  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.
