Electrostatic properties of the structure of the docking and dimerization domain of protein kinase A IIα

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Abstract
The structure of the N‐terminal docking and dimerization domain of the type IIα regulatory subunit (RIIα D/D) of protein kinase A (PKA) forms a noncovalent stand‐alone X‐type four‐helix bundle structural motif, consisting of two helix‐loop‐helix monomers. RIIα D/D possesses a strong hydrophobic core and two distinct, exposed faces. A hydrophobic face with a groove is the site of protein–protein interactions necessary for subcellular localization. A highly charged face, opposite to the former, may be involved in regulation of protein–protein interactions as a result of changes in phosphorylation state of the regulatory subunit. Although recent studies have addressed the hydrophobic character of packing of RIIα D/D and revealed the function of the hydrophobic face as the binding site to A‐kinase anchoring proteins (AKAPs), little attention has been paid to the charges involved in structure and function. To examine the electrostatic character of the structure of RIIα D/D we have predicted mean apparent pKa values, based on Poisson–Boltzmann electrostatic calculations, using an ensemble of calculated dimer structures. We propose that the helix promoting sequence Glu34‐X‐X‐X‐Arg38 stabilizes the second helix of each monomer, through the formation of a (i, i +4) side chain salt bridge. We show that a weak inter‐helical hydrogen bond between Tyr35–Glu19 of each monomer contributes to tertiary packing and may be responsible for discriminating from alternative quaternary packing of the two monomers. We also show that an inter‐monomer hydrogen bond between Asp30–Arg40 contributes to quaternary packing. We propose that the charged face comprising of Asp27‐Asp30‐Glu34‐Arg38‐Arg40‐Glu41‐Arg43‐Arg44 may be necessary to provide flexibility or stability in the region between the C‐terminus and the interdomain/autoinhibitory sequence of RIIα, depending on the activation state of PKA. We also discuss the structural requirements necessary for the formation of a stacked (rather than intertwined) dimer, which has consequences for the orientation of the functionally important and distinct faces.