Dynamics and Cooperativity of the Catalytic Subunit of Protein Kinase A

Abstract

The protein kinase family is a large and diverse family of enzymes that regulate almost all facets of cellular signaling. Protein kinases function as molecular switches by attaching a phosphate group to a Ser/Thr/Tyr hydroxyl group by using ATP as a co-factor to increase or decrease the activity of their protein substrates. Over 500 kinases have been discovered, including pseudo-kinases that share the same fold but are catalytic inactive, and the kinome comprises of 2% of the human genome. As such this family of enzymes has attracted much interest for understanding cellular signaling and for disease therapeutics. Of these kinases, the catalytic-subunit of cAMP-dependent Protein Kinase A (PKA-C) has been a benchmark for the study of conserved features of eukaryotic protein kinases. The overall goal of this thesis is to understand the conformational landscape, dynamics and cooperativity present in PKA-C. This work has been accomplished by utilizing two different techniques; NMR spectroscopy and isothermal titration calorimetry (ITC). NMR spectroscopy was used to define the conformational landscape of PKA-C by using backbone and methyl side chain chemical shifts and the conformational dynamics of each of the states have been studied by using relaxation studies.. The role of binding cooperativity was studied extensively using ITC for substrate and kinase mutants as well as for different nucleotides and ATP-competitive inhibitors.