Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states

Abstract

The main principles of protein-protein recognition are elucidated by the studies of homooligomers which in turn mediate and regulate gene expression, activity of enzymes, ion channels, receptors, and cell-cell adhesion processes. Here we explore oligomeric states of homologous proteins in various organisms to better understand the functional roles and evolutionary mechanisms of homooligomerization. We observe a great diversity in mechanisms controlling oligomerization and focus in our study on insertions and deletions in homologous proteins and how they enable or disable complex formation. We show that insertions and deletions which differentiate monomers and dimers have a significant tendency to be located on the interaction interfaces and about a quarter of all proteins studied and forty percent of enzymes have regions which mediate or disrupt the formation of oligomers. We suggest that relatively small insertions or deletions may have a profound effect on complex stability and/or specificity. Indeed removal of complex enabling regions from protein structures in many cases resulted in the complete or partial loss of stability. Moreover, we find that insertions and deletions modulating oligomerization have a lower aggregation propensity and contain a larger fraction of polar, charged residues, glycine and proline compared to conventional interfaces and protein surface. Most likely, these regions may mediate specific interactions, prevent nonspecific dysfunctional aggregation and preclude undesired interactions between close paralogs therefore separating their functional pathways. Last, we show how the presence or absence of insertions and deletions on interfaces might be of practical value in annotating protein oligomeric states.

Fig. 1.

The length distribution of the enabling and disabling regions in the nonredundant set.

Fig. 2.

Percentage of secondary structures in the enabling and disabling regions in the nonredundant set. Percentage of secondary structures in the full dataset is shown in Fig. S2. In all cases including the full dataset, more than half of enabling and disabling regions are located in loops, approximately 30–40% in α-helices, and 10% in β-strands.

Fig. 3.

The amino acid propensities in the nonredundant set for (A) enabling regions (B) disabling regions. The propensities of the full dataset are shown in Fig. S3 C and D. The propensities are calculated as the log ratio between frequencies of a particular amino acid in enabling/disabling regions and frequency of the same amino acid in aligned conventional interfaces.

Fig. 4.

Aggregation propensities calculated using the nonredundant set for four different regions: enabling, disabling, aligned interface, and overall molecular surface. The distributions of aggregation propensities are smoothed by the Gaussian kernel density estimation. Conventional interfaces have the highest aggregation propensity, whereas disabling regions have the lowest aggregation propensity. Aggregation propensities for the full dataset are also shown in Fig. S4B.

Fig. 5.

Illustration of enabling features with insertion of new secondary structure elements, 1P3C—1FQ3 pair from the trypsin-like serine protease family (cd00190). Two subunits of the homodimers are shown in light-blue and light-red. Enabling regions and their surrounding residues are represented by the red tubes, whereas corresponding residues in the monomer are represented by the yellow tubes. A small β-sheet contributing to the enabling interaction (shown in red tube) is absent from the monomer (shown in the yellow tube).

Fig. 6.

Illustration of enabling features with the extension of existing secondary structure elements. (A) 2D73—3A24 from the glycoside hydrolase family (pfam10566). Two longer loops create an interface that is absent from the monomer (B) 1TYY—2QHP from the Fructokinases family (cd01167). The β-sheet is more extensive in the homodimer than in the monomer. (C) 3E3A—3E0X from the Esterases and lipases family (cd00312). Two α-helices are extended in the homodimer compared to the monomer. In all figures, the two subunits of the homodimers are shown in light-blue and light-red. Enabling regions are represented by red tubes, whereas corresponding regions in the monomer are shown by yellow tubes.

Fig. 7.

Illustration of disabling features of 2VQR—3B5Q from the phosphonate monoester hydrolase family (cd00016). (A) Front view of the interface in 2VQR (homodimer) with several disabling residues shown in yellow for 3B5Q (monomer). (B) Side view of the interface. Interface and surface on one subunit of the homodimer are shown in dark-red and light-red. The binding region (C-terminal region) of the other subunit is represented by the blue tube. A disabling region that fills a part of the interface is shown in yellow.