Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces. Phys Biol 8:035006

Koc University, Center for Computational Biology and Bioinformatics, and College of Engineering, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey.
Physical Biology (Impact Factor: 2.54). 06/2011; 8(3):035006. DOI: 10.1088/1478-3975/8/3/035006
Source: PubMed


The vast majority of the chores in the living cell involve protein-protein interactions. Providing details of protein interactions at the residue level and incorporating them into protein interaction networks are crucial toward the elucidation of a dynamic picture of cells. Despite the rapid increase in the number of structurally known protein complexes, we are still far away from a complete network. Given experimental limitations, computational modeling of protein interactions is a prerequisite to proceed on the way to complete structural networks. In this work, we focus on the question 'how do proteins interact?' rather than 'which proteins interact?' and we review structure-based protein-protein interaction prediction approaches. As a sample approach for modeling protein interactions, PRISM is detailed which combines structural similarity and evolutionary conservation in protein interfaces to infer structures of complexes in the protein interaction network. This will ultimately help us to understand the role of protein interfaces in predicting bound conformations.

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    • "Using only interface architectures as templates, independent of global sequence or structure homology, is a significant improvement on this scheme, because it was found that similar protein interface architectures are reused by structurally and functionally different protein pairs (Tuncbag et al., 2011a,b; Gunther et al., 2007; Kundrotas and Vakser, 2010; Sinha et al., 2010, 2012). In the PRISM protocol (Tuncbag et al., 2011a,b) the target proteins, after being transformed onto the template complex, additionally undergo flexible refinement. The performance of various docking and scoring methods, servers and groups are evaluated in a community-wide experiment , the Critical Assessment of Predicted Interactions (CAPRI) (Lensink and Wodak, 2013; Janin, 2013). "
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    ABSTRACT: Understanding the molecular basis of protein function remains a central goal of biology, with the hope to elucidate the role of human genes in health and in disease, and to rationally design therapies through targeted molecular perturbations. We review here some of the computational techniques and resources available for characterizing a critical aspect of protein function - those mediated by protein-protein interactions (PPI). We describe several applications and recent successes of the Evolutionary Trace (ET) in identifying molecular events and shapes that underlie protein function and specificity in both eukaryotes and prokaryotes. ET is a part of analytical approaches based on the successes and failures of evolution that enable the rational control of PPI.
    Progress in Biophysics and Molecular Biology 05/2014; 116(2-3). DOI:10.1016/j.pbiomolbio.2014.05.004 · 2.27 Impact Factor
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    • "In this study, we constructed the structural pathway based on protein-protein interactions (PPIs). The commonly used node-and-edge description of pathways, where nodes represent proteins and edges the interactions between them, are useful, but do not provide structural interaction detail [33,34]. Further, in many cases, such as IL-10 and the receptors in this study, the available structural interaction data of the proteins are incomplete. "
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    ABSTRACT: Background Inflammation has significant roles in all phases of tumor development, including initiation, progression and metastasis. Interleukin-10 (IL-10) is a well-known immuno-modulatory cytokine with an anti-inflammatory activity. Lack of IL-10 allows induction of pro-inflammatory cytokines and hinders anti-tumor immunity, thereby favoring tumor growth. The IL-10 network is among the most important paths linking cancer and inflammation. The simple node-and-edge network representation is useful, but limited, hampering the understanding of the mechanistic details of signaling pathways. Structural networks complete the missing parts, and provide details. The IL-10 structural network may shed light on the mechanisms through which disease-related mutations work and the pathogenesis of malignancies. Results Using PRISM (a PRotein Interactions by Structural Matching tool), we constructed the structural network of IL-10, which includes its first and second degree protein neighbor interactions. We predicted the structures of complexes involved in these interactions, thereby enriching the available structural data. In order to reveal the significance of the interactions, we exploited mutations identified in cancer patients, mapping them onto key proteins of this network. We analyzed the effect of these mutations on the interactions, and demonstrated a relation between these and inflammation and cancer. Our results suggest that mutations that disrupt the interactions of IL-10 with its receptors (IL-10RA and IL-10RB) and α2-macroglobulin (A2M) may enhance inflammation and modulate anti-tumor immunity. Likewise, mutations that weaken the A2M-APP (amyloid precursor protein) association may increase the proliferative effect of APP through preventing β-amyloid degradation by the A2M receptor, and mutations that abolish the A2M-Kallikrein-13 (KLK13) interaction may lead to cell proliferation and metastasis through the destructive effect of KLK13 on the extracellular matrix. Conclusions Prediction of protein-protein interactions through structural matching can enrich the available cellular pathways. In addition, the structural data of protein complexes suggest how oncogenic mutations influence the interactions and explain their potential impact on IL-10 signaling in cancer and inflammation.
    BMC Genomics 05/2014; 15 Suppl 4(Suppl 4):S2. DOI:10.1186/1471-2164-15-S4-S2 · 3.99 Impact Factor
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    • "The downsides of the docking algorithms are that exploring the large conformation space consumes huge computational resources and that binding geometry evaluations based on various ranking systems are not clearly effective in distinguishing the actual structures from a large set of possibilities. Template-based prediction approaches reduce the solution space of the docking approaches [2] on the premise that PPI sites are relatively conserved throughout proteins with similar sequence and structural features [28]. With the template-based approaches, high-throughput modeling of PPI sites based on protein docking have been shown with accuracy feasible for low to medium resolution models [34]. "
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    ABSTRACT: Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors.
    PLoS ONE 06/2012; 7(6):e37706. DOI:10.1371/journal.pone.0037706 · 3.23 Impact Factor
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