ArticleScientific reports2017
Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 21 citations in OpenAlex.
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- Ibetazol, a novel inhibitor of importin β1-mediated nuclear import.Communications biology · 2024Article
- Contextual AI models for single-cell protein biology.Nature methods · 2024Article
- Contextual AI models for single-cell protein biology.bioRxiv : the preprint server for biology · 2024Article
- Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology.JACS Au · 2024Review
- Nanoparticular and other carriers to deliver lactoferrin for antimicrobial, antibiofilm and bone-regenerating effects: a review.Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine · 2023Review
- Modeling the Dynamics of Protein-Protein Interfaces, How and Why?Molecules (Basel, Switzerland) · 2022Review
- Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing.Methods in molecular biology (Clifton, N.J.) · 2019Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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