High-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants

Mihkel Örd, Matthew J. Winters, Mythili S. Subbanna, Natàlia Martín Garrido, Victoria I. Cushing, Johanna Kliche, Caroline Benz, Ylva Ivarsson, Basil J. Greber, Peter M. Pryciak () and Norman E. Davey ()
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Mihkel Örd: University of Cambridge, CRUK Cambridge Institute
Matthew J. Winters: University of Massachusetts Chan Medical School
Mythili S. Subbanna: University of Massachusetts Chan Medical School
Natàlia Martín Garrido: The Institute of Cancer Research, Chester Beatty Laboratories
Victoria I. Cushing: The Institute of Cancer Research, Chester Beatty Laboratories
Johanna Kliche: Department of Chemistry - BMC, Uppsala University, Husargatan 3
Caroline Benz: Department of Chemistry - BMC, Uppsala University, Husargatan 3
Ylva Ivarsson: Department of Chemistry - BMC, Uppsala University, Husargatan 3
Basil J. Greber: The Institute of Cancer Research, Chester Beatty Laboratories
Peter M. Pryciak: University of Massachusetts Chan Medical School
Norman E. Davey: The Institute of Cancer Research, Chester Beatty Laboratories

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-62765-z

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