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Oxidant sensor in the cGMP-binding pocket of PKGIα regulates nitroxyl-mediated kinase activity. Sci Rep 2017; 7:9938. [PMID: 28855531 PMCID: PMC5577323 DOI: 10.1038/s41598-017-09275-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/18/2017] [Indexed: 12/15/2022] Open
Abstract
Despite the mechanisms for endogenous nitroxyl (HNO) production and action being incompletely understood, pharmacological donors show broad therapeutic promise and are in clinical trials. Mass spectrometry and site-directed mutagenesis showed that chemically distinct HNO donors 1-nitrosocyclohexyl acetate or Angeli’s salt induced disulfides within cGMP-dependent protein kinase I-alpha (PKGIα), an interdisulfide between Cys42 of the two identical subunits of the kinase and a previously unobserved intradisulfide between Cys117 and Cys195 in the high affinity cGMP-binding site. Kinase activity was monitored in cells transfected with wildtype (WT), Cys42Ser or Cys117/195Ser PKGIα that cannot form the inter- or intradisulfide, respectively. HNO enhanced WT kinase activity, an effect significantly attenuated in inter- or intradisulfide-deficient PKGIα. To investigate whether the intradisulfide modulates cGMP binding, real-time imaging was performed in vascular smooth muscle cells expressing a FRET-biosensor comprising the cGMP-binding sites of PKGIα. HNO induced FRET changes similar to those elicited by an increase of cGMP, suggesting that intradisulfide formation is associated with activation of PKGIα. Intradisulfide formation in PKGIα correlated with enhanced HNO-mediated vasorelaxation in mesenteric arteries in vitro and arteriolar dilation in vivo in mice. HNO induces intradisulfide formation in PKGIα, inducing the same effect as cGMP binding, namely kinase activation and thus vasorelaxation.
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2
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Burgers PP, Bruystens J, Burnley RJ, Nikolaev VO, Keshwani M, Wu J, Janssen BJC, Taylor SS, Heck AJR, Scholten A. Structure of smAKAP and its regulation by PKA-mediated phosphorylation. FEBS J 2016; 283:2132-48. [PMID: 27028580 DOI: 10.1111/febs.13726] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/04/2016] [Accepted: 03/29/2016] [Indexed: 12/27/2022]
Abstract
UNLABELLED The A-kinase anchoring protein (AKAP) smAKAP has three extraordinary features; it is very small, it is anchored directly to membranes by acyl motifs, and it interacts almost exclusively with the type I regulatory subunits (RI) of cAMP-dependent kinase (PKA). Here, we determined the crystal structure of smAKAP's A-kinase binding domain (smAKAP-AKB) in complex with the dimerization/docking (D/D) domain of RIα which reveals an extended hydrophobic interface with unique interaction pockets that drive smAKAP's high specificity for RI subunits. We also identify a conserved PKA phosphorylation site at Ser66 in the AKB domain which we predict would cause steric clashes and disrupt binding. This correlates with in vivo colocalization and fluorescence polarization studies, where Ser66 AKB phosphorylation ablates RI binding. Hydrogen/deuterium exchange studies confirm that the AKB helix is accessible and dynamic. Furthermore, full-length smAKAP as well as the unbound AKB is predicted to contain a break at the phosphorylation site, and circular dichroism measurements confirm that the AKB domain loses its helicity following phosphorylation. As the active site of PKA's catalytic subunit does not accommodate α-helices, we predict that the inherent flexibility of the AKB domain enables its phosphorylation by PKA. This represents a novel mechanism, whereby activation of anchored PKA can terminate its binding to smAKAP affecting the regulation of localized cAMP signaling events. DATABASE Structural data are available in the PDB under accession number 5HVZ.
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Affiliation(s)
- Pepijn P Burgers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Jessica Bruystens
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Rebecca J Burnley
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
| | | | - Malik Keshwani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Jian Wu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Bert J C Janssen
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA.,Department of Pharmacology, University of California San Diego, La Jolla, California, USA.,The Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, USA
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Arjen Scholten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.,Netherlands Proteomics Centre, Utrecht, The Netherlands
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3
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Corradini E, Heck AJR, Scholten A. Separation of PKA and PKG signaling nodes by chemical proteomics. Methods Mol Biol 2015; 1294:191-201. [PMID: 25783887 DOI: 10.1007/978-1-4939-2537-7_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The chemically quite similar cyclic nucleotides cAMP and cGMP are two second messengers that activate the homologous cAMP- and cGMP-dependent protein kinases (PKA and PKG, respectively). To gain specificity in space and time in vivo, PKA is compartmentalized by the interaction of its regulatory subunits with A-kinase-anchoring proteins (AKAPs), which often form the core of larger signaling protein machineries. In a similar manner, PKG is also found to be compartmentalized close to specific, local pools of cGMP through interaction with G-kinase-anchoring proteins (GKAPs), although the extent and mechanisms mediating these interactions are only marginally understood. In affinity-based chemical proteomics strategies, small molecules are immobilized on solid supports in order to enrich for specific target proteins. We have shown the utility of immobilized cAMP and cGMP to enrich for PKA and PKG and their associated proteins. Unfortunately, both PKA and PKG are enriched in the pull downs with both immobilized compounds. Although this proved sufficient to identify novel AKAPs, the lower abundance of PKG has seriously hampered the enrichment and identification of novel GKAPs. Here we present an improved chemical proteomics method involving in-solution competition with low doses of different free cyclic nucleotides to segregate the cAMP/PKA- and cGMP/PKG-based signaling nodes, allowing the purification and subsequent identification of new scaffold proteins for PKG.
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Affiliation(s)
- Eleonora Corradini
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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4
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Prysyazhna O, Eaton P. Redox regulation of cGMP-dependent protein kinase Iα in the cardiovascular system. Front Pharmacol 2015; 6:139. [PMID: 26236235 PMCID: PMC4505079 DOI: 10.3389/fphar.2015.00139] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/22/2015] [Indexed: 11/13/2022] Open
Abstract
Elevated levels of oxidants in biological systems have been historically referred to as “oxidative stress,” a choice of words that perhaps conveys an imbalanced view of reactive oxygen species in cells and tissues. The term stress suggests a harmful role, whereas a contemporary view is that oxidants are also crucial for the maintenance of homeostasis or adaptive signaling that can actually limit injury. This regulatory role for oxidants is achieved in part by them inducing oxidative post-translational modifications of proteins which may alter their function or interactions. Such mechanisms allow changes in cell oxidant levels to be coupled to regulated alterations in enzymatic function (i.e., signal transduction), which enables “redox signaling.” In this review we focus on the role of cGMP-dependent protein kinase (PKG) Ia disulfide dimerisation, an oxidative modification that is induced by oxidants that directly activates the enzyme, discussing how this impacts on the cardiovascular system. Additionally, how this oxidative activation of PKG may coordinate with or differ from classical activation of this kinase by cGMP is also considered.
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Affiliation(s)
- Oleksandra Prysyazhna
- Cardiovascular Division, King's College London, The British Heart Foundation Centre of Excellence, The Rayne Institute, St Thomas' Hospital , London, UK
| | - Philip Eaton
- Cardiovascular Division, King's College London, The British Heart Foundation Centre of Excellence, The Rayne Institute, St Thomas' Hospital , London, UK
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5
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Peng M, Aye TT, Snel B, van Breukelen B, Scholten A, Heck AJR. Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution. J Proteome Res 2015; 14:2976-87. [DOI: 10.1021/acs.jproteome.5b00370] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mao Peng
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
- Department
of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Thin Thin Aye
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Berend Snel
- Theoretical
Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bas van Breukelen
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Arjen Scholten
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
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6
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Burgers PP, van der Heyden MAG, Kok B, Heck AJR, Scholten A. A Systematic Evaluation of Protein Kinase A–A-Kinase Anchoring Protein Interaction Motifs. Biochemistry 2014; 54:11-21. [DOI: 10.1021/bi500721a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Pepijn P. Burgers
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Marcel A. G. van der Heyden
- Department
of Medical Physiology, Division of Heart and Lungs, University Medical Centre Utrecht, Yalelaan 50, 3584 CM Utrecht, The Netherlands
| | - Bart Kok
- Department
of Medical Physiology, Division of Heart and Lungs, University Medical Centre Utrecht, Yalelaan 50, 3584 CM Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Arjen Scholten
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
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7
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Niu S, Rabuck JN, Ruotolo BT. Ion mobility-mass spectrometry of intact protein–ligand complexes for pharmaceutical drug discovery and development. Curr Opin Chem Biol 2013; 17:809-17. [DOI: 10.1016/j.cbpa.2013.06.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/17/2013] [Accepted: 06/18/2013] [Indexed: 11/30/2022]
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8
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Muhn F, Klopocki E, Graul-Neumann L, Uhrig S, Colley A, Castori M, Lankes E, Henn W, Gruber-Sedlmayr U, Seifert W, Horn D. Novel mutations of thePRKAR1Agene in patients with acrodysostosis. Clin Genet 2013; 84:531-8. [DOI: 10.1111/cge.12106] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/18/2013] [Accepted: 01/18/2013] [Indexed: 01/06/2023]
Affiliation(s)
- F Muhn
- Institute for Medical and Human Genetics; Charité Universitätsmedizin Berlin; Berlin Germany
| | - E Klopocki
- Institute for Medical and Human Genetics; Charité Universitätsmedizin Berlin; Berlin Germany
- Max-Planck-Institute for Molecular Genetics; Berlin Germany
| | - L Graul-Neumann
- Institute for Medical and Human Genetics; Charité Universitätsmedizin Berlin; Berlin Germany
| | - S Uhrig
- Institute of Human Genetics; Medical University; Graz Austria
| | - A Colley
- Department of Clinical Genetics, South Western Sydney LHD; Liverpool Hospital; Liverpool Australia
| | - M Castori
- Department of Molecular Medicine, San Camillo-Forlanini Hospital; Sapienza University; Rome Italy
| | - E Lankes
- Pediatric Endocrinology; Otto Heubner Center for Pediatrics, Charité Universitätsmedizin Berlin; Berlin Germany
| | - W Henn
- Institute of Human Genetics; Saarland University; Homburg Saar Germany
| | | | - W Seifert
- Institute for Vegetative Anatomy, Charité; University Medicine of Berlin; Berlin Germany
| | - D Horn
- Institute for Medical and Human Genetics; Charité Universitätsmedizin Berlin; Berlin Germany
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9
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Burgers PP, Ma Y, Margarucci L, Mackey M, van der Heyden MAG, Ellisman M, Scholten A, Taylor SS, Heck AJR. A small novel A-kinase anchoring protein (AKAP) that localizes specifically protein kinase A-regulatory subunit I (PKA-RI) to the plasma membrane. J Biol Chem 2012; 287:43789-97. [PMID: 23115245 DOI: 10.1074/jbc.m112.395970] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Protein kinase A-anchoring proteins (AKAPs) provide spatio-temporal specificity for the omnipotent cAMP-dependent protein kinase (PKA) via high affinity interactions with PKA regulatory subunits (PKA-RI, RII). Many PKA-RII-AKAP complexes are heavily tethered to cellular substructures, whereas PKA-RI-AKAP complexes have remained largely undiscovered. Here, using a cAMP affinity-based chemical proteomics strategy in human heart and platelets, we uncovered a novel, ubiquitously expressed AKAP, termed small membrane (sm)AKAP due to its specific localization at the plasma membrane via potential myristoylation/palmitoylation anchors. In vitro binding studies revealed specificity of smAKAP for PKA-RI (K(d) = 7 nM) over PKA-RII (K(d) = 53 nM) subunits, co-expression of smAKAP with the four PKA R subunits revealed an even more exclusive specificity of smAKAP for PKA-RIα/β in the cellular context. Applying the singlet oxygen-generating electron microscopy probe miniSOG indicated that smAKAP is tethered to the plasma membrane and is particularly dense at cell-cell junctions and within filopodia. Our preliminary functional characterization of smAKAP provides evidence that, like PKA-RII, PKA-RI can be tightly tethered by a novel repertoire of AKAPs, providing a new perspective on spatio-temporal control of cAMP signaling.
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Affiliation(s)
- Pepijn P Burgers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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10
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Kovanich D, Cappadona S, Raijmakers R, Mohammed S, Scholten A, Heck AJR. Applications of stable isotope dimethyl labeling in quantitative proteomics. Anal Bioanal Chem 2012; 404:991-1009. [DOI: 10.1007/s00216-012-6070-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 04/13/2012] [Accepted: 04/23/2012] [Indexed: 01/03/2023]
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11
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Aye TT, Soni S, van Veen TAB, van der Heyden MAG, Cappadona S, Varro A, de Weger RA, de Jonge N, Vos MA, Heck AJR, Scholten A. Reorganized PKA-AKAP associations in the failing human heart. J Mol Cell Cardiol 2011; 52:511-8. [PMID: 21712045 DOI: 10.1016/j.yjmcc.2011.06.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 05/20/2011] [Accepted: 06/02/2011] [Indexed: 10/18/2022]
Abstract
Here we reveal that the characterization of large-scale re-arrangements of signaling scaffolds induced by heart failure can serve as a novel concept to identify more specific therapeutic targets. In the mammalian heart, the cAMP pathway, with the cAMP-dependent protein kinase (PKA) in a central role, acts directly downstream of adrenergic receptors to mediate cardiac contractility and rhythm. Heart failure, characterized by severe alterations in adrenergic stimulation is, amongst other interventions, often treated with β-blockers. Contrasting results, however, have shown both beneficial and detrimental effects of decreased cAMP levels in failing hearts. We hypothesize that the origin of this behavior lies in the complex spatiotemporal organization of the regulatory subunit of PKA (PKA-R), which associates tightly with various A-kinase anchoring proteins (AKAPs) to specifically localize PKA's activity. Using chemical proteomics directly applied to human patient and control heart tissue we demonstrate that the association profile of PKA-R with several AKAPs is severely altered in the failing heart, for instance effecting the interaction between PKA and the novel AKAP SPHKAP was 6-fold upregulated upon failing heart conditions. Also a significant increase in captured cGMP-dependent protein kinase (PKG) and phosphodiesterase 2 (PDE2) was observed. The observed altered profiles can already explain many aspects of the aberrant cAMP-response in the failing human heart, validating that this dataset may provide a resource for several novel, more specific, treatment options. This article is part of a Special Issue entitled "Local Signaling in Myocytes".
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Affiliation(s)
- Thin-Thin Aye
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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12
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Hanke SE, Bertinetti D, Badel A, Schweinsberg S, Genieser HG, Herberg FW. Cyclic nucleotides as affinity tools: phosphorothioate cAMP analogues address specific PKA subproteomes. N Biotechnol 2010; 28:294-301. [PMID: 21147280 DOI: 10.1016/j.nbt.2010.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/02/2010] [Accepted: 12/05/2010] [Indexed: 11/29/2022]
Abstract
cAMP (adenosine-3',5'-cyclic monophosphate) is a general second messenger controlling distinct targets in eukaryotic cells. In a (sub)proteomic approach, two classes of phosphorothioate cAMP affinity tools were used to isolate and to identify signalling complexes of the main cAMP target, cAMP dependent protein kinase (PKA). Agonist analogues (here: Sp-cAMPS) bind to the regulatory subunits of PKA (PKA-R), together with their interaction partners, and cause dissociation of a holoenzyme complex comprising PKA-R and catalytic subunits of PKA (PKA-C). Antagonist analogues (here: Rp-cAMPS) bind to the holoenzyme without dissociating the complex and were developed to identify interaction partners that bind to the entire complex or to PKA-C. More than 80 different proteins were isolated from tissue extracts including several PKA isoforms and known as well as potentially new interaction partners. Nevertheless, unspecific binding of general nucleotide binding proteins limited the outcome of this chemical proteomics approach. Surface plasmon resonance (SPR) was employed to optimise the entire workflow of pull down proteomics and to quantify the effects of different nucleotides (ATP, ADP, GTP and NADH) on PKA-R binding to affinity material. We could demonstrate that the addition of NADH to lysates improved specificity in pull down experiments. Using a combination of SPR studies and pull down experiments it was shown unambiguously that it is possible to specifically elute protein complexes with cAMP or cGMP from cAMPS analogue matrices. The side-by-side analysis of the PKA-R interactome and the holoenzyme complexed with interacting proteins will contribute to a further dissection of the multifaceted PKA signalling network.
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Affiliation(s)
- Susanne E Hanke
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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13
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van der Spoel D, Marklund EG, Larsson DSD, Caleman C. Proteins, Lipids, and Water in the Gas Phase. Macromol Biosci 2010; 11:50-9. [DOI: 10.1002/mabi.201000291] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Kovanich D, van der Heyden MAG, Aye TT, van Veen TAB, Heck AJR, Scholten A. Sphingosine kinase interacting protein is an A-kinase anchoring protein specific for type I cAMP-dependent protein kinase. Chembiochem 2010; 11:963-71. [PMID: 20394097 DOI: 10.1002/cbic.201000058] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The compartmentalization of kinases and phosphatases plays an important role in the specificity of second-messenger-mediated signaling events. Localization of the cAMP-dependent protein kinase is mediated by interaction of its regulatory subunit (PKA-R) with the versatile family of A-kinase-anchoring proteins (AKAPs). Most AKAPs bind avidly to PKA-RII, while some have dual specificity for both PKA-RI and PKA-RII; however, no mammalian PKA-RI-specific AKAPs have thus far been assigned. This has mainly been attributed to the observation that PKA-RI is more cytosolic than the more heavily compartmentalized PKA-RII. Chemical proteomics screens of the cAMP interactome in mammalian heart tissue recently identified sphingosine kinase type 1-interacting protein (SKIP, SPHKAP) as a putative novel AKAP. Biochemical characterization now shows that SPHKAP can be considered as the first mammalian AKAP that preferentially binds to PKA-RIalpha. Recombinant human SPHKAP functions as an RI-specific AKAP that utilizes the characteristic AKAP amphipathic helix for interaction. Further chemical proteomic screening utilizing differential binding characteristics of specific cAMP resins confirms SPHKAPs endogenous specificity for PKA-RI directly in mammalian heart and spleen tissue. Immunolocalization studies revealed that recombinant SPHKAP is expressed in the cytoplasm, where PKA-RIalpha also mainly resides. Alignment of SPHKAPs' amphipathic helix with peptide models of PKA-RI- or PKA-RII-specific anchoring domains shows that it has largely only PKA-RIalpha characteristics. Being the first mammalian PKA-RI-specific AKAP with cytosolic localization, SPHKAP is a very promising model for studying the function of the less explored cytosolic PKA-RI signaling nodes.
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Affiliation(s)
- Duangnapa Kovanich
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center forBiomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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15
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Chen H, Yang S, Li M, Hu B, Li J, Wang J. Sensitive Detection of Native Proteins Using Extractive Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2010; 49:3053-6. [DOI: 10.1002/anie.200906886] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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16
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Chen H, Yang S, Li M, Hu B, Li J, Wang J. Sensitive Detection of Native Proteins Using Extractive Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906886] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Uetrecht C, Rose RJ, van Duijn E, Lorenzen K, Heck AJR. Ion mobility mass spectrometry of proteins and proteinassemblies. Chem Soc Rev 2010; 39:1633-55. [DOI: 10.1039/b914002f] [Citation(s) in RCA: 381] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Aye TT, Scholten A, Taouatas N, Varro A, Van Veen TAB, Vos MA, Heck AJR. Proteome-wide protein concentrations in the human heart. MOLECULAR BIOSYSTEMS 2010; 6:1917-27. [DOI: 10.1039/c004495d] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Pinkse MWH, Rijkers DTS, Dostmann WR, Heck AJR. Mode of action of cGMP-dependent protein kinase-specific inhibitors probed by photoaffinity cross-linking mass spectrometry. J Biol Chem 2009; 284:16354-16368. [PMID: 19369251 DOI: 10.1074/jbc.m808521200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The inhibitor peptide DT-2 (YGRKKRRQRRRPPLRKKKKKH) is the most potent and selective inhibitor of the cGMP-dependent protein kinase (PKG) known today. DT-2 is a construct of a PKG tight binding sequence (W45, LRKKKKKH, KI=0.8 microM) and a membrane translocating sequence (DT-6, YGRKKRRQRRRPP, KI=1.1 microM), that combined strongly inhibits PKG catalyzed phosphorylation (KI=12.5 nM) with approximately 1000-fold selectivity toward PKG over protein kinase A, the closest relative of PKG. However, the molecular mechanism behind this inhibition is not entirely understood. Using a combination of photoaffinity labeling, stable isotope labeling, and mass spectrometry, we have located the binding sites of PKG-specific substrate and inhibitor peptides. Covalent linkage of a PKG-specific substrate analogue was localized in the catalytic core on residues 356-372, also known as the glycine-rich loop, essential for ATP binding. By analogy, the individual inhibitor peptides W45 and DT-6 were also found to cross-link near the glycine-rich loop, suggesting these are both substrate competitive inhibitors. A bifunctional photoreactive analogue of DT-2 was found to generate dimers of PKG. This cross-linking induced covalent PKG dimerization was not observed for an N-terminal deletion mutant of PKG, which lacks the dimerization domain. In addition, non-covalent mass spectrometry was used to determine binding stoichiometry and binding order of the inhibitor peptides. Dimeric PKG binds two W45 and DT-6 peptides, whereas only one DT-2 molecule was observed to bind to the dimeric PKG. Taken together, these findings imply that (i) the two individual components making up DT-2 are both targeted against the substrate-binding site and (ii) binding of a single DT-2 molecule inactivates both PKG monomers simultaneously, which is an indication that (iii) in cGMP-activated PKG the catalytic centers of both subunits may be in each other's proximity.
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Affiliation(s)
- Martijn W H Pinkse
- From the Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnnelaan 16, Utrecht 3584 CA, The Netherlands; Department of Biotechnology, Delft, University of Technology, Delft 2628 BC, The Netherlands
| | - Dirk T S Rijkers
- Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht 3584 CA, The Netherlands
| | - Wolfgang R Dostmann
- Department of Pharmacology, College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Albert J R Heck
- From the Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnnelaan 16, Utrecht 3584 CA, The Netherlands.
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Aye TT, Mohammed S, van den Toorn HWP, van Veen TAB, van der Heyden MAG, Scholten A, Heck AJR. Selectivity in enrichment of cAMP-dependent protein kinase regulatory subunits type I and type II and their interactors using modified cAMP affinity resins. Mol Cell Proteomics 2008; 8:1016-28. [PMID: 19119138 DOI: 10.1074/mcp.m800226-mcp200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
cAMP regulates cellular functions primarily by activating PKA. The involvement of PKAs in various signaling pathways occurring simultaneously in different cellular compartments necessitates stringent spatial and temporal regulation. This specificity is largely achieved by binding of PKA to protein scaffolds, whereby a distinct group of proteins called A kinase anchoring proteins (AKAPs) play a dominant role. AKAPs are a diverse family of proteins that all bind via a small PKA binding domain to the regulatory subunits of PKA. The binding affinities between PKA and several AKAPs can be different for different isoforms of the regulatory subunits of PKA. Here we employ a combination of affinity chromatography and mass spectrometry-based quantitative proteomics to investigate specificity in PKA-AKAP interactions. Three different immobilized cAMP analogs were used to enrich for PKA and its interacting proteins from several systems; HEK293 and RCC10 cells and rat lung and testis tissues. Stable isotope labeling was used to confidently identify and differentially quantify target proteins and their preferential binding affinity for the three different cAMP analogs. We were able to enrich all four isoforms of the regulatory subunits of PKA and concomitantly identify more than 10 AKAPs. A selective enrichment of the PKA RI isoforms could be achieved; which allowed us to unravel which AKAPs bind preferentially to the RI or RII regulatory domains of PKA. Of the twelve AKAPs detected, seven preferentially bound to RII, whereas the remaining five displayed at least dual specificity with a potential preference for RI. For some of these AKAPs our data provide the first insights into their specificity.
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Affiliation(s)
- Thin Thin Aye
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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