High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants
Abstract Many regulatory protein-protein interactions depend on Short Linear Motifs (SLiMs). In the cell cycle, cyclin-CDKs recognize SLiMs to control substrate recruitment and phosphorylation timing. Here, we measure the relative binding strength of ~100,000 peptides to 11 human cyclins from five f...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-08-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-62765-z |
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| author | Mihkel Örd Matthew J. Winters Mythili S. Subbanna Natàlia de Martín Garrido Victoria I. Cushing Johanna Kliche Caroline Benz Ylva Ivarsson Basil J. Greber Peter M. Pryciak Norman E. Davey |
| author_facet | Mihkel Örd Matthew J. Winters Mythili S. Subbanna Natàlia de Martín Garrido Victoria I. Cushing Johanna Kliche Caroline Benz Ylva Ivarsson Basil J. Greber Peter M. Pryciak Norman E. Davey |
| author_sort | Mihkel Örd |
| collection | DOAJ |
| description | Abstract Many regulatory protein-protein interactions depend on Short Linear Motifs (SLiMs). In the cell cycle, cyclin-CDKs recognize SLiMs to control substrate recruitment and phosphorylation timing. Here, we measure the relative binding strength of ~100,000 peptides to 11 human cyclins from five families (D, E, A, B, and F). Using a quantitative intracellular binding assay and large-scale tiled peptide screening, we identify multiple non-canonical binders unveiling a broader repertoire of cyclin docking motif types. Cryo-electron microscopy and saturation mutagenesis studies reveal distinct binding modes and sequence features governing motif recognition, binding strength, and cyclin preference. Docking motifs vary from highly selective to pan-cyclin, thereby fine-tuning the timing of CDK phosphorylation during cell cycle. Overall, these findings provide insights into the rules encoding specificity and affinity of SLiM-mediated interactions and offer a framework for understanding motif-driven protein networks across the proteome. |
| format | Article |
| id | doaj-art-4d9c871f4c3c407489e814723825c2c2 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-4d9c871f4c3c407489e814723825c2c22025-08-20T03:46:09ZengNature PortfolioNature Communications2041-17232025-08-0116111910.1038/s41467-025-62765-zHigh-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinantsMihkel Örd0Matthew J. Winters1Mythili S. Subbanna2Natàlia de Martín Garrido3Victoria I. Cushing4Johanna Kliche5Caroline Benz6Ylva Ivarsson7Basil J. Greber8Peter M. Pryciak9Norman E. Davey10University of Cambridge, CRUK Cambridge InstituteDepartment of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolDepartment of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolThe Institute of Cancer Research, Chester Beatty LaboratoriesThe Institute of Cancer Research, Chester Beatty LaboratoriesDepartment of Chemistry - BMC, Uppsala University, Husargatan 3Department of Chemistry - BMC, Uppsala University, Husargatan 3Department of Chemistry - BMC, Uppsala University, Husargatan 3The Institute of Cancer Research, Chester Beatty LaboratoriesDepartment of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolThe Institute of Cancer Research, Chester Beatty LaboratoriesAbstract Many regulatory protein-protein interactions depend on Short Linear Motifs (SLiMs). In the cell cycle, cyclin-CDKs recognize SLiMs to control substrate recruitment and phosphorylation timing. Here, we measure the relative binding strength of ~100,000 peptides to 11 human cyclins from five families (D, E, A, B, and F). Using a quantitative intracellular binding assay and large-scale tiled peptide screening, we identify multiple non-canonical binders unveiling a broader repertoire of cyclin docking motif types. Cryo-electron microscopy and saturation mutagenesis studies reveal distinct binding modes and sequence features governing motif recognition, binding strength, and cyclin preference. Docking motifs vary from highly selective to pan-cyclin, thereby fine-tuning the timing of CDK phosphorylation during cell cycle. Overall, these findings provide insights into the rules encoding specificity and affinity of SLiM-mediated interactions and offer a framework for understanding motif-driven protein networks across the proteome.https://doi.org/10.1038/s41467-025-62765-z |
| spellingShingle | Mihkel Örd Matthew J. Winters Mythili S. Subbanna Natàlia de Martín Garrido Victoria I. Cushing Johanna Kliche Caroline Benz Ylva Ivarsson Basil J. Greber Peter M. Pryciak Norman E. Davey High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants Nature Communications |
| title | High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants |
| title_full | High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants |
| title_fullStr | High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants |
| title_full_unstemmed | High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants |
| title_short | High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants |
| title_sort | high throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants |
| url | https://doi.org/10.1038/s41467-025-62765-z |
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