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Störmer E, Weng JH, Wu J, Bertinetti D, Kaila Sharma P, Ma W, Herberg FW, Taylor SS. Capturing the domain crosstalk in full length LRRK2 and LRRK2RCKW. Biochem J 2023; 480:BCJ20230126. [PMID: 37212165 PMCID: PMC10317166 DOI: 10.1042/bcj20230126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/10/2023] [Accepted: 05/19/2023] [Indexed: 05/23/2023]
Abstract
LRRK2 is a multi-domain protein with three catalytically inert N-terminal domains (NtDs) and four C-terminal domains, including a kinase and a GTPase domain. LRRK2 mutations are linked to Parkinson's Disease. Recent structures of LRRK2RCKW and a full-length inactive LRRK2 (fl-LRRK2INACT) monomer revealed that the kinase domain drives LRRK2 activation. The LRR domain and also an ordered LRR- COR linker, wrap around the C-lobe of the kinase domain and sterically block the substrate binding surface in fl-LRRK2INACT. Here we focus on the crosstalk between domains. Our biochemical studies of GTPase and kinase activities of fl-LRRK2 and LRRK2RCKW reveal how mutations influence this crosstalk differently depending on the domain borders investigated. Furthermore, we demonstrate that removing the NtDs leads to altered intramolecular regulation. To further investigate the crosstalk, we used Hydrogen-Deuterium exchange Mass Spectrometry (HDX-MS) to characterize the conformation of LRRK2RCKW and Gaussian Accelerated Molecular Dynamics (GaMD) to create dynamic portraits of fl-LRRK2 and LRRK2RCKW. These models allowed us to investigate the dynamic changes in wild type and mutant LRRK2s. Our data show that the a3ROC helix, the Switch II motif in the ROC domain, and the LRR-ROC linker play crucial roles in mediating local and global conformational changes. We demonstrate how these regions are affected by other domains in fl-LRRK2 and LRRK2RCKW and show how unleashing of the NtDs as well as PD mutations lead to changes in conformation and dynamics of the ROC and kinase domains which ultimately impact kinase and GTPase activities. These allosteric sites are potential therapeutic targets.
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Affiliation(s)
- Eliza Störmer
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, U.S.A
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, U.S.A
| | | | | | - Wen Ma
- Department of Chemistry and Biochemistry, University of California, San Diego, U.S.A
| | | | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, U.S.A
- Department of Chemistry and Biochemistry, University of California, San Diego, U.S.A
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2
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Happ JT, Arveseth CD, Bruystens J, Bertinetti D, Nelson IB, Olivieri C, Zhang J, Hedeen DS, Zhu JF, Capener JL, Bröckel JW, Vu L, King CC, Ruiz-Perez VL, Ge X, Veglia G, Herberg FW, Taylor SS, Myers BR. A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction. Nat Struct Mol Biol 2022; 29:990-999. [PMID: 36202993 PMCID: PMC9696579 DOI: 10.1038/s41594-022-00838-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/22/2022] [Indexed: 02/03/2023]
Abstract
The Hedgehog (Hh) cascade is central to development, tissue homeostasis and cancer. A pivotal step in Hh signal transduction is the activation of glioma-associated (GLI) transcription factors by the atypical G protein-coupled receptor (GPCR) SMOOTHENED (SMO). How SMO activates GLI remains unclear. Here we show that SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity. As a result, GLI is released from phosphorylation-induced inhibition. Using a combination of in vitro, cellular and organismal models, we demonstrate that interfering with SMO-PKA pseudosubstrate interactions prevents Hh signal transduction. The mechanism uncovered echoes one used by the Wnt cascade, revealing an unexpected similarity in how these two essential developmental and cancer pathways signal intracellularly. More broadly, our findings define a mode of GPCR-PKA communication that may be harnessed by a range of membrane receptors and kinases.
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Affiliation(s)
- John T Happ
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Corvin D Arveseth
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
- Washington University School of Medicine, St. Louis, MO, USA
| | - Jessica Bruystens
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Daniela Bertinetti
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Isaac B Nelson
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Jingyi Zhang
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA
| | - Danielle S Hedeen
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ju-Fen Zhu
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jacob L Capener
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA
- Biological and Biomedical Sciences Program, University of North Carolina, Chapel Hill, NC, USA
| | - Jan W Bröckel
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Lily Vu
- Department of Neurobiology, University of California, San Diego, La Jolla, CA, USA
| | - C C King
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Victor L Ruiz-Perez
- Instituto de Investigaciones Biomédicas 'Alberto Sols,' Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Xuecai Ge
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Friedrich W Herberg
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
| | - Benjamin R Myers
- Department of Oncological Sciences, Department of Biochemistry, and Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA.
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3
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Bruystens JH, Wu J, Wallbott M, Bertinetti D, Herberg FW, Taylor SS. The Forgotten PKAs: New Insights Revealed by the First Crystal Structure of a PKA C Beta Splice Variant, Cβ4ab. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r6147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Jian Wu
- PharmacologyUniversity of California, San DiegoLa JollaCA
| | | | | | | | - Susan S. Taylor
- PharmacologyUniversity of California, San DiegoLa JollaCA
- Chemistry and BiochemistryUniversity of California, San DiegoLa JollaCA
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4
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Myers B, Happ J, Arveseth C, Bruystens J, Bertinetti D, Nelson I, Olivieri C, Hedeen D, Zhu J, Capener J, Broeckel J, Vu L, King CC, Ruiz‐Perez V, Veglia G, Herberg F, Taylor S. Unconventional GPCR‐PKA Signaling in the Hedgehog Pathway. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r2978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - John Happ
- University of Utah School of MedicineSalt Lake CityUT
| | | | | | | | - Isaac Nelson
- University of Utah School of MedicineSalt Lake CityUT
| | | | | | - Ju‐Fen Zhu
- University of Utah School of MedicineSalt Lake CityUT
| | - Jacob Capener
- University of Utah School of MedicineSalt Lake CityUT
| | | | - Lily Vu
- University of CaliforniaSan DiegoCA
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5
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Reginka M, Hoang H, Efendi Ö, Merkel M, Huhnstock R, Holzinger D, Dingel K, Sick B, Bertinetti D, Herberg FW, Ehresmann A. Transport Efficiency of Biofunctionalized Magnetic Particles Tailored by Surfactant Concentration. Langmuir 2021; 37:8498-8507. [PMID: 34231364 DOI: 10.1021/acs.langmuir.1c00900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Controlled transport of surface-functionalized magnetic beads in a liquid medium is a central requirement for the handling of captured biomolecular targets in microfluidic lab-on-chip biosensors. Here, the influence of the physiological liquid medium on the transport characteristics of functionalized magnetic particles and on the functionality of the coupled protein is studied. These aspects are theoretically modeled and experimentally investigated for prototype superparamagnetic beads, surface-functionalized with green fluorescent protein immersed in buffer solution with different concentrations of a surfactant. The model reports on the tunability of the steady-state particle substrate separation distance to prevent their surface sticking via the choice of surfactant concentration. Experimental and theoretical average velocities are discussed for a ratchet-like particle motion induced by a dynamic external field superposed on a static locally varying magnetic field landscape. The developed model and experiment may serve as a basis for quantitative forecasts on the functionality of magnetic particle transport-based lab-on-chip devices.
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Affiliation(s)
- Meike Reginka
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
| | - Hai Hoang
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
| | - Özge Efendi
- Institute of Biology and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
| | - Maximilian Merkel
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
| | - Rico Huhnstock
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
| | - Dennis Holzinger
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
| | - Kristina Dingel
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
- Intelligent Embedded Systems, University of Kassel, Wilhelmshöher Allee 71-73, D-34121 Kassel, Germany
| | - Bernhard Sick
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
- Intelligent Embedded Systems, University of Kassel, Wilhelmshöher Allee 71-73, D-34121 Kassel, Germany
| | - Daniela Bertinetti
- Institute of Biology and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
| | - Friedrich W Herberg
- Institute of Biology and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
| | - Arno Ehresmann
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, D-34132 Kassel, Germany
- Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and Kassel University, cc Gregor Hartmann, Hahn-Meitner Platz 1, 14109 Berlin, Germany
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6
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Lasonder E, More K, Singh S, Haidar M, Bertinetti D, Kennedy EJ, Herberg FW, Holder AA, Langsley G, Chitnis CE. cAMP-Dependent Signaling Pathways as Potential Targets for Inhibition of Plasmodium falciparum Blood Stages. Front Microbiol 2021; 12:684005. [PMID: 34108954 PMCID: PMC8183823 DOI: 10.3389/fmicb.2021.684005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/30/2021] [Indexed: 11/13/2022] Open
Abstract
We review the role of signaling pathways in regulation of the key processes of merozoite egress and red blood cell invasion by Plasmodium falciparum and, in particular, the importance of the second messengers, cAMP and Ca2+, and cyclic nucleotide dependent kinases. cAMP-dependent protein kinase (PKA) is comprised of cAMP-binding regulatory, and catalytic subunits. The less well conserved cAMP-binding pockets should make cAMP analogs attractive drug leads, but this approach is compromised by the poor membrane permeability of cyclic nucleotides. We discuss how the conserved nature of ATP-binding pockets makes ATP analogs inherently prone to off-target effects and how ATP analogs and genetic manipulation can be useful research tools to examine this. We suggest that targeting PKA interaction partners as well as substrates, or developing inhibitors based on PKA interaction sites or phosphorylation sites in PKA substrates, may provide viable alternative approaches for the development of anti-malarial drugs. Proximity of PKA to a substrate is necessary for substrate phosphorylation, but the P. falciparum genome encodes few recognizable A-kinase anchor proteins (AKAPs), suggesting the importance of PKA-regulatory subunit myristylation and membrane association in determining substrate preference. We also discuss how Pf14-3-3 assembles a phosphorylation-dependent signaling complex that includes PKA and calcium dependent protein kinase 1 (CDPK1) and how this complex may be critical for merozoite invasion, and a target to block parasite growth. We compare altered phosphorylation levels in intracellular and egressed merozoites to identify potential PKA substrates. Finally, as host PKA may have a critical role in supporting intracellular parasite development, we discuss its role at other stages of the life cycle, as well as in other apicomplexan infections. Throughout our review we propose possible new directions for the therapeutic exploitation of cAMP-PKA-signaling in malaria and other diseases caused by apicomplexan parasites.
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Affiliation(s)
- Edwin Lasonder
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Kunal More
- Unité de Biologie de Plasmodium et Vaccins, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Malak Haidar
- Laboratoire de Biologie Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France.,INSERM U1016, CNRS UMR 8104, Cochin Institute, Paris, France
| | | | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, United States
| | | | - Anthony A Holder
- Malaria Parasitology Laboratory, Francis Crick Institute, London, United Kingdom
| | - Gordon Langsley
- Laboratoire de Biologie Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France.,INSERM U1016, CNRS UMR 8104, Cochin Institute, Paris, France
| | - Chetan E Chitnis
- Unité de Biologie de Plasmodium et Vaccins, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France
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7
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Palencia-Campos A, Aoto PC, Machal EMF, Rivera-Barahona A, Soto-Bielicka P, Bertinetti D, Baker B, Vu L, Piceci-Sparascio F, Torrente I, Boudin E, Peeters S, Van Hul W, Huber C, Bonneau D, Hildebrand MS, Coleman M, Bahlo M, Bennett MF, Schneider AL, Scheffer IE, Kibæk M, Kristiansen BS, Issa MY, Mehrez MI, Ismail S, Tenorio J, Li G, Skålhegg BS, Otaify GA, Temtamy S, Aglan M, Jønch AE, De Luca A, Mortier G, Cormier-Daire V, Ziegler A, Wallis M, Lapunzina P, Herberg FW, Taylor SS, Ruiz-Perez VL. Germline and Mosaic Variants in PRKACA and PRKACB Cause a Multiple Congenital Malformation Syndrome. Am J Hum Genet 2020; 107:977-988. [PMID: 33058759 DOI: 10.1016/j.ajhg.2020.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/09/2020] [Indexed: 12/19/2022] Open
Abstract
PRKACA and PRKACB code for two catalytic subunits (Cα and Cβ) of cAMP-dependent protein kinase (PKA), a pleiotropic holoenzyme that regulates numerous fundamental biological processes such as metabolism, development, memory, and immune response. We report seven unrelated individuals presenting with a multiple congenital malformation syndrome in whom we identified heterozygous germline or mosaic missense variants in PRKACA or PRKACB. Three affected individuals were found with the same PRKACA variant, and the other four had different PRKACB mutations. In most cases, the mutations arose de novo, and two individuals had offspring with the same condition. Nearly all affected individuals and their affected offspring shared an atrioventricular septal defect or a common atrium along with postaxial polydactyly. Additional features included skeletal abnormalities and ectodermal defects of variable severity in five individuals, cognitive deficit in two individuals, and various unusual tumors in one individual. We investigated the structural and functional consequences of the variants identified in PRKACA and PRKACB through the use of several computational and experimental approaches, and we found that they lead to PKA holoenzymes which are more sensitive to activation by cAMP than are the wild-type proteins. Furthermore, expression of PRKACA or PRKACB variants detected in the affected individuals inhibited hedgehog signaling in NIH 3T3 fibroblasts, thereby providing an underlying mechanism for the developmental defects observed in these cases. Our findings highlight the importance of both Cα and Cβ subunits of PKA during human development.
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Affiliation(s)
- Adrian Palencia-Campos
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, 28029, Spain; CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain
| | - Phillip C Aoto
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, CA 92093-0654, USA
| | - Erik M F Machal
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, 34132, Germany
| | - Ana Rivera-Barahona
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, 28029, Spain; CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain
| | - Patricia Soto-Bielicka
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, 28029, Spain
| | - Daniela Bertinetti
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, 34132, Germany
| | - Blaine Baker
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, CA 92093-0654, USA
| | - Lily Vu
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, CA 92093-0654, USA
| | - Francesca Piceci-Sparascio
- Medical Genetics Unit, Casa Sollievo della Sofferenza Foundation, IRCCS, San Giovanni Rotondo, 71013, Italy
| | - Isabella Torrente
- Medical Genetics Unit, Casa Sollievo della Sofferenza Foundation, IRCCS, San Giovanni Rotondo, 71013, Italy
| | - Eveline Boudin
- Department of Medical Genetics, University of Antwerp, Edegem, 2650, Belgium
| | - Silke Peeters
- Department of Medical Genetics, University of Antwerp, Edegem, 2650, Belgium
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Edegem, 2650, Belgium
| | - Celine Huber
- Clinical Genetics and Reference Center for Skeletal Dysplasia, AP-HP, Necker-Enfants Malades Hospital, Paris, 75015, France; Université De Paris, INSERM UMR1163, Institut Imagine, Paris, 75015, France
| | - Dominique Bonneau
- Biochemistry and Genetics Department, Angers Hospital, Angers Cedex 9, 49933, France; UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers Cedex 9, 49933, France
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, 3084, Victoria, Australia; Murdoch Children's Research Institute, Parkville, 3052, Victoria, Australia
| | - Matthew Coleman
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, 3084, Victoria, Australia; Murdoch Children's Research Institute, Parkville, 3052, Victoria, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Victoria, Australia; Department of Medical Biology, University of Melbourne, Melbourne, 3010, Victoria, Australia
| | - Mark F Bennett
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, 3084, Victoria, Australia; Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Victoria, Australia; Department of Medical Biology, University of Melbourne, Melbourne, 3010, Victoria, Australia
| | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, 3084, Victoria, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Heidelberg, 3084, Victoria, Australia; Murdoch Children's Research Institute, Parkville, 3052, Victoria, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, and Florey Institute of Neuroscience and Mental Health, Parkville, 3052, Victoria, Australia
| | - Maria Kibæk
- Children's Hospital of H.C. Andersen, Odense University Hospital, 5000 Odense, Denmark
| | - Britta S Kristiansen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Mahmoud Y Issa
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Mennat I Mehrez
- Department of Oro-dental Genetics, Division of Human Genetics and Genome Research. Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Samira Ismail
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Jair Tenorio
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain; Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, 28046, Spain; ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability
| | - Gaoyang Li
- Division for Molecular Nutrition, Institute for Basic Medical Sciences, University of Oslo, Oslo, 0316, Norway
| | - Bjørn Steen Skålhegg
- Division for Molecular Nutrition, Institute for Basic Medical Sciences, University of Oslo, Oslo, 0316, Norway
| | - Ghada A Otaify
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Samia Temtamy
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Mona Aglan
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt
| | - Aia E Jønch
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Alessandro De Luca
- Medical Genetics Unit, Casa Sollievo della Sofferenza Foundation, IRCCS, San Giovanni Rotondo, 71013, Italy
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp, Edegem, 2650, Belgium; Antwerp University Hospital, Edegem, 2650, Belgium
| | - Valérie Cormier-Daire
- Clinical Genetics and Reference Center for Skeletal Dysplasia, AP-HP, Necker-Enfants Malades Hospital, Paris, 75015, France; Université De Paris, INSERM UMR1163, Institut Imagine, Paris, 75015, France
| | - Alban Ziegler
- Biochemistry and Genetics Department, Angers Hospital, Angers Cedex 9, 49933, France; UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers Cedex 9, 49933, France
| | - Mathew Wallis
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, 7001, Australia; Clinical Genetics Service, Austin Health, Heidelberg, 3084, Victoria, Australia
| | - Pablo Lapunzina
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain; Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, 28046, Spain; ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability
| | - Friedrich W Herberg
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, 34132, Germany
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, CA 92093-0654, USA; Department of Chemistry and Biochemistry, University of California, San Diego, 9400 Gilman Drive, La Jolla, CA 92093-0654, USA
| | - Victor L Ruiz-Perez
- Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, 28029, Spain; CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain; Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, 28046, Spain; ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability.
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Knape MJ, Wallbott M, Burghardt NCG, Bertinetti D, Hornung J, Schmidt SH, Lorenz R, Herberg FW. Molecular Basis for Ser/Thr Specificity in PKA Signaling. Cells 2020; 9:cells9061548. [PMID: 32630525 PMCID: PMC7361990 DOI: 10.3390/cells9061548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
cAMP-dependent protein kinase (PKA) is the major receptor of the second messenger cAMP and a prototype for Ser/Thr-specific protein kinases. Although PKA strongly prefers serine over threonine substrates, little is known about the molecular basis of this substrate specificity. We employ classical enzyme kinetics and a surface plasmon resonance (SPR)-based method to analyze each step of the kinase reaction. In the absence of divalent metal ions and nucleotides, PKA binds serine (PKS) and threonine (PKT) substrates, derived from the heat-stable protein kinase inhibitor (PKI), with similar affinities. However, in the presence of metal ions and adenine nucleotides, the Michaelis complex for PKT is unstable. PKA phosphorylates PKT with a higher turnover due to a faster dissociation of the product complex. Thus, threonine substrates are not necessarily poor substrates of PKA. Mutation of the DFG+1 phenylalanine to β-branched amino acids increases the catalytic efficiency of PKA for a threonine peptide substrate up to 200-fold. The PKA Cα mutant F187V forms a stable Michaelis complex with PKT and shows no preference for serine versus threonine substrates. Disease-associated mutations of the DFG+1 position in other protein kinases underline the importance of substrate specificity for keeping signaling pathways segregated and precisely regulated.
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Affiliation(s)
| | | | | | | | | | | | - Robin Lorenz
- Correspondence: (R.L.); (F.W.H.); Tel.: +49-561-804-4539 (R.L.); +49-561-804-4511 (F.W.H.)
| | - Friedrich W. Herberg
- Correspondence: (R.L.); (F.W.H.); Tel.: +49-561-804-4539 (R.L.); +49-561-804-4511 (F.W.H.)
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9
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Manschwetus JT, Wallbott M, Fachinger A, Obergruber C, Pautz S, Bertinetti D, Schmidt SH, Herberg FW. Binding of the Human 14-3-3 Isoforms to Distinct Sites in the Leucine-Rich Repeat Kinase 2. Front Neurosci 2020; 14:302. [PMID: 32317922 PMCID: PMC7155755 DOI: 10.3389/fnins.2020.00302] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 03/16/2020] [Indexed: 12/25/2022] Open
Abstract
Proteins of the 14-3-3 family are well known modulators of the leucine-rich repeat kinase 2 (LRRK2) regulating kinase activity, cellular localization, and ubiquitylation. Although binding between those proteins has been investigated, a comparative study of all human 14-3-3 isoforms interacting with LRRK2 is lacking so far. In a comprehensive approach, we quantitatively analyzed the interaction between the seven human 14-3-3 isoforms and LRRK2-derived peptides covering both, reported and putative 14-3-3 binding sites. We observed that phosphorylation is an absolute prerequisite for 14-3-3 binding and generated binding patterns of 14-3-3 isoforms to interact with peptides derived from the N-terminal phosphorylation cluster (S910 and S935), the Roc domain (S1444) and the C-terminus. The tested 14-3-3 binding sites in LRRK2 preferentially were recognized by the isoforms γ and η, whereas the isoforms ϵ and especially σ showed the weakest or no binding. Interestingly, the possible pathogenic mutation Q930R in LRRK2 drastically increases binding affinity to a peptide encompassing pS935. We then identified the autophosphorylation site T2524 as a so far not described 14-3-3 binding site at the very C-terminus of LRRK2. Binding affinities of all seven 14-3-3 isoforms were quantified for all three binding regions with pS1444 displaying the highest affinity of all measured singly phosphorylated peptides. The strongest binding was detected for the combined phosphosites S910 and S935, suggesting that avidity effects are important for high affinity interaction between 14-3-3 proteins and LRRK2.
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Affiliation(s)
| | | | | | | | | | | | | | - Friedrich W. Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
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10
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Lelle M, Otte M, Thon S, Bertinetti D, Herberg FW, Benndorf K. Chemical synthesis and biological activity of novel brominated 7-deazaadenosine-3',5'-cyclic monophosphate derivatives. Bioorg Med Chem 2019; 27:1704-1713. [PMID: 30879860 DOI: 10.1016/j.bmc.2019.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 11/19/2022]
Abstract
Synthetic derivatives of cyclic adenosine monophosphate, such as halogenated or other more hydrophobic analogs, are widely used compounds, to investigate diverse signal transduction pathways of eukaryotic cells. This inspired us to develop cyclic nucleotides, which exhibit chemical structures composed of brominated 7-deazaadenines and the phosphorylated ribosugar. The synthesized 8-bromo- and 7-bromo-7-deazaadenosine-3',5'-cyclic monophosphates rank among the most potent activators of cyclic nucleotide-regulated ion channels as well as cAMP-dependent protein kinase. Moreover, these substances bind tightly to exchange proteins directly activated by cAMP.
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Affiliation(s)
- Marco Lelle
- Institute of Physiology II, University Hospital Jena, Kollegiengasse 9, 07743 Jena, Germany
| | - Maik Otte
- Institute of Physiology II, University Hospital Jena, Kollegiengasse 9, 07743 Jena, Germany
| | - Susanne Thon
- Institute of Physiology II, University Hospital Jena, Kollegiengasse 9, 07743 Jena, Germany
| | - Daniela Bertinetti
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Friedrich W Herberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Klaus Benndorf
- Institute of Physiology II, University Hospital Jena, Kollegiengasse 9, 07743 Jena, Germany.
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11
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Knape MJ, Ballez M, Burghardt NC, Zimmermann B, Bertinetti D, Kornev AP, Herberg FW. Divalent metal ions control activity and inhibition of protein kinases. Metallomics 2018; 9:1576-1584. [PMID: 29043344 DOI: 10.1039/c7mt00204a] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein kinases are key enzymes in the regulation of eukaryotic signal transduction. As metalloenzymes they employ divalent cations for catalysis and regulation. We used the catalytic (C) subunit of cAMP-dependent protein kinase (PKA) as a model protein to investigate the role of a variety of physiologically or pathophysiologically relevant divalent metal ions in distinct steps within the catalytic cycle. It is established that divalent metal ions play a crucial role in co-binding of nucleotides and also assist in catalysis. Our studies reveal that besides the physiologically highly relevant magnesium, metals like zinc and manganese can assist in phosphoryl transfer, however, only a few support efficient substrate turnover (turnover catalysis). Those trace metals allow for substrate binding and phosphotransfer but hamper product release. We further established the unique role of magnesium as the common biologically relevant divalent metal ideally enabling (co-) substrate binding and orientation. Magnesium allows stable substrate binding and, on the other hand accelerates product release, thus being extremely efficient in turnover catalysis. We extended our studies to non-catalytic functions of protein kinases looking at pseudokinases, a subfamily of protein kinases inherently lacking critical residues for catalysis. Recently, pseudokinases have been linked to human diseases. Some pseudokinases are still capable of binding metal ions, yet have lost the ability to transfer the phosphoryl group from ATP to a given substrate. Here metal ions stabilize an active like, though catalytically unproductive conformation and are therefore crucial to maintain non-catalytic function. Finally, we demonstrate for the canonical kinase PKA that the trace metal manganese alone can stabilize protein kinases in an active like conformation allowing them to bind substrates even in the absence of nucleotides.
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Affiliation(s)
- Matthias J Knape
- Department of Biochemistry, University of Kassel, 34132 Kassel, Germany.
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12
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Kailing LL, Bertinetti D, Paul CE, Manszewski T, Jaskolski M, Herberg FW, Pavlidis IV. S-Adenosyl-L-Homocysteine Hydrolase Inhibition by a Synthetic Nicotinamide Cofactor Biomimetic. Front Microbiol 2018; 9:505. [PMID: 29619018 PMCID: PMC5871694 DOI: 10.3389/fmicb.2018.00505] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/06/2018] [Indexed: 11/13/2022] Open
Abstract
S-adenosyl-L-homocysteine (SAH) hydrolases (SAHases) are involved in the regulation of methylation reactions in many organisms and are thus crucial for numerous cellular functions. Consequently, their dysregulation is associated with severe health problems. The SAHase-catalyzed reaction is reversible and both directions depend on the redox activity of nicotinamide adenine dinucleotide (NAD+) as a cofactor. Therefore, nicotinamide cofactor biomimetics (NCB) are a promising tool to modulate SAHase activity. In the present in vitro study, we investigated 10 synthetic truncated NAD+ analogs against a SAHase from the root-nodulating bacterium Bradyrhizobium elkanii. Among this set of analogs, one was identified to inhibit the SAHase in both directions. Isothermal titration calorimetry (ITC) and crystallography experiments suggest that the inhibitory effect is not mediated by a direct interaction with the protein. Neither the apo-enzyme (i.e., deprived of the natural cofactor), nor the holo-enzyme (i.e., in the NAD+-bound state) were found to bind the inhibitor. Yet, enzyme kinetics point to a non-competitive inhibition mechanism, where the inhibitor acts on both, the enzyme and enzyme-SAH complex. Based on our experimental results, we hypothesize that the NCB inhibits the enzyme via oxidation of the enzyme-bound NADH, which may be accessible through an open molecular gate, leaving the enzyme stalled in a configuration with oxidized cofactor, where the reaction intermediate can be neither converted nor released. Since the reaction mechanism of SAHase is quite uncommon, this kind of inhibition could be a viable pharmacological route, with a low risk of off-target effects. The NCB presented in this work could be used as a template for the development of more potent SAHase inhibitors.
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Affiliation(s)
- Lyn L Kailing
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | | | - Caroline E Paul
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Tomasz Manszewski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.,Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University in Poznań, Poznań, Poland
| | | | - Ioannis V Pavlidis
- Department of Biochemistry, University of Kassel, Kassel, Germany.,Department of Chemistry, University of Crete, Heraklion, Greece
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Todd Milne G, Sandner P, Lincoln KA, Harrison PC, Chen H, Wang H, Clifford H, Qian HS, Wong D, Sarko C, Fryer R, Richman J, Reinhart GA, Boustany CM, Pullen SS, Andresen H, Moltzau LR, Cataliotti A, Levy FO, Lukowski R, Frankenreiter S, Friebe A, Calamaras T, Baumgartner R, McLaughlin A, Aronovitz M, Baur W, Wang GR, Kapur N, Karas R, Blanton R, Hell S, Waldman SA, Lin JE, Colon-Gonzalez F, Kim GW, Blomain ES, Merlino D, Snook A, Erdmann J, Wobst J, Kessler T, Schunkert H, Walter U, Pagel O, Walter E, Gambaryan S, Smolenski A, Jurk K, Zahedi R, Klinger JR, Benza RL, Corris PA, Langleben D, Naeije R, Simonneau G, Meier C, Colorado P, Chang MK, Busse D, Hoeper MM, Masferrer JL, Jacobson S, Liu G, Sarno R, Bernier S, Zhang P, Todd Milne G, Flores-Costa R, Currie M, Hall K, Möhrle D, Reimann K, Wolter S, Wolters M, Mergia E, Eichert N, Geisler HS, Ruth P, Friebe A, Feil R, Zimmermann U, Koesling D, Knipper M, Rüttiger L, Tanaka Y, Okamoto A, Nojiri T, Kumazoe M, Tokudome T, Miura K, Hino J, Hosoda H, Miyazato M, Kangawa K, Kapil V, Ahluwalia A, Paolocci N, Eaton P, Campbell JC, Henning P, Franz E, Sankaran B, Herberg FW, Kim C, Wittwer M, Luo Q, Kaila V, Dames SA, Tobin A, Alam M, Rudyk O, Krasemann S, Hartmann K, Prysyazhna O, Zhang M, Zhao L, Weiss A, Schermuly R, Eaton P, Moyes AJ, Chu SM, Baliga RS, Hobbs AJ, Michalakis S, Mühlfriedel R, Schön C, Fischer DM, Wilhelm B, Zobor D, Kohl S, Peters T, Zrenner E, Bartz-Schmidt KU, Ueffing M, Wissinger B, Seeliger M, Biel M, Ranek MJ, Kokkonen KM, Lee DI, Holewinski RJ, Agrawal V, Virus C, Stevens DA, Sasaki M, Zhang H, Mannion MM, Rainer PP, Page RC, Schisler JC, Van Eyk JE, Willis MS, Kass DA, Zaccolo M, Russwurm M, Giesen J, Russwurm C, Füchtbauer EM, Koesling D, Bork NI, Nikolaev VO, Agulló L, Floor M, Villà-Freixa J, Manfra O, Calamera G, Surdo NC, Meier S, Froese A, Nikolaev VO, Zaccolo M, Levy FO, Andressen KW, Aue A, Schwiering F, Groneberg D, Friebe A, Bajraktari G, Burhenne J, Haefeli WE, Weiss J, Beck K, Voussen B, Vincent A, Parsons SP, Huizinga JD, Friebe A, Mónica FZ, Seto E, Murad F, Bian K, Burgoyne JR, Prysyazhna O, Richards D, Eaton P, Calamera G, Bjørnerem M, Ulsund AH, Kim JJ, Kim C, Levy FO, Andressen KW, Donzelli S, Goetz M, Schmidt K, Wolters M, Stathopoulou K, Prysyazhna O, Scotcher J, Dees C, Subramanian H, Butt E, Kamynina A, Bruce King S, Nikolaev VO, de Witt C, Leichert LI, Feil R, Eaton P, Cuello F, Dobrowinski H, Lehners M, Schmidt MPH, Feil R, Feil S, Wen L, Wolters M, Thunemann M, Schmidt K, Olbrich M, Langer H, Gawaz M, Friebe A, de Wit C, Feil R, Franz E, Kim JJ, Bertinetti D, Kim C, Herberg FW, Ghofrani HA, Grimminger F, Grünig E, Huang Y, Jansa P, Jing ZC, Kilpatrick D, Langleben D, Rosenkranz S, Menezes F, Fritsch A, Nikkho S, Frey R, Humbert M, Groneberg D, Aue A, Schwiering F, Friebe A, Harloff M, Reinders J, Schlossmann J, Jung J, Wales JA, Chen CY, Breci L, Weichsel A, Bernier SG, Solinga R, Sheppeck JE, Renhowe PA, Montfort WR, Qin L, Sung YJ, Casteel D, Kim C, Kollau A, Neubauer A, Schrammel A, Russwurm M, Koesling D, Mayer B, Kumazoe M, Takai M, Takeuchi C, Kadomatsu M, Hiroi S, Takamatsu K, Nojiri T, Kangawa K, Tachibana H, Opelt M, Eroglu E, Waldeck-Weiermair M, Russwurm M, Koesling D, Malli R, Graier WF, Fassett JT, Schrammel A, Mayer B, Sollie SJ, Moltzau LR, Hernandez-Valladares M, Berven F, Levy FO, Andressen KW, Nojiri T, Tokudome T, Kumazoe M, Arai M, Suzuki Y, Miura K, Hino J, Hosoda H, Miyazato M, Okumura M, Kawaoka S, Kangawa K, Peters S, Schmidt H, Selin Kenet B, Nies SH, Frank K, Wen L, Rathjen FG, Feil R, Petrova ON, Lamarre I, Négrerie M, Robinson JW, Egbert JR, Davydova J, Jaffe LA, Potter LR, Robinson JW, Blixt N, Shuhaibar LC, Warren GL, Mansky KC, Jaffe LA, Potter LR, Romoli S, Bauch T, Dröbner K, Eitner F, Ruppert M, Radovits T, Korkmaz-Icöz S, Li S, Hegedűs P, Loganathan S, Németh BT, Oláh A, Mátyás C, Benke K, Merkely B, Karck M, Szabó G, Scheib U, Broser M, Mukherjee S, Stehfest K, Gee CE, Körschen HG, Oertner TG, Hegemann P, Schmidt H, Dickey DM, Dumoulin A, Kühn R, Jaffe L, Potter LR, Rathjen FG, Schobesberger S, Wright P, Poulet C, Mansfield C, Friebe A, Harding SE, Nikolaev VO, Gorelik J, Kollau A, Opelt M, Wölkart G, Gorren ACF, Russwurm M, Koesling D, Schrammel A, Mayer B, Schwaerzer GK, Casteel DE, Dalton ND, Gu Y, Zhuang S, Milewicz DM, Peterson KL, Pilz R, Schwiering F, Aue A, Groneberg D, Friebe A, Argyriou AI, Makrynitsa G, Alexandropoulos II, Stamopoulou A, Bantzi M, Giannis A, Topouzis S, Papapetropoulos A, Spyroulias GA, Stuehr DJ, Ghosh A, Dai Y, Misra S, Tchernychev B, Jung J, Liu G, Silos-Santiago I, Hannig G, Dao VTV, Deile M, Nedvetsky PI, Güldner A, Ibarra-Alvarado C, Gödecke A, Schmidt HHHW, Vachaviolos A, Gerling A, Thunemann M, Lutz SZ, Häring HU, Krüger MA, Pichler BJ, Shipston MJ, Feil S, Feil R, Vandenwijngaert S, Ledsky CD, Agha O, Hu D, Domian IJ, Buys ES, Newton-Cheh C, Bloch DB, Voussen B, Beck K, Mauro N, Keppler J, Friebe A, Ferreira WA, Chweih H, Brito PL, Almeida CB, Penteado CFF, Saad SSO, Costa FF, Frenette PS, Brockschnieder D, Stasch JP, Sandner P, Conran N, Zimmer DP, Tobin J, Shea C, Sarno R, Long K, Jacobson S, Tang K, Germano P, Wakefield J, Banijamali A, Im GYJ, Sheppeck JE, Profy AT, Todd Milne G, Currie MG, Masferrer JL. Abstracts from the 8th International Conference on cGMP Generators, Effectors and Therapeutic Implications : Bamberg, Germany. 23-25 June, 2017. BMC Pharmacol Toxicol 2017; 18:64. [PMID: 29035170 PMCID: PMC5667593 DOI: 10.1186/s40360-017-0170-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Pérez-Mendoza D, Bertinetti D, Lorenz R, Gallegos MT, Herberg FW, Sanjuán J. A novel c-di-GMP binding domain in glycosyltransferase BgsA is responsible for the synthesis of a mixed-linkage β-glucan. Sci Rep 2017; 7:8997. [PMID: 28827694 PMCID: PMC5567048 DOI: 10.1038/s41598-017-09290-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/14/2017] [Indexed: 12/04/2022] Open
Abstract
BgsA is the glycosyltransferase (GT) involved in the synthesis of a linear mixed-linkage β-glucan (MLG), a recently described exopolysaccharide activated by c-di-GMP in Sinorhizobium meliloti and other Rhizobiales. Although BgsA displays sequence and structural homology with bacterial cellulose synthases (CS), it does not contain any predictable c-di-GMP binding domain. In this work we demonstrate that the cytoplasmic C-terminal domain of BgsA (C-BgsA) binds c-di-GMP with both high affinity (KD = 0.23 μM) and specificity. C-BgsA is structurally different to the otherwise equivalent cytoplasmic C-terminal domain of CS, and does not contain PilZ motifs for c-di-GMP recognition. A combination of random and site-directed mutagenesis with surface plasmon resonance (SPR) allowed identification of the C-BgsA residues which are important not only for c-di-GMP binding, but also for BgsA GT activity. The results suggest that the C-BgsA domain is important for both, c-di-GMP binding and GT activity of BgsA. In contrast to bacterial CS where c-di-GMP has been proposed as a derepressor of GT activity, we hypothesize that the C-terminal domain of BgsA plays an active role in BgsA GT activity upon binding c-di-GMP.
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Affiliation(s)
- Daniel Pérez-Mendoza
- Department of Biochemistry, University of Kassel, Kassel, Germany. .,Dpto. Microbiología del Suelo y Sistemas Simbióticos. Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
| | | | - Robin Lorenz
- Department of Biochemistry, University of Kassel, Kassel, Germany.,Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - María-Trinidad Gallegos
- Dpto. Microbiología del Suelo y Sistemas Simbióticos. Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | - Juan Sanjuán
- Dpto. Microbiología del Suelo y Sistemas Simbióticos. Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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Kailing LL, Bertinetti D, Herberg FW, Pavlidis IV. A coupled photometric assay for characterization of S-adenosyl-l-homocysteine hydrolases in the physiological hydrolytic direction. N Biotechnol 2017; 39:11-17. [PMID: 28461153 DOI: 10.1016/j.nbt.2017.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 10/19/2022]
Abstract
S-Adenosyl-l-homocysteine hydrolases (SAHases) are important metabolic enzymes and their dysregulation is associated with some severe diseases. In vivo they catalyze the hydrolysis of S-adenosyl-l-homocysteine (SAH), the by-product of methylation reactions in various organisms. SAH is a potent inhibitor of methyltransferases, thus its removal from the equilibrium is an important requirement for methylation reactions. SAH hydrolysis is also the first step in the cellular regeneration process of the methyl donor S-adenosyl-l-methionine (SAM). However, in vitro the equilibrium lies towards the synthetic direction. To enable characterization of SAHases in the physiologically relevant direction, we have developed a coupled photometric assay that shifts the equilibrium towards hydrolysis by removing the product adenosine, using a high affinity adenosine kinase (AK). This converts adenosine to AMP and thereby forms equimolar amounts of ADP, which is phosphorylated by a pyruvate kinase (PK), in turn releasing pyruvate. The readout of the assay is the consumption of NADH during the lactate dehydrogenase (LDH) catalyzed reduction of pyruvate to lactic acid. The applicability of the assay is showcased for the determination of the kinetic constants of an SAHase from Bradyrhizobium elkanii (KM,SAH 41±5μM, vmax,SAH 25±1μM/min with 0.13mg/mL enzyme). This assay is a valuable tool for in vitro characterization of SAHases with biotechnological potential, and for monitoring SAHase activity in diagnostics.
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Affiliation(s)
- Lyn L Kailing
- Group of Biotechnology, Dept. of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Daniela Bertinetti
- Dept. of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Friedrich W Herberg
- Dept. of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Ioannis V Pavlidis
- Group of Biotechnology, Dept. of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany.
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Autenrieth K, Bendzunas NG, Bertinetti D, Herberg FW, Kennedy EJ. Defining A-Kinase Anchoring Protein (AKAP) Specificity for the Protein Kinase A Subunit RI (PKA-RI). Chembiochem 2016; 17:693-697. [PMID: 26611881 PMCID: PMC4836982 DOI: 10.1002/cbic.201500632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 01/18/2023]
Abstract
A-Kinase anchoring proteins (AKAPs) act as spatial and temporal regulators of protein kinase A (PKA) by localizing PKA along with multiple proteins into discrete signaling complexes. AKAPs interact with the PKA holoenzyme through an α-helix that docks into a groove formed on the dimerization/docking domain of PKA-R in an isoform-dependent fashion. In an effort to understand isoform selectivity at the molecular level, a library of protein-protein interaction (PPI) disruptors was designed to systematically probe the significance of an aromatic residue on the AKAP docking sequence for RI selectivity. The stapled peptide library was designed based on a high affinity, RI-selective disruptor of AKAP binding, RI-STAD-2. Phe, Trp and Leu were all found to maintain RI selectivity, whereas multiple intermediate-sized hydrophobic substitutions at this position either resulted in loss of isoform selectivity (Ile) or a reversal of selectivity (Val). As a limited number of RI-selective sequences are currently known, this study aids in our understanding of isoform selectivity and establishing parameters for discovering additional RI-selective AKAPs.
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Affiliation(s)
- Karolin Autenrieth
- Dept. of Biochemistry, Universitat Kassel, Heinrich Plett Strasse 40, Kassel 34132 (Germany)
| | - N. George Bendzunas
- Dept. of Pharmaceutical and Biomedical Sciences, University of Georgia, College of Pharmacy, 240 W. Green St, Athens, GA 30602 (USA)
| | - Daniela Bertinetti
- Dept. of Biochemistry, Universitat Kassel, Heinrich Plett Strasse 40, Kassel 34132 (Germany)
| | - Friedrich W. Herberg
- Dept. of Biochemistry, Universitat Kassel, Heinrich Plett Strasse 40, Kassel 34132 (Germany)
| | - Eileen J. Kennedy
- Dept. of Pharmaceutical and Biomedical Sciences, University of Georgia, College of Pharmacy, 240 W. Green St, Athens, GA 30602 (USA)
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18
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Kilisch M, Lytovchenko O, Arakel EC, Bertinetti D, Schwappach B. A dual phosphorylation switch controls 14-3-3-dependent cell surface expression of TASK-1. J Cell Sci 2016; 129:831-42. [PMID: 26743085 PMCID: PMC4760375 DOI: 10.1242/jcs.180182] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/29/2015] [Indexed: 11/20/2022] Open
Abstract
The transport of the K+ channels TASK-1 and TASK-3 (also known as KCNK3 and KCNK9, respectively) to the cell surface is controlled by the binding of 14-3-3 proteins to a trafficking control region at the extreme C-terminus of the channels. The current model proposes that phosphorylation-dependent binding of 14-3-3 sterically masks a COPI-binding motif. However, the direct effects of phosphorylation on COPI binding and on the binding parameters of 14-3-3 isoforms are still unknown. We find that phosphorylation of the trafficking control region prevents COPI binding even in the absence of 14-3-3, and we present a quantitative analysis of the binding of all human 14-3-3 isoforms to the trafficking control regions of TASK-1 and TASK-3. Surprisingly, the affinities of 14-3-3 proteins for TASK-1 are two orders of magnitude lower than for TASK-3. Furthermore, we find that phosphorylation of a second serine residue in the C-terminus of TASK-1 inhibits 14-3-3 binding. Thus, phosphorylation of the trafficking control region can stimulate or inhibit transport of TASK-1 to the cell surface depending on the target serine residue. Our findings indicate that control of TASK-1 trafficking by COPI, kinases, phosphatases and 14-3-3 proteins is highly dynamic. Summary: Phosphorylation of a previously neglected serine residue in the trafficking control region of TASK-1 interferes with the binding of trafficking machinery and enables complex regulation by physiological stimuli.
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Affiliation(s)
- Markus Kilisch
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen 37073, Germany
| | - Olga Lytovchenko
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen 37073, Germany
| | - Eric C Arakel
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen 37073, Germany
| | | | - Blanche Schwappach
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen 37073, Germany Max-Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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19
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Kibat J, Schirrmann T, Knape MJ, Helmsing S, Meier D, Hust M, Schröder C, Bertinetti D, Winter G, Pardes K, Funk M, Vala A, Giese N, Herberg FW, Dübel S, Hoheisel JD. Utilisation of antibody microarrays for the selection of specific and informative antibodies from recombinant library binders of unknown quality. N Biotechnol 2015; 33:574-81. [PMID: 26709003 DOI: 10.1016/j.nbt.2015.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/04/2015] [Accepted: 12/08/2015] [Indexed: 12/22/2022]
Abstract
Many diagnostic and therapeutic concepts require antibodies of high specificity. Recombinant binder libraries and related selection approaches allow the efficient isolation of antibodies against almost every target of interest. Nevertheless, it cannot be guaranteed that selected antibodies perform well and interact specifically enough with analytes unless an elaborate characterisation is performed. Here, we present an approach to shorten this process by combining the selection of suitable antibodies with the identification of informative target molecules by means of antibody microarrays, thereby reducing the effort of antibody characterisation by concentrating on relevant molecules. In a pilot scheme, a library of 456 single-chain variable fragment (scFv) binders to 134 antigens was used. They were arranged in a microarray format and incubated with the protein content of clinical tissue samples isolated from pancreatic ductal adenocarcinoma and healthy pancreas, as well as recurrent and non-recurrent bladder tumours. We observed significant variation in the expression of the E3 ubiquitin-protein ligase (CHFR) as well as the glutamate receptor interacting protein 2 (GRIP2), for example, always with more than one of the scFvs binding to these targets. Only the relevant antibodies were then characterised further on antigen microarrays and by surface plasmon resonance experiments so as to select the most specific and highest affinity antibodies. These binders were in turn used to confirm a microarray result by immunohistochemistry analysis.
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Affiliation(s)
- Janek Kibat
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ) , Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Department of Pharmacy, Pharmaceutical Technology & Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Thomas Schirrmann
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany; YUMAB GmbH, Rebenring 33, 38106 Braunschweig, Germany
| | - Matthias J Knape
- Department of Biochemistry, Universität Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Saskia Helmsing
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Doris Meier
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Michael Hust
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Christoph Schröder
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ) , Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Sciomics GmbH, Im Neuenheimer Feld 583, 69120 Heidelberg, Germany
| | - Daniela Bertinetti
- Department of Biochemistry, Universität Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Gerhard Winter
- Department of Pharmacy, Pharmaceutical Technology & Biopharmaceutics, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Khalid Pardes
- The Novo Nordisk Foundation Centre for Protein Research, Protein Structure and Function Program, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Mia Funk
- The Novo Nordisk Foundation Centre for Protein Research, Protein Structure and Function Program, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Andrea Vala
- The Novo Nordisk Foundation Centre for Protein Research, Protein Structure and Function Program, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nathalia Giese
- Department of Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 110, 69120 Heidelberg, Germany
| | - Friedrich W Herberg
- Department of Biochemistry, Universität Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Stefan Dübel
- Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ) , Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
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20
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Franz E, Kim JJ, Schneider O, Bertinetti D, Kim C, Herberg FW. The role of a parasite-specific D-site in activation of Plasmodium falciparum cGMP-dependent protein kinase. BMC Pharmacol Toxicol 2015. [PMCID: PMC4565114 DOI: 10.1186/2050-6511-16-s1-a51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Knape MJ, Ahuja LG, Bertinetti D, Burghardt NC, Zimmermann B, Taylor SS, Herberg FW. Divalent Metal Ions Mg²⁺ and Ca²⁺ Have Distinct Effects on Protein Kinase A Activity and Regulation. ACS Chem Biol 2015. [PMID: 26200257 DOI: 10.1021/acschembio.5b00271] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
cAMP-dependent protein kinase (PKA) is regulated primarily in response to physiological signals while nucleotides and metals may provide fine-tuning. PKA can use different metal ions for phosphoryl transfer, yet some, like Ca(2+), do not support steady-state catalysis. Fluorescence Polarization (FP) and Surface Plasmon Resonance (SPR) were used to study inhibitor and substrate interactions with PKA. The data illustrate how metals can act differentially as a result of their inherent coordination properties. We found that Ca(2+), in contrast to Mg(2+), does not induce high-affinity binding of PKA to pseudosubstrate inhibitors. However, Ca(2+) works in a single turnover mode to allow for phosphoryl-transfer. Using a novel SPR approach, we were able to directly monitor the interaction of PKA with a substrate in the presence of Mg(2+)ATP. This allows us to depict the entire kinase reaction including complex formation as well as release of the phosphorylated substrate. In contrast to Mg(2+), Ca(2+) apparently slows down the enzymatic reaction. A focus on individual reaction steps revealed that Ca(2+) is not as efficient as Mg(2+) in stabilizing the enzyme:substrate complex. The opposite holds true for product dissociation where Mg(2+) easily releases the phospho-substrate while Ca(2+) traps both reaction products at the active site. This explains the low steady-state activity in the presence of Ca(2+). Furthermore, Ca(2+) is able to modulate kinase activity as well as inhibitor binding even in the presence of Mg(2+). We therefore hypothesize that the physiological metal ions Mg(2+) and Ca(2+) both play a role in kinase activity and regulation. Since PKA is localized close to calcium channels and may render PKA activity susceptible to Ca(2+), our data provide a possible mechanism for novel crosstalk between cAMP and calcium signaling.
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Affiliation(s)
- Matthias J. Knape
- Department
of Biochemistry, University of Kassel, 34132 Kassel, Germany
| | - Lalima G. Ahuja
- Department
of Pharmacology, University of California at San Diego, La Jolla, California 92093, United States
| | | | | | | | - Susan S. Taylor
- Department
of Pharmacology, University of California at San Diego, La Jolla, California 92093, United States
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22
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Wang Y, Ho TG, Franz E, Hermann JS, Smith FD, Hehnly H, Esseltine JL, Hanold LE, Murph MM, Bertinetti D, Scott JD, Herberg FW, Kennedy EJ. PKA-type I selective constrained peptide disruptors of AKAP complexes. ACS Chem Biol 2015; 10:1502-10. [PMID: 25765284 DOI: 10.1021/acschembio.5b00009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A-Kinase Anchoring Proteins (AKAPs) coordinate complex signaling events by serving as spatiotemporal modulators of cAMP-dependent protein kinase activity in cells. Although AKAPs organize a plethora of diverse pathways, their cellular roles are often elusive due to the dynamic nature of these signaling complexes. AKAPs can interact with the type I or type II PKA holoenzymes by virtue of high-affinity interactions with the R-subunits. As a means to delineate AKAP-mediated PKA signaling in cells, we sought to develop isoform-selective disruptors of AKAP signaling. Here, we report the development of conformationally constrained peptides named RI-STapled Anchoring Disruptors (RI-STADs) that target the docking/dimerization domain of the type 1 regulatory subunit of PKA. These high-affinity peptides are isoform-selective for the RI isoforms, can outcompete binding by the classical AKAP disruptor Ht31, and can selectively displace RIα, but not RIIα, from binding the dual-specific AKAP149 complex. Importantly, these peptides are cell-permeable and disrupt Type I PKA-mediated phosphorylation events in the context of live cells. Hence, RI-STAD peptides are versatile cellular tools to selectively probe anchored type I PKA signaling events.
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Affiliation(s)
- Yuxiao Wang
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Tienhuei G. Ho
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Eugen Franz
- Department
of Biochemistry, University of Kassel, 34132 Kassel, Germany
| | | | - F. Donelson Smith
- Howard
Hughes Medical Institute, Department of Pharmacology, University of Washington School of Medicine, Seattle, Washington 98195, United States
| | - Heidi Hehnly
- Howard
Hughes Medical Institute, Department of Pharmacology, University of Washington School of Medicine, Seattle, Washington 98195, United States
| | - Jessica L. Esseltine
- Howard
Hughes Medical Institute, Department of Pharmacology, University of Washington School of Medicine, Seattle, Washington 98195, United States
| | - Laura E. Hanold
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Mandi M. Murph
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | | | - John D. Scott
- Howard
Hughes Medical Institute, Department of Pharmacology, University of Washington School of Medicine, Seattle, Washington 98195, United States
| | | | - Eileen J. Kennedy
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
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23
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Schwede F, Chepurny OG, Kaufholz M, Bertinetti D, Leech CA, Cabrera O, Zhu Y, Mei F, Cheng X, Manning Fox JE, MacDonald PE, Genieser HG, Herberg FW, Holz GG. Rp-cAMPS Prodrugs Reveal the cAMP Dependence of First-Phase Glucose-Stimulated Insulin Secretion. Mol Endocrinol 2015; 29:988-1005. [PMID: 26061564 DOI: 10.1210/me.2014-1330] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
cAMP-elevating agents such as the incretin hormone glucagon-like peptide-1 potentiate glucose-stimulated insulin secretion (GSIS) from pancreatic β-cells. However, a debate has existed since the 1970s concerning whether or not cAMP signaling is essential for glucose alone to stimulate insulin secretion. Here, we report that the first-phase kinetic component of GSIS is cAMP-dependent, as revealed through the use of a novel highly membrane permeable para-acetoxybenzyl (pAB) ester prodrug that is a bioactivatable derivative of the cAMP antagonist adenosine-3',5'-cyclic monophosphorothioate, Rp-isomer (Rp-cAMPS). In dynamic perifusion assays of human or rat islets, a step-wise increase of glucose concentration leads to biphasic insulin secretion, and under these conditions, 8-bromoadenosine-3',5'-cyclic monophosphorothioate, Rp-isomer, 4-acetoxybenzyl ester (Rp-8-Br-cAMPS-pAB) inhibits first-phase GSIS by up to 80%. Surprisingly, second-phase GSIS is inhibited to a much smaller extent (≤20%). Using luciferase, fluorescence resonance energy transfer, and bioluminescence resonance energy transfer assays performed in living cells, we validate that Rp-8-Br-cAMPS-pAB does in fact block cAMP-dependent protein kinase activation. Novel effects of Rp-8-Br-cAMPS-pAB to block the activation of cAMP-regulated guanine nucleotide exchange factors (Epac1, Epac2) are also validated using genetically encoded Epac biosensors, and are independently confirmed in an in vitro Rap1 activation assay using Rp-cAMPS and Rp-8-Br-cAMPS. Thus, in addition to revealing the cAMP dependence of first-phase GSIS from human and rat islets, these findings establish a pAB-based chemistry for the synthesis of highly membrane permeable prodrug derivatives of Rp-cAMPS that act with micromolar or even nanomolar potency to inhibit cAMP signaling in living cells.
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Affiliation(s)
- Frank Schwede
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Oleg G Chepurny
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Melanie Kaufholz
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Daniela Bertinetti
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Colin A Leech
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Over Cabrera
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Yingmin Zhu
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Fang Mei
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Xiaodong Cheng
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Jocelyn E Manning Fox
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Patrick E MacDonald
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Hans-G Genieser
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - Friedrich W Herberg
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
| | - George G Holz
- BIOLOG Life Science Institute (F.S., H.-G.G.), 28199 Bremen, Germany; Departments of Medicine (O.G.C., C.A.L., G.G.H.) and Pharmacology (G.G.H.), State University of New York, Upstate Medical University, Syracuse, New York 13210; Department of Biochemistry (M.K., D.B., F.W.H.), University of Kassel, 34132 Kassel, Germany; Eli Lilly and Company (O.C.), Indianapolis, Indiana 46225; Department of Integrative Biology and Pharmacology (Y.Z., F.M., X.C.), Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, Texas 77030; Department of Pharmacology and the Alberta Diabetes Institute (J.E.M.F., P.E.M.), University of Alberta, Edmonton, Canada AB T6G 2E1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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Schwede F, Bertinetti D, Langerijs CN, Hadders MA, Wienk H, Ellenbroek JH, de Koning EJP, Bos JL, Herberg FW, Genieser HG, Janssen RAJ, Rehmann H. Structure-guided design of selective Epac1 and Epac2 agonists. PLoS Biol 2015; 13:e1002038. [PMID: 25603503 PMCID: PMC4300089 DOI: 10.1371/journal.pbio.1002038] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 12/03/2014] [Indexed: 12/25/2022] Open
Abstract
The second messenger cAMP is known to augment glucose-induced insulin secretion. However, its downstream targets in pancreatic β-cells have not been unequivocally determined. Therefore, we designed cAMP analogues by a structure-guided approach that act as Epac2-selective agonists both in vitro and in vivo. These analogues activate Epac2 about two orders of magnitude more potently than cAMP. The high potency arises from increased affinity as well as increased maximal activation. Crystallographic studies demonstrate that this is due to unique interactions. At least one of the Epac2-specific agonists, Sp-8-BnT-cAMPS (S-220), enhances glucose-induced insulin secretion in human pancreatic cells. Selective targeting of Epac2 is thus proven possible and may be an option in diabetes treatment. cAMP is a small molecule produced by cells that activates proteins involved in a wide range of biological processes, including olfaction, pacemaker activity, regulation of gene expression, insulin secretion, and many others. In the case of insulin secretion, cAMP seems to impinge on different stages of the signalling cascade to regulate secretory activity in pancreatic β-cells. Here we have developed a chemically modified version of cAMP that specifically only activates Epac2, one of the cAMP-responsive proteins in this cascade. Furthermore, our cAMP analogue activates Epac2 more potently than cAMP itself does. We have determined several crystal structures of Epac2 in complex with cAMP analogues to help us explain the molecular basis of the observed selectivity and the strong activation potential. In addition, we were able to show that the analogue is able to potentiate glucose-induced secretion of insulin from human pancreatic islets. The principal challenge during this study was identifying and understanding small differences in the cAMP-binding domains of cAMP-regulated proteins and matching these differences with suitable modifications of the cAMP molecule. A newly developed analogue of cAMP that selectively activates Epac2 can potentiate glucose-induced insulin secretion from human pancreatic β-cells.
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Affiliation(s)
| | | | | | - Michael A. Hadders
- Department of Chemistry, Laboratory of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Hans Wienk
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | | | - Eelco J. P. de Koning
- Department of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
- Hubrecht Institute/KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johannes L. Bos
- Molecular Cancer Research and Cancer Genomics Netherlands, Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
| | | | | | | | - Holger Rehmann
- Molecular Cancer Research and Cancer Genomics Netherlands, Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
- * E-mail:
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26
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Möller S, Alfieri A, Bertinetti D, Aquila M, Schwede F, Lolicato M, Rehmann H, Moroni A, Herberg FW. Cyclic nucleotide mapping of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels. ACS Chem Biol 2014; 9:1128-37. [PMID: 24605759 DOI: 10.1021/cb400904s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels play a central role in the regulation of cardiac and neuronal firing rate, and these channels can be dually activated by membrane hyperpolarization and by binding of cyclic nucleotides. cAMP has been shown to directly bind HCN channels and modulate their activity. Despite this, while there are selective inhibitors that block the activation potential of the HCN channels, regulation by cAMP analogs has not been well investigated. A comprehensive screen of 47 cyclic nucleotides with modifications in the nucleobase, ribose moiety, and cyclic phosphate was tested on the three isoforms HCN1, HCN2, and HCN4. 7-CH-cAMP was identified to be a high affinity binder for HCN channels and crosschecked for its ability to act on other cAMP receptor proteins. While 7-CH-cAMP is a general activator for cAMP- and cGMP-dependent protein kinases as well as for the guanine nucleotide exchange factors Epac1 and Epac2, it displays the highest affinity to HCN channels. The molecular basis of the high affinity was investigated by determining the crystal structure of 7-CH-cAMP in complex with the cyclic nucleotide binding domain of HCN4. Electrophysiological studies demonstrate a strong activation potential of 7-CH-cAMP for the HCN4 channel in vivo. So, this makes 7-CH-cAMP a promising activator of the HCN channels in vitro whose functionality can be translated in living cells.
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Affiliation(s)
- Stefan Möller
- Department
of Biochemistry, University of Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Andrea Alfieri
- Department
of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Daniela Bertinetti
- Department
of Biochemistry, University of Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Marco Aquila
- Department
of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Frank Schwede
- Biolog Life Science Institute, Flughafendamm 9a, 28199 Bremen, Germany
| | - Marco Lolicato
- Cardiovascular
Research Institute, University of California San Francisco, 555 Mission
Bay Boulevard South, Rm 482, San Francisco, CA 94158, United States
| | - Holger Rehmann
- Molecular
Cancer Research, Centre of Biomedical Genetics and Cancer Genomics
Centre, University Medical Center Utrecht, Universiteitsweg 100, 3584CG Utrecht, The Netherlands
| | - Anna Moroni
- Department
of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Friedrich W. Herberg
- Department
of Biochemistry, University of Kassel, Heinrich-Plett-Straße 40, 34132 Kassel, Germany
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27
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Wang Y, Ho TG, Bertinetti D, Neddermann M, Franz E, Mo GCH, Schendowich LP, Sukhu A, Spelts RC, Zhang J, Herberg FW, Kennedy EJ. Correction to Isoform-Selective Disruption of AKAP-Localized PKA Using Hydrocarbon Stapled Peptides. ACS Chem Biol 2014. [PMCID: PMC4126737 DOI: 10.1021/cb500329z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Wang Y, Ho TG, Bertinetti D, Neddermann M, Franz E, Mo GCH, Schendowich LP, Sukhu A, Spelts RC, Zhang J, Herberg FW, Kennedy EJ. Isoform-selective disruption of AKAP-localized PKA using hydrocarbon stapled peptides. ACS Chem Biol 2014; 9:635-42. [PMID: 24422448 PMCID: PMC3985448 DOI: 10.1021/cb400900r] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
A-kinase
anchoring proteins (AKAPs) play an important role in the
spatial and temporal regulation of protein kinase A (PKA) by scaffolding
critical intracellular signaling complexes. Here we report the design
of conformationally constrained peptides that disrupt interactions
between PKA and AKAPs in an isoform-selective manner. Peptides derived
from the A Kinase Binding (AKB) domain of several AKAPs were chemically
modified to contain an all-hydrocarbon staple and target the docking/dimerization
domain of PKA-R, thereby occluding AKAP interactions. The peptides
are cell-permeable against diverse human cell lines, are highly isoform-selective
for PKA-RII, and can effectively inhibit interactions between AKAPs
and PKA-RII in intact cells. These peptides can be applied as useful
reagents in cell-based studies to selectively disrupt AKAP-localized
PKA-RII activity and block AKAP signaling complexes. In summary, the
novel hydrocarbon-stapled peptides developed in this study represent
a new class of AKAP disruptors to study compartmentalized RII-regulated
PKA signaling in cells.
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Affiliation(s)
- Yuxiao Wang
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Tienhuei G. Ho
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | | | | | - Eugen Franz
- Department
of Biochemistry, University of Kassel, 34132 Kassel, Germany
| | - Gary C. H. Mo
- Department
of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Lewis P. Schendowich
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Avinash Sukhu
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Raybun C. Spelts
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
| | - Jin Zhang
- Department
of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | | | - Eileen J. Kennedy
- Department
of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602, United States
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29
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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30
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Kim JJ, Figueroa ES, Franz E, Bertinetti D, Herberg F, Kim C. Crystal structures of the carboxyl cGMP binding domain of plasmodium falciparumcGMP-dependent protein kinase reveals a novel salt bridge crucial for activation. BMC Pharmacol Toxicol 2013. [PMCID: PMC3765566 DOI: 10.1186/2050-6511-14-s1-p33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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Lorenz R, Moon EW, Huang GY, Reger AS, Kim JJ, Franz E, Bertinetti D, Kim C, Herberg FW. Transforming PKA into PKG – a structure-function approach to understand cyclic nucleotide selectivity. BMC Pharmacol Toxicol 2013. [PMCID: PMC3765617 DOI: 10.1186/2050-6511-14-s1-p41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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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. Structures of human PKG reveal cGMP-selectived activation mechanisms. BMC Pharmacol Toxicol 2013. [PMCID: PMC3765643 DOI: 10.1186/2050-6511-14-s1-o16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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33
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Chepurny OG, Bertinetti D, Diskar M, Leech CA, Afshari P, Tsalkova T, Cheng X, Schwede F, Genieser HG, Herberg FW, Holz GG. Stimulation of proglucagon gene expression by human GPR119 in enteroendocrine L-cell line GLUTag. Mol Endocrinol 2013; 27:1267-82. [PMID: 23798572 DOI: 10.1210/me.2013-1029] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
GPR119 is a G protein-coupled receptor expressed on enteroendocrine L-cells that synthesize and secrete the incretin hormone glucagon-like peptide-1 (GLP-1). Although GPR119 agonists stimulate L-cell GLP-1 secretion, there is uncertainty concerning whether GLP-1 biosynthesis is under the control of GPR119. Here we report that GPR119 is functionally coupled to increased proglucagon (PG) gene expression that constitutes an essential first step in GLP-1 biosynthesis. Using a mouse L-cell line (GLUTag) that expresses endogenous GPR119, we demonstrate that PG gene promoter activity is stimulated by GPR119 agonist AS1269574. Surprisingly, transfection of GLUTag cells with recombinant human GPR119 (hGPR119) results in a constitutive and apparently ligand-independent increase of PG gene promoter activity and PG mRNA content. These constitutive actions of hGPR119 are mediated by cAMP-dependent protein kinase (PKA) but not cAMP sensor Epac2. Thus, the constitutive action of hGPR119 to stimulate PG gene promoter activity is diminished by: 1) a dominant-negative Gαs protein, 2) a dominant-negative PKA regulatory subunit, and 3) a dominant-negative A-CREB. Interestingly, PG gene promoter activity is stimulated by 6-Bn-cAMP-AM, a cAMP analog that selectively activates α and β isoforms of type II, but not type I PKA regulatory subunits expressed in GLUTag cells. Finally, our analysis reveals that a specific inhibitor of Epac2 activation (ESI-05) fails to block the stimulatory action of 6-Bn-cAMP-AM at the PG gene promoter, nor is PG gene promoter activity stimulated by: 1) a constitutively active Epac2, or 2) cAMP analogs that selectively activate Epac proteins. Such findings are discussed within the context of ongoing controversies concerning the relative contributions of PKA and Epac2 to the control of PG gene expression.
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Affiliation(s)
- Oleg G Chepurny
- Department of Medicine, State University of New York, Upstate Medical University, Syracuse, New York 13210, USA
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34
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Düvel J, Bertinetti D, Möller S, Schwede F, Morr M, Wissing J, Radamm L, Zimmermann B, Genieser HG, Jänsch L, Herberg FW, Häussler S. A chemical proteomics approach to identify c-di-GMP binding proteins in Pseudomonas aeruginosa. J Microbiol Methods 2011; 88:229-36. [PMID: 22178430 DOI: 10.1016/j.mimet.2011.11.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/28/2011] [Accepted: 11/29/2011] [Indexed: 12/16/2022]
Abstract
In many bacteria, high levels of the ubiquitous second messenger c-di-GMP have been demonstrated to suppress motility and to promote the establishment of surface-adherent biofilm communities. While molecular mechanisms underlying the synthesis and degradation of c-di-GMP have been comprehensively characterized, little is known about how c-di-GMP mediates its regulatory effects. In this study, we have established a chemical proteomics approach to identify c-di-GMP interacting proteins in the opportunistic pathogen Pseudomonas aeruginosa. A functionalized c-di-GMP analog, 2'-aminohexylcarbamoyl-c-di-GMP (2'-AHC-c-di-GMP), was chemically synthesized and following its immobilization used to perform affinity pull down experiments. Enriched proteins were subsequently identified by high-resolution mass spectrometry. 2'-AHC-c-di-GMP was also employed in surface plasmon resonance studies to evaluate and quantify the interaction of c-di-GMP with its potential target molecules in vitro. The biochemical tools presented here may serve the identification of novel classes of c-di-GMP effectors and thus contribute to a better characterization and understanding of the complex c-di-GMP signaling network.
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Affiliation(s)
- Juliane Düvel
- Department of Cell Biology, Helmholtz Center for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany
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35
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Lolicato M, Nardini M, Gazzarrini S, Möller S, Bertinetti D, Herberg FW, Bolognesi M, Martin H, Fasolini M, Bertrand JA, Arrigoni C, Thiel G, Moroni A. Tetramerization dynamics of C-terminal domain underlies isoform-specific cAMP gating in hyperpolarization-activated cyclic nucleotide-gated channels. J Biol Chem 2011; 286:44811-20. [PMID: 22006928 DOI: 10.1074/jbc.m111.297606] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are dually activated by hyperpolarization and binding of cAMP to their cyclic nucleotide binding domain (CNBD). HCN isoforms respond differently to cAMP; binding of cAMP shifts activation of HCN2 and HCN4 by 17 mV but shifts that of HCN1 by only 2-4 mV. To explain the peculiarity of HCN1, we solved the crystal structures and performed a biochemical-biophysical characterization of the C-terminal domain (C-linker plus CNBD) of the three isoforms. Our main finding is that tetramerization of the C-terminal domain of HCN1 occurs at basal cAMP concentrations, whereas those of HCN2 and HCN4 require cAMP saturating levels. Therefore, HCN1 responds less markedly than HCN2 and HCN4 to cAMP increase because its CNBD is already partly tetrameric. This is confirmed by voltage clamp experiments showing that the right-shifted position of V(½) in HCN1 is correlated with its propensity to tetramerize in vitro. These data underscore that ligand-induced CNBD tetramerization removes tonic inhibition from the pore of HCN channels.
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Affiliation(s)
- Marco Lolicato
- Department of Biology and Consiglio Nazionale delle Ricerche-Istituto di Biofisica, University of Milan, Via Celoria 26, 20133 Milan, Italy
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36
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Schmidt J, Müsken M, Becker T, Magnowska Z, Bertinetti D, Möller S, Zimmermann B, Herberg FW, Jänsch L, Häussler S. The Pseudomonas aeruginosa chemotaxis methyltransferase CheR1 impacts on bacterial surface sampling. PLoS One 2011; 6:e18184. [PMID: 21445368 PMCID: PMC3062574 DOI: 10.1371/journal.pone.0018184] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 02/22/2011] [Indexed: 12/27/2022] Open
Abstract
The characterization of factors contributing to the formation and development of surface-associated bacterial communities known as biofilms has become an area of intense interest since biofilms have a major impact on human health, the environment and industry. Various studies have demonstrated that motility, including swimming, swarming and twitching, seems to play an important role in the surface colonization and establishment of structured biofilms. Thereby, the impact of chemotaxis on biofilm formation has been less intensively studied. Pseudomonas aeruginosa has a very complex chemosensory system with two Che systems implicated in flagella-mediated motility. In this study, we demonstrate that the chemotaxis protein CheR1 is a methyltransferase that binds S-adenosylmethionine and transfers a methyl group from this methyl donor to the chemoreceptor PctA, an activity which can be stimulated by the attractant serine but not by glutamine. We furthermore demonstrate that CheR1 does not only play a role in flagella-mediated chemotaxis but that its activity is essential for the formation and maintenance of bacterial biofilm structures. We propose a model in which motility and chemotaxis impact on initial attachment processes, dispersion and reattachment and increase the efficiency and frequency of surface sampling in P. aeruginosa.
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Affiliation(s)
- Juliane Schmidt
- Department of Cell Biology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Mathias Müsken
- Department of Cell Biology, Helmholtz Center for Infection Research, Braunschweig, Germany
- TWINCORE, Center for Experimental and Clinical Infection Research, a Joint Venture of the Helmholtz Center for Infection Research and Medical School Hannover, Hannover, Germany
| | - Tanja Becker
- Department of Cell Biology, Helmholtz Center for Infection Research, Braunschweig, Germany
- TWINCORE, Center for Experimental and Clinical Infection Research, a Joint Venture of the Helmholtz Center for Infection Research and Medical School Hannover, Hannover, Germany
| | - Zofia Magnowska
- Department of Cell Biology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Stefan Möller
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | | | | | - Lothar Jänsch
- Department of Cell Biology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Department of Cell Biology, Helmholtz Center for Infection Research, Braunschweig, Germany
- TWINCORE, Center for Experimental and Clinical Infection Research, a Joint Venture of the Helmholtz Center for Infection Research and Medical School Hannover, Hannover, Germany
- * E-mail:
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Hanke SE, Bertinetti D, Badel A, Schweinsberg S, Genieser HG, Herberg FW. Cyclic nucleotides as affinity tools: phosphorothioate cAMP analogues address specific PKA subproteomes. N Biotechnol 2010; 28:294-301. [PMID: 21147280 DOI: 10.1016/j.nbt.2010.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/02/2010] [Accepted: 12/05/2010] [Indexed: 11/29/2022]
Abstract
cAMP (adenosine-3',5'-cyclic monophosphate) is a general second messenger controlling distinct targets in eukaryotic cells. In a (sub)proteomic approach, two classes of phosphorothioate cAMP affinity tools were used to isolate and to identify signalling complexes of the main cAMP target, cAMP dependent protein kinase (PKA). Agonist analogues (here: Sp-cAMPS) bind to the regulatory subunits of PKA (PKA-R), together with their interaction partners, and cause dissociation of a holoenzyme complex comprising PKA-R and catalytic subunits of PKA (PKA-C). Antagonist analogues (here: Rp-cAMPS) bind to the holoenzyme without dissociating the complex and were developed to identify interaction partners that bind to the entire complex or to PKA-C. More than 80 different proteins were isolated from tissue extracts including several PKA isoforms and known as well as potentially new interaction partners. Nevertheless, unspecific binding of general nucleotide binding proteins limited the outcome of this chemical proteomics approach. Surface plasmon resonance (SPR) was employed to optimise the entire workflow of pull down proteomics and to quantify the effects of different nucleotides (ATP, ADP, GTP and NADH) on PKA-R binding to affinity material. We could demonstrate that the addition of NADH to lysates improved specificity in pull down experiments. Using a combination of SPR studies and pull down experiments it was shown unambiguously that it is possible to specifically elute protein complexes with cAMP or cGMP from cAMPS analogue matrices. The side-by-side analysis of the PKA-R interactome and the holoenzyme complexed with interacting proteins will contribute to a further dissection of the multifaceted PKA signalling network.
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Affiliation(s)
- Susanne E Hanke
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CAK, Bourbeillon J, Bradbury ARM, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H. A community standard format for the representation of protein affinity reagents. Mol Cell Proteomics 2009; 9:1-10. [PMID: 19674966 DOI: 10.1074/mcp.m900185-mcp200] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site.
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Affiliation(s)
- David E Gloriam
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
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Bertinetti D, Schweinsberg S, Hanke SE, Schwede F, Bertinetti O, Drewianka S, Genieser HG, Herberg FW. Chemical tools selectively target components of the PKA system. BMC Chem Biol 2009; 9:3. [PMID: 19216744 PMCID: PMC2660902 DOI: 10.1186/1472-6769-9-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 02/12/2009] [Indexed: 11/23/2022]
Abstract
Background In the eukaryotic cell the cAMP-dependent protein kinase (PKA) is a key enzyme in signal transduction and represents the main target of the second messenger cAMP. Here we describe the design, synthesis and characterisation of specifically tailored cAMP analogs which can be utilised as a tool for affinity enrichment and purification as well as for proteomics based analyses of cAMP binding proteins. Results Two sets of chemical binders were developed based on the phosphorothioate derivatives of cAMP, Sp-cAMPS and Rp-cAMPS acting as cAMP-agonists and -antagonists, respectively. These compounds were tested via direct surface plasmon resonance (SPR) analyses for their binding properties to PKA R-subunits and holoenzyme. Furthermore, these analogs were used in an affinity purification approach to analyse their binding and elution properties for the enrichment and improvement of cAMP binding proteins exemplified by the PKA R-subunits. As determined by SPR, all tested Sp-analogs provide valuable tools for affinity chromatography. However, Sp-8-AEA-cAMPS displayed (i) superior enrichment properties while maintaining low unspecific binding to other proteins in crude cell lysates, (ii) allowing mild elution conditions and (iii) providing the capability to efficiently purify all four isoforms of active PKA R-subunit in milligram quantities within 8 h. In a chemical proteomics approach both sets of binders, Rp- and Sp-cAMPS derivatives, can be employed. Whereas Sp-8-AEA-cAMPS preferentially binds free R-subunit, Rp-AHDAA-cAMPS, displaying antagonist properties, not only binds to the free PKA R-subunits but also to the intact PKA holoenzyme both from recombinant and endogenous sources. Conclusion In summary, all tested cAMP analogs were useful for their respective application as an affinity reagent which can enhance purification of cAMP binding proteins. Sp-8-AEA-cAMPS was considered the most efficient analog since Sp-8-AHA-cAMPS and Sp-2-AHA-cAMPS, demonstrated incomplete elution from the matrix, as well as retaining notable amounts of bound protein contaminants. Furthermore it could be demonstrated that an affinity resin based on Rp-8-AHDAA-cAMPS provides a valuable tool for chemical proteomics approaches.
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Affiliation(s)
- Daniela Bertinetti
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Sonja Schweinsberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Susanne E Hanke
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Frank Schwede
- Biolog Life Science Institute, Flughafendamm 9a, P.O. Box 107125, Bremen, Germany
| | - Oliver 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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