The complexity of protein interactions unravelled from structural disorder

The importance of unstructured biology has quickly grown during the last decades accompanying the explosion of the number of experimentally resolved protein structures. The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the literature, although the number of statistically significant structural studies supporting this idea is surprisingly low. At variance with previous works, our conclusions rely exclusively on a large-scale analysis of all the 134337 X-ray crystallographic structures of the Protein Data Bank averaged over clusters of almost identical protein sequences. In this work, we explore the complexity of the organisation of all the interaction interfaces observed when a protein lies in alternative complexes, showing that interfaces progressively add up in a hierarchical way, which is reflected in a logarithmic law for the size of the union of the interface regions on the number of distinct interfaces. We further investigate the connection of this complexity with different measures of structural disorder: the standard missing residues and a new definition, called soft disorder, that covers all the flexible and structurally amorphous residues of a protein. We show evidences that both the interaction interfaces and the soft disordered regions tend to involve roughly the same amino-acids of the protein, and preliminary results suggesting that soft disorder spots those surface regions where new interfaces are progressively accommodated by complex formation. In fact, our results suggest that structurally disordered regions not only carry crucial information about the location of alternative interfaces within complexes, but also about the order of the assembly. We verify these hypotheses in several examples, such as the DNA binding domains of P53 and P73, the C3 exoenzyme, and two known biological orders of assembly. We finally compare our measures of structural disorder with several disorder bioinformatics predictors, showing that these latter are optimised to predict the residues that are missing in all the alternative structures of a protein and they are not able to catch the progressive evolution of the disordered regions upon complex formation. Yet, the predicted residues, when not missing, tend to be characterised as soft disordered regions. Author summary The Protein Data Bank (PDB) is crowded with proteins that are partially or totally structurally disordered. Nowadays it is widely accepted that Nature uses this disorder to increase a protein's number of possible conformations and interaction interfaces. In this work, we show that the relation between interfaces and structural disorder goes much deeper: the existence of soft structural disorder might be necessary to make an interface. Indeed, interactions with partners take place in the floppy parts of a protein, which means that soft structural disorder might determine the order at which complexes are assembled. Our results are supported by a large-scale analysis of all the crystallographic structures of the PDB and uses no fine-tuning nor learning algorithms.

Automated summary

The study explores the relationship between incomplete protein structure and the interaction interfaces in multiple complexes, revealing that interaction interfaces and soft disordered regions often involve the same amino acids and soft structural disorder may influence the assembly order of complexes.