1
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Meudt M, Pannek M, Glogowski N, Higel F, Thanisch K, Knape MJ. CE methods for charge variant analysis of mAbs and complex format biotherapeutics. Electrophoresis 2024. [PMID: 38233206 DOI: 10.1002/elps.202300170] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/21/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024]
Abstract
Charge heterogeneity analysis of monoclonal antibodies (mAbs) and complex formats, such as bispecifics, is crucial for therapeutic applications. In this study, we developed two capillary electrophoresis (CE)-based methods, capillary zone electrophoresis (CZE) and imaged capillary isoelectric focusing (iCIEF), for analyzing a broad spectrum of mAbs and complex mAb formats. For CZE, we introduced a new buffer system and optimized the background electrolyte (BGE) with an alternative dynamic coating agent and a superior polymeric additive. The pH of the BGE was increased, leading to enhanced resolution of high pI and complex format mAbs. In iCIEF, we identified an ampholyte combination offering a highly linear pH gradient and covering a suitable pH range. We also investigated alternatives to denaturing stabilizers and found that non-detergent sulfobetaine 195 exhibited excellent properties for iCIEF applications. These optimized methods provide a framework for the charge heterogeneity analysis of therapeutic mAbs and complex formats.
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Affiliation(s)
- Maximilian Meudt
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Martin Pannek
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
- Rentschler Biopharma SE, Laupheim, Germany
| | - Nina Glogowski
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Fabian Higel
- Global CMC Experts NBE, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Katharina Thanisch
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Matthias J Knape
- Analytical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
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2
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Yang J, Knape MJ, Burkert O, Mazzini V, Jung A, Craig VSJ, Miranda-Quintana RA, Bluhmki E, Smiatek J. Artificial neural networks for the prediction of solvation energies based on experimental and computational data. Phys Chem Chem Phys 2020; 22:24359-24364. [PMID: 33084665 DOI: 10.1039/d0cp03701j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The knowledge of thermodynamic properties for novel electrolyte formulations is of fundamental interest for industrial applications as well as academic research. Herewith, we present an artificial neural networks (ANN) approach for the prediction of solvation energies and entropies for distinct ion pairs in various protic and aprotic solvents. The considered feed-forward ANN is trained either by experimental data or computational results from conceptual density functional theory calculations. The proposed concept of mapping computed values to experimental data lowers the amount of time-consuming and costly experiments and helps to overcome certain limitations. Our findings reveal high correlation coefficients between predicted and experimental values which demonstrate the validity of our approach.
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Affiliation(s)
- Jiyoung Yang
- Boehringer Ingelheim Pharma GmbH & Co. KG, Analytical Development Biologicals, Birkendorfer Strasse 65, D-88397 Biberach (Riss), Germany
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3
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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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4
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Manschwetus JT, Bendzunas GN, Limaye AJ, Knape MJ, Herberg FW, Kennedy EJ. A Stapled Peptide Mimic of the Pseudosubstrate Inhibitor PKI Inhibits Protein Kinase A. Molecules 2019; 24:molecules24081567. [PMID: 31009996 PMCID: PMC6514771 DOI: 10.3390/molecules24081567] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 11/16/2022] Open
Abstract
Kinases regulate multiple and diverse signaling pathways and misregulation is implicated in a multitude of diseases. Although significant efforts have been put forth to develop kinase-specific inhibitors, specificity remains a challenge. As an alternative to catalytic inhibition, allosteric inhibitors can target areas on the surface of an enzyme, thereby providing additional target diversity. Using cAMP-dependent protein kinase A (PKA) as a model system, we sought to develop a hydrocarbon-stapled peptide targeting the pseudosubstrate domain of the kinase. A library of peptides was designed from a Protein Kinase Inhibitor (PKI), a naturally encoded protein that serves as a pseudosubstrate inhibitor for PKA. The binding properties of these peptide analogs were characterized by fluorescence polarization and surface plasmon resonance, and two compounds were identified with KD values in the 500-600 pM range. In kinase activity assays, both compounds demonstrated inhibition with 25-35 nM IC50 values. They were also found to permeate cells and localize within the cytoplasm and inhibited PKA activity within the cellular environment. To the best of our knowledge, these stapled peptide inhibitors represent some of the highest affinity binders reported to date for hydrocarbon stapled peptides.
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Affiliation(s)
- Jascha T Manschwetus
- Department of Biochemistry, Institute for Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany.
| | - George N Bendzunas
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 240 W. Green St, Athens, GA 30602, USA.
| | - Ameya J Limaye
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 240 W. Green St, Athens, GA 30602, USA.
| | - Matthias J Knape
- Department of Biochemistry, Institute for Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany.
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany.
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, 240 W. Green St, Athens, GA 30602, USA.
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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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6
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Espiard S, Knape MJ, Bathon K, Assié G, Rizk-Rabin M, Faillot S, Luscap-Rondof W, Abid D, Guignat L, Calebiro D, Herberg FW, Stratakis CA, Bertherat J. Activating PRKACB somatic mutation in cortisol-producing adenomas. JCI Insight 2018; 3:98296. [PMID: 29669941 DOI: 10.1172/jci.insight.98296] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/20/2018] [Indexed: 12/13/2022] Open
Abstract
Mutations in the gene encoding the protein kinase A (PKA) catalytic subunit α have been found to be responsible for cortisol-producing adenomas (CPAs). In this study, we identified by whole-exome sequencing the somatic mutation p.S54L in the PRKACB gene, encoding the catalytic subunit β (Cβ) of PKA, in a CPA from a patient with severe Cushing syndrome. Bioluminescence resonance energy transfer and surface plasmon resonance assays revealed that the mutation hampers formation of type I holoenzymes and that these holoenzymes were highly sensitive to cAMP. PKA activity, measured both in cell lysates and with recombinant proteins, based on phosphorylation of a synthetic substrate, was higher under basal conditions for the mutant enzyme compared with the WT, while maximal activity was lower. These data suggest that at baseline the PRKACB p.S54L mutant drove the adenoma cells to higher cAMP signaling activity, probably contributing to their autonomous growth. Although the role of PRKACB in tumorigenesis has been suggested, we demonstrated for the first time to our knowledge that a PRKACB mutation can lead to an adrenal tumor. Moreover, this observation describes another mechanism of PKA pathway activation in CPAs and highlights the particular role of residue Ser54 for the function of PKA.
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Affiliation(s)
- Stéphanie Espiard
- Cochin Institute, Paris Descartes University, CNRS (UMR 8104)/Inserm (U1016), Paris, France.,Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Matthias J Knape
- University of Kassel, Department of Biochemistry, Kassel, Germany
| | - Kerstin Bathon
- Institute of Pharmacology and Toxicology and Bio-Imaging Center/Rudolf Virchow Center, University of Würzburg, Würzburg, Germany
| | - Guillaume Assié
- Cochin Institute, Paris Descartes University, CNRS (UMR 8104)/Inserm (U1016), Paris, France.,Center for Rare Adrenal Diseases, Endocrinology Department, Cochin Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Marthe Rizk-Rabin
- Cochin Institute, Paris Descartes University, CNRS (UMR 8104)/Inserm (U1016), Paris, France
| | - Simon Faillot
- Cochin Institute, Paris Descartes University, CNRS (UMR 8104)/Inserm (U1016), Paris, France
| | - Windy Luscap-Rondof
- Cochin Institute, Paris Descartes University, CNRS (UMR 8104)/Inserm (U1016), Paris, France
| | - Daniel Abid
- University of Kassel, Department of Biochemistry, Kassel, Germany
| | - Laurence Guignat
- Center for Rare Adrenal Diseases, Endocrinology Department, Cochin Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Davide Calebiro
- Institute of Pharmacology and Toxicology and Bio-Imaging Center/Rudolf Virchow Center, University of Würzburg, Würzburg, Germany.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom.,Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, United Kingdom
| | | | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Jérôme Bertherat
- Cochin Institute, Paris Descartes University, CNRS (UMR 8104)/Inserm (U1016), Paris, France.,Center for Rare Adrenal Diseases, Endocrinology Department, Cochin Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
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7
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Isensee J, Kaufholz M, Knape MJ, Hasenauer J, Hammerich H, Gonczarowska-Jorge H, Zahedi RP, Schwede F, Herberg FW, Hucho T. PKA-RII subunit phosphorylation precedes activation by cAMP and regulates activity termination. J Cell Biol 2018; 217:2167-2184. [PMID: 29615473 PMCID: PMC5987717 DOI: 10.1083/jcb.201708053] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 02/18/2018] [Accepted: 03/15/2018] [Indexed: 11/22/2022] Open
Abstract
Activity of endogenous protein kinase A (PKA) could never be analyzed directly in the cellular environment. Isensee et al. used antibodies to quantify conformational changes leading to an open conformation of endogenous PKA-II holoenzymes, which allowed them to analyze and model its activation cycle in primary sensory neurons. Type II isoforms of cyclic adenosine monophosphate (cAMP)–dependent protein kinase A (PKA-II) contain a phosphorylatable epitope within the inhibitory domain of RII subunits (pRII) with still unclear function. In vitro, RII phosphorylation occurs in the absence of cAMP, whereas staining of cells with pRII-specific antibodies revealed a cAMP-dependent pattern. In sensory neurons, we found that increased pRII immunoreactivity reflects increased accessibility of the already phosphorylated RII epitope during cAMP-induced opening of the tetrameric RII2:C2 holoenzyme. Accordingly, induction of pRII by cAMP was sensitive to novel inhibitors of dissociation, whereas blocking catalytic activity was ineffective. Also in vitro, cAMP increased the binding of pRII antibodies to RII2:C2 holoenzymes. Identification of an antibody specific for the glycine-rich loop of catalytic subunits facing the pRII-epitope confirmed activity-dependent binding with similar kinetics, proving that the reassociation is rapid and precisely controlled. Mechanistic modeling further supported that RII phosphorylation precedes cAMP binding and controls the inactivation by modulating the reassociation involving the coordinated action of phosphodiesterases and phosphatases.
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Affiliation(s)
- Jörg Isensee
- Department of Anesthesiology and Intensive Care Medicine, Experimental Anesthesiology and Pain Research, University Hospital of Cologne, Cologne, Germany
| | - Melanie Kaufholz
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Matthias J Knape
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Center for Mathematics, Technische Universität München, Garching, Germany
| | - Hanna Hammerich
- Department of Anesthesiology and Intensive Care Medicine, Experimental Anesthesiology and Pain Research, University Hospital of Cologne, Cologne, Germany
| | - Humberto Gonczarowska-Jorge
- ISAS, Leibniz-Institut für Analytische Wissenschaften, Dortmund, Germany.,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - René P Zahedi
- ISAS, Leibniz-Institut für Analytische Wissenschaften, Dortmund, Germany
| | | | | | - Tim Hucho
- Department of Anesthesiology and Intensive Care Medicine, Experimental Anesthesiology and Pain Research, University Hospital of Cologne, Cologne, Germany
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Abstract
cGMP-dependent protein kinase from Plasmodium falciparum ( PfPKG) plays a crucial role in the sexual as well as the asexual proliferation of this human malaria causing parasite. However, function and regulation of PfPKG are largely unknown. Previous studies showed that the domain organization of PfPKG significantly differs from human PKG ( hPKG) and indicated a critical role of the cyclic nucleotide binding domain D (CNB-D). We identified a novel mechanism, where the CNB-D controls activation and regulation of the parasite specific protein kinase. Here, kinase activity is not dependent on a pseudosubstrate autoinhibitory sequence (IS), as reported for human PKG. A construct lacking the putative IS and containing only the CNB-D and the catalytic domain is inactive in the absence of cGMP and can efficiently be activated with cGMP. On the basis of structural evidence, we describe a regulatory mechanism, whereby cGMP binding to CNB-D induces a conformational change involving the αC-helix of the CNB-D. The inactive state is defined by a unique interaction between Asp597 of the catalytic domain and Arg528 of the αC-helix. The same arginine (R528), however, stabilizes cGMP binding by interacting with Tyr480 of the phosphate binding cassette (PBC). This represents the active state of PfPKG. Our results unveil fundamental differences in the activation mechanism between PfPKG and hPKG, building the basis for the development of strategies for targeted drug design in fighting malaria.
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Affiliation(s)
- Eugen Franz
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Matthias J. Knape
- 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
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9
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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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10
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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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11
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Zhang P, Knape MJ, Ahuja LG, Keshwani MM, King CC, Sastri M, Herberg FW, Taylor SS. Single Turnover Autophosphorylation Cycle of the PKA RIIβ Holoenzyme. PLoS Biol 2015; 13:e1002192. [PMID: 26158466 PMCID: PMC4497662 DOI: 10.1371/journal.pbio.1002192] [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] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 06/01/2015] [Indexed: 01/10/2023] Open
Abstract
To provide tight spatiotemporal signaling control, the cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) holoenzyme typically nucleates a macromolecular complex or a "PKA signalosome." Using the RIIβ holoenzyme as a prototype, we show how autophosphorylation/dephosphorylation of the RIIβ subunit, as well as cAMP and metal ions, contribute to the dynamics of PKA signaling. While we showed previously that the RIIβ holoenzyme could undergo a single turnover autophosphorylation with adenosine triphosphate and magnesium (MgATP) and trap both products in the crystal lattice, we asked here whether calcium could trap an ATP:RIIβ holoenzyme since the RIIβ holoenzyme is located close to ion channels. The 2.8Å structure of an RIIβp2:C2:(Ca2ADP)2 holoenzyme, supported by biochemical and biophysical data, reveals a trapped single phosphorylation event similar to MgATP. Thus, calcium can mediate a single turnover event with either ATP or adenosine-5'-(β,γ-imido)triphosphate (AMP-PNP), even though it cannot support steady-state catalysis efficiently. The holoenzyme serves as a "product trap" because of the slow off-rate of the pRIIβ subunit, which is controlled by cAMP, not by phosphorylation of the inhibitor site. By quantitatively defining the RIIβ signaling cycle, we show that release of pRIIβ in the presence of cAMP is reduced by calcium, whereas autophosphorylation at the phosphorylation site (P-site) inhibits holoenzyme reassociation with the catalytic subunit. Adding a single phosphoryl group to the preformed RIIβ holoenzyme thus creates a signaling cycle in which phosphatases become an essential partner. This previously unappreciated molecular mechanism is an integral part of PKA signaling for type II holoenzymes.
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Affiliation(s)
- Ping Zhang
- Department of Pharmacology, University of California at San Diego, La Jolla, California, United States of America
| | | | - Lalima G. Ahuja
- Department of Pharmacology, University of California at San Diego, La Jolla, California, United States of America
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, United States of America
| | - Malik M. Keshwani
- Department of Pharmacology, University of California at San Diego, La Jolla, California, United States of America
| | - Charles C. King
- Department of Pediatrics, University of California at San Diego, La Jolla, California, United States of America
| | - Mira Sastri
- Department of Pharmacology, University of California at San Diego, La Jolla, California, United States of America
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, United States of America
| | - Friedrich W. Herberg
- Department of Biochemistry, University of Kassel, Kassel, Germany
- * E-mail: (FWH); (SST)
| | - Susan S. Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, California, United States of America
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, United States of America
- * E-mail: (FWH); (SST)
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