Decoding the dynamic mechanism of allosteric activation in the cyclin-dependent kinase Cdk2

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Project Abstract This project reaches towards a new paradigm for how conformational dynamics of protein kinases drive their catalytic activation, and provides an important case study of how protein dynamics can be commandeered to artificially control kinase activity with allosteric small molecules. The protein kinases are a large family of signaling proteins that control cell growth and proliferation in all eukaryotic cells. Kinases behave like molecular switches, transitioning between catalytically active “on” and inactive “off” states in a tightly controlled fashion to bring about prescribed changes in cell physiology. This stringent regulatory control is widely disrupted in cancer, and targeting aberrant kinase activity with small- molecule drugs is now an important component of many cancer treatments. Crystal structures have given us static pictures of the on and off states of kinases, but they tell us little about how the proteins transition between these states, which is an inherently dynamic process. The nature of these dynamic transitions and how they are perturbed in disease remain largely obscure, a fact that has impeded our ability to design allosteric therapeutics that switch kinases to the off state by mimicking their natural control mechanisms. Instead, existing kinase inhibitors work by binding to the highly conserved active site, a mode of action that makes them poorly selective. The goal of this project is to use a combination of experimental methods that provide complementary information about protein dynamics to determine how kinases transition between different conformational states, and to understand how kinase dynamics can be commandeered by small-molecule drugs to artificially modulate kinase function. Using nuclear magnetic resonance and optical spectroscopy applied to the cyclin- dependent kinase Cdk2, a key regulator of cell cycle progression, we aim to reveal 1) the allosteric coupling mechanism that links cyclin binding to activation of Cdk2, 2) how phosphorylation cooperates with the cyclin subunit to tune protein dynamics and promote catalytic activity, and 3) how dynamic conformational changes in Cdk2 control access of small-molecule ligands to allosteric pockets in the kinase. The insights from this work will fundamentally advance our understanding of allosteric control mechanisms in proteins, and help set the stage for the design of advanced allosteric therapeutics that effectively harness allostery to modulate kinase function.