Differences in Binding Affinity Among Cell-cycle CDK and Cyclin Pairs
Sivasankar Putta1, Carina A Villegas1, Seth M Rubin1
1Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, United States.
Journal of Molecular Biology
|January 18, 2025
Summary
This study quantifies cell-cycle cyclin-dependent kinase (CDK) and cyclin interactions, revealing canonical pairs exhibit highest affinity. Findings provide insights into noncanonical pair activation in cancer.
Area of Science:
- Cell Biology
- Molecular Biology
- Biochemistry
Background:
- Mammalian cell cycle control relies on cyclin-dependent kinases (CDKs) activated by cyclins.
- Previous studies qualitatively suggested specific CDK-cyclin pairings, but quantitative data on binding kinetics and affinity were lacking.
Purpose of the Study:
- To quantitatively measure binding kinetics and affinity for all cell-cycle CDK-cyclin pairings.
- To explore the structural basis for CDK-cyclin interaction preferences.
- To assess the catalytic activity of CDK-cyclin complexes.
Main Methods:
- Biolayer interferometry (BLI) assay to quantify association/dissociation rates and binding constants.
- Structural modeling and mutagenesis to investigate sequence-specific interactions.
- Assay of ATP phosphotransfer activity for CDK-cyclin complexes.
Main Results:
- Highest affinity interactions confirmed for canonical CDK-cyclin pairs (e.g., CDK1/CycB, CDK2/CycA, CDK2/CycE, CDK4/CycD).
- Specific sequence differences identified as key determinants for preferential binding, exemplified by CDK2/CycA versus CDK2/CycD.
- Most CDK-cyclin complexes demonstrated competence in ATP phosphotransfer, with variations in catalytic efficiency observed.
Conclusions:
- Quantitative binding data validates canonical CDK-cyclin interactions.
- Structural insights explain specific binding preferences.
- The catalytic competence of various complexes suggests potential roles for noncanonical pairings in cell proliferation, particularly in cancer.
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