Soft disorder modulates the assembly path of protein complexes

TL;DR

This study reveals that soft disordered regions in proteins play a crucial role in the assembly of protein complexes, with disordered regions becoming more involved as complexes grow, and links this to structure prediction confidence metrics.

Contribution

It provides the first large-scale statistical evidence connecting soft disorder regions to protein assembly pathways and suggests using AF2 confidence scores to predict assembly routes.

Findings

Disordered regions are involved in new interface formation during oligomerization.

Location of soft disordered residues changes with increasing number of partners.

AF2's pLDDT scores correlate with soft disorder regions, aiding assembly path prediction.

Abstract

The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide statistical evidence for the involvement of highly mobile and disordered regions in complex assembly. We ordered the entire set of X-ray crystallographic structures in the PDB into hierarchies of progressive interactions involving identical or very similar protein chains, yielding 40205 hierarchies of complexes with increasing numbers of partners. We then examine them as proxies for the assembly pathways. Using this database, we show that upon oligomerisation, new interfaces tend to be observed at residues that were characterised as softly disordered (flexible, amorphous or missing residues) in the complexes preceding them in the hierarchy. We also rule out the possibility that this correlation is just a surface effect by restricting the analysis to residues on the surface. Interestingly, we find that the location of soft disordered residues in the sequence changes as the number of partners increases. Our results show that there is a general mechanism for protein assembly that involves soft disorder and modulates the way protein complexes are assembled. This work highlights the difficulty of predicting the structure of large protein complexes from sequence and emphasises the importance of linking predictors of disorder to the next generation of predictors of complex structure. Finally, we investigate the relationship between the AF2's confidence metric pLDDT for structure prediction in unbound vs. bound structures, and soft disorder. We show a strong correlation between AF2 low confidence residues and the union of all regions of soft disorder observed in the hierarchy. This paves the way for using the pLDDT metric as a proxy for predicting assembly paths.