ALLOSTERIC MECHANISMS FOR THE cAMP-DEPENDENT CONTROL OF FUNCTIONAL INTER-DOMAIN LINKERS

Abstract

The activation of Protein Kinase A (PKA) and of Hyperpolarization-activated and Cyclic Nucleotide-modulated channels (HCN) is controlled by cAMP through cAMP binding domains (CBDs), which serve as cAMP-dependent conformational switches to regulate downstream signaling pathways. The binding of the cAMP allosteric effector removes the auto-inhibition imposed by linkers that are adjacent to the CBDs of PKA and HCN. However, our understanding of how cAMP binding to the structured CBD controls the adjacent inhibitory linkers is currently limited. Herein, we investigate through NMR spectroscopy the interactions between the CBDs of HCN and PKA and the respective adjacent linkers. Chapters 2 and 3 of this thesis focus on the linkers N-terminal to PKA CBD-A and CBD-B, respectively, while Chapter 4 centers on the linker N-terminal to the HCN CBD. We show that in the case of PKA the linker N-terminal to CBD-A is flexible, but is coupled to the CBD-A through state active selective interactions. In the case of the CBD-B of PKA the state selective interactions with the linker N-terminal to it are to a large extent lost and replaced by state-selective inter-CBD interactions, which in turn control the conformational ensemble accessible to the inter-domain linker. Unlike PKA, in the case of HCN, the primary mechanism of cAMP-dependent linker control is through the state-selective destabilization of the structured tetrameric N-terminal linker. Overall, this thesis reports three distinct mechanisms through which linkers in HCN and PKA serve not only as simple covalent threads, but also as integral parts of the allosteric networks underlying auto-inhibition and cAMP dependent activation.