1
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Qin J, Zhang J, Lin L, Haji-Ghassemi O, Lin Z, Woycechowsky KJ, Van Petegem F, Zhang Y, Yuchi Z. Structures of PKA-phospholamban complexes reveal a mechanism of familial dilated cardiomyopathy. eLife 2022; 11:75346. [PMID: 35297759 PMCID: PMC8970585 DOI: 10.7554/elife.75346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/16/2022] [Indexed: 01/07/2023] Open
Abstract
Several mutations identified in phospholamban (PLN) have been linked to familial dilated cardiomyopathy (DCM) and heart failure, yet the underlying molecular mechanism remains controversial. PLN interacts with sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) and regulates calcium uptake, which is modulated by the protein kinase A (PKA)-dependent phosphorylation of PLN during the fight-or-flight response. Here, we present the crystal structures of the catalytic domain of mouse PKA in complex with wild-type and DCM-mutant PLNs. Our structures, combined with the results from other biophysical and biochemical assays, reveal a common disease mechanism: the mutations in PLN reduce its phosphorylation level by changing its conformation and weakening its interactions with PKA. In addition, we demonstrate that another more ubiquitous SERCA-regulatory peptide, called another-regulin (ALN), shares a similar mechanism mediated by PKA in regulating SERCA activity.
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Affiliation(s)
- Juan Qin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency; Collaborative Innovation Center of Chemical Science and Engineering; School of Pharmaceutical Science and Technology, Tianjin UniversityTianjinChina
| | - Jingfeng Zhang
- Wuhan Institute of Physics and Mathematics, Chinese Academy of SciencesWuhanChina
| | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency; Collaborative Innovation Center of Chemical Science and Engineering; School of Pharmaceutical Science and Technology, Tianjin UniversityTianjinChina
| | - Omid Haji-Ghassemi
- Department of Biochemistry and Molecular Biology, The Life Sciences Centre, University of British ColumbiaVancouverCanada
| | - Zhi Lin
- School of Life Sciences, Tianjin UniversityTianjinChina
| | - Kenneth J Woycechowsky
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency; Collaborative Innovation Center of Chemical Science and Engineering; School of Pharmaceutical Science and Technology, Tianjin UniversityTianjinChina
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, The Life Sciences Centre, University of British ColumbiaVancouverCanada
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency; Collaborative Innovation Center of Chemical Science and Engineering; School of Pharmaceutical Science and Technology, Tianjin UniversityTianjinChina
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency; Collaborative Innovation Center of Chemical Science and Engineering; School of Pharmaceutical Science and Technology, Tianjin UniversityTianjinChina,Department of Molecular Pharmacology, Tianjin Medical University Cancer Institute & Hospital; National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin’s Clinical Research Center for CancerTianjinChina
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2
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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] [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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3
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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] [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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4
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Plasmodium falciparum Cyclic GMP-Dependent Protein Kinase Interacts with a Subunit of the Parasite Proteasome. Infect Immun 2018; 87:IAI.00523-18. [PMID: 30323024 DOI: 10.1128/iai.00523-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/29/2018] [Indexed: 12/20/2022] Open
Abstract
Malaria is caused by the protozoan parasite Plasmodium, which undergoes a complex life cycle in a human host and a mosquito vector. The parasite's cyclic GMP (cGMP)-dependent protein kinase (PKG) is essential at multiple steps of the life cycle. Phosphoproteomic studies in Plasmodium falciparum erythrocytic stages and Plasmodium berghei ookinetes have identified proteolysis as a major biological pathway dependent on PKG activity. To further understand PKG's mechanism of action, we screened a yeast two-hybrid library for P. falciparum proteins that interact with P. falciparum PKG (PfPKG) and tested peptide libraries to identify its phosphorylation site preferences. Our data suggest that PfPKG has a distinct phosphorylation site and that PfPKG directly phosphorylates parasite RPT1, one of six AAA+ ATPases present in the 19S regulatory particle of the proteasome. PfPKG and RPT1 interact in vitro, and the interacting fragment of RPT1 carries a PfPKG consensus phosphorylation site; a peptide carrying this consensus site competes with the RPT1 fragment for binding to PfPKG and is efficiently phosphorylated by PfPKG. These data suggest that PfPKG's phosphorylation of RPT1 could contribute to its regulation of parasite proteolysis. We demonstrate that proteolysis plays an important role in a biological process known to require Plasmodium PKG: invasion by sporozoites of hepatocytes. A small-molecule inhibitor of proteasomal activity blocks sporozoite invasion in an additive manner when combined with a Plasmodium PKG-specific inhibitor. Mining the previously described parasite PKG-dependent phosphoproteomes using the consensus phosphorylation motif identified additional proteins that are likely to be direct substrates of the enzyme.
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5
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Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. Understanding how cAMP-dependent protein kinase can catalyze phosphoryl transfer in the presence of Ca2+and Sr2+: a QM/MM study. Phys Chem Chem Phys 2017; 19:10377-10394. [DOI: 10.1039/c7cp00666g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Theoretical results demonstrate for the first time at the molecular level that the overall PKAc-catalyzed phosphoryl-transfer reaction is plausible with Ca2+and Sr2+, alkaline earth metal ions other than Mg2+, which is in good agreement with experiments.
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Affiliation(s)
- Ayax Pérez-Gallegos
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
| | - Mireia Garcia-Viloca
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
| | - Àngels González-Lafont
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona
- 08193 Bellaterra (Barcelona)
- Spain
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6
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Haubrich BA, Swinney DC. Enzyme Activity Assays for Protein Kinases: Strategies to Identify Active Substrates. Curr Drug Discov Technol 2016; 13:2-15. [PMID: 26768716 DOI: 10.2174/1570163813666160115125930] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 11/22/2022]
Abstract
Protein kinases are an important class of enzymes and drug targets. New opportunities to discover medicines for neglected diseases can be leveraged by the extensive kinase tools and knowledge created in targeting human kinases. A valuable tool for kinase drug discovery is an enzyme assay that measures catalytic function. The functional assay can be used to identify inhibitors, estimate affinity, characterize molecular mechanisms of action (MMOAs) and evaluate selectivity. However, establishing an enzyme assay for a new kinases requires identification of a suitable substrate. Identification of a new kinase's endogenous physiologic substrate and function can be extremely costly and time consuming. Fortunately, most kinases are promiscuous and will catalyze the phosphotransfer from ATP to alternative substrates with differing degrees of catalytic efficiency. In this manuscript we review strategies and successes in the identification of alternative substrates for kinases from organisms responsible for many of the neglected tropical diseases (NTDs) towards the goal of informing strategies to identify substrates for new kinases. Approaches for establishing a functional kinase assay include measuring auto-activation and use of generic substrates and peptides. The most commonly used generic substrates are casein, myelin basic protein, and histone. Sequence homology modeling can provide insights into the potential substrates and the requirement for activation. Empirical approaches that can identify substrates include screening of lysates (which may also help identify native substrates) and use of peptide arrays. All of these approaches have been used with a varying degree of success to identify alternative substrates.
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Affiliation(s)
- Brad A Haubrich
- Institute for Rare and Neglected Diseases Drug Discovery, 897 Independence Ave, Suite 2C, Mountain View, CA 94043, USA.
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Reactivation of flagellar motility in demembranated Leishmania reveals role of cAMP in flagellar wave reversal to ciliary waveform. Sci Rep 2016; 6:37308. [PMID: 27849021 PMCID: PMC5110981 DOI: 10.1038/srep37308] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/27/2016] [Indexed: 12/20/2022] Open
Abstract
The flagellum of parasitic trypanosomes is a multifunctional appendage essential for its viability and infectivity. However, the biological mechanisms that make the flagellum so dynamic remains unexplored. No method is available to access and induce axonemal motility at will to decipher motility regulation in trypanosomes. For the first time we report the development of a detergent-extracted/demembranated ATP-reactivated model for studying flagellar motility in Leishmania. Flagellar beat parameters of reactivated parasites were similar to live ones. Using this model we discovered that cAMP (both exogenous and endogenous) induced flagellar wave reversal to a ciliary waveform in reactivated parasites via cAMP-dependent protein kinase A. The effect was reversible and highly specific. Such an effect of cAMP on the flagellar waveform has never been observed before in any organism. Flagellar wave reversal allows parasites to change direction of swimming. Our findings suggest a possible cAMP-dependent mechanism by which Leishmania responds to its surrounding microenvironment, necessary for its survival. Our demembranated-reactivated model not only serves as an important tool for functional studies of flagellated eukaryotic parasites but has the potential to understand ciliary motility regulation with possible implication on human ciliopathies.
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Araujo NA, Guevara A, Lorenzo MA, Calabokis M, Bubis J. Fluram-Kemptide-Lys8 Non-radioactive Assay for Protein Kinase A. Protein J 2016; 35:247-55. [DOI: 10.1007/s10930-016-9667-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Gerlits O, Das A, Keshwani MM, Taylor S, Waltman MJ, Langan P, Heller WT, Kovalevsky A. Metal-free cAMP-dependent protein kinase can catalyze phosphoryl transfer. Biochemistry 2014; 53:3179-86. [PMID: 24786636 PMCID: PMC4030786 DOI: 10.1021/bi5000965] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
X-ray structures of several ternary product complexes of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have been determined with no bound metal ions and with Na(+) or K(+) coordinated at two metal-binding sites. The metal-free PKAc and the enzyme with alkali metals were able to facilitate the phosphoryl transfer reaction. In all studied complexes, the ATP and the substrate peptide (SP20) were modified into the products ADP and the phosphorylated peptide. The products of the phosphotransfer reaction were also found when ATP-γS, a nonhydrolyzable ATP analogue, reacted with SP20 in the PKAc active site containing no metals. Single turnover enzyme kinetics measurements utilizing (32)P-labeled ATP confirmed the phosphotransferase activity of the enzyme in the absence of metal ions and in the presence of alkali metals. In addition, the structure of the apo-PKAc binary complex with SP20 suggests that the sequence of binding events may become ordered in a metal-free environment, with SP20 binding first to prime the enzyme for subsequent ATP binding. Comparison of these structures reveals conformational and hydrogen bonding changes that might be important for the mechanism of catalysis.
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Affiliation(s)
- Oksana Gerlits
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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10
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Wong A, Zhang YW, Jeschke GR, Turk BE, Rudnick G. Cyclic GMP-dependent stimulation of serotonin transport does not involve direct transporter phosphorylation by cGMP-dependent protein kinase. J Biol Chem 2012; 287:36051-8. [PMID: 22942288 DOI: 10.1074/jbc.m112.394726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The serotonin transporter (SERT) is responsible for reuptake of serotonin (5-hydroxytryptamine) after its exocytotic release from neurons. It is the primary target for antidepressants and stimulants, including "ecstasy" (3,4-methylenedioxymethamphetamine). SERT is regulated by several processes, including a cyclic GMP signaling pathway involving nitric oxide synthase, guanylyl cyclase, and cGMP-dependent protein kinase (PKG). Here, we show that SERT was phosphorylated in a PKG Iα-dependent manner in vitro, but that SERT was not a direct substrate of PKG. We generated an analog-sensitive gatekeeper residue mutant of PKG Iα (M438G) that efficiently used the ATP analog N(6)-benzyl-ATP. This mutant, but not the wild type (WT) kinase, used the ATP analog to phosphorylate both a model peptide substrate as well as an established protein substrate of PKG (vasodilator-stimulated phosphoprotein). PKG Iα M438G effectively substituted for the WT kinase in stimulating SERT-mediated 5-hydroxytryptamine transport in cultured cells. Addition of either WT or mutant PKG Iα M438G to membranes containing SERT in vitro led to radiolabel incorporation from [γ-(33)P]ATP but not from similarly labeled N(6)-benzyl-ATP, indicating that SERT was phosphorylated by another kinase that could not utilize the ATP analog. These results are consistent with the proposed SERT phosphorylation site, Thr-276, being highly divergent from the consensus PKG phosphorylation site sequence, which we verified through peptide library screening. Another proposed SERT kinase, the p38 mitogen-activated protein kinase, could not substitute for PKG in this assay, and p38 inhibitors did not block PKG-dependent phosphorylation of SERT. The results suggest that PKG initiates a kinase cascade that leads to phosphorylation of SERT by an as yet unidentified protein kinase.
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Affiliation(s)
- Albert Wong
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, USA
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11
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Puthenveetil S, Liu DS, White KA, Thompson S, Ting AY. Yeast display evolution of a kinetically efficient 13-amino acid substrate for lipoic acid ligase. J Am Chem Soc 2010; 131:16430-8. [PMID: 19863063 DOI: 10.1021/ja904596f] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Escherichia coli lipoic acid ligase (LplA) catalyzes ATP-dependent covalent ligation of lipoic acid onto specific lysine side chains of three acceptor proteins involved in oxidative metabolism. Our lab has shown that LplA and engineered mutants can ligate useful small-molecule probes such as alkyl azides ( Nat. Biotechnol. 2007 , 25 , 1483 - 1487 ) and photo-cross-linkers ( Angew. Chem., Int. Ed. 2008 , 47 , 7018 - 7021 ) in place of lipoic acid, facilitating imaging and proteomic studies. Both to further our understanding of lipoic acid metabolism, and to improve LplA's utility as a biotechnological platform, we have engineered a novel 13-amino acid peptide substrate for LplA. LplA's natural protein substrates have a conserved beta-hairpin structure, a conformation that is difficult to recapitulate in a peptide, and thus we performed in vitro evolution to engineer the LplA peptide substrate, called "LplA Acceptor Peptide" (LAP). A approximately 10(7) library of LAP variants was displayed on the surface of yeast cells, labeled by LplA with either lipoic acid or bromoalkanoic acid, and the most efficiently labeled LAP clones were isolated by fluorescence activated cell sorting. Four rounds of evolution followed by additional rational mutagenesis produced a "LAP2" sequence with a k(cat)/K(m) of 0.99 muM(-1) min(-1), >70-fold better than our previous rationally designed 22-amino acid LAP1 sequence (Nat. Biotechnol. 2007, 25, 1483-1487), and only 8-fold worse than the k(cat)/K(m) values of natural lipoate and biotin acceptor proteins. The kinetic improvement over LAP1 allowed us to rapidly label cell surface peptide-fused receptors with quantum dots.
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Affiliation(s)
- Sujiet Puthenveetil
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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12
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Malki-Feldman L, Jaffe CL. Leishmania major: Effect of protein kinase A and phosphodiesterase activity on infectivity and proliferation of promastigotes. Exp Parasitol 2009; 123:39-44. [DOI: 10.1016/j.exppara.2009.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 04/30/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022]
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13
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Pinkse MWH, Rijkers DTS, Dostmann WR, Heck AJR. Mode of action of cGMP-dependent protein kinase-specific inhibitors probed by photoaffinity cross-linking mass spectrometry. J Biol Chem 2009; 284:16354-16368. [PMID: 19369251 DOI: 10.1074/jbc.m808521200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The inhibitor peptide DT-2 (YGRKKRRQRRRPPLRKKKKKH) is the most potent and selective inhibitor of the cGMP-dependent protein kinase (PKG) known today. DT-2 is a construct of a PKG tight binding sequence (W45, LRKKKKKH, KI=0.8 microM) and a membrane translocating sequence (DT-6, YGRKKRRQRRRPP, KI=1.1 microM), that combined strongly inhibits PKG catalyzed phosphorylation (KI=12.5 nM) with approximately 1000-fold selectivity toward PKG over protein kinase A, the closest relative of PKG. However, the molecular mechanism behind this inhibition is not entirely understood. Using a combination of photoaffinity labeling, stable isotope labeling, and mass spectrometry, we have located the binding sites of PKG-specific substrate and inhibitor peptides. Covalent linkage of a PKG-specific substrate analogue was localized in the catalytic core on residues 356-372, also known as the glycine-rich loop, essential for ATP binding. By analogy, the individual inhibitor peptides W45 and DT-6 were also found to cross-link near the glycine-rich loop, suggesting these are both substrate competitive inhibitors. A bifunctional photoreactive analogue of DT-2 was found to generate dimers of PKG. This cross-linking induced covalent PKG dimerization was not observed for an N-terminal deletion mutant of PKG, which lacks the dimerization domain. In addition, non-covalent mass spectrometry was used to determine binding stoichiometry and binding order of the inhibitor peptides. Dimeric PKG binds two W45 and DT-6 peptides, whereas only one DT-2 molecule was observed to bind to the dimeric PKG. Taken together, these findings imply that (i) the two individual components making up DT-2 are both targeted against the substrate-binding site and (ii) binding of a single DT-2 molecule inactivates both PKG monomers simultaneously, which is an indication that (iii) in cGMP-activated PKG the catalytic centers of both subunits may be in each other's proximity.
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Affiliation(s)
- Martijn W H Pinkse
- From the Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnnelaan 16, Utrecht 3584 CA, The Netherlands; Department of Biotechnology, Delft, University of Technology, Delft 2628 BC, The Netherlands
| | - Dirk T S Rijkers
- Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht 3584 CA, The Netherlands
| | - Wolfgang R Dostmann
- Department of Pharmacology, College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Albert J R Heck
- From the Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnnelaan 16, Utrecht 3584 CA, The Netherlands.
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14
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Asano J, Niisato N, Nakajima KI, Miyazaki H, Yasuda M, Iwasaki Y, Hama T, Dejima K, Hisa Y, Marunaka Y. Quercetin stimulates Na+/K+/2Cl- cotransport via PTK-dependent mechanisms in human airway epithelium. Am J Respir Cell Mol Biol 2009; 41:688-95. [PMID: 19251944 DOI: 10.1165/rcmb.2008-0338oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We investigated regulatory mechanisms of Cl(-) secretion playing an essential role in the maintenance of surface fluid in human airway epithelial Calu-3 cells. The present study reports that quercetin (a flavonoid) stimulated bumetanide-sensitive Cl(-) secretion with reduction of apical Cl(-) conductance, suggesting that quercetin stimulates Cl(-) secretion by activating an entry step of Cl(-) across the basolateral membrane through Na(+)/K(+)/2Cl(-) cotransporter (NKCC1). To clarify the mechanism stimulating NKCC1 by quercetin, we verified involvement of protein kinase (PK)A, PKC, protein tyrosine kinase (PTK), and cytosolic Ca(2+)-dependent pathways. A PKA inhibitor (PKI-14-22 amide), a PKC inhibitor (Gö 6983) or a Ca(2+) chelating agent did not affect the quercetin-stimulated Cl(-) secretion. On the other hand, a PTK inhibitor (AG18) significantly diminished the stimulatory action of quercetin on Cl(-) secretion without inhibitory effects on apical Cl(-) conductance, suggesting that a PTK-mediated pathway is involved in the stimulatory action of quercetin. The quercetin action on Cl(-) secretion was suppressed with brefeldin A (BFA, an inhibitor of vesicular transport from ER to Golgi), and the BFA-sensitive Cl(-) secretion was not observed in the presence of an epidermal growth factor receptor (EGFR) kinase inhibitor (AG1478), suggesting that quercetin stimulates Cl(-) secretion by causing the EGFR kinase-mediated translocation of NKCC1 or an NKC1-activating factor to the basolateral membrane in human airway epithelial Calu-3 cells. However, the surface density of NKCC1 was not increased by quercetin, but quercetin elevated the activity of NKCC1. These observations indicate that quercetin stimulates Cl(-) secretion by activating NKCC1 via translocation of an NKCC1-activating factor through an EGFR kinase-dependent pathway.
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Affiliation(s)
- Junji Asano
- Department of Molecular Cell Physiology, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
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15
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Abstract
Pharmaceutical companies are facing an increasing interest in new target identification and validation. In particular, extensive efforts are being made in the field of protein kinase inhibitors research and development, and the past ten years of effort in this field have altered our perception of the potential of kinases as drug targets. Therefore, in the drug discovery process, the selection of relevant, susceptible protein kinase targets combined with searches for leads and candidates have become a crucial approach. The success of recent launches of protein kinase inhibitors (Gleevec, Imatinib, Sutent, Iressa, Nexavar, Sprycel) gave another push to this field. Numerous other kinase inhibitors are currently undergoing clinical trials or clinical development. Some questions are nevertheless unanswered, mostly related to the great number of known kinases in the human genome, to their similarity with each other, to the existence of functionally redundant kinases for specific pathways, and also because the connection between particular pathways and diseases is not always clear. The review is leading the reader through a panoramic view of protein kinase inhibition with a major focus on MAPK, successful examples and clinical candidates.
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Affiliation(s)
- Simona Margutti
- Institute of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry; Eberhard Karls University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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Alverdi V, Mazon H, Versluis C, Hemrika W, Esposito G, van den Heuvel R, Scholten A, Heck AJR. cGMP-binding prepares PKG for substrate binding by disclosing the C-terminal domain. J Mol Biol 2007; 375:1380-93. [PMID: 18082764 DOI: 10.1016/j.jmb.2007.11.053] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Revised: 10/23/2007] [Accepted: 11/15/2007] [Indexed: 10/22/2022]
Abstract
Type I cyclic guanosine 3',5'-monophosphate (cGMP)-dependent protein kinase (PKG) is involved in the nitric oxide/cGMP signaling pathway. PKG has been identified in many different species, ranging from unicelölular organisms to mammals. The enzyme serves as one of the major receptor proteins for intracellular cGMP and controls a variety of cellular responses, ranging from smooth-muscle relaxation to neuronal synaptic plasticity. In the absence of a crystal structure, the three-dimensional structure of the homodimeric 152-kDa kinase PKG is unknown; however, there is evidence that the kinase adopts a distinct cGMP-dependent active conformation when compared to the inactive conformation. We performed mass-spectrometry-based hydrogen/deuterium exchange experiments to obtain detailed information on the structural changes in PKG I alpha induced by cGMP activation. Site-specific exchange measurements confirmed that the autoinhibitory domain and the hinge region become more solvent exposed, whereas the cGMP-binding domains become more protected in holo-PKG (dimeric PKG saturated with four cGMP molecules bound). More surprisingly, our data revealed a specific disclosure of the substrate-binding region of holo-PKG, shedding new light into the kinase-activation process of PKG.
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Affiliation(s)
- Vera Alverdi
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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17
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Sharma V, Agnes RS, Lawrence DS. Deep quench: an expanded dynamic range for protein kinase sensors. J Am Chem Soc 2007; 129:2742-3. [PMID: 17305340 PMCID: PMC2517079 DOI: 10.1021/ja068280r] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vyas Sharma
- Department of Biochemistry, The Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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18
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Branham MT, Mayorga LS, Tomes CN. Calcium-induced acrosomal exocytosis requires cAMP acting through a protein kinase A-independent, Epac-mediated pathway. J Biol Chem 2006; 281:8656-66. [PMID: 16407249 DOI: 10.1074/jbc.m508854200] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Epac, a guanine nucleotide exchange factor for the small GTPase Rap, binds to and is activated by the second messenger cAMP. In sperm, there are a number of signaling pathways required to achieve egg-fertilizing ability that depend upon an intracellular rise of cAMP. Most of these processes were thought to be mediated by cAMP-dependent protein kinases. Here we report a new dependence for the cAMP-induced acrosome reaction involving Epac. The acrosome reaction is a specialized type of regulated exocytosis leading to a massive fusion between the outer acrosomal and the plasma membranes of sperm cells. Ca2+ is the archetypical trigger of regulated exocytosis, and we show here that its effects on acrosomal release are fully mediated by cAMP. Ca2+ failed to trigger acrosomal exocytosis when intracellular cAMP was depleted by an exogenously added phosphodiesterase or when Epac was sequestered by specific blocking antibodies. The nondiscriminating dibutyryl-cAMP and the Epac-selective 8-(p-chlorophenylthio)-2'-O-methyladenosine-3',5'-cyclic monophosphate analogues triggered the acrosome reaction in the effective absence of extracellular Ca2+. This indicates that cAMP, via Epac activation, has the ability to drive the whole cascade of events necessary to bring exocytosis to completion, including tethering and docking of the acrosome to the plasma membrane, priming of the fusion machinery, mobilization of intravesicular Ca2+, and ultimately, bilayer mixing and fusion. cAMP-elicited exocytosis was sensitive to anti-alpha-SNAP, anti-NSF, and anti-Rab3A antibodies, to intra-acrosomal Ca2+ chelators, and to botulinum toxins but was resistant to cAMP-dependent protein kinase blockers. These experiments thus identify Epac in human sperm and evince its indispensable role downstream of Ca2+ in exocytosis.
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Affiliation(s)
- María T Branham
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Médicas, CC 56, Universidad Nacional de Cuyo, Mendoza 5500, Argentina
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19
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Chen X, Ye H, Kuruvilla R, Ramanan N, Scangos KW, Zhang C, Johnson NM, England PM, Shokat KM, Ginty DD. A chemical-genetic approach to studying neurotrophin signaling. Neuron 2005; 46:13-21. [PMID: 15820690 DOI: 10.1016/j.neuron.2005.03.009] [Citation(s) in RCA: 186] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Revised: 02/07/2005] [Accepted: 03/10/2005] [Indexed: 10/25/2022]
Abstract
Trk tyrosine kinases are receptors for members of the neurotrophin family and are crucial for growth and survival of specific populations of neurons. Yet, the functions of neurotrophin-Trk signaling in postnatal development as well as maintenance and plasticity of the adult nervous system are less clear. We report here the generation of mice harboring Trk knockin alleles that allow for pharmacological control of Trk kinase activity. Nanomolar concentrations of either 1NMPP1 or 1NaPP1, derivatives of the general kinase inhibitor PP1, inhibit NGF and BDNF signaling in TrkA(F592A) and TrkB(F616A) neurons, respectively, while no such Trk inhibition is observed in wild-type neurons. Moreover, oral administration of 1NMPP1 leads to specific inhibition of TrkA(F592A), TrkB(F616A), and TrkC(F167A) signaling in vivo. Thus, Trk knockin mice provide valuable tools for selective, rapid, and reversible inhibition of neurotrophin signaling in vitro and in vivo.
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Affiliation(s)
- Xi Chen
- Department of Neuroscience, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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20
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Taylor MK, Ahmed R, Begley M, Uhler MD. Autoinhibition and isoform-specific dominant negative inhibition of the type II cGMP-dependent protein kinase. J Biol Chem 2002; 277:37242-53. [PMID: 12093798 DOI: 10.1074/jbc.m202060200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the absence of cyclic nucleotides, the cAMP-dependent protein kinase and cGMP-dependent protein kinases (cGKs) suppress phosphotransfer activity at the catalytic cleft by competitive inhibition of substrate binding with a pseudosubstrate sequence within the holoenzyme. The magnitude of inhibition can be diminished by autophosphorylation near this pseudosubstrate sequence. Activation of type I cGK (cGKI) and type II cGK (cGKII) are differentially regulated by their cyclic nucleotide-binding sites. To address the possibility that the distinct activation mechanisms of cGKII and cGKI result from differences in the autophosphorylation of the inhibitory domain, we investigated the effects of autophosphorylation on the kinetics of activation. Unlike the type I cGKs (cGKIalpha and Ibeta), cGKII autophosphorylation did not alter the basal activity, nor the sensitivity of the enzyme to cyclic nucleotide activation. To determine residues responsible for autoinhibition of cGKII, Ala was substituted for basic residues (Lys(122), Arg(118), and Arg(119)) or a hydrophobic residue (Val(125)) within the putative pseudosubstrate domain of cGKII. The integrity of these residues was essential for full cGKII autoinhibition. Furthermore, a cGKII truncation mutant containing this autoinhibitory region demonstrated a nanomolar IC(50) toward a constitutively active form of cGKII. Finally, we present evidence that the dominant negative properties of this truncation mutant are specific to cGKII when compared with cAMP-dependent protein kinase Calpha and cGKIbeta. These findings extend the known differences in the activation mechanisms among cGK isoforms and allow the design of an isoform-specific cGKII inhibitor.
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Affiliation(s)
- Merritt K Taylor
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan 48104, USA
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21
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Scott JW, Norman DG, Hawley SA, Kontogiannis L, Hardie DG. Protein kinase substrate recognition studied using the recombinant catalytic domain of AMP-activated protein kinase and a model substrate. J Mol Biol 2002; 317:309-23. [PMID: 11902845 DOI: 10.1006/jmbi.2001.5316] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have expressed a truncated form of the alpha1 kinase domain of AMP-activated protein kinase (AMPK) in Escherichia coli as a glutathione-S-transferase fusion (GST-KD). A T172D mutant version did not require prior phosphorylation and was utilized for most subsequent studies. We have also created a recombinant substrate (GST-ACC) by expressing 34 residues around the major phosphorylation site (Ser79) on rat acetyl-CoA carboxylase-1/alpha (ACC1) as a GST fusion. This was an excellent substrate that was phosphorylated with similar kinetic parameters to ACC1 by both native AMPK and the bacterially expressed kinase domain. We also constructed a structural model for the binding of the ACC1 sequence to the kinase domain, based on crystal structures for related protein kinases. The model was tested by making a total of 25 mutants of GST-ACC and seven mutants of GST-KD, and measuring kinetic parameters with different combinations. The results reveal that AMPK and ACC1 interact over a much wider region than previously realized (>20 residues). The features of the interaction can be summarised as follows: (i) an amphipathic helix from P-16 to P-5 on the substrate binds in a hydrophobic groove on the large lobe of the kinase; (ii) basic residues at P-6 and P-4 bind to two acidic patches (D215/D216/D217 and E103/D100/E143, respectively), on the large lobe; (iii) a histidine at P+3 interacts with D56 on the small lobe; (iv) the side-chain of P+4 leucine could not be precisely positioned, but a new finding was that asparagine or glutamine could replace a hydrophobic residue at this position. These interactions position the serine residue to be phosphorylated in close proximity to the gamma-phosphate group of ATP. Although based on modelling rather than a determined structure, this represents one of the most detailed studies of the interaction between a kinase and its substrate achieved to date.
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Affiliation(s)
- John W Scott
- Division of Molecular Physiology, School of Life Sciences and Wellcome Trust Biocentre, Dundee University, Scotland, UK
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22
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Dostmann WRG, Tegge W, Frank R, Nickl CK, Taylor MS, Brayden JE. Exploring the mechanisms of vascular smooth muscle tone with highly specific, membrane-permeable inhibitors of cyclic GMP-dependent protein kinase Ialpha. Pharmacol Ther 2002; 93:203-15. [PMID: 12191612 DOI: 10.1016/s0163-7258(02)00189-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural similarity of cyclic GMP-dependent protein kinase (cGPK) and cyclic AMP-dependent protein kinase (cAPK) has made it difficult to study cGPK pathways independent of those mediated by cAPK, primarily due to the lack of potent and selective cGPK inhibitors. We recently reported a novel peptide library screen specifically designed to select for tight-binding peptides that identified selective inhibitors of cGPK [Proc Natl Acad Sci USA, 97 (2000) 14772]. Iterative deconvolution of octameric library arrays on paper identified the sequence LRK(5)H (W45). Binding of W45 to cGPK resulted in selective inhibition of the kinase, with K(i) values of 0.8 microM and 560 microM for cGPK and cAPK, respectively. Cellular internalization of highly charged W45 was accomplished by N-terminal fusion of membrane translocation sequences from either the human immunodeficiency virus tyrosine aminotransferase protein (47-59) DT-2 or from the Drosophila Antennapedia homeodomain (43-58) DT-3, respectively. For both fusion peptides, DT-2 and DT-3, we observed a potentiating effect with respect to the inhibitory potency, with K(i) values 40- to 80-fold lower than W45. Fluorescein-labeled DT-2 and DT-3 demonstrated rapid translocation through the cytosol and nuclei in a time-dependent manner using cultured cells and intact tissue samples (cerebral arteries). The physiological effects of DT-2 and DT-3 as selective cGPK inhibitors in smooth muscle were studied in small intact arteries. Nitric oxide, a cyclic GMP/cGPK activator, elicited a concentration-dependent dilation of isolated rat cerebral arteries, which was markedly inhibited by DT-2 and DT-3. Collectively, these results indicate that DT-2 and DT-3 effectively inhibit nitric oxide-induced vasodilation, further emphasizing the central role for cGPK in the modulation of vascular contractility.
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Affiliation(s)
- Wolfgang R G Dostmann
- Department of Pharmacology, University of Vermont, College of Medicine, Given Building, 89 Beaumont Avenue, Burlington, VT 05405, USA.
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23
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Affiliation(s)
- J A Adams
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0506, USA.
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24
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Layne J, Yip S, Crook RB. Down-regulation of Na-K-Cl cotransport by protein kinase C is mediated by protein phosphatase 1 in pigmented ciliary epithelial cells. Exp Eye Res 2001; 72:371-9. [PMID: 11273665 DOI: 10.1006/exer.2000.0966] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The role of protein phosphatases in the regulation of Na-K-Cl cotransport was examined in human pigmented ciliary epithelial (PE) cells. Both a 37 kDa form and a 72 kDa form of protein phosphatase 1 (PP1) could be immunologically detected. The protein phosphatase inhibitor calyculin A stimulated Na-K-Cl cotransport by 89 +/- 12% at 10 n M, whereas okadaic acid had no effect at concentrations less than 100 n M. Calyculin A had no significant effect on either Na-K ATPase or ouabain-insensitive, bumetanide-insensitive 86Rb+uptake. These data suggest that PP1 plays a role in the inhibition of Na-K-Cl cotransport in PE cells. Treatment of cells with phorbol 12-myristate, 13-acetate (PMA), a protein kinase C (PKC) activator caused an 82% inhibition of Na-K-Cl cotransport. When cells were first treated for 5 min with PMA, 10 n M calyculin A stimulated Na-K-Cl cotransport by 53% compared to 101% by calyculin A alone. Treatment of cells with PMA after stimulation of Na-K-Cl cotransport by calyculin A resulted in a prompt 56% drop in cotransport activity. These data suggest that maximal inhibition of Na-K-Cl cotransport by PKC requires PP1 activity, but that a part of PKCs inhibitory effect is independent of PP1. The effect of PKC activation on PP1 was further examined by determining PP1 activity in cells pretreated with PMA. PP1 activity increased 38+/-8% in cells exposed to 1 microM PMA for 5 min. This stimulation was blocked by 100 n M staurosporine or 1 microM bisindolylmaleimide, two PKC inhibitors. An isomer which does not activate PKC (4 alpha phorbol didecanoate), did not stimulate PP1 activity. Thus PKC activation leads to an increase in PP1 activity in PE cells. Pretreatment of cells with the protein kinase A (PKA) inhibitor PHI 14-22 resulted in a partial reduction in calyculin A stimulation of cotransport, suggesting that PP1 and PKA function in a kinase-phosphatase regulatory loop. To determine whether other protein kinases might also be involved, several protein kinase inhibitors were tested, including KT5823 (protein kinase G, type II-specific), KN62 (calmodulin activated kinase-specific) and ML7 (myosin light chain kinase-specific). None prevented activation of Na-K-Cl cotransport by calyculin A, suggesting that these kinases are not involved in the activation of Na-K-Cl cotransport.
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Affiliation(s)
- J Layne
- Beckman Vision Center, Box 0730, University of California, San Francisco, San Francisco, CA 94143, USA
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25
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Dostmann WR, Taylor MS, Nickl CK, Brayden JE, Frank R, Tegge WJ. Highly specific, membrane-permeant peptide blockers of cGMP-dependent protein kinase Ialpha inhibit NO-induced cerebral dilation. Proc Natl Acad Sci U S A 2000; 97:14772-7. [PMID: 11121077 PMCID: PMC18994 DOI: 10.1073/pnas.97.26.14772] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arrays of octameric peptide libraries on cellulose paper were screened by using (32)P-autophosphorylated cGMP-dependent protein kinase Ialpha (cGPK) to identify peptide sequences with high binding affinity for cGPK. Iterative deconvolution of every amino acid position in the peptides identified the sequence LRK(5)H (W45) as having the highest binding affinity. Binding of W45 to cGPK resulted in selective inhibition of the kinase with K(i) values of 0.8 microM and 560 microM for cGPK and cAMP-dependent protein kinase (cAPK), respectively. Fusion of W45 to membrane translocation signals from HIV-1 tat protein (YGRKKRRQRRRPP-LRK(5)H, DT-2) or Drosophila Antennapedia homeo-domain (RQIKIWFQNRRMKWKK-LRK(5)H, DT-3) proved to be an efficient method for intracellular delivery of these highly charged peptides. Rapid translocation of the peptides into intact cerebral arteries was demonstrated by using fluorescein-labeled DT-2 and DT-3. The inhibitory potency of the fusion peptides was even greater than that for W45, with K(i) values of 12.5 nM and 25 nM for DT-2 and DT-3, respectively. Both peptides were still poor inhibitors of cAPK. Selective inhibition of cGPK by DT-2 or DT-3 in the presence of cAPK was demonstrated in vitro. In pressurized cerebral arteries, DT-2 and DT-3 substantially decreased NO-induced dilation. This study provides functional characterization of a class of selective cGPK inhibitor peptides in vascular smooth muscle and reveals a central role for cGPK in the modulation of vascular contractility.
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Affiliation(s)
- W R Dostmann
- Department of Pharmacology, Department of Molecular Physiology and Biophysics, University of Vermont, College of Medicine, Burlington, VT 05405-0068, USA.
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26
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Ni Q, Shaffer J, Adams JA. Insights into nucleotide binding in protein kinase A using fluorescent adenosine derivatives. Protein Sci 2000; 9:1818-27. [PMID: 11045627 PMCID: PMC2144695 DOI: 10.1110/ps.9.9.1818] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The binding of the methylanthraniloyl derivatives of ATP (mant-ATP), ADP (mant-ADP), 2'deoxyATP (mant-2'deoxyATP), and 3'deoxyATP (mant-3'deoxyATP) to the catalytic subunit of protein kinase A was studied to gain insights into the mechanism of nucleotide binding. The binding of the mant nucleotides leads to a large increase in fluorescence energy transfer at 440 nm, allowing direct measurements of nucleotide affinity. The dissociation constant of mant-ADP is identical to that for ADP, while that for mant-ATP is approximately threefold higher than that for ATP. The dissociation constant for mant-3'deoxyATP is approximately fivefold higher than that for 3'deoxyATP while derivatization of 2'deoxyATP does not affect affinity. The time-dependent binding of mant-ATP, mant-2'deoxyATP, and mant-ADP, measured using stopped-flow fluorescence spectroscopy, is best fit to three exponentials. The fast phase is ligand dependent, while the two slower phases are ligand independent. The slower phases are similar but not identical in rate, and have opposite fluorescence amplitudes. Both isomers of mant-ATP are equivalent substrates, as judged by reversed-phase chromatography, although the rate of phosphorylation is approximately 20-fold lower than the natural nucleotide. The kinetic data are consistent with a three-step binding mechanism in which initial association of the nucleotide derivatives produces a highly fluorescent complex. Either one or two conformational changes can occur after the formation of this binary species, but one of the isomerized forms must have low fluorescence compared to the initial binary complex. These data soundly attest to the structural plasticity within the kinase core that may be essential for catalysis. Overall, the mant nucleotides present a useful reporter system for gauging these conformational changes in light of the prevailing three-dimensional models for the enzyme.
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Affiliation(s)
- Q Ni
- Department of Pharmacology, University of California, San Diego, La Jolla 92093-0506, USA
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27
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Dostmann WR, Nickl C, Thiel S, Tsigelny I, Frank R, Tegge WJ. Delineation of selective cyclic GMP-dependent protein kinase Ialpha substrate and inhibitor peptides based on combinatorial peptide libraries on paper. Pharmacol Ther 1999; 82:373-87. [PMID: 10454213 DOI: 10.1016/s0163-7258(98)00063-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Peptide libraries on cellulose paper have proven to be valuable tools for the a priori determination of substrate specificities of cyclic AMP- and cyclic GMP-dependent protein kinases (cAMP-kinase and cGMP-kinase) on the basis of octa-peptide sequences. Here, we report the extension of our peptide library screens to 12-mer and 14-mer peptide sequences, resulting in highly cGMP-kinase Ialpha selective peptides. The sequences TQAKRKKSLAMA-amide and TQAKRKKSLAMFLR-amide, with Km values for cGMP-kinase Ialpha of 0.7 and 0.26 microM and Vmax values of 11.5 and 10.9 micromol/min/mg, respectively, display a high specificity for this enzyme. Furthermore, replacing the phosphate acceptor residue serine with alanine in TQAKRKKSLAMA-amide resulted in the highly cGMP-kinase Ialpha selective inhibitor peptide TQAKRKKALAMA-amide, with inhibitor constants for cGMP-kinase Ialpha and cAMP-kinase of 7.5 microM and 750 microM, respectively. Selective cGMP-kinase inhibitors have the potential to play an important role in the elucidation of the distinct cellular functions of cGMP-kinase separate from those activated by cAMP-kinases, and, therefore, may play an important role as pharmaceutical targets. Molecular docking experiments of the most cGMP-kinase selective sequences on a molecular model of the catalytic domain of cGMP-kinase Ialpha suggest that they adopt unique conformations, which differ significantly from those observed for the cAMP-kinase-specific inhibitor PKI(5-24). Our results suggest that despite their structural similarities, cAMP-kinase and cGMP-kinase use distinct peptide substrate and inhibitor conformations, which could account for their unique substrate specificities. These findings are further supported by cAMP- and cGMP-kinase-selective inhibitor analogs with (D)-Ala residues at the inhibitory positions.
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Affiliation(s)
- W R Dostmann
- Department of Pharmacology, University of Vermont, College of Medicine, Burlington 05405, USA
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28
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Pfeifer A, Ruth P, Dostmann W, Sausbier M, Klatt P, Hofmann F. Structure and function of cGMP-dependent protein kinases. Rev Physiol Biochem Pharmacol 1999; 135:105-49. [PMID: 9932482 DOI: 10.1007/bfb0033671] [Citation(s) in RCA: 154] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- A Pfeifer
- Institut für Pharmakologie und Toxikologie der TU, München, Germany
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29
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Zhao J, Trewhella J, Corbin J, Francis S, Mitchell R, Brushia R, Walsh D. Progressive cyclic nucleotide-induced conformational changes in the cGMP-dependent protein kinase studied by small angle X-ray scattering in solution. J Biol Chem 1997; 272:31929-36. [PMID: 9395542 DOI: 10.1074/jbc.272.50.31929] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Small angle scattering data from bovine lung type Ialpha cGMP-dependent protein kinase (PKG) in the absence of cGMP show the protein to have a highly asymmetric structure with a radius of gyration (Rg) of 45 A and a maximum linear dimension (dmax) of 165 A. The addition of cGMP induces a marked conformational change in PKG. The Rg and dmax increase 25-30%, and the protein's mass moves further away from the center of mass; this results in an even more asymmetric structure. Fourier transform infrared spectroscopy data suggest that the conformational change induced by cGMP binding is primarily due to a topographical movement of the structural domains of PKG rather than to secondary structural changes within one or more of the individual domains. Each monomer of the dimeric PKG contains one high and one low affinity cGMP-binding site. A prominent increase in the asymmetry of PKG occurs with binding to high affinity cGMP-binding sites alone, but the full domain movements require the binding to both sets of sites. These conformational changes occurring in PKG with the progressive binding of cGMP to both sets of cGMP-binding sites correlate with past data, which have indicated that cGMP binding to both sets of sites is required for the full activation of the enzyme. These results provide the first quantitative measurement of the overall PKG structure, as well as an assessment of the structural events that accompany the activation of a protein kinase upon binding a small molecular weight ligand.
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Affiliation(s)
- J Zhao
- Chemical Science and Technology Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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30
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Kumar P, Van Patten SM, Walsh DA. Multiplicity of the beta form of the cAMP-dependent protein kinase inhibitor protein generated by post-translational modification and alternate translational initiation. J Biol Chem 1997; 272:20011-20. [PMID: 9242671 DOI: 10.1074/jbc.272.32.20011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Two distinct species of the thermostable inhibitor of the cAMP-dependent protein kinase, PKIalpha and PKIbeta, exist that are the products of separate genes. The PKIbeta form, as first isolated from rat testis, is a 70-amino acid protein, but the genomic sequence suggested that an alternate form might exist, arising as a consequence of alternate translational initiation. This species, now termed PKIbeta-78, has been synthesized by bacterial expression, demonstrated to be equipotent with PKIbeta-70, and also now demonstrated to occur in vivo. By Western blot analyses, six additional species of PKIbeta are also evident in tissues. Two of these represent the phospho forms of PKIbeta-78 and PKIbeta-70. The other four represent phospho and dephospho forms of two higher molecular mass PKIbeta species. These latter forms are currently termed PKIbeta-X and PKIbeta-Y, awaiting the full elucidation of their molecular identity. In adult rat testis and cerebellum, PKIbeta-70, PKIbeta-X, and PKIbeta-Y constitute 39, 23, and 32% and 15, 29, and 54% of the total tissue levels, respectively. In adult rat testis, 35-42% of each of these three species is present as a monophospho form, whereas no phosphorylation of them is evident in cerebellum. PKIbeta-78 is present at much lower levels in both rat testis and cerebellum (approximately 6 and 2% of the total, respectively) and almost entirely as a monophospho species. PKIbeta-78, like PKIbeta-70, is a high affinity and specific inhibitor of the cAMP-dependent protein kinase. PKIbeta-Y and PKIbeta-X, in contrast, also significantly inhibit the cGMP-dependent protein kinase.
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Affiliation(s)
- P Kumar
- Department of Biological Chemistry, School of Medicine, University of California, Davis, California 95616, USA
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31
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Lew J, Coruh N, Tsigelny I, Garrod S, Taylor SS. Synergistic binding of nucleotides and inhibitors to cAMP-dependent protein kinase examined by acrylodan fluorescence spectroscopy. J Biol Chem 1997; 272:1507-13. [PMID: 8999821 DOI: 10.1074/jbc.272.3.1507] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have engineered an acrylodan-modified derivative of the catalytic subunit of cyclic AMP-dependent protein kinase (cAPK) whose fluorescence emission signal has allowed the synergistic binding between nucleotides and physiological inhibitors of cAPK to be examined (Whitehouse, S., and Walsh, D. A. (1983) J. Biol. Chem. 258, 3682-3692). In the presence of the regulatory subunit, RI, the affinity of cAPK for adenosine, ADP, AMPPNP (adenosine 5'-(beta, gamma-imino)triphosphate), or ATP was 5-, 50-, 120-, and 15,000-fold enhanced, while in the presence of the heat-stable inhibitor protein of cAPK (PKI), there was a 3-, 20-, 33-, and 2000-fold enhancement in the binding of these nucleotides, respectively. A short inhibitor peptide, PKI-(14-22), enhanced the binding of ADP to the same degree as did full-length PKI (20-fold) but, in contrast, did not significantly enhance the binding of ATP or AMPPNP. The full binding synergism between PKI and either ATP (2000-fold) or AMPPNP (33-fold) to cAPK could, however, be mimicked by a longer peptide, PKI-(5-24), suggesting that the PKI NH2 terminus (residues 5-13) is most likely critical. Since this region is remote from the ATP gamma-phosphate, the binding synergism must arise through an extended network communication mechanism between the PKI NH2 terminus and the ATP binding site.
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Affiliation(s)
- J Lew
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0654, USA
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Pinna LA, Ruzzene M. How do protein kinases recognize their substrates? BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1314:191-225. [PMID: 8982275 DOI: 10.1016/s0167-4889(96)00083-3] [Citation(s) in RCA: 342] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- L A Pinna
- Dipartimento di Chimica Biologica, Università di Padova, Italy.
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Ruth P, Kamm S, Nau U, Pfeifer A, Hofmann F. A cGMP kinase mutant with increased sensitivity to the protein kinase inhibitor peptide PKI(5-24). Biol Chem 1996; 377:513-20. [PMID: 8922286 DOI: 10.1515/bchm3.1996.377.7-8.513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Synthetic peptides corresponding to the active domain of the heat-stable inhibitor protein PKI are very potent inhibitors of cAMP-dependent protein kinase, but are extremely weak inhibitors of cGMP-dependent protein kinase. In this study, we tried to confer PKI sensitivity to cGMP kinase by site-directed mutagenesis. The molecular requirements for high affinity inhibition by PKI were deduced from the crystal structure of the cAMP kinase/PKI complex. A prominent site of interaction are residues Tyr235 and Phe239 in the catalytic subunit, which from a sandwich-like structure with Phe10 of the PKI(5-24) peptide. To increase the sensitivity for PKI, the cGMP kinase codons at the corresponding sites, Ser555 and Ser559, were changed to Tyr and Phe. The mutant cGMP kinase was stimulated half maximally by cGMP at 3-fold higher concentrations (240 nM) than the wild type (77 nM). Wild type and mutant cGMP kinase did not differ significantly in their Km and Vmax for three different substrate peptides. The PKI(5-24) peptide inhibited phosphotransferase activity of the mutant cGMP kinase with higher potency than that of wild type, with Ki values of 42 +/- .3 microM and 160 +/- .7 microM, respectively. The increased affinity of the mutant cGMP kinase was specific for the PKI(5-24) peptide. Mutation of the essential Phe10 in the PKI(5-24) sequence to an Ala yielded a peptide that inhibited mutant and wild type cGMP kinase with similar potency, with Ki values of 160 +/- 11 and 169 +/- 27 microM, respectively. These results suggest that the mutations Ser555Tyr and Ser559Phe are required, but not sufficient, for high affinity inhibition of cGMP kinase by PKI.
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Affiliation(s)
- P Ruth
- Institut für Pharmakologie und Toxikologie, Technischen Universität München, Germany
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Werner DS, Lee TR, Lawrence DS. Is protein kinase substrate efficacy a reliable barometer for successful inhibitor design? J Biol Chem 1996; 271:180-5. [PMID: 8550556 DOI: 10.1074/jbc.271.1.180] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have addressed the question of whether protein kinase substrate efficacy is a reliable barometer for successful inhibitor design by assessing the dependence of kcat and kcat/Km for eight separate alcohol-bearing residues on solvent viscosity. We have found that the Km for three structurally distinct primary alcohol-containing peptides overestimates the affinity that these species exhibit for the cAMP-dependent protein kinase. In all three cases, the rate-determining step is product release, and substrate binding is best described as rapid equilibrium. In contrast, peptides containing the following phosphorylatable residues all provide Km values that are accurate assessments of substrate affinity for the protein kinase: a secondary alcohol, a simple phenol, and a primary alcohol with a relatively long side chain. In the latter three instances, the rate-determining step is phosphoryl transfer. Finally, two aromatic alcohol-containing residues that possess lipophilic side chains exhibit Michaelis constants that underestimate enzyme affinity. These results demonstrate that while it may be tempting to employ structural elements from the most efficient substrates (e.g. primary alcohols) for inhibitor design, less effective substrates may serve as a more accurate assessment of inhibitory success.
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Affiliation(s)
- D S Werner
- Department of Chemistry, State University of New York, Buffalo 14260, USA
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