Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins

Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling. In this study, we proposed a new representation for structural PPI networks inspecting the alternative conformations of proteins. We performed a large-scale study by creating breast cancer metastasis network and equipped it with different conformers of proteins. Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. However, using even this small set of alternative conformations we observed a considerable increase in our protein docking predictions. Our protein-protein interaction predictions increased from 54% to 76% using the alternative conformations. We also showed the benefits of investigating structural data and alternative conformations of proteins through three case studies

WNT signalling control by KDM5C during development affects cognition

Although KDM5C is one of the most frequently mutated genes in X-linked intellectual disability, the exact mechanisms that lead to cognitive impairment remain unknown. Here we use human patient-derived induced pluripotent stem cells and Kdm5c knockout mice to conduct cellular, transcriptomic, chromatin and behavioural studies. KDM5C is identified as a safeguard to ensure that neurodevelopment occurs at an appropriate timescale, the disruption of which leads to intellectual disability. Specifically, there is a developmental window during which KDM5C directly controls WNT output to regulate the timely transition of primary to intermediate progenitor cells and consequently neurogenesis. Treatment with WNT signalling modulators at specific times reveal that only a transient alteration of the canonical WNT signalling pathway is sufficient to rescue the transcriptomic and chromatin landscapes in patient-derived cells and to induce these changes in wild-type cells. Notably, WNT inhibition during this developmental period also rescues behavioural changes of Kdm5c knockout mice. Conversely, a single injection of WNT3A into the brains of wild-type embryonic mice cause anxiety and memory alterations. Our work identifies KDM5C as a crucial sentinel for neurodevelopment and sheds new light on KDM5C mutation-associated intellectual disability. The results also increase our general understanding of memory and anxiety formation, with the identification of WNT functioning in a transient nature to affect long-lasting cognitive function

Multi-interface binding strategy for the same protein pairs.

<p>(<b>a</b>) Histogram of protein-protein interactions which have different binding structures at the same shared site or different binding sites. 7962 protein-protein pairwise interactions use more than one interface conformation in order to interact with the same partner. Complex with one interface structure is pair of Phenylethanolamine N-methyltransferase with Phenylethanolamine N-methyltransferase, with two interface structures are pairs of probable two-component response regulator with probable two-component response regulator, with three interface structures are pairs of Hypothetical oxidoreductase yiaK with Hypothetical oxidoreductase yiaK, with four interface structures are pairs of Neurotoxin BoNT/A with Neurotoxin BoNT/A, with five different interface structures are pairs of Cytochrome P450 3A4 with Cytochrome P450 3A4 and eighteen interface structures are pairs of Calmodulin 2 with Calmodulin 2. (<b>b</b>) Multiple interaction sites of Histone deacetylase 8 (red-1VKGA). Six different interface architectures of interaction between Histone deacetylase 8 and Histone deacetylase 8 are shown. One of the binding sites is shared by three partners. The others are different. Gray-1VKGB, orange-3RQDB, green-1W22B are at binding site A, yellow-3F0RC is at binding site B, blue-3F07B is at binding site C, purple-1T64B is at binding site D. The balls represent the carbon alpha atoms of the interface residues of the complexes. Carbon alpha atoms are labeled according to interaction partners of the 1VKGA. (<b>c</b>) Histone deacetylase 8 (red monomer) uses the same binding site to bind different partners. Small conformational changes in the interface residues assist binding the partners. On the left hand-side, protein complexes are shown and in the center, interface structures are shown in ball and stick. Blue and yellow balls are the interface residues of histone deacetylase 8 (red), and yellow balls also showed the hotspot residues of the interface. Pink and purple balls are the interface residues of the partner monomer shown in gray, orange and green, and pink balls also show the hotspot residues of the interface. In the right side, hotspot residues of the interfaces are given.</p

Similar interfaces with similar and dissimilar global protein folds.

<p>Complexes are shown in cartoon representation and interface residues are shown in ball representation. (a) Bence-Jones Kappa I Protein Bre complex (1BRECF) and Immunoglobulin Light and Heavy chain complex (43C9AC) have 79% interface similarity. (b) Asportakinase complex (3AB2CG) and Thioredoxin complex (3O6TCD) which have different global fold have 77% interface similarity.</p

Network of Interfaces.

<p>(a) Community structure. (b) Node and edge representation in protein interface network. (c) The nodes in the left network which have similarity values higher than 0.80 are grouped as a single node in the right network. The new node and the neighbors’ similarity values are chosen as the maximum similarity value of the edges between the two nodes which were grouped and the neighbor nodes (e.g. Node G and node H).</p

Comparison of the average relative accessible surface areas.

<p>The average relative accessible surface area of the representative interfaces and their nearby residues are showed. We suggested using 40% RASA value which corresponded to 99% of the average interface RASA values in order to extract interface residues using RASA values of the residues.</p

Comparison of the silhouette values.

<p>The silhouette value distribution over the protein interfaces generated by hierarchical clustering and community finding algorithm is presented. The new clusters are better clustered according to the silhouette values.</p

Protein interfaces and interface clusters based on years.

<p>(a) Protein interface and interface clusters evaluation during years. (b) Distribution of protein interface cluster sizes throughout years. While the number of protein interface clusters is increasing, the cluster sizes are getting denser. The largest cluster in 1999 had 238 members that increased to 1361 in 2011. The minimum cluster size criterion is used to stop the algorithm in order to prevent the network nodes as network size of 1. During separation of the networks, for example, if one of the networks divided into two networks which have 4 and 6 nodes respectively, the algorithm only tries to divide the network which is above 5 (if it is possible) because the other network reached its final state according to our stopping criterion.</p