Related Experiment Video

Updated: Jun 1, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

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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
PubMed

Insights

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.
Keywords:
bilayer interferometrycell cyclekinasesprotein–protein interactions

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