Structural disorder promotes assembly of protein complexes

Abstract

Background: The idea that the assembly of protein complexes is linked with protein disorder has been inferred from a few large complexes, such as the viral capsid or bacterial flagellar system, only. The relationship, which suggests that larger complexes have more disorder, has never been systematically tested. The recent high-throughput analyses of protein-protein interactions and protein complexes in the cell generated data that enable to address this issue by bioinformatic means.

Results: In this work we predicted structural disorder for both E. coli and S. cerevisiae, and correlated it with the size of complexes. Using IUPred to predict the disorder for each complex, we found a statistically significant correlation between disorder and the number of proteins assembled into complexes. The distribution of disorder has a median value of 10% in yeast for complexes of 2-4 components (6% in E. coli), but 18% for complexes in the size range of 11-100 proteins (12% in E. coli). The level of disorder as assessed for regions longer than 30 consecutive disordered residues shows an even stronger division between small and large complexes (median values about 4% for complexes of 2-4 components, but 12% for complexes of 11-100 components in yeast). The predicted correlation is also supported by experimental evidence, by observing the structural disorder in protein components of complexes that can be found in the Protein Data Bank (median values 1. 5% for complexes of 2-4 components, and 9.6% for complexes of 11-100 components in yeast). Further analysis shows that this correlation is not directly linked with the increased disorder in hub proteins, but reflects a genuine systemic property of the proteins that make up the complexes.

Conclusion: Overall, it is suggested and discussed that the assembly of protein-protein complexes is enabled and probably promoted by protein disorder.

Figure 1

Distribution of the complex-averaged disorder for complexes of different sizes. The distributions are grouped by the sizes of complexes and singular proteins for which no evidence of complex-forming has been found. Magenta – singular proteins, cyan – complexes size 2–4, orange – complexes size 5–10, blue – complexes size 11–100, red: unique to complexes of size 11–100. The average disorder for each complex has been calculated by predicting the individual protein components and averaging them for each complex individually. A) E. coli complexes, taken from the IntAct database (significant differences among the different distributions with chi-square tests, p-value < 0.02). B) Yeast complexes (significantly different distributions, p-value < 0.01).

Figure 2

Median values for predicted and observed disorder of complexes. Median values were calculated for distributions of IUPred-predicted disorder of complexes of various numbers of components (Figure 1). Green – yeast predicted, yellow – E. coli predicted, purple – E. coli observed. For E. coli, we also recorded the complex average and median values for the different size groups derived from the observed values of matching PDB structures (with at least 90% sequence identity between the complex components and the PDB-s and almost full coverage, i.e. the length difference between the protein components and the PDB-s was less than 50 amino acids).

Figure 3

Distributions of complex-averaged disorder of long disordered regions for complexes of different sizes. The distributions are grouped by the sizes of complexes and singular proteins for which no evidence of complex-forming has been found. Magenta - singular proteins, cyan - complexes size 2-4, orange - complexes size 5-10, blue - complexes size 11-100. The average disorder for each complex has been calculated by predicting the individual protein components, and averaging them for each complex individually by considering only residues which fall into segments longer than 30 consecutive disordered residues. Complex averages were calculated and their % distributions are presented here. Medians are indicated in parentheses. A) E. coli complexes (significantly different distributions, p-value<0.001). B) Yeast complexes (significantly different distributions, p-value<0.001).

Figure 4

Distribution of the relative disorder of the proteins in complexes of various sizes. Individual proteins were taken from the complexes, their levels of disorder were predicted by the IUPred server, and are shown grouped according to the size of the complexes they were found in. Median values are indicated in parentheses. Magenta - singular proteins, cyan - complexes size 2-4, orange - complexes size 5-10, blue - complexes size 11-100. A) E. coli complexes (significantly different distributions, p-value<0.001, with the exception of difference between complexes of 2-4 and 5-10 proteins). B) Yeast complexes (significantly different distributions, p-value<0.001).

Figure 5

Distribution of the experimentally observed average disorder of proteins in complexes of various sizes. Averages of disorder were determined for those E. coli complexes, in which at least one component had an at least 90% sequence identity with a PDB chain whose length differed at most by 50 amino acids. Magenta – singular proteins, cyan – complexes size 2–4, orange – complexes size 5–10, blue – complexes size 11–100. The average disorder of the complexes was calculated by averaging the observed disorder of the matching PDB-s only.

Figure 6

The maximum complex size each E. coli protein occurs in, as a function of its "hubness". Only those E. coli proteins are presented here that appear in both pairwise interactions and complexes in the IntAct database (852 proteins altogether). For each protein the size of the largest complex it appears in is presented as the function of the number of interacting partners in pairwise interactions. Data are presented on a log-log scale. The fitted curve represents a linear relationship but a negligible one, apparent from the very small value of R², 0.02.