101
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Cui J, Zhu Q, Zhang H, Cianfrocco MA, Leschziner AE, Dixon JE, Xiao J. Structure of Fam20A reveals a pseudokinase featuring a unique disulfide pattern and inverted ATP-binding. eLife 2017; 6. [PMID: 28432788 PMCID: PMC5413348 DOI: 10.7554/elife.23990] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/20/2017] [Indexed: 12/19/2022] Open
Abstract
Mutations in FAM20A cause tooth enamel defects known as Amelogenesis Imperfecta (AI) and renal calcification. We previously showed that Fam20A is a secretory pathway pseudokinase and allosterically activates the physiological casein kinase Fam20C to phosphorylate secreted proteins important for biomineralization (Cui et al., 2015). Here we report the nucleotide-free and ATP-bound structures of Fam20A. Fam20A exhibits a distinct disulfide bond pattern mediated by a unique insertion region. Loss of this insertion due to abnormal mRNA splicing interferes with the structure and function of Fam20A, resulting in AI. Fam20A binds ATP in the absence of divalent cations, and strikingly, ATP is bound in an inverted orientation compared to other kinases. Fam20A forms a dimer in the crystal, and residues in the dimer interface are critical for Fam20C activation. Together, these results provide structural insights into the function of Fam20A and shed light on the mechanism by which Fam20A mutations cause disease. DOI:http://dx.doi.org/10.7554/eLife.23990.001
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Affiliation(s)
- Jixin Cui
- Department of Pharmacology, University of California, San Diego, United States
| | - Qinyu Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Hui Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Michael A Cianfrocco
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States
| | - Jack E Dixon
- Department of Pharmacology, University of California, San Diego, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, United States
| | - Junyu Xiao
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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102
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Murphy JM, Farhan H, Eyers PA. Bio-Zombie: the rise of pseudoenzymes in biology. Biochem Soc Trans 2017; 45:537-544. [PMID: 28408493 DOI: 10.1042/bst20160400] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/19/2017] [Accepted: 02/21/2017] [Indexed: 11/17/2022]
Abstract
Pseudoenzymes are catalytically dead counterparts of enzymes. Despite their first description some 50 years ago, the importance and functional diversity of these 'fit-for-purpose' polypeptides is only now being appreciated. Pseudoenzymes have been identified throughout all the kingdoms of life and, owing to predicted deficits in enzyme activity due to the absence of catalytic residues, have been variously referred to as pseudoenzymes, non-enzymes, dead enzymes, prozymes or 'zombie' proteins. An important goal of the recent Biochemical Society Pseudoenzymes-focused meeting was to explore the functional and evolutionary diversity of pseudoenzymes and to begin to evaluate their functions in biology, including cell signalling and metabolism. Here, we summarise the impressive breadth of enzyme classes that are known to have pseudoenzyme counterparts and present examples of known cellular functions. We predict that the next decades will represent golden years for the analysis of pseudoenzymes.
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Affiliation(s)
- James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Hesso Farhan
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
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103
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Kaufmann C, Motzkus M, Sauter M. Phosphorylation of the phytosulfokine peptide receptor PSKR1 controls receptor activity. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1411-1423. [PMID: 28338789 PMCID: PMC5441923 DOI: 10.1093/jxb/erx030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The phytosulfokine peptide receptor PSKR1 is modified by phosphorylation of its cytoplasmic kinase domain. We analyzed defined phosphorylation sites by site-directed mutagenesis with regard to kinase activity in vitro and receptor activity in planta. S696 and S698 in the juxtamembrane (JM) domain are phosphorylated in planta. The phosphomimetic S696D/S698D replacements resulted in reduced transphosphorylation activity of PSKR1 kinase in vitro but did not reduce autophosphorylation activity. Growth-promoting activity of the PSKR1(S696D/S698D) receptor isoform was impaired in the shoot but not in the root. The JM domain thus seems to be important for phosphorylation of a target protein required for shoot growth promotion. The phosphomimetic replacement T998D at the C-terminus (CT) abolished kinase activity in vitro but not receptor function in planta, indicating that additional levels of regulation exist in planta. A possible mode of receptor regulation is the interaction with regulatory proteins such as the calcium sensor calmodulin (CaM). We show that the previously reported binding of CaM2 to PSKR1 is calcium-dependent, occurs predominately to the hypophosphorylated soluble PSKR1 kinase, and does not significantly change PSKR1 kinase activity. In conclusion, our results show that peptide signaling of growth by PSKR1 is regulated by differential phosphorylation of the juxtamembrane and C-terminal domains of the intracellular receptor part and suggest that interaction of PSKR1 with CaM serves a function other than the regulation of kinase activity.
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Affiliation(s)
- Christine Kaufmann
- Entwicklungsbiologie und Physiologie der Pflanzen, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 5, 24118 Kiel, Germany
| | - Michael Motzkus
- Entwicklungsbiologie und Physiologie der Pflanzen, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 5, 24118 Kiel, Germany
| | - Margret Sauter
- Entwicklungsbiologie und Physiologie der Pflanzen, Christian-Albrechts-Universität Kiel, Am Botanischen Garten 5, 24118 Kiel, Germany
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104
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Abstract
The pseudokinase complement of the human kinase superfamily consists of approximately 60 signaling proteins, which lacks one or more of the amino acids typically required to correctly align ATP and metal ions, and phosphorylate protein substrates. Recent studies in the pseudokinase field have begun to expose the biological relevance of pseudokinases, which are now thought to perform a diverse range of physiological roles and are connected to a multitude of human diseases, including cancer. In this review, we discuss how and why members of the 'pseudokinome' represent important new targets for drug discovery, and describe how knowledge of protein structure and function provides informative clues to help guide the rational chemical design or repurposing of inhibitors to target pseudokinases.
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105
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Volkov OA, Kinch L, Ariagno C, Deng X, Zhong S, Grishin N, Tomchick DR, Chen Z, Phillips MA. Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog. eLife 2016; 5. [PMID: 27977001 PMCID: PMC5201418 DOI: 10.7554/elife.20198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 12/11/2016] [Indexed: 02/06/2023] Open
Abstract
Catalytically inactive enzyme paralogs occur in many genomes. Some regulate their active counterparts but the structural principles of this regulation remain largely unknown. We report X-ray structures of Trypanosoma brucei S-adenosylmethionine decarboxylase alone and in functional complex with its catalytically dead paralogous partner, prozyme. We show monomeric TbAdoMetDC is inactive because of autoinhibition by its N-terminal sequence. Heterodimerization with prozyme displaces this sequence from the active site through a complex mechanism involving a cis-to-trans proline isomerization, reorganization of a β-sheet, and insertion of the N-terminal α-helix into the heterodimer interface, leading to enzyme activation. We propose that the evolution of this intricate regulatory mechanism was facilitated by the acquisition of the dimerization domain, a single step that can in principle account for the divergence of regulatory schemes in the AdoMetDC enzyme family. These studies elucidate an allosteric mechanism in an enzyme and a plausible scheme by which such complex cooperativity evolved. DOI:http://dx.doi.org/10.7554/eLife.20198.001
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Affiliation(s)
- Oleg A Volkov
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Lisa Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carson Ariagno
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shihua Zhong
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nick Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute,University of Texas Southwestern Medical Center, Dallas, United States
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
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106
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Abstract
Pseudoenzymes are catalytically deficient variants of enzymes that are represented in all major enzyme families. Their regulatory functions in signalling pathways are shedding new light on the non-catalytic functions of active enzymes, and are suggesting new ways to target cellular signalling mechanisms with drugs.
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Affiliation(s)
- Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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107
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Dos Santos HG, Siltberg-Liberles J. Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family. Genome Biol Evol 2016; 8:2806-25. [PMID: 27519537 PMCID: PMC5630953 DOI: 10.1093/gbe/evw194] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/21/2022] Open
Abstract
One of the largest multigene families in Metazoa are the tyrosine kinases (TKs). These are important multifunctional proteins that have evolved as dynamic switches that perform tyrosine phosphorylation and other noncatalytic activities regulated by various allosteric mechanisms. TKs interact with each other and with other molecules, ultimately activating and inhibiting different signaling pathways. TKs are implicated in cancer and almost 30 FDA-approved TK inhibitors are available. However, specific binding is a challenge when targeting an active site that has been conserved in multiple protein paralogs for millions of years. A cassette domain (CD) containing SH3-SH2-Tyrosine Kinase domains reoccurs in vertebrate nonreceptor TKs. Although part of the CD function is shared between TKs, it also presents TK specific features. Here, the evolutionary dynamics of sequence, structure, and phosphorylation across the CD in 17 TK paralogs have been investigated in a large-scale study. We establish that TKs often have ortholog-specific structural disorder and phosphorylation patterns, while secondary structure elements, as expected, are highly conserved. Further, domain-specific differences are at play. Notably, we found the catalytic domain to fluctuate more in certain secondary structure elements than the regulatory domains. By elucidating how different properties evolve after gene duplications and which properties are specifically conserved within orthologs, the mechanistic understanding of protein evolution is enriched and regions supposedly critical for functional divergence across paralogs are highlighted.
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Affiliation(s)
- Helena G Dos Santos
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University
| | - Jessica Siltberg-Liberles
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University
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108
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Feldman HC, Tong M, Wang L, Meza-Acevedo R, Gobillot TA, Lebedev I, Gliedt MJ, Hari SB, Mitra AK, Backes BJ, Papa FR, Seeliger MA, Maly DJ. Structural and Functional Analysis of the Allosteric Inhibition of IRE1α with ATP-Competitive Ligands. ACS Chem Biol 2016; 11:2195-205. [PMID: 27227314 DOI: 10.1021/acschembio.5b00940] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The accumulation of unfolded proteins under endoplasmic reticulum (ER) stress leads to the activation of the multidomain protein sensor IRE1α as part of the unfolded protein response (UPR). Clustering of IRE1α lumenal domains in the presence of unfolded proteins promotes kinase trans-autophosphorylation in the cytosol and subsequent RNase domain activation. Interestingly, there is an allosteric relationship between the kinase and RNase domains of IRE1α, which allows ATP-competitive inhibitors to modulate the activity of the RNase domain. Here, we use kinase inhibitors to study how ATP-binding site conformation affects the activity of the RNase domain of IRE1α. We find that diverse ATP-competitive inhibitors of IRE1α promote dimerization and activation of RNase activity despite blocking kinase autophosphorylation. In contrast, a subset of ATP-competitive ligands, which we call KIRAs, allosterically inactivate the RNase domain through the kinase domain by stabilizing monomeric IRE1α. Further insight into how ATP-competitive inhibitors are able to divergently modulate the RNase domain through the kinase domain was gained by obtaining the first structure of apo human IRE1α in the RNase active back-to-back dimer conformation. Comparison of this structure with other existing structures of IRE1α and integration of our extensive structure activity relationship (SAR) data has led us to formulate a model to rationalize how ATP-binding site ligands are able to control the IRE1α oligomeric state and subsequent RNase domain activity.
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Affiliation(s)
- Hannah C. Feldman
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Michael Tong
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York, United States
| | - Likun Wang
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Diabetes
Center, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
- California
Institute for Quantitative Biosciences, University of California−San Francisco, San Francisco, California, United States
| | - Rosa Meza-Acevedo
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Diabetes
Center, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
- California
Institute for Quantitative Biosciences, University of California−San Francisco, San Francisco, California, United States
| | - Theodore A. Gobillot
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Ivan Lebedev
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York, United States
| | - Micah J. Gliedt
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
| | - Sanjay B. Hari
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Arinjay K. Mitra
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Bradley J. Backes
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
| | - Feroz R. Papa
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Diabetes
Center, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
- California
Institute for Quantitative Biosciences, University of California−San Francisco, San Francisco, California, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington, United States
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109
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Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, Jaeg-Ehret T, Minogue CE, Ulbrich A, Hutchins PD, Wilkerson EM, Ruan Z, Aydin D, Hebert AS, Guo X, Freiberger EC, Reutenauer L, Jochem A, Chergova M, Johnson IE, Lohman DC, Rush MJP, Kwiecien NW, Singh PK, Schlagowski AI, Floyd BJ, Forsman U, Sindelar PJ, Westphall MS, Pierrel F, Zoll J, Dal Peraro M, Kannan N, Bingman CA, Coon JJ, Isope P, Puccio H, Pagliarini DJ. Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity. Mol Cell 2016; 63:608-620. [PMID: 27499294 DOI: 10.1016/j.molcel.2016.06.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/27/2016] [Accepted: 06/21/2016] [Indexed: 10/21/2022]
Abstract
The UbiB protein kinase-like (PKL) family is widespread, comprising one-quarter of microbial PKLs and five human homologs, yet its biochemical activities remain obscure. COQ8A (ADCK3) is a mammalian UbiB protein associated with ubiquinone (CoQ) biosynthesis and an ataxia (ARCA2) through unclear means. We show that mice lacking COQ8A develop a slowly progressive cerebellar ataxia linked to Purkinje cell dysfunction and mild exercise intolerance, recapitulating ARCA2. Interspecies biochemical analyses show that COQ8A and yeast Coq8p specifically stabilize a CoQ biosynthesis complex through unorthodox PKL functions. Although COQ8 was predicted to be a protein kinase, we demonstrate that it lacks canonical protein kinase activity in trans. Instead, COQ8 has ATPase activity and interacts with lipid CoQ intermediates, functions that are likely conserved across all domains of life. Collectively, our results lend insight into the molecular activities of the ancient UbiB family and elucidate the biochemical underpinnings of a human disease.
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Affiliation(s)
- Jonathan A Stefely
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Floriana Licitra
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Leila Laredj
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Andrew G Reidenbach
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zachary A Kemmerer
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anais Grangeray
- Université de Strasbourg, 67081 Strasbourg, France; Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212, 67084 Strasbourg, France
| | - Tiphaine Jaeg-Ehret
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Catherine E Minogue
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arne Ulbrich
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul D Hutchins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Emily M Wilkerson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Deniz Aydin
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Alexander S Hebert
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiao Guo
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Elyse C Freiberger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Laurence Reutenauer
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Adam Jochem
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Maya Chergova
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Isabel E Johnson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Danielle C Lohman
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew J P Rush
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicholas W Kwiecien
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Pankaj K Singh
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France
| | - Anna I Schlagowski
- Fédération de Medicine Translationnelle de Strasbourg, EA3072, Faculté de Médicine et Faculté des Sciences du Sport, Université de Strasbourg, 67084 Strasbourg, France
| | - Brendan J Floyd
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ulrika Forsman
- University Grenoble Alpes, LCBM, UMR 5249, 38000 Grenoble, France
| | - Pavel J Sindelar
- University Grenoble Alpes, LCBM, UMR 5249, 38000 Grenoble, France; Laboratoire de Chimie des Processus Biologiques, CNRS UMR 8229, Collège de France, 75252 Paris, France
| | - Michael S Westphall
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fabien Pierrel
- University Grenoble Alpes, LCBM, UMR 5249, 38000 Grenoble, France; TIMC-IMAG, CNRS UMR 5525, UFR de Médecine, University Joseph Fourier, 38706 La Tronche, France
| | - Joffrey Zoll
- Fédération de Medicine Translationnelle de Strasbourg, EA3072, Faculté de Médicine et Faculté des Sciences du Sport, Université de Strasbourg, 67084 Strasbourg, France
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Philippe Isope
- Université de Strasbourg, 67081 Strasbourg, France; Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212, 67084 Strasbourg, France
| | - Hélène Puccio
- Département de Médecine Translationnelle et Neurogénétique, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596, CNRS UMR 7104, 67400 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France; Chaire de Génétique Humaine, Collège de France, 67404 Illkirch, France.
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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110
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cAMP-dependent protein kinase (PKA) complexes probed by complementary differential scanning fluorimetry and ion mobility-mass spectrometry. Biochem J 2016; 473:3159-75. [PMID: 27444646 PMCID: PMC5095912 DOI: 10.1042/bcj20160648] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022]
Abstract
cAMP-dependent protein kinase (PKA) is an archetypal biological signaling module and a model for understanding the regulation of protein kinases. In the present study, we combine biochemistry with differential scanning fluorimetry (DSF) and ion mobility–mass spectrometry (IM–MS) to evaluate effects of phosphorylation and structure on the ligand binding, dynamics and stability of components of heteromeric PKA protein complexes in vitro. We uncover dynamic, conformationally distinct populations of the PKA catalytic subunit with distinct structural stability and susceptibility to the physiological protein inhibitor PKI. Native MS of reconstituted PKA R2C2 holoenzymes reveals variable subunit stoichiometry and holoenzyme ablation by PKI binding. Finally, we find that although a ‘kinase-dead’ PKA catalytic domain cannot bind to ATP in solution, it interacts with several prominent chemical kinase inhibitors. These data demonstrate the combined power of IM–MS and DSF to probe PKA dynamics and regulation, techniques that can be employed to evaluate other protein-ligand complexes, with broad implications for cellular signaling.
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111
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Ivan T, Enkvist E, Viira B, Manoharan GB, Raidaru G, Pflug A, Alam KA, Zaccolo M, Engh RA, Uri A. Bifunctional Ligands for Inhibition of Tight-Binding Protein-Protein Interactions. Bioconjug Chem 2016; 27:1900-10. [PMID: 27389935 DOI: 10.1021/acs.bioconjchem.6b00293] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The acknowledged potential of small-molecule therapeutics targeting disease-related protein-protein interactions (PPIs) has promoted active research in this field. The strategy of using small molecule inhibitors (SMIs) to fight strong (tight-binding) PPIs tends to fall short due to the flat and wide interfaces of PPIs. Here we propose a biligand approach for disruption of strong PPIs. The potential of this approach was realized for disruption of the tight-binding (KD = 100 pM) tetrameric holoenzyme of cAMP-dependent protein kinase (PKA). Supported by X-ray analysis of cocrystals, bifunctional inhibitors (ARC-inhibitors) were constructed that simultaneously associated with both the ATP-pocket and the PPI interface area of the catalytic subunit of PKA (PKAc). Bifunctional inhibitor ARC-1411, possessing a KD value of 3 pM toward PKAc, induced the dissociation of the PKA holoenzyme with a low-nanomolar IC50, whereas the ATP-competitive inhibitor H89 bound to the PKA holoenzyme without disruption of the protein tetramer.
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Affiliation(s)
- Taavi Ivan
- Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia
| | - Birgit Viira
- Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia
| | | | - Gerda Raidaru
- Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia
| | - Alexander Pflug
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø , N-9019 Tromsø, Norway
| | - Kazi Asraful Alam
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø , N-9019 Tromsø, Norway
| | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics, University of Oxford , OX1 3QX Oxford, United Kingdom
| | - Richard Alan Engh
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø , N-9019 Tromsø, Norway
| | - Asko Uri
- Institute of Chemistry, University of Tartu , 50410 Tartu, Estonia
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