ArticleProceedings of the National Academy of Sciences of the United States of America2008
Built-in loops allow versatility in domain-domain interactions: lessons from self-interacting domains.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
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- Designed Loop Extension Followed by Combinatorial Screening Confers High Specificity to a Broad Matrix MetalloproteinaseInhibitor.Journal of molecular biology · 2023Article
- SH2 Domains: Folding, Binding and Therapeutical Approaches.International journal of molecular sciences · 2022Review
- How gene duplication diversifies the landscape of protein oligomeric state and function.Current opinion in genetics & development · 2022Review
- Oligomeric interactions maintain active-site structure in a noncooperative enzyme family.The EMBO journal · 2022Article
- Conserved Molecular Signatures in the Spike, Nucleocapsid, and Polymerase Proteins Specific for the GenusGenes · 2022Article
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- Homodimerization of a glycoside hydrolase family GH1 β-glucosidase suggests distinct activity of enzyme different states.Protein science : a publication of the Protein Society · 2020Article
- DIP/Dpr interactions and the evolutionary design of specificity in protein families.Nature communications · 2020Article
- Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles.Microorganisms · 2019Article
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- Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering.Angewandte Chemie (International ed. in English) · 2019Review
- Dopamine transporter forms stable dimers in the live cell plasma membrane in a phosphatidylinositol 4,5-bisphosphate-independent manner.The Journal of biological chemistry · 2019Article
- Ultrahigh specificity in a network of computationally designed protein-interaction pairs.Nature communications · 2018Article
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Authors and funding
3 authors.
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Abstract
Compilations of domain-domain interactions based on solved structures suggest there are distinct domain pairs that are used repeatedly in different protein contexts to mediate protein-protein interactions. However, not all protein pairs with the corresponding domains that can potentially mediate interaction do interact, even when they are colocalized and coexpressed. It is conceivable that there are structural and sequence features, below the domain level, that play a role in determining the potential of domains to mediate protein-protein interactions. Here, we discover such features by comparing domains that, on the one hand, mediate homodimerization of proteins and, on the other, occur in different proteins that are documented as monomers. Intriguingly, this comparison uncovered surface loops that can be considered as determinants of the interactions. There are enabling loops, which mediate the domain interactions, and disabling loops that prevent the interactions. The presence of the enabling/disabling loops is consistent with the fulfillment/prevention of the interaction and is highly preserved in evolution. This suggests that, along with the preservation of structural elements that enable interaction, evolution maintains elements intended to prevent unwanted interactions. The enabling and disabling loops discovered in this study have implications in prediction of protein-protein interactions, by pointing to the protein regions that determine the interaction. Our results extend the hierarchy of attributes that collectively establish the modularity of domain-mediated protein-protein interactions.
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