1
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Rasmussen M, Tolone A, Paquet-Durand F, Welinder C, Schwede F, Ekström P. The photoreceptor protective cGMP-analog Rp-8-Br-PET-cGMPS interacts with cGMP-interactors PKGI, PDE1, PDE6, and PKAI in the degenerating mouse retina. J Comp Neurol 2023; 531:935-951. [PMID: 36989379 DOI: 10.1002/cne.25475] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/12/2022] [Accepted: 03/06/2023] [Indexed: 03/31/2023]
Abstract
The inherited eye disease retinitis pigmentosa (RP) causes the loss of photoreceptors by a still unknown cell death mechanism. During this degeneration, cyclic guanosine-3',5'-monophosphate (cGMP) levels become elevated, leading to over-activation of the cGMP-binding protein cGMP-dependent protein kinase (PKG). cGMP analogs selectively modified to have inhibitory actions on PKG have aided in impeding photoreceptor death, and one such cGMP analog is Rp-8-Br-PET-cGMPS. However, cGMP analogs have previously been shown to interact with numerous targets, so to better understand the therapeutic action of Rp-8-Br-PET-cGMPS, it is necessary to elucidate its target-selectivity and hence what potential cellular mechanism(s) it may affect within the photoreceptors. Here, we, therefore, applied affinity chromatography together with mass spectrometry to isolate and identify Rp-8-Br-PET-cGMPS interactors from retinas derived from three different murine RP models (i.e., rd1, rd2, and rd10 mice). Our findings revealed that Rp-8-Br-PET-cGMPS bound seven known cGMP-binding proteins, including PKG1β, PDE1β, PDE1c, PDE6α, and PKA1α. Furthermore, an additional 28 proteins were found to be associated with Rp-8-Br-PET-cGMPS. This latter group included MAPK1/3, which is known to connect with cGMP/PKG in other systems. However, in organotypic retinal cultures, Rp-8-Br-PET-cGMPS had no effect on photoreceptor MAPK1/3 expression or activity. To summarize, Rp-8-Br-PET-cGMPS is more target specific compared to regular cGMP.
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Affiliation(s)
- Michel Rasmussen
- Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden
| | - Arianna Tolone
- Insitute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | | | - Charlotte Welinder
- Faculty of Medicine, Department of Clinical Sciences Lund, Mass Spectrometry, Lund University, Lund, Sweden
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH & Co. KG, Bremen, Germany
| | - Per Ekström
- Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden
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2
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Sharma R, Kim JJ, Qin L, Henning P, Akimoto M, VanSchouwen B, Kaur G, Sankaran B, MacKenzie KR, Melacini G, Casteel DE, Herberg FW, Kim CW. An auto-inhibited state of protein kinase G and implications for selective activation. eLife 2022; 11:79530. [PMID: 35929723 PMCID: PMC9417419 DOI: 10.7554/elife.79530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 08/04/2022] [Indexed: 11/29/2022] Open
Abstract
Cyclic GMP-dependent protein kinases (PKGs) are key mediators of the nitric oxide/cyclic guanosine monophosphate (cGMP) signaling pathway that regulates biological functions as diverse as smooth muscle contraction, cardiac function, and axon guidance. Understanding how cGMP differentially triggers mammalian PKG isoforms could lead to new therapeutics that inhibit or activate PKGs, complementing drugs that target nitric oxide synthases and cyclic nucleotide phosphodiesterases in this signaling axis. Alternate splicing of PRKG1 transcripts confers distinct leucine zippers, linkers, and auto-inhibitory (AI) pseudo-substrate sequences to PKG Iα and Iβ that result in isoform-specific activation properties, but the mechanism of enzyme auto-inhibition and its alleviation by cGMP is not well understood. Here, we present a crystal structure of PKG Iβ in which the AI sequence and the cyclic nucleotide-binding (CNB) domains are bound to the catalytic domain, providing a snapshot of the auto-inhibited state. Specific contacts between the PKG Iβ AI sequence and the enzyme active site help explain isoform-specific activation constants and the effects of phosphorylation in the linker. We also present a crystal structure of a PKG I CNB domain with an activating mutation linked to Thoracic Aortic Aneurysms and Dissections. Similarity of this structure to wildtype cGMP-bound domains and differences with the auto-inhibited enzyme provide a mechanistic basis for constitutive activation. We show that PKG Iβ auto-inhibition is mediated by contacts within each monomer of the native full-length dimeric protein, and using the available structural and biochemical data we develop a model for the regulation and cooperative activation of PKGs.
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Affiliation(s)
- Rajesh Sharma
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
| | - Jeong Joo Kim
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
| | - Liying Qin
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
| | - Philipp Henning
- Department of Biochemistry, University of Kassel, kassel, Germany
| | - Madoka Akimoto
- Department of Chemistry and Chemical Biology, McMaster University, Ontario, Canada
| | - Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Ontario, Canada
| | - Gundeep Kaur
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Kevin R MacKenzie
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Darren E Casteel
- Department of Medicine, University of California, San Diego, San Diego, United States
| | - Fritz W Herberg
- Department of Biochemistry, University of Kassel, kassel, Germany
| | - Choel W Kim
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, United States
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3
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Mak VW, Patel AM, Yen R, Hanisak J, Lim YH, Bao J, Zheng R, Seganish WM, Yu Y, Healy DR, Ogawa A, Ren Z, Soriano A, Ermakov GP, Beaumont M, Metwally E, Cheng AC, Verras A, Fischmann T, Zebisch M, Silvestre HL, McEwan PA, Barker J, Rearden P, Greshock TJ. Optimization and Mechanistic Investigations of Novel Allosteric Activators of PKG1α. J Med Chem 2022; 65:10318-10340. [PMID: 35878399 DOI: 10.1021/acs.jmedchem.1c02109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Activation of PKG1α is a compelling strategy for the treatment of cardiovascular diseases. As the main effector of cyclic guanosine monophosphate (cGMP), activation of PKG1α induces smooth muscle relaxation in blood vessels, lowers pulmonary blood pressure, prevents platelet aggregation, and protects against cardiac stress. The development of activators has been mostly limited to cGMP mimetics and synthetic peptides. Described herein is the optimization of a piperidine series of small molecules to yield activators that demonstrate in vitro phosphorylation of vasodilator-stimulated phosphoprotein as well as antiproliferative effects in human pulmonary arterial smooth muscle cells. Hydrogen/deuterium exchange mass spectrometry experiments with the small molecule activators revealed a mechanism of action consistent with cGMP-induced activation, and an X-ray co-crystal structure with a construct encompassing the regulatory domains illustrated a binding mode in an allosteric pocket proximal to the low-affinity cyclic nucleotide-binding domain.
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Affiliation(s)
- Victor W Mak
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Akash M Patel
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Rose Yen
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Jennifer Hanisak
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yeon-Hee Lim
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Jianming Bao
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States.,Ionova Life Science, Shenzhen 518122, Guangdong, China
| | - Rong Zheng
- IDSU, Wuxi AppTec Co., Ltd, Shanghai 200131, China
| | - W Michael Seganish
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Yang Yu
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - David R Healy
- Discovery Biology, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Aimie Ogawa
- Quantitative Biosciences, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Zhao Ren
- Quantitative Biosciences, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Aileen Soriano
- Mass Spectrometry and Biophysics, Computation and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Grigori P Ermakov
- PPDM Discovery Bioanalytics, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Maribel Beaumont
- PPDM Discovery Bioanalytics, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Essam Metwally
- Computational and Structural Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Alan C Cheng
- Computational and Structural Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Andreas Verras
- Schrodinger Inc., 120 West 45th Street, 17th Floor, New York, New York 10036-4041, United States.,Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Thierry Fischmann
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Matthias Zebisch
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - H Leonardo Silvestre
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Paul A McEwan
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - John Barker
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Paul Rearden
- DMPK, Recursion Pharmaceuticals, Salt Lake City, Utah 84101, United States.,PPDM, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Thomas J Greshock
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
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4
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Khamina M, Martinez Pomier K, Akimoto M, VanSchouwen B, Melacini G. Non-Canonical Allostery in Cyclic Nucleotide Dependent Kinases. J Mol Biol 2022; 434:167584. [DOI: 10.1016/j.jmb.2022.167584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 12/28/2022]
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5
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Rasmussen M, Welinder C, Schwede F, Ekström P. The stereospecific interaction sites and target specificity of cGMP analogs in mouse cortex. Chem Biol Drug Des 2021; 99:206-221. [PMID: 34687134 DOI: 10.1111/cbdd.13976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/29/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022]
Abstract
cGMP interactors play a role in several pathologies and may be targets for cGMP analog-based drugs, but the success of targeting depends on the biochemical stereospecificity between the cGMP-analog and the interactor. The stereospecificity between general cGMP analogs-or such that are selectivity-modified to obtain, for example, inhibitory actions on a specific target, like the cGMP-dependent protein kinase-have previously been investigated. However, the importance of stereospecificity for cGMP-analog binding to interactors is not known. We, therefore, applied affinity chromatography on mouse cortex proteins utilizing analogs with cyclic phosphate (8-AET-cGMP, 2-AH-cGMP, 2'-AHC-cGMP) and selectivity-modified analogs with sulfur-containing cyclic phosphorothioates (Rp/Sp-8-AET-cGMPS, Rp/Sp-2'-AHC-cGMPS) immobilized to agaroses. The results illustrate the cGMP analogs' stereospecific binding for PKG, PKA regulatory subunits and PKA catalytic subunits, PDEs, and EPAC2 and the involvement of these in various KEGG pathways. For the seven agaroses, PKG, PKA regulatory subunits, and PKA catalytic subunits were more prone to be enriched by 2-AH-, 8-AET-, Rp-8-AET-, and Sp-8-AET-cGMP, whereas PDEs and EPAC2 were more likely to be enriched by 2-AH-, Rp-2'-AHC-, and Rp-8-AET-cGMP. Our findings help elucidate the stereospecific-binding sites essential for the interaction between individual cGMP analogs and cGMP-binding proteins, as well as the cGMP analogs' target specificity, which are two crucial parameters in drug design.
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Affiliation(s)
- Michel Rasmussen
- Faculty of Medicine, Department of Clinical Sciences Lund, Ophthalmology, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University, Lund, Sweden
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH & Co. KG, Bremen, Germany
| | - Per Ekström
- Faculty of Medicine, Department of Clinical Sciences Lund, Ophthalmology, Lund University, Lund, Sweden
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6
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Development of Phosphodiesterase-Protein-Kinase Complexes as Novel Targets for Discovery of Inhibitors with Enhanced Specificity. Int J Mol Sci 2021; 22:ijms22105242. [PMID: 34063491 PMCID: PMC8156604 DOI: 10.3390/ijms22105242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/25/2021] [Accepted: 05/13/2021] [Indexed: 11/29/2022] Open
Abstract
Phosphodiesterases (PDEs) hydrolyze cyclic nucleotides to modulate multiple signaling events in cells. PDEs are recognized to actively associate with cyclic nucleotide receptors (protein kinases, PKs) in larger macromolecular assemblies referred to as signalosomes. Complexation of PDEs with PKs generates an expanded active site that enhances PDE activity. This facilitates signalosome-associated PDEs to preferentially catalyze active hydrolysis of cyclic nucleotides bound to PKs and aid in signal termination. PDEs are important drug targets, and current strategies for inhibitor discovery are based entirely on targeting conserved PDE catalytic domains. This often results in inhibitors with cross-reactivity amongst closely related PDEs and attendant unwanted side effects. Here, our approach targeted PDE–PK complexes as they would occur in signalosomes, thereby offering greater specificity. Our developed fluorescence polarization assay was adapted to identify inhibitors that block cyclic nucleotide pockets in PDE–PK complexes in one mode and disrupt protein-protein interactions between PDEs and PKs in a second mode. We tested this approach with three different systems—cAMP-specific PDE8–PKAR, cGMP-specific PDE5–PKG, and dual-specificity RegA–RD complexes—and ranked inhibitors according to their inhibition potency. Targeting PDE–PK complexes offers biochemical tools for describing the exquisite specificity of cyclic nucleotide signaling networks in cells.
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7
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Kim C, Sharma R. Cyclic nucleotide selectivity of protein kinase G isozymes. Protein Sci 2020; 30:316-327. [PMID: 33271627 DOI: 10.1002/pro.4008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 11/07/2022]
Abstract
The intrinsic activity of the C-terminal catalytic (C) domain of cyclic guanosine monophosphate (cGMP)-dependent protein kinases (PKG) is inhibited by interactions with the N-terminal regulatory (R) domain. Selective binding of cGMP to cyclic nucleotide binding (CNB) domains within the R-domain disrupts the inhibitory R-C interaction, leading to the release and activation of the C-domain. Affinity measurements of mammalian and plasmodium PKG CNB domains reveal different degrees of cyclic nucleotide affinity and selectivity; the CNB domains adjacent to the C-domain are more cGMP selective and therefore critical for cGMP-dependent activation. Crystal structures of isolated CNB domains in the presence and absence of cyclic nucleotides reveal isozyme-specific contacts that explain cyclic nucleotide selectivity and conformational changes that accompany CNB. Crystal structures of tandem CNB domains identify two types of CNB-mediated dimeric contacts that indicate cGMP-driven reorganization of domain-domain interfaces that include large conformational changes. Here, we review the available structural and functional information of PKG CNB domains that further advance our understanding of cGMP mediated regulation and activation of PKG isozymes.
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Affiliation(s)
- Choel Kim
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Rajesh Sharma
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
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8
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Rasmussen M, Welinder C, Schwede F, Ekström P. The cGMP system in normal and degenerating mouse neuroretina: New proteins with cGMP interaction potential identified by a proteomics approach. J Neurochem 2020; 157:2173-2186. [PMID: 33230839 PMCID: PMC8359485 DOI: 10.1111/jnc.15251] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022]
Abstract
The hereditary disease Retinitis pigmentosa results in severe vision loss due to photoreceptor degeneration by unclear mechanisms. In several disease models, the second messenger cGMP accumulates in the degenerating photoreceptors, where it may over‐activate specific cGMP‐interacting proteins, like cGMP‐dependent protein kinase. Moreover, interventions that counteract the activity of these proteins lead to reduced photoreceptor cell death. Yet there is little or no information whether other than such regular cGMP‐interactors are present in the retina, which we, therefore, investigated in wild‐type and retinal degeneration (rd1, rd10, and rd2) mouse models. An affinity chromatography based proteomics approach that utilized immobilized cGMP analogs was applied to enrich and select for regular and potentially new cGMP‐interacting proteins as identified by mass spectrometry. This approach revealed 12 regular and 10 potentially new retinal cGMP‐interacting proteins (e.g., EPAC2 and CaMKIIα). Several of the latter were found to be expressed in the photoreceptors and to have proximity to cGMP and may thus be of interest when defining prospective therapeutic targets or biomarkers for retinal degeneration.
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Affiliation(s)
- Michel Rasmussen
- Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden
| | - Charlotte Welinder
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University, Lund, Sweden
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH & Co. KG, Bremen, Germany
| | - Per Ekström
- Faculty of Medicine, Department of Clinical Sciences Lund, Lund University, Ophthalmology, Lund, Sweden
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9
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Betolngar DB, Mota É, Fabritius A, Nielsen J, Hougaard C, Christoffersen CT, Yang J, Kehler J, Griesbeck O, Castro LRV, Vincent P. Phosphodiesterase 1 Bridges Glutamate Inputs with NO- and Dopamine-Induced Cyclic Nucleotide Signals in the Striatum. Cereb Cortex 2020; 29:5022-5036. [PMID: 30877787 DOI: 10.1093/cercor/bhz041] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/14/2019] [Indexed: 12/15/2022] Open
Abstract
The calcium-regulated phosphodiesterase 1 (PDE1) family is highly expressed in the brain, but its functional role in neurones is poorly understood. Using the selective PDE1 inhibitor Lu AF64196 and biosensors for cyclic nucleotides including a novel biosensor for cGMP, we analyzed the effect of PDE1 on cAMP and cGMP in individual neurones in brain slices from male newborn mice. Release of caged NMDA triggered a transient increase of intracellular calcium, which was associated with a decrease in cAMP and cGMP in medium spiny neurones in the striatum. Lu AF64196 alone did not increase neuronal cyclic nucleotide levels, but blocked the NMDA-induced reduction in cyclic nucleotides indicating that this was mediated by calcium-activated PDE1. Similar effects were observed in the prefrontal cortex and the hippocampus. Upon corelease of dopamine and NMDA, PDE1 was shown to down-regulate the D1-receptor mediated increase in cAMP. PDE1 inhibition increased long-term potentiation in rat ventral striatum, showing that PDE1 is implicated in the regulation of synaptic plasticity. Overall, our results show that PDE1 reduces cyclic nucleotide signaling in the context of glutamate and dopamine coincidence. This effect could have a therapeutic value for treating brain disorders related to dysfunctions in dopamine neuromodulation.
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Affiliation(s)
| | - Élia Mota
- Sorbonne Université, CNRS, Biological Adaptation and Ageing, Paris, France
| | - Arne Fabritius
- Max Planck Institute for Neurobiology, Tools for Bio-Imaging, Am Klopferspitz 18, Martinsried, Germany
| | | | | | | | - Jun Yang
- Shanghai Chempartner Co. Ltd., Shanghai, China
| | - Jan Kehler
- H. Lundbeck A/S, Ottiliavej 9, Valby, Denmark
| | - Oliver Griesbeck
- Max Planck Institute for Neurobiology, Tools for Bio-Imaging, Am Klopferspitz 18, Martinsried, Germany
| | - Liliana R V Castro
- Sorbonne Université, CNRS, Biological Adaptation and Ageing, Paris, France
| | - Pierre Vincent
- Sorbonne Université, CNRS, Biological Adaptation and Ageing, Paris, France
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10
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Datta A, Yang CR, Limbutara K, Chou CL, Rinschen MM, Raghuram V, Knepper MA. PKA-independent vasopressin signaling in renal collecting duct. FASEB J 2020; 34:6129-6146. [PMID: 32219907 PMCID: PMC9200475 DOI: 10.1096/fj.201902982r] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 11/11/2022]
Abstract
Vasopressin regulates renal water excretion by binding to a Gα s-coupled receptor (V2R) in collecting duct cells, resulting in increased water permeability through regulation of the aquaporin-2 (AQP2) water channel. This action is widely accepted to be associated with cAMP-mediated activation of protein kinase A (PKA). Here, we use phosphoproteomics in collecting duct cells in which PKA has been deleted (CRISPR-Cas9) to identify PKA-independent responses to vasopressin. The results show that V2R-mediated vasopressin signaling is predominantly, but not entirely, PKA-dependent. Upregulated sites in PKA-null cells include Ser256 of AQP2, which is critical to regulation of AQP2 trafficking. In addition, phosphorylation changes in the protein kinases Stk39 (SPAK) and Prkci (an atypical PKC) are consistent with PKA-independent regulation of these protein kinases. Target motif analysis of the phosphopeptides increased in PKA-null cells indicates that vasopressin activates one or more members of the AMPK/SNF1-subfamily of basophilic protein kinases. In vitro phosphorylation assays using recombinant, purified SNF1-subfamily kinases confirmed postulated target specificities. Of interest, measured IBMX-dependent cAMP levels were an order of magnitude higher in PKA-null than in PKA-intact cells, indicative of a PKA-dependent feedback mechanism. Overall, the findings support the conclusion that V2-receptor mediated signaling in collecting duct cells is in part PKA-independent.
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Affiliation(s)
- Arnab Datta
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Yenepoya Research Center, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore 575018, Karnataka, India
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Kavee Limbutara
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Markus M. Rinschen
- Department of Chemistry, Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Mark A. Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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11
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Kim C, Sharma R, Casteel DE. Correction to: Crystal structure of PKG Iβ holoenzyme reveals a trans‑inhibiting dimer assembly. J Transl Med 2020; 18:27. [PMID: 31948450 PMCID: PMC6966794 DOI: 10.1186/s12967-019-02198-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Choel Kim
- Baylor College of Medicine, Pharmacology and Chemical Biology, Houston, TX, USA. .,Baylor College of Medicine, Biochemistry and Molecular Biology, Houston, TX, USA.
| | - Rajesh Sharma
- Baylor College of Medicine, Pharmacology and Chemical Biology, Houston, TX, USA
| | - Darren E Casteel
- University of California, San Diego, Medicine, La Jolla, CA, USA
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12
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Cadby IT, Basford SM, Nottingham R, Meek R, Lowry R, Lambert C, Tridgett M, Till R, Ahmad R, Fung R, Hobley L, Hughes WS, Moynihan PJ, Sockett RE, Lovering AL. Nucleotide signaling pathway convergence in a cAMP-sensing bacterial c-di-GMP phosphodiesterase. EMBO J 2019; 38:e100772. [PMID: 31355487 PMCID: PMC6717892 DOI: 10.15252/embj.2018100772] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 01/06/2023] Open
Abstract
Bacterial usage of the cyclic dinucleotide c‐di‐GMP is widespread, governing the transition between motile/sessile and unicellular/multicellular behaviors. There is limited information on c‐di‐GMP metabolism, particularly on regulatory mechanisms governing control of EAL c‐di‐GMP phosphodiesterases. Herein, we provide high‐resolution structures for an EAL enzyme Bd1971, from the predatory bacterium Bdellovibrio bacteriovorus, which is controlled by a second signaling nucleotide, cAMP. The full‐length cAMP‐bound form reveals the sensory N‐terminus to be a domain‐swapped variant of the cNMP/CRP family, which in the cAMP‐activated state holds the C‐terminal EAL enzyme in a phosphodiesterase‐active conformation. Using a truncation mutant, we trap both a half‐occupied and inactive apo‐form of the protein, demonstrating a series of conformational changes that alter juxtaposition of the sensory domains. We show that Bd1971 interacts with several GGDEF proteins (c‐di‐GMP producers), but mutants of Bd1971 do not share the discrete phenotypes of GGDEF mutants, instead having an elevated level of c‐di‐GMP, suggesting that the role of Bd1971 is to moderate these levels, allowing “action potentials” to be generated by each GGDEF protein to effect their specific functions.
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Affiliation(s)
- Ian T Cadby
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Sarah M Basford
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Ruth Nottingham
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Richard Meek
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Rebecca Lowry
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Carey Lambert
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Matthew Tridgett
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Rob Till
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Rashidah Ahmad
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Rowena Fung
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Laura Hobley
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - William S Hughes
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Patrick J Moynihan
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - R Elizabeth Sockett
- Centre for Genetics and Genomics, School of Biology, Medical School, Queen's Medical Centre, Nottingham University, Nottingham, UK
| | - Andrew L Lovering
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
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13
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Structures of the cGMP-dependent protein kinase in malaria parasites reveal a unique structural relay mechanism for activation. Proc Natl Acad Sci U S A 2019; 116:14164-14173. [PMID: 31239348 PMCID: PMC6628679 DOI: 10.1073/pnas.1905558116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cyclic guanosine-3',5'-monophosphate (cGMP)-dependent protein kinase (PKG) was identified >25 y ago; however, efforts to obtain a structure of the entire PKG enzyme or catalytic domain from any species have failed. In malaria parasites, cooperative activation of PKG triggers crucial developmental transitions throughout the complex life cycle. We have determined the cGMP-free crystallographic structures of PKG from Plasmodium falciparum and Plasmodium vivax, revealing how key structural components, including an N-terminal autoinhibitory segment (AIS), four predicted cyclic nucleotide-binding domains (CNBs), and a kinase domain (KD), are arranged when the enzyme is inactive. The four CNBs and the KD are in a pentagonal configuration, with the AIS docked in the substrate site of the KD in a swapped-domain dimeric arrangement. We show that although the protein is predominantly a monomer (the dimer is unlikely to be representative of the physiological form), the binding of the AIS is necessary to keep Plasmodium PKG inactive. A major feature is a helix serving the dual role of the N-terminal helix of the KD as well as the capping helix of the neighboring CNB. A network of connecting helices between neighboring CNBs contributes to maintaining the kinase in its inactive conformation. We propose a scheme in which cooperative binding of cGMP, beginning at the CNB closest to the KD, transmits conformational changes around the pentagonal molecule in a structural relay mechanism, enabling PKG to orchestrate rapid, highly regulated developmental switches in response to dynamic modulation of cGMP levels in the parasite.
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14
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Establishing a Split Luciferase Assay for Proteinkinase G (PKG) Interaction Studies. Int J Mol Sci 2018; 19:ijms19041180. [PMID: 29649180 PMCID: PMC5979328 DOI: 10.3390/ijms19041180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/04/2018] [Accepted: 04/04/2018] [Indexed: 02/06/2023] Open
Abstract
Nitric oxide (NO/cyclic guanosine monophosphate (cGMP)-regulated cellular mechanisms are involved in a variety of (patho-) physiological processes. One of the main effector molecules in this system, proteinkinase G (PKG), serves as a molecular switch by phosphorylating different target proteins and thereby turning them on or off. To date, only a few interaction partners of PKG have been described although the identification of protein–protein interactions (PPI) is indispensable for the understanding of cellular processes and diseases. Conventionally used methods to detect PPIs exhibit several disadvantages, e.g., co-immunoprecipitations, which depend on suitable high-affinity antibodies. Therefore, we established a cell-based protein-fragment complementation assay (PCA) for the identification of PKG target proteins. Here, a reporter protein (click beetle luciferase) is split into two fragments and fused to two different possible interaction partners. If interaction occurs, the reporter protein is functionally complemented and the catalyzed reaction can then be quantitatively measured. By using this technique, we confirmed the regulator of G-Protein signaling 2 (RGS2) as an interaction partner of PKGIα (a PKG-isoform) following stimulation with 8-Br-cGMP and 8-pCPT-cGMP. Hence, our results support the conclusion that the established approach could serve as a novel tool for the rapid, easy and cost-efficient detection of novel PKG target proteins.
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15
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Moon TM, Sheehe JL, Nukareddy P, Nausch LW, Wohlfahrt J, Matthews DE, Blumenthal DK, Dostmann WR. An N-terminally truncated form of cyclic GMP-dependent protein kinase Iα (PKG Iα) is monomeric and autoinhibited and provides a model for activation. J Biol Chem 2018; 293:7916-7929. [PMID: 29602907 DOI: 10.1074/jbc.ra117.000647] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/26/2018] [Indexed: 01/08/2023] Open
Abstract
The type I cGMP-dependent protein kinases (PKG I) serve essential physiological functions, including smooth muscle relaxation, cardiac remodeling, and platelet aggregation. These enzymes form homodimers through their N-terminal dimerization domains, a feature implicated in regulating their cooperative activation. Previous investigations into the activation mechanisms of PKG I isoforms have been largely influenced by structures of the cAMP-dependent protein kinase (PKA). Here, we examined PKG Iα activation by cGMP and cAMP by engineering a monomeric form that lacks N-terminal residues 1-53 (Δ53). We found that the construct exists as a monomer as assessed by whole-protein MS, size-exclusion chromatography, and small-angle X-ray scattering (SAXS). Reconstruction of the SAXS 3D envelope indicates that Δ53 has a similar shape to the heterodimeric RIα-C complex of PKA. Moreover, we found that the Δ53 construct is autoinhibited in its cGMP-free state and can bind to and be activated by cGMP in a manner similar to full-length PKG Iα as assessed by surface plasmon resonance (SPR) spectroscopy. However, we found that the Δ53 variant does not exhibit cooperative activation, and its cyclic nucleotide selectivity is diminished. These findings support a model in which, despite structural similarities, PKG Iα activation is distinct from that of PKA, and its cooperativity is driven by in trans interactions between protomers.
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Affiliation(s)
- Thomas M Moon
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405.
| | - Jessica L Sheehe
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Praveena Nukareddy
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405
| | - Lydia W Nausch
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Jessica Wohlfahrt
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Dwight E Matthews
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405
| | - Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah 84112
| | - Wolfgang R Dostmann
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405.
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16
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Gerlits O, Campbell JC, Blakeley MP, Kim C, Kovalevsky A. Neutron Crystallography Detects Differences in Protein Dynamics: Structure of the PKG II Cyclic Nucleotide Binding Domain in Complex with an Activator. Biochemistry 2018. [PMID: 29517905 DOI: 10.1021/acs.biochem.8b00010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As one of the main receptors of a second messenger, cGMP, cGMP-dependent protein kinase (PKG) isoforms I and II regulate distinct physiological processes. The design of isoform-specific activators is thus of great biomedical importance and requires detailed structural information about PKG isoforms bound with activators, including accurate positions of hydrogen atoms and a description of the hydrogen bonding and water architecture. Here, we determined a 2.2 Å room-temperature joint X-ray/neutron (XN) structure of the human PKG II carboxyl cyclic nucleotide binding (CNB-B) domain bound with a potent PKG II activator, 8-pCPT-cGMP. The XN structure directly visualizes intermolecular interactions and reveals changes in hydrogen bonding patterns upon comparison to the X-ray structure determined at cryo-temperatures. Comparative analysis of the backbone hydrogen/deuterium exchange patterns in PKG II:8-pCPT-cGMP and previously reported PKG Iβ:cGMP XN structures suggests that the ability of these agonists to activate PKG is related to how effectively they quench dynamics of the cyclic nucleotide binding pocket and the surrounding regions.
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Affiliation(s)
- Oksana Gerlits
- Bredesen Center , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - James C Campbell
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Matthew P Blakeley
- Large-Scale Structures Group , Institut Laue Langevin , 38042 Grenoble Cedex 9, France
| | - Choel Kim
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , Houston , Texas 77030 , United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Neutron Sciences Directorate , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
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17
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He D, Lorenz R, Kim C, Herberg FW, Lim CJ. Switching Cyclic Nucleotide-Selective Activation of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Holoenzyme Reveals Distinct Roles of Tandem Cyclic Nucleotide-Binding Domains. ACS Chem Biol 2017; 12:3057-3066. [PMID: 29111666 DOI: 10.1021/acschembio.7b00732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cyclic adenosine monophosphate (cAMP)- and cyclic guanosine monophosphate (cGMP)-dependent protein kinases (PKA and PKG) are key effectors of cyclic nucleotide signaling. Both share structural features that include tandem cyclic nucleotide-binding (CNB) domains, CNB-A and CNB-B, yet their functions are separated through preferential activation by either cAMP or cGMP. Based on structural studies and modeling, key CNB contact residues have been identified for both kinases. In this study, we explored the requirements for conversion of PKA activation from cAMP-dependent to cGMP-dependent. The consequences of the residue substitutions T192R/A212T within CNB-A or G316R/A336T within CNB-B of PKA-RIα on cyclic nucleotide binding and holoenzyme activation were assessed in vitro using purified recombinant proteins, and ex vivo using RIα-deficient mouse embryonic fibroblasts genetically reconstituted with wild-type or mutant PKA-RIα. In vitro, a loss of binding and activation selectivity was observed when residues in either one of the CNB domains were mutated, while mutations in both CNB domains resulted in a complete switch of selectivity from cAMP to cGMP. The switch in selectivity was also recapitulated ex vivo, confirming their functional roles in cells. Our results highlight the importance of key cyclic nucleotide contacts within each CNB domain and suggest that these domains may have evolved from an ancestral gene product to yield two distinct cyclic nucleotide-dependent protein kinases.
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Affiliation(s)
- Daniel He
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Robin Lorenz
- Department of Biochemistry, University of Kassel, 34132 Kassel, Germany
| | - Choel Kim
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | | | - Chinten James Lim
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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18
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Lorenz R, Bertinetti D, Herberg FW. cAMP-Dependent Protein Kinase and cGMP-Dependent Protein Kinase as Cyclic Nucleotide Effectors. Handb Exp Pharmacol 2017; 238:105-122. [PMID: 27885524 DOI: 10.1007/164_2015_36] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The cAMP-dependent protein kinase (PKA) and the cGMP-dependent protein kinase (PKG) are homologous enzymes with different binding and activation specificities for cyclic nucleotides. Both enzymes harbor conserved cyclic nucleotide-binding (CNB) domains. Differences in amino acid composition of these CNB domains mediate cyclic nucleotide selectivity in PKA and PKG, respectively. Recently, the presence of the noncanonical cyclic nucleotides cCMP and cUMP in eukaryotic cells has been proven, while the existence of cellular cIMP and cXMP remains unclear. It was shown that the main effectors of cyclic nucleotide signaling, PKA and PKG, can be activated by each of these noncanonical cyclic nucleotides. With unique effector proteins still missing, such cross-activation effects might have physiological relevance. Therefore, we approach PKA and PKG as cyclic nucleotide effectors in this chapter. The focus of this chapter is the general cyclic nucleotide-binding properties of both kinases as well as the selectivity for cAMP or cGMP, respectively. Furthermore, we discuss the binding affinities and activation potencies of noncanonical cyclic nucleotides.
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Affiliation(s)
- Robin Lorenz
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Daniela Bertinetti
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Friedrich W Herberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany.
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19
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Grundmann M, Kostenis E. Holistic Methods for the Analysis of cNMP Effects. Handb Exp Pharmacol 2017; 238:339-357. [PMID: 26721676 DOI: 10.1007/164_2015_42] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cyclic nucleotide monophosphates (cNMPs) typify the archetype second messenger in living cells and serve as molecular switches with broad functionality. cAMP and cGMP are the best-described cNMPs; however, there is a growing body of evidence indicating that also cCMP and cUMP play a substantial role in signal transduction. Despite research efforts, to date, relatively little is known about the biology of these noncanonical cNMPs, which is due, at least in part, to methodological issues in the past entailing setbacks of the entire field. Only recently, with the use of state-of-the-art techniques, it was possible to revive noncanonical cNMP research. While high-sensitive detection methods disclosed relevant levels of cCMP and cUMP in mammalian cells, knowledge about the biological effectors and their physiological interplay is still incomplete. Holistic biophysical readouts capture cell responses label-free and in an unbiased fashion with the advantage to detect concealed aspects of cell signaling that are arduous to access via traditional biochemical assay approaches. In this chapter, we introduce the dynamic mass redistribution (DMR) technology to explore cell signaling beyond established receptor-controlled mechanisms. Both common and distinctive features in the signaling structure of cCMP and cUMP were identified. Moreover, the integrated response of whole live cells revealed a hitherto undisclosed additional effector of the noncanonical cNMPs. Future studies will show how holistic methods will become integrated into the methodological arsenal of contemporary cNMP research.
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Affiliation(s)
- Manuel Grundmann
- Molecular-, Cellular- and Pharmacobiology Section, Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany.
| | - Evi Kostenis
- Molecular-, Cellular- and Pharmacobiology Section, Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
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20
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Campbell JC, Henning P, Franz E, Sankaran B, Herberg FW, Kim C. Structural Basis of Analog Specificity in PKG I and II. ACS Chem Biol 2017; 12:2388-2398. [PMID: 28793191 PMCID: PMC5896746 DOI: 10.1021/acschembio.7b00369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cyclic GMP analogs, 8-Br, 8-pCPT, and PET-cGMP, have been widely used for characterizing cellular functions of cGMP-dependent protein kinase (PKG) I and II isotypes. However, interpreting results obtained using these analogs has been difficult due to their low isotype specificity. Additionally, each isotype has two binding sites with different cGMP affinities and analog selectivities, making understanding the molecular basis for isotype specificity of these compounds even more challenging. To determine isotype specificity of cGMP analogs and their structural basis, we generated the full-length regulatory domains of PKG I and II isotypes with each binding site disabled, determined their affinities for these analogs, and obtained cocrystal structures of both isotypes bound with cGMP analogs. Our affinity and activation measurements show that PET-cGMP is most selective for PKG I, whereas 8-pCPT-cGMP is most selective for PKG II. Our structures of cyclic nucleotide binding (CNB) domains reveal that the B site of PKG I is more open and forms a unique π/π interaction through Arg285 at β4 with the PET moiety, whereas the A site of PKG II has a larger β5/β6 pocket that can better accommodate the bulky 8-pCPT moiety. Our structural and functional results explain the selectivity of these analogs for each PKG isotype and provide a starting point for the rational design of isotype selective activators.
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Affiliation(s)
- James C. Campbell
- Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, Texas, United States
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, United States
| | - Philipp Henning
- Department of Biochemistry, University of Kassel, Kassel, Hesse, Germany
| | - Eugen Franz
- Department of Biochemistry, University of Kassel, Kassel, Hesse, Germany
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States
| | | | - Choel Kim
- Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, Texas, United States
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, United States
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States
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21
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Kalyanaraman H, Zhuang S, Pilz RB, Casteel DE. The activity of cGMP-dependent protein kinase Iα is not directly regulated by oxidation-induced disulfide formation at cysteine 43. J Biol Chem 2017; 292:8262-8268. [PMID: 28360102 DOI: 10.1074/jbc.c117.787358] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 03/28/2017] [Indexed: 12/20/2022] Open
Abstract
The type I cGMP-dependent protein kinases (PKGs) are key regulators of smooth muscle tone, cardiac hypertrophy, and other physiological processes. The two isoforms PKGIα and PKGIβ are thought to have unique functions because of their tissue-specific expression, different cGMP affinities, and isoform-specific protein-protein interactions. Recently, a non-canonical pathway of PKGIα activation has been proposed, in which PKGIα is activated in a cGMP-independent fashion via oxidation of Cys43, resulting in disulfide formation within the PKGIα N-terminal dimerization domain. A "redox-dead" knock-in mouse containing a C43S mutation exhibits phenotypes consistent with decreased PKGIα signaling, but the detailed mechanism of oxidation-induced PKGIα activation is unknown. Therefore, we examined oxidation-induced activation of PKGIα, and in contrast to previous findings, we observed that disulfide formation at Cys43 does not directly activate PKGIα in vitro or in intact cells. In transfected cells, phosphorylation of Ras homolog gene family member A (RhoA) and vasodilator-stimulated phosphoprotein was increased in response to 8-CPT-cGMP treatment, but not when disulfide formation in PKGIα was induced by H2O2 Using purified enzymes, we found that the Cys43 oxidation had no effect on basal kinase activity or Km and Vmax values; however, PKGIα containing the C43S mutation was less responsive to cGMP-induced activation. This reduction in cGMP affinity may in part explain the PKGIα loss-of-function phenotype of the C43S knock-in mouse. In conclusion, disulfide formation at Cys43 does not directly activate PKGIα, and the C43S-mutant PKGIα has a higher Ka for cGMP. Our results highlight that mutant enzymes should be carefully biochemically characterized before making in vivo inferences.
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Affiliation(s)
- Hema Kalyanaraman
- Department of Medicine, University of California, San Diego, La Jolla, California 92093
| | - Shunhui Zhuang
- Department of Medicine, University of California, San Diego, La Jolla, California 92093
| | - Renate B Pilz
- Department of Medicine, University of California, San Diego, La Jolla, California 92093
| | - Darren E Casteel
- Department of Medicine, University of California, San Diego, La Jolla, California 92093.
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22
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Sharma S, Visweswariah SS. Illuminating Cyclic Nucleotides: Sensors for cAMP and cGMP and Their Application in Live Cell Imaging. J Indian Inst Sci 2017. [DOI: 10.1007/s41745-016-0014-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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23
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Campbell JC, VanSchouwen B, Lorenz R, Sankaran B, Herberg FW, Melacini G, Kim C. Crystal structure of cGMP-dependent protein kinase Iβ cyclic nucleotide-binding-B domain : Rp-cGMPS complex reveals an apo-like, inactive conformation. FEBS Lett 2016; 591:221-230. [PMID: 27914169 DOI: 10.1002/1873-3468.12505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/13/2016] [Accepted: 11/18/2016] [Indexed: 12/23/2022]
Abstract
The R-diastereomer of phosphorothioate analogs of cGMP, Rp-cGMPS, is one of few known inhibitors of cGMP-dependent protein kinase I (PKG I); however, its mechanism of inhibition is currently not fully understood. Here, we determined the crystal structure of the PKG Iβ cyclic nucleotide-binding domain (PKG Iβ CNB-B), considered a 'gatekeeper' for cGMP activation, bound to Rp-cGMPS at 1.3 Å. Our structural and NMR data show that PKG Iβ CNB-B bound to Rp-cGMPS displays an apo-like structure with its helical domain in an open conformation. Comparison with the cAMP-dependent protein kinase regulatory subunit (PKA RIα) showed that this conformation resembles the catalytic subunit-bound inhibited state of PKA RIα more closely than the apo or Rp-cAMPS-bound conformations. These results suggest that Rp-cGMPS inhibits PKG I by stabilizing the inactive conformation of CNB-B.
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Affiliation(s)
- James C Campbell
- Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Robin Lorenz
- Department of Biochemistry, University of Kassel, Kassel, Hesse, Germany
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, CA, USA
| | | | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Choel Kim
- Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
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24
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Kim JJ, Lorenz R, Arold ST, Reger AS, Sankaran B, Casteel DE, Herberg FW, Kim C. Crystal Structure of PKG I:cGMP Complex Reveals a cGMP-Mediated Dimeric Interface that Facilitates cGMP-Induced Activation. Structure 2016; 24:710-720. [PMID: 27066748 DOI: 10.1016/j.str.2016.03.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 01/21/2016] [Accepted: 03/04/2016] [Indexed: 10/22/2022]
Abstract
Cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG) is a key regulator of smooth muscle and vascular tone and represents an important drug target for treating hypertensive diseases and erectile dysfunction. Despite its importance, its activation mechanism is not fully understood. To understand the activation mechanism, we determined a 2.5 Å crystal structure of the PKG I regulatory (R) domain bound with cGMP, which represents the activated state. Although we used a monomeric domain for crystallization, the structure reveals that two R domains form a symmetric dimer where the cGMP bound at high-affinity pockets provide critical dimeric contacts. Small-angle X-ray scattering and mutagenesis support this dimer model, suggesting that the dimer interface modulates kinase activation. Finally, structural comparison with the homologous cyclic AMP-dependent protein kinase reveals that PKG is drastically different from protein kinase A in its active conformation, suggesting a novel activation mechanism for PKG.
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Affiliation(s)
- Jeong Joo Kim
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry, University of Kassel, Kassel, Hesse 34132, Germany
| | - Robin Lorenz
- Department of Biochemistry, University of Kassel, Kassel, Hesse 34132, Germany
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal 23955-6900, Saudi Arabia
| | - Albert S Reger
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Darren E Casteel
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Friedrich W Herberg
- Department of Biochemistry, University of Kassel, Kassel, Hesse 34132, Germany
| | - Choel Kim
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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25
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Campbell JC, Kim JJ, Li KY, Huang GY, Reger AS, Matsuda S, Sankaran B, Link TM, Yuasa K, Ladbury JE, Casteel DE, Kim C. Structural Basis of Cyclic Nucleotide Selectivity in cGMP-dependent Protein Kinase II. J Biol Chem 2016; 291:5623-5633. [PMID: 26769964 PMCID: PMC4786703 DOI: 10.1074/jbc.m115.691303] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/13/2016] [Indexed: 02/04/2023] Open
Abstract
Membrane-bound cGMP-dependent protein kinase (PKG) II is a key regulator of bone growth, renin secretion, and memory formation. Despite its crucial physiological roles, little is known about its cyclic nucleotide selectivity mechanism due to a lack of structural information. Here, we find that the C-terminal cyclic nucleotide binding (CNB-B) domain of PKG II binds cGMP with higher affinity and selectivity when compared with its N-terminal CNB (CNB-A) domain. To understand the structural basis of cGMP selectivity, we solved co-crystal structures of the CNB domains with cyclic nucleotides. Our structures combined with mutagenesis demonstrate that the guanine-specific contacts at Asp-412 and Arg-415 of the αC-helix of CNB-B are crucial for cGMP selectivity and activation of PKG II. Structural comparison with the cGMP selective CNB domains of human PKG I and Plasmodium falciparum PKG (PfPKG) shows different contacts with the guanine moiety, revealing a unique cGMP selectivity mechanism for PKG II.
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Affiliation(s)
- James C Campbell
- From the Structural and Computational Biology and Molecular Biophysics Program
| | - Jeong Joo Kim
- Department of Pharmacology, and; the Department of Biochemistry, University of Kassel, Kassel, Hesse 34132, Germany
| | - Kevin Y Li
- the Department of Biochemistry & Cell Biology, Rice University, Houston, Texas 77005
| | - Gilbert Y Huang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | | | - Shinya Matsuda
- the Department of Biological Science and Technology, the University of Tokushima Graduate School, Tokushima 770-8506, Japan
| | - Banumathi Sankaran
- the Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Todd M Link
- the Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, and
| | - Keizo Yuasa
- the Department of Biological Science and Technology, the University of Tokushima Graduate School, Tokushima 770-8506, Japan
| | - John E Ladbury
- From the Structural and Computational Biology and Molecular Biophysics Program,; the Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, and
| | - Darren E Casteel
- the Department of Medicine, University of California, San Diego, La Jolla, California 92093
| | - Choel Kim
- From the Structural and Computational Biology and Molecular Biophysics Program,; Department of Pharmacology, and; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030,.
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26
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Crystal structure of cyclic nucleotide-binding-like protein from Brucella abortus. Biochem Biophys Res Commun 2015; 468:647-52. [PMID: 26549229 DOI: 10.1016/j.bbrc.2015.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 10/22/2022]
Abstract
The cyclic nucleotide-binding (CNB)-like protein (CNB-L) from Brucella abortus shares sequence homology with CNB domain-containing proteins. We determined the crystal structure of CNB-L at 2.0 Å resolution in the absence of its C-terminal helix and nucleotide. The 3D structure of CNB-L is in a two-fold symmetric form. Each protomer shows high structure similarity to that of cGMP-binding domain-containing proteins, and likely mimics their nucleotide-free conformation. A key residue, Glu17, mediates the dimerization and prevents binding of cNMP to the canonical ligand-pocket. The structurally observed dimer of CNB-L is stable in solution, and thus is likely to be biologically relevant.
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27
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VanSchouwen B, Selvaratnam R, Giri R, Lorenz R, Herberg FW, Kim C, Melacini G. Mechanism of cAMP Partial Agonism in Protein Kinase G (PKG). J Biol Chem 2015; 290:28631-41. [PMID: 26370085 DOI: 10.1074/jbc.m115.685305] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 11/06/2022] Open
Abstract
Protein kinase G (PKG) is a major receptor of cGMP and controls signaling pathways often distinct from those regulated by cAMP. Hence, the selective activation of PKG by cGMP versus cAMP is critical. However, the mechanism of cGMP-versus-cAMP selectivity is only limitedly understood. Although the C-terminal cyclic nucleotide-binding domain B of PKG binds cGMP with higher affinity than cAMP, the intracellular concentrations of cAMP are typically higher than those of cGMP, suggesting that the cGMP-versus-cAMP selectivity of PKG is not controlled uniquely through affinities. Here, we show that cAMP is a partial agonist for PKG, and we elucidate the mechanism for cAMP partial agonism through the comparative NMR analysis of the apo, cGMP-, and cAMP-bound forms of the PKG cyclic nucleotide-binding domain B. We show that although cGMP activation is adequately explained by a two-state conformational selection model, the partial agonism of cAMP arises from the sampling of a third, partially autoinhibited state.
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Affiliation(s)
| | | | - Rajanish Giri
- From the Departments of Chemistry and Chemical Biology and
| | - Robin Lorenz
- the Department of Biochemistry, Kassel University, Heinrich Plett Strasse 40, 34132 Kassel, Germany, and
| | - Friedrich W Herberg
- the Department of Biochemistry, Kassel University, Heinrich Plett Strasse 40, 34132 Kassel, Germany, and
| | - Choel Kim
- the Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030
| | - Giuseppe Melacini
- From the Departments of Chemistry and Chemical Biology and Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada,
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28
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Chardonnet F, Capdevielle-Dulac C, Chouquet B, Joly N, Harry M, Le Ru B, Silvain JF, Kaiser L. Food searching behaviour of a Lepidoptera pest species is modulated by the foraging gene polymorphism. ACTA ACUST UNITED AC 2015; 217:3465-73. [PMID: 25274324 DOI: 10.1242/jeb.108258] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The extent of damage to crop plants from pest insects depends on the foraging behaviour of the insect's feeding stage. Little is known, however, about the genetic and molecular bases of foraging behaviour in phytophagous pest insects. The foraging gene (for), a candidate gene encoding a PKG-I, has an evolutionarily conserved function in feeding strategies. Until now, for had never been studied in Lepidoptera, which includes major pest species. The cereal stem borer Sesamia nonagrioides is therefore a relevant species within this order with which to study conservation of and polymorphism in the for gene, and its role in foraging - a behavioural trait that is directly associated with plant injuries. Full sequencing of for cDNA in S. nonagrioides revealed a high degree of conservation with other insect taxa. Activation of PKG by a cGMP analogue increased larval foraging activity, measured by how frequently larvae moved between food patches in an actimeter. We found one non-synonymous allelic variation in a natural population that defined two allelic variants. These variants presented significantly different levels of foraging activity, and the behaviour was positively correlated to gene expression levels. Our results show that for gene function is conserved in this species of Lepidoptera, and describe an original case of a single nucleotide polymorphism associated with foraging behaviour variation in a pest insect. By illustrating how variation in this single gene can predict phenotype, this work opens new perspectives into the evolutionary context of insect adaptation to plants, as well as pest management.
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Affiliation(s)
- Floriane Chardonnet
- Laboratoire Evolution Génome et Spéciation, CNRS UPR 9034, IRD UR 072 and Université Paris Sud Orsay, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Claire Capdevielle-Dulac
- Laboratoire Evolution Génome et Spéciation, CNRS UPR 9034, IRD UR 072 and Université Paris Sud Orsay, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Bastien Chouquet
- Laboratoire Evolution Génome et Spéciation, CNRS UPR 9034, IRD UR 072 and Université Paris Sud Orsay, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Nicolas Joly
- Laboratoire Evolution Génome et Spéciation, CNRS UPR 9034, IRD UR 072 and Université Paris Sud Orsay, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Myriam Harry
- Laboratoire Evolution Génome et Spéciation, CNRS UPR 9034, IRD UR 072 and Université Paris Sud Orsay, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Bruno Le Ru
- Laboratoire Evolution Génome et Spéciation, CNRS UPR 9034, IRD UR 072 and Université Paris Sud Orsay, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, France icipe - African Insect Science for Food and Health, Duduville Campus, Kasarani, PO Box 30772-00100, Nairobi, Kenya
| | - Jean-François Silvain
- Laboratoire Evolution Génome et Spéciation, CNRS UPR 9034, IRD UR 072 and Université Paris Sud Orsay, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, France
| | - Laure Kaiser
- Laboratoire Evolution Génome et Spéciation, CNRS UPR 9034, IRD UR 072 and Université Paris Sud Orsay, 1 Avenue de la Terrasse, 91198 Gif sur Yvette, France INRA, UMR 1392, Institut d'Ecologie et des Sciences de l'Environnement de Paris, France
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29
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Kim JJ, Flueck C, Franz E, Sanabria-Figueroa E, Thompson E, Lorenz R, Bertinetti D, Baker DA, Herberg FW, Kim C. Crystal structures of the carboxyl cGMP binding domain of the Plasmodium falciparum cGMP-dependent protein kinase reveal a novel capping triad crucial for merozoite egress. PLoS Pathog 2015; 11:e1004639. [PMID: 25646845 PMCID: PMC4412288 DOI: 10.1371/journal.ppat.1004639] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/20/2014] [Indexed: 01/05/2023] Open
Abstract
The Plasmodium falciparum cGMP-dependent protein kinase (PfPKG) is a key regulator across the malaria parasite life cycle. Little is known about PfPKG’s activation mechanism. Here we report that the carboxyl cyclic nucleotide binding domain functions as a “gatekeeper” for activation by providing the highest cGMP affinity and selectivity. To understand the mechanism, we have solved its crystal structures with and without cGMP at 2.0 and 1.9 Å, respectively. These structures revealed a PfPKG-specific capping triad that forms upon cGMP binding, and disrupting the triad reduces kinase activity by 90%. Furthermore, mutating these residues in the parasite prevents blood stage merozoite egress, confirming the essential nature of the triad in the parasite. We propose a mechanism of activation where cGMP binding allosterically triggers the conformational change at the αC-helix, which bridges the regulatory and catalytic domains, causing the capping triad to form and stabilize the active conformation. Malaria causes up to a million fatalities per year worldwide. Most of these deaths are caused by Plasmodium falciparum, which has a complex life cycle in both humans and mosquitoes. One key regulator of this process is P. falciparum cGMP-dependent protein kinase (PfPKG), the main effector of the cGMP-signaling pathway. Specifically blocking this kinase stops both replication and transmission of the parasites, suggesting that PfPKG is a promising drug target. Here we identified the carboxyl cGMP-binding domain of PfPKG serving as a gatekeeper for activation of the entire kinase by having the highest affinity and selectivity for cGMP. High-resolution crystal structures with and without cGMP allowed us to identify a novel cGMP capping triad that dynamically forms upon binding cGMP and stabilizes the activated conformation. Mutation of the capping triad forming residues not only reduces its kinase activity, but also prevents blood stage merozoite egress, demonstrating its crucial role in PfPKG activation.
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Affiliation(s)
- Jeong Joo Kim
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Biochemistry, University of Kassel, Kassel, Hesse, Germany
| | - Christian Flueck
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Eugen Franz
- Department of Biochemistry, University of Kassel, Kassel, Hesse, Germany
| | | | - Eloise Thompson
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Robin Lorenz
- Department of Biochemistry, University of Kassel, Kassel, Hesse, Germany
| | - Daniela Bertinetti
- Department of Biochemistry, University of Kassel, Kassel, Hesse, Germany
| | - David A. Baker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Choel Kim
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, United States of America
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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30
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Seifert R, Schneider EH, Bähre H. From canonical to non-canonical cyclic nucleotides as second messengers: pharmacological implications. Pharmacol Ther 2014; 148:154-84. [PMID: 25527911 DOI: 10.1016/j.pharmthera.2014.12.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 12/11/2014] [Indexed: 02/07/2023]
Abstract
This review summarizes our knowledge on the non-canonical cyclic nucleotides cCMP, cUMP, cIMP, cXMP and cTMP. We place the field into a historic context and discuss unresolved questions and future directions of research. We discuss the implications of non-canonical cyclic nucleotides for experimental and clinical pharmacology, focusing on bacterial infections, cardiovascular and neuropsychiatric disorders and reproduction medicine. The canonical cyclic purine nucleotides cAMP and cGMP fulfill the criteria of second messengers. (i) cAMP and cGMP are synthesized by specific generators, i.e. adenylyl and guanylyl cyclases, respectively. (ii) cAMP and cGMP activate specific effector proteins, e.g. protein kinases. (iii) cAMP and cGMP exert specific biological effects. (iv) The biological effects of cAMP and cGMP are terminated by phosphodiesterases and export. The effects of cAMP and cGMP are mimicked by (v) membrane-permeable cyclic nucleotide analogs and (vi) bacterial toxins. For decades, the existence and relevance of cCMP and cUMP have been controversial. Modern mass-spectrometric methods have unequivocally demonstrated the existence of cCMP and cUMP in mammalian cells. For both, cCMP and cUMP, the criteria for second messenger molecules are now fulfilled as well. There are specific patterns by which nucleotidyl cyclases generate cNMPs and how they are degraded and exported, resulting in unique cNMP signatures in biological systems. cNMP signaling systems, specifically at the level of soluble guanylyl cyclase, soluble adenylyl cyclase and ExoY from Pseudomonas aeruginosa are more promiscuous than previously appreciated. cUMP and cCMP are evolutionary new molecules, probably reflecting an adaption to signaling requirements in higher organisms.
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Affiliation(s)
- Roland Seifert
- Institute of Pharmacology, Hannover Medical School, D-30625 Hannover, Germany.
| | - Erich H Schneider
- Institute of Pharmacology, Hannover Medical School, D-30625 Hannover, Germany
| | - Heike Bähre
- Institute of Pharmacology, Hannover Medical School, D-30625 Hannover, Germany
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31
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Chen J, Roberts JD. cGMP-dependent protein kinase I gamma encodes a nuclear localization signal that regulates nuclear compartmentation and function. Cell Signal 2014; 26:2633-44. [PMID: 25172423 PMCID: PMC4254301 DOI: 10.1016/j.cellsig.2014.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 08/15/2014] [Indexed: 10/24/2022]
Abstract
cGMP-dependent protein kinase I (PKGI) plays an important role in regulating how cGMP specifies vascular smooth muscle cell (SMC) phenotype. Although studies indicate that PKGI nuclear localization controls how cGMP regulates gene expression in SMC, information about the mechanisms that regulate PKGI nuclear compartmentation and its role in directly regulating cell phenotype is limited. Here we characterize a nuclear localization signal sequence (NLS) in PKGIγ, a proteolytically cleaved PKGI kinase fragment that translocates to the nucleus of SMC. Immuno-localization studies using cells expressing native and NLS-mutant PKGIγ, and treated with a small molecule nuclear transport inhibitor, indicated that PKGIγ encodes a constitutively active NLS that requires importin α and β for regulation of its compartmentation. Moreover, studies utilizing a genetically encoded nuclear phospho-CREB biosensor probe and fluorescence lifetime imaging microscopy demonstrated that this NLS controls PKGIγ nuclear function. In addition, although cytosolic PKGIγ-activity was observed to stimulate MAPK/ERK-mediated nuclear CREB signaling in SMC, NLS-mediated PKGIγ nuclear activity alone was determined to increase the expression of differentiation marker proteins in these cells. These results indicate that NLS-mediated nuclear PKGIγ localization plays an important role in how PKGI regulates vascular SMC phenotype.
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Affiliation(s)
- Jingsi Chen
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Cambridge, MA, USA
| | - Jesse D Roberts
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Cambridge, MA, USA; Departments of Anesthesia, Pediatrics, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
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32
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Huang GY, Gerlits OO, Blakeley MP, Sankaran B, Kovalevsky AY, Kim C. Neutron diffraction reveals hydrogen bonds critical for cGMP-selective activation: insights for cGMP-dependent protein kinase agonist design. Biochemistry 2014; 53:6725-7. [PMID: 25271401 PMCID: PMC4222537 DOI: 10.1021/bi501012v] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
High selectivity of cyclic-nucleotide
binding (CNB) domains for
cAMP and cGMP are required for segregating signaling pathways; however,
the mechanism of selectivity remains unclear. To investigate the mechanism
of high selectivity in cGMP-dependent protein kinase (PKG), we determined
a room-temperature joint X-ray/neutron (XN) structure of PKG Iβ
CNB-B, a domain 200-fold selective for cGMP over cAMP, bound to cGMP
(2.2 Å), and a low-temperature X-ray structure of CNB-B with
cAMP (1.3 Å). The XN structure directly describes the hydrogen
bonding interactions that modulate high selectivity for cGMP, while
the structure with cAMP reveals that all these contacts are disrupted,
explaining its low affinity for cAMP.
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Affiliation(s)
- Gilbert Y Huang
- Verna and Mars McClean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , One Baylor Plaza, Houston, Texas 77004, United States
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33
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Double electron-electron resonance reveals cAMP-induced conformational change in HCN channels. Proc Natl Acad Sci U S A 2014; 111:9816-21. [PMID: 24958877 DOI: 10.1073/pnas.1405371111] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Binding of 3',5'-cyclic adenosine monophosphate (cAMP) to hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels regulates their gating. cAMP binds to a conserved intracellular cyclic nucleotide-binding domain (CNBD) in the channel, increasing the rate and extent of activation of the channel and shifting activation to less hyperpolarized voltages. The structural mechanism underlying this regulation, however, is unknown. We used double electron-electron resonance (DEER) spectroscopy to directly map the conformational ensembles of the CNBD in the absence and presence of cAMP. Site-directed, double-cysteine mutants in a soluble CNBD fragment were spin-labeled, and interspin label distance distributions were determined using DEER. We found motions of up to 10 Å induced by the binding of cAMP. In addition, the distributions were narrower in the presence of cAMP. Continuous-wave electron paramagnetic resonance studies revealed changes in mobility associated with cAMP binding, indicating less conformational heterogeneity in the cAMP-bound state. From the measured DEER distributions, we constructed a coarse-grained elastic-network structural model of the cAMP-induced conformational transition. We find that binding of cAMP triggers a reorientation of several helices within the CNBD, including the C-helix closest to the cAMP-binding site. These results provide a basis for understanding how the binding of cAMP is coupled to channel opening in HCN and related channels.
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34
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Akimoto M, Zhang Z, Boulton S, Selvaratnam R, VanSchouwen B, Gloyd M, Accili EA, Lange OF, Melacini G. A mechanism for the auto-inhibition of hyperpolarization-activated cyclic nucleotide-gated (HCN) channel opening and its relief by cAMP. J Biol Chem 2014; 289:22205-20. [PMID: 24878962 DOI: 10.1074/jbc.m114.572164] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels control neuronal and cardiac electrical rhythmicity. There are four homologous isoforms (HCN1-4) sharing a common multidomain architecture that includes an N-terminal transmembrane tetrameric ion channel followed by a cytoplasmic "C-linker," which connects a more distal cAMP-binding domain (CBD) to the inner pore. Channel opening is primarily stimulated by transmembrane elements that sense membrane hyperpolarization, although cAMP reduces the voltage required for HCN activation by promoting tetramerization of the intracellular C-linker, which in turn relieves auto-inhibition of the inner pore gate. Although binding of cAMP has been proposed to relieve auto-inhibition by affecting the structure of the C-linker and CBD, the nature and extent of these cAMP-dependent changes remain limitedly explored. Here, we used NMR to probe the changes caused by the binding of cAMP and of cCMP, a partial agonist, to the apo-CBD of HCN4. Our data indicate that the CBD exists in a dynamic two-state equilibrium, whose position as gauged by NMR chemical shifts correlates with the V½ voltage measured through electrophysiology. In the absence of cAMP, the most populated CBD state leads to steric clashes with the activated or "tetrameric" C-linker, which becomes energetically unfavored. The steric clashes of the apo tetramer are eliminated either by cAMP binding, which selects for a CBD state devoid of steric clashes with the tetrameric C-linker and facilitates channel opening, or by a transition of apo-HCN to monomers or dimer of dimers, in which the C-linker becomes less structured, and channel opening is not facilitated.
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Affiliation(s)
- Madoka Akimoto
- From the Departments of Chemistry and Chemical Biology and
| | - Zaiyong Zhang
- the Biomolecular NMR and Munich Center for Integrated Protein Science, Department of Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Stephen Boulton
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | | | | | - Melanie Gloyd
- From the Departments of Chemistry and Chemical Biology and Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Eric A Accili
- the Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada, and
| | - Oliver F Lange
- the Biomolecular NMR and Munich Center for Integrated Protein Science, Department of Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany, the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Giuseppe Melacini
- From the Departments of Chemistry and Chemical Biology and Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada,
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35
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Seok SH, Im H, Won HS, Seo MD, Lee YS, Yoon HJ, Cha MJ, Park JY, Lee BJ. Structures of inactive CRP species reveal the atomic details of the allosteric transition that discriminates cyclic nucleotide second messengers. ACTA ACUST UNITED AC 2014; 70:1726-42. [PMID: 24914983 DOI: 10.1107/s139900471400724x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 04/01/2014] [Indexed: 11/10/2022]
Abstract
The prokaryotic global transcription factor CRP has been considered to be an ideal model for in-depth study of both the allostery of the protein and the differential utilization of the homologous cyclic nucleotide second messengers cAMP and cGMP. Here, atomic details from the crystal structures of two inactive CRP species, an apo form and a cGMP-bound form, in comparison with a known active conformation, the cAMP-CRP complex, provide macroscopic and microscopic insights into CRP allostery, which is coupled to specific discrimination between the two effectors. The cAMP-induced conformational transition, including dynamic fluctuations, can be driven by the fundamental folding forces that cause water-soluble globular proteins to construct an optimized hydrophobic core, including secondary-structure formation. The observed conformational asymmetries underlie a negative cooperativity in the sequential binding of cyclic nucleotides and a stepwise manner of binding with discrimination between the effector molecules. Additionally, the finding that cGMP, which is specifically recognized in a syn conformation, induces an inhibitory conformational change, rather than a null effect, on CRP supports the intriguing possibility that cGMP signalling could be widely utilized in prokaryotes, including in aggressive inhibition of CRP-like proteins.
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Affiliation(s)
- Seung-Hyeon Seok
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hookang Im
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Hyung-Sik Won
- Department of Biotechnology, RIBHS and RIID, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 380-701, Republic of Korea
| | - Min-Duk Seo
- College of Pharmacy, Ajou University, Suwon, Kyeonggi 443-749, Republic of Korea
| | - Yoo-Sup Lee
- Department of Biotechnology, RIBHS and RIID, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 380-701, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Min-Jeong Cha
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jin-Young Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
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36
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Aggarwal S, Gross CM, Rafikov R, Kumar S, Fineman JR, Ludewig B, Jonigk D, Black SM. Nitration of tyrosine 247 inhibits protein kinase G-1α activity by attenuating cyclic guanosine monophosphate binding. J Biol Chem 2014; 289:7948-61. [PMID: 24469460 DOI: 10.1074/jbc.m113.534313] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The cGMP-dependent protein kinase G-1α (PKG-1α) is a downstream mediator of nitric oxide and natriuretic peptide signaling. Alterations in this pathway play a key role in the pathogenesis and progression of vascular diseases associated with increased vascular tone and thickness, such as pulmonary hypertension. Previous studies have shown that tyrosine nitration attenuates PKG-1α activity. However, little is known about the mechanisms involved in this event. Utilizing mass spectrometry, we found that PKG-1α is susceptible to nitration at tyrosine 247 and 425. Tyrosine to phenylalanine mutants, Y247F- and Y425F-PKG-1α, were both less susceptible to nitration than WT PKG-1α, but only Y247F-PKG-1α exhibited preserved activity, suggesting that the nitration of Tyr(247) is critical in attenuating PKG-1α activity. The overexpression of WT- or Y247F-PKG-1α decreased the proliferation of pulmonary artery smooth muscle cells (SMC), increased the expression of SMC contractile markers, and decreased the expression of proliferative markers. Nitrosative stress induced a switch from a contractile to a synthetic phenotype in cells expressing WT- but not Y247F-PKG-1α. An antibody generated against 3-NT-Y247 identified increased levels of nitrated PKG-1α in humans with pulmonary hypertension. Finally, to gain a more mechanistic understanding of how nitration attenuates PKG activity, we developed a homology model of PKG-1α. This model predicted that the nitration of Tyr(247) would decrease the affinity of PKG-1α for cGMP, which we confirmed using a [(3)H]cGMP binding assay. Our study shows that the nitration of Tyr(247) and the attenuation of cGMP binding is an important mechanism regulating in PKG-1α activity and SMC proliferation/differentiation.
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Affiliation(s)
- Saurabh Aggarwal
- From the Pulmonary Disease Program, Vascular Biology Center, Georgia Regents University, Augusta, Georgia 30912
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37
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Huang GY, Kim JJ, Reger AS, Lorenz R, Moon EW, Zhao C, Casteel DE, Bertinetti D, Vanschouwen B, Selvaratnam R, Pflugrath JW, Sankaran B, Melacini G, Herberg FW, Kim C. Structural basis for cyclic-nucleotide selectivity and cGMP-selective activation of PKG I. Structure 2013; 22:116-24. [PMID: 24239458 DOI: 10.1016/j.str.2013.09.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/18/2013] [Accepted: 09/23/2013] [Indexed: 10/26/2022]
Abstract
Cyclic guanosine monophosphate (cGMP) and cyclic AMP (cAMP)-dependent protein kinases (PKG and PKA) are closely related homologs, and the cyclic nucleotide specificity of each kinase is crucial for keeping the two signaling pathways segregated, but the molecular mechanism of cyclic nucleotide selectivity is unknown. Here, we report that the PKG Iβ C-terminal cyclic nucleotide binding domain (CNB-B) is highly selective for cGMP binding, and we have solved crystal structures of CNB-B with and without bound cGMP. These structures, combined with a comprehensive mutagenic analysis, allowed us to identify Leu296 and Arg297 as key residues that mediate cGMP selectivity. In addition, by comparing the cGMP bound and unbound structures, we observed large conformational changes in the C-terminal helices in response to cGMP binding, which were stabilized by recruitment of Tyr351 as a "capping residue" for cGMP. The observed rearrangements of the C-terminal helices provide a mechanical insight into release of the catalytic domain and kinase activation.
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Affiliation(s)
- Gilbert Y Huang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeong Joo Kim
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Albert S Reger
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robin Lorenz
- Department of Biochemistry, University of Kassel, Kassel 34132, Germany
| | - Eui-Whan Moon
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chi Zhao
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Darren E Casteel
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Bryan Vanschouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Rajeevan Selvaratnam
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | | | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Building 6R2100, Berkeley, CA 94720, USA
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4M1, Canada
| | | | - Choel Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA.
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38
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Guo DC, Regalado E, Casteel D, Santos-Cortez R, Gong L, Kim J, Dyack S, Horne S, Chang G, Jondeau G, Boileau C, Coselli J, Li Z, Leal S, Shendure J, Rieder M, Bamshad M, Nickerson D, Kim C, Milewicz D. Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections. Am J Hum Genet 2013; 93:398-404. [PMID: 23910461 PMCID: PMC3738837 DOI: 10.1016/j.ajhg.2013.06.019] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/21/2013] [Accepted: 06/20/2013] [Indexed: 01/08/2023] Open
Abstract
Gene mutations that lead to decreased contraction of vascular smooth-muscle cells (SMCs) can cause inherited thoracic aortic aneurysms and dissections. Exome sequencing of distant relatives affected by thoracic aortic disease and subsequent Sanger sequencing of additional probands with familial thoracic aortic disease identified the same rare variant, PRKG1 c.530G>A (p.Arg177Gln), in four families. This mutation segregated with aortic disease in these families with a combined two-point LOD score of 7.88. The majority of affected individuals presented with acute aortic dissections (63%) at relatively young ages (mean 31 years, range 17-51 years). PRKG1 encodes type I cGMP-dependent protein kinase (PKG-1), which is activated upon binding of cGMP and controls SMC relaxation. Although the p.Arg177Gln alteration disrupts binding to the high-affinity cGMP binding site within the regulatory domain, the altered PKG-1 is constitutively active even in the absence of cGMP. The increased PKG-1 activity leads to decreased phosphorylation of the myosin regulatory light chain in fibroblasts and is predicted to cause decreased contraction of vascular SMCs. Thus, identification of a gain-of-function mutation in PRKG1 as a cause of thoracic aortic disease provides further evidence that proper SMC contractile function is critical for maintaining the integrity of the thoracic aorta throughout a lifetime.
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Affiliation(s)
- Dong-chuan Guo
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ellen Regalado
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Darren E. Casteel
- Department of Medicine and Cancer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Regie L. Santos-Cortez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Limin Gong
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jeong Joo Kim
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Dyack
- Department of Pediatrics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - S. Gabrielle Horne
- Department of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Guijuan Chang
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Guillaume Jondeau
- Institut National de la Santé et de la Recherche Médicale Unité 698, Hôpital Bichat, 46 Rue Henri Huchard, 75018 Paris, France
- Centre de Référence pour les Syndromes de Marfan et Apparentés, Service de Cardiologie, Hôpital Bichat, Assistance Publique – Hôpitaux de Paris, 75018 Paris, France
- Service de Cardiologie, Hopital Bichat, Assistance Publique – Hôpitaux de Paris, 75018 Paris, France
- Unité de Formation et de Recherche de Médecine, Université Paris Diderot – Paris 7, 75010 Paris, France
| | - Catherine Boileau
- Institut National de la Santé et de la Recherche Médicale Unité 698, Hôpital Bichat, 46 Rue Henri Huchard, 75018 Paris, France
- Centre de Référence pour les Syndromes de Marfan et Apparentés, Service de Cardiologie, Hôpital Bichat, Assistance Publique – Hôpitaux de Paris, 75018 Paris, France
- Service de Biochimie, d’Hormonologie, et de Génétique Moléculaire, Hôpital Ambroise Paré, Assistance Publique – Hôpitaux de Paris 9, Avenue Charles de Gaulle, 92100 Boulogne, France
- Université Versailles Saint-Quentin-en-Yvelines, Unité de Formation et de Recherche des Sciences de la Santé, 78280 Guyancourt, France
| | - Joseph S. Coselli
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhenyu Li
- Department of Internal Medicine, University of Kentucky, Lexington, KY 40508, USA
| | - Suzanne M. Leal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Mark J. Rieder
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | | | | | - Choel Kim
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dianna M. Milewicz
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Memorial Hermann Heart and Vascular Institute, Houston, TX 77030, USA
- Texas Heart Institute at St. Luke’s Episcopal Hospital, Houston, TX 77030, USA
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39
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Kato S, Zhang R, Roberts JD. Proprotein convertases play an important role in regulating PKGI endoproteolytic cleavage and nuclear transport. Am J Physiol Lung Cell Mol Physiol 2013; 305:L130-40. [PMID: 23686857 PMCID: PMC3726948 DOI: 10.1152/ajplung.00391.2012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 05/15/2013] [Indexed: 12/27/2022] Open
Abstract
Nitric oxide and cGMP modulate vascular smooth muscle cell (SMC) phenotype by regulating cell differentiation and proliferation. Recent studies suggest that cGMP-dependent protein kinase I (PKGI) cleavage and the nuclear translocation of a constitutively active kinase fragment, PKGIγ, are required for nuclear cGMP signaling in SMC. However, the mechanisms that control PKGI proteolysis are unknown. Inspection of the amino acid sequence of a PKGI cleavage site that yields PKGIγ and a protease database revealed a putative minimum consensus sequence for proprotein convertases (PCs). Therefore we investigated the role of PCs in regulating PKGI proteolysis. We observed that overexpression of PCs, furin and PC5, but not PC7, which are all expressed in SMC, increase PKGI cleavage in a dose-dependent manner in human embryonic kidney (HEK) 293 cells. Moreover, furin-induced proteolysis of mutant PKGI, in which alanines were substituted into the putative PC consensus sequence, was decreased in these cells. In addition, overexpression of furin increased PKGI proteolysis in LoVo cells, which is an adenocarcinoma cell line expressing defective furin without PC activity. Also, expression of α1-PDX, an engineered serpin-like PC inhibitor, reduced PC activity and decreased PKGI proteolysis in HEK293 cells. Last, treatment of low-passage rat aortic SMC with membrane-permeable PC inhibitor peptides decreased cGMP-stimulated nuclear PKGIγ translocation. These data indicate for the first time that PCs have a role in regulating PKGI proteolysis and the nuclear localization of its active cleavage product, which are important for cGMP-mediated SMC phenotype.
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Affiliation(s)
- Shin Kato
- Cardiovascular Research Center of the General Medical Services, Massachusetts General Hospital, Boston, MA, USA
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40
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Puljung MC, Zagotta WN. A secondary structural transition in the C-helix promotes gating of cyclic nucleotide-regulated ion channels. J Biol Chem 2013; 288:12944-56. [PMID: 23525108 DOI: 10.1074/jbc.m113.464123] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Cyclic nucleotide-regulated ion channels bind second messengers like cAMP to a C-terminal domain, consisting of a β-roll, followed by two α-helices (B- and C-helices). We monitored the cAMP-dependent changes in the structure of the C-helix of a C-terminal fragment of HCN2 channels using transition metal ion FRET between fluorophores on the C-helix and metal ions bound between histidine pairs on the same helix. cAMP induced a change in the dimensions of the C-helix and an increase in the metal binding affinity of the histidine pair. cAMP also caused an increase in the distance between a fluorophore on the C-helix and metal ions bound to the B-helix. Stabilizing the C-helix of intact CNGA1 channels by metal binding to a pair of histidines promoted channel opening. These data suggest that ordering of the C-helix is part of the gating conformational change in cyclic nucleotide-regulated channels.
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Affiliation(s)
- Michael C Puljung
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195-7290, USA
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41
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Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annu Rev Biophys 2013; 42:265-87. [PMID: 23451892 DOI: 10.1146/annurev-biophys-083012-130253] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Advances in our understanding of macromolecular structure come from experimental methods, such as X-ray crystallography, and also computational analysis of the growing number of atomic models obtained from such experiments. The later analyses have made it possible to develop powerful tools for structure prediction and optimization in the absence of experimental data. In recent years, a synergy between these computational methods for crystallographic structure determination and structure prediction and optimization has begun to be exploited. We review some of the advances in the algorithms used for crystallographic structure determination in the Phenix and Crystallography & NMR System software packages and describe how methods from ab initio structure prediction and refinement in Rosetta have been applied to challenging crystallographic problems. The prospects for future improvement of these methods are discussed.
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Affiliation(s)
- Paul D Adams
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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42
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Moon TM, Osborne BW, Dostmann WR. The switch helix: a putative combinatorial relay for interprotomer communication in cGMP-dependent protein kinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1346-51. [PMID: 23416533 DOI: 10.1016/j.bbapap.2013.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/04/2013] [Indexed: 11/26/2022]
Abstract
For over three decades the isozymes of cGMP-dependent protein kinase (PKG) have been studied using an array of biochemical and biophysical techniques. When compared to its closest cousin, cAMP-dependent protein kinase (PKA), these studies revealed a set of identical domain types, yet containing distinct, sequence-specific features. The recently solved structure of the PKG regulatory domain showed the presence of the switch helix (SW), a novel motif that promotes the formation of a domain-swapped dimer in the asymmetric unit. This dimer is mediated by the interaction of a knob motif on the C-terminal locus of the SW, with a hydrophobic nest on the opposing protomer. This nest sits adjacent to the cGMP binding pocket of the B-site. Priming of this site by cGMP may influence the geometry of the hydrophobic nest. Moreover, this unique interaction may have wide implications for the architecture of the inactive and active forms of PKG. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Affiliation(s)
- Thomas M Moon
- Department of Pharmacology, The University of Vermont, Burlington, VT 05405, USA
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43
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Abstract
The cyclic-AMP binding domain (CBD) is the central regulatory unit of exchange proteins activated by cAMP (EPAC). The CBD maintains EPAC in a state of auto-inhibition in the absence of the allosteric effector, cAMP. When cAMP binds to the CBD such auto-inhibition is released, leading to EPAC activation. It has been shown that a key feature of such cAMP-dependent activation process is the partial destabilization of a structurally conserved hinge helix at the C-terminus of the CBD. However, the role of this helix in auto-inhibition is currently not fully understood. Here we utilize a series of progressive deletion mutants that mimic the hinge helix destabilization caused by cAMP to show that such helix is also a pivotal auto-inhibitory element of apo-EPAC. The effect of the deletion mutations on the auto-inhibitory apo/inactive vs. apo/active equilibrium was evaluated using recently developed NMR chemical shift projection and covariance analysis methods. Our results show that, even in the absence of cAMP, the C-terminal region of the hinge helix is tightly coupled to other conserved allosteric structural elements of the CBD and perturbations that destabilize the hinge helix shift the auto-inhibitory equilibrium toward the apo/active conformations. These findings explain the apparently counterintuitive observation that cAMP binds more tightly to shorter than longer EPAC constructs. These results are relevant for CBDs in general and rationalize why substrates sensitize CBD-containing systems to cAMP. Furthermore, the NMR analyses presented here are expected to be generally useful to quantitatively evaluate how mutations affect conformational equilibria.
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Affiliation(s)
- Rajeevan Selvaratnam
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | | | - Rahul Das
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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44
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Elkins JM, Knapp S. The Structure of the Full-Length Tetrameric PKA Regulatory RIIβ Complex Reveals the Mechanism of Allosteric PKA Activation. Sci Signal 2012; 5:pe21. [DOI: 10.1126/scisignal.2003053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The conformational changes caused by cAMP binding to the regulatory subunit in the PKA holoenzyme are shown.
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Affiliation(s)
- Jonathan M. Elkins
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
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45
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Hopp CS, Bowyer PW, Baker DA. The role of cGMP signalling in regulating life cycle progression of Plasmodium. Microbes Infect 2012; 14:831-7. [PMID: 22613210 PMCID: PMC3484397 DOI: 10.1016/j.micinf.2012.04.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/13/2012] [Accepted: 04/17/2012] [Indexed: 11/25/2022]
Abstract
The 3′-5′-cyclic guanosine monophosphate (cGMP)-dependent protein kinase (PKG) is the main mediator of cGMP signalling in the malaria parasite. This article reviews the role of PKG in Plasmodium falciparum during gametogenesis and blood stage schizont rupture, as well as the role of the Plasmodium berghei orthologue in ookinete differentiation and motility, and liver stage schizont development. The current views on potential effector proteins downstream of PKG and the mechanisms that may regulate cyclic nucleotide levels are presented.
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Affiliation(s)
- Christine S Hopp
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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46
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Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:381-90. [PMID: 22505258 PMCID: PMC3322597 DOI: 10.1107/s0907444911047834] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 11/10/2011] [Indexed: 11/10/2022]
Abstract
Traditional methods for macromolecular refinement often have limited success at low resolution (3.0-3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine. Firstly, a `reference-model' method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a ϕ,ψ term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from nonredundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered R(free) and a decreased gap between R(work) and R(free).
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Affiliation(s)
- Jeffrey J Headd
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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47
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Abstract
Signaling by nitric oxide (NO) determines several cardiovascular functions including blood pressure regulation, cardiac and smooth muscle hypertrophy, and platelet function. NO stimulates the synthesis of cGMP by soluble guanylyl cyclases and thereby activates cGMP-dependent protein kinases (PKGs), mediating most of the cGMP functions. Hence, an elucidation of the PKG signaling cascade is essential for the understanding of the (patho)physiological aspects of NO. Several PKG signaling pathways were identified, meanwhile regulating the intracellular calcium concentration, mediating calcium desensitization or cytoskeletal rearrangement. During the last decade it emerged that the inositol trisphosphate receptor-associated cGMP-kinase substrate (IRAG), an endoplasmic reticulum-anchored 125-kDa membrane protein, is a main signal transducer of PKG activity in the cardiovascular system. IRAG interacts specifically in a trimeric complex with the PKG1β isoform and the inositol 1,4,5-trisphosphate receptor I and, upon phosphorylation, reduces the intracellular calcium release from the intracellular stores. IRAG motifs for phosphorylation and for targeting to PKG1β and 1,4,5-trisphosphate receptor I were identified by several approaches. The (patho)physiological functions for the regulation of smooth muscle contractility and the inhibition of platelet activation were perceived. In this review, the IRAG recognition, targeting, and function are summarized compared with PKG and several PKG substrates in the cardiovascular system.
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Affiliation(s)
- Jens Schlossmann
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Regensburg, Regensburg, Germany.
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