Mapping Intersubunit Interactions of the Regulatory Subunit (RIα) in the Type I Holoenzyme of Protein Kinase A by Amide Hydrogen/Deuterium Exchange Mass Spectrometry (DXMS)

• Published in: Journal of molecular biology Vol. 340; no. 5; pp. 1185 - 1196
• Main Authors: Hamuro, Yoshimoto, Anand, Ganesh S, Kim, Jack S, Juliano, Celina, Stranz, David D, Taylor, Susan S, Woods, Virgil L
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 23.07.2004
• Subjects: amide hydrogen/deuterium exchange mass spectometry; Amides - chemistry; Amino Acid Sequence; cAPK; Cyclic AMP - metabolism; Cyclic AMP-Dependent Protein Kinase RIalpha Subunit; Cyclic AMP-Dependent Protein Kinases - chemistry; Cyclic AMP-Dependent Protein Kinases - metabolism; Deuterium - chemistry; Deuterium Exchange Measurement; DXMS; Holoenzymes - chemistry; Holoenzymes - metabolism; Mass Spectrometry; Models, Molecular; Molecular Sequence Data; Peptide Fragments - chemistry; Peptide Fragments - metabolism; PKA; Protein Structure, Quaternary; Protein Subunits - chemistry; Protein Subunits - metabolism; C-subunit, catalytic subunit; Mops, 3-( N-morpholino)propane sulfonic acid; cAMP, adenosine 3′,5′-cyclic monophosphate; H/D exchange, hydrogen/deuterium exchange; PKA; βX:Y, β-sheet X in cAMP-binding domain Y; amide hydrogen/deuterium exchange mass spectometry; cGMP, guanosine 3′,5′-cyclic monophosphate; GuHCl, guanidine hydrochloride; D/D domain, dimerization/docking domain; R-subunit, regulatory-subunit; cAPK; PBC, phosphate-binding cassette; cAMP:A, cAMP-binding domain A; cAMP:B, cAMP-binding domain B; DXMS; αX:Y, α-helix X in cAMP-binding domain Y; DXMS, amide hydrogen/deuterium exchange mass spectrometry; PKA, protein kinase A; TFA, trifluoroacetic acid
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2004.05.042

Protein kinase A (PKA), a central locus for cAMP signaling in the cell, is composed of regulatory (R) and catalytic (C) subunits. The C-subunits are maintained in an inactive state by binding to the R-subunit dimer in a tetrameric holoenzyme complex (R 2C 2). PKA is activated by cAMP binding to the R-subunits which induces a conformational change leading to release of the active C-subunit. Enzymatic activity of the C-subunit is thus regulated by cAMP via the R-subunit, which toggles between cAMP and C-subunit bound states. The R-subunit is composed of a dimerization/docking (D/D) domain connected to two cAMP-binding domains (cAMP:A and cAMP:B). While crystal structures of the free C-subunit and cAMP-bound states of a deletion mutant of the R-subunit are known, there is no structure of the holoenzyme complex or of the cAMP-free state of the R-subunit. An important step in understanding the cAMP-dependent activation of PKA is to map the R–C interface and characterize the mutually exclusive interactions of the R-subunit with cAMP and C-subunit. Amide hydrogen/deuterium exchange mass spectrometry is a suitable method that has provided insights into the different states of the R-subunit in solution, thereby allowing mapping of the effects of cAMP and C-subunit on different regions of the R-subunit. Our study has localized interactions with the C-subunit to a small contiguous surface on the cAMP:A domain and the linker region. In addition, C-subunit binding causes increased amide hydrogen exchange within both cAMP-domains, suggesting that these regions become more flexible in the holoenzyme and are primed to bind cAMP. Furthermore, the difference in the protection patterns between RIα and the previously studied RIIβ upon cAMP-binding suggests isoform-specific differences in cAMP-dependent regulation of PKA activity.