of the interface relative to the protein termini (N=0 and C=1), and it was calculated as previously described (Badonyi and Marsh 2022). To ensure the analysis is not biased by homologous proteins, we generated a distance matrix based on the sequences of the chains from the structures using Clustal Omega version 1.2.4 (Sievers et al 2011).…”

“…We are beginning to understand which structural properties are important for or predispose subunits to undergo this mode of assembly. Thus far, these include N-terminally exposed interface residues (Bertolini et al 2021; Kamenova et al 2019; Natan et al 2018; Shiber et al 2018), a large interface area (Badonyi and Marsh 2022), a high alpha helix content and presence of coiled coil motifs (Bertolini et al 2021) or domain invasion motifs (Seidel et al 2022). Although many studies have provided insight into the functional and evolutionary aspects of cotranslational assembly, our understanding of the genetic impact of its allele-specific nature is lacking.…”