ArticleProceedings of the National Academy of Sciences of the United States of America2016
Evolution of domain-peptide interactions to coadapt specificity and affinity to functional diversity.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 46 citations in OpenAlex.
- Article
- Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network.Cell · 2025Article
- Dissection of the role of a Src homology 3 domain in the evolution of binding preference of paralogous proteins.Genetics · 2024Article
- Data-driven design of orthogonal protein-protein interactions.Science signaling · 2023Article
- Short Linear Motifs Orchestrate Functioning of Human Proteins during Embryonic Development, Redox Regulation, and Cancer.Metabolites · 2022Article
- Article
- CellectSeq: In silico discovery of antibodies targeting integral membrane proteins combining in situ selections and next-generation sequencing.Communications biology · 2021Article
- Protein context shapes the specificity of SH3 domain-mediated interactions in vivo.Nature communications · 2021Article
- Large-scale survey and database of high affinity ligands for peptide recognition modules.Molecular systems biology · 2020Article
- Interactions by Disorder - A Matter of Context.Frontiers in molecular biosciences · 2020Review
- Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions.Journal of molecular biology · 2019Article
- MotifAnalyzer-PDZ: A computational program to investigate the evolution of PDZ-binding target specificity.Protein science : a publication of the Protein Society · 2019Article
- The PCNA interaction motifs revisited: thinking outside the PIP-box.Cellular and molecular life sciences : CMLS · 2019Article
- Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling.Journal of biosciences · 2018Review
- Article
- Article
- Molecular basis of interactions between SH3 domain-containing proteins and the proline-rich region of the ubiquitin ligase Itch.The Journal of biological chemistry · 2017Article
- Exhaustive search of linear information encoding protein-peptide recognition.PLoS computational biology · 2017Article
- Linking molecular evolution to molecular grafting.The Journal of biological chemistryReview
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Evolution of complexity in eukaryotic proteomes has arisen, in part, through emergence of modular independently folded domains mediating protein interactions via binding to short linear peptides in proteins. Over 30 years, structural properties and sequence preferences of these peptides have been extensively characterized. Less successful, however, were efforts to establish relationships between physicochemical properties and functions of domain-peptide interactions. To our knowledge, we have devised the first strategy to exhaustively explore the binding specificity of protein domain-peptide interactions. We applied the strategy to SH3 domains to determine the properties of their binding peptides starting from various experimental data. The strategy identified the majority (∼70%) of experimentally determined SH3 binding sites. We discovered mutual relationships among binding specificity, binding affinity, and structural properties and evolution of linear peptides. Remarkably, we found that these properties are also related to functional diversity, defined by depth of proteins within hierarchies of gene ontologies. Our results revealed that linear peptides evolved to coadapt specificity and affinity to functional diversity of domain-peptide interactions. Thus, domain-peptide interactions follow human-constructed gene ontologies, which suggest that our understanding of biological process hierarchies reflect the way chemical and thermodynamic properties of linear peptides and their interaction networks, in general, have evolved.
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