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Póti ÁL, Dénes L, Papp K, Bató C, Bánóczi Z, Reményi A, Alexa A. Phosphorylation-Assisted Luciferase Complementation Assay Designed to Monitor Kinase Activity and Kinase-Domain-Mediated Protein-Protein Binding. Int J Mol Sci 2023; 24:14854. [PMID: 37834301 PMCID: PMC10573712 DOI: 10.3390/ijms241914854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023] Open
Abstract
Protein kinases are key regulators of cell signaling and have been important therapeutic targets for three decades. ATP-competitive drugs directly inhibit the activity of kinases but these enzymes work as part of complex protein networks in which protein-protein interactions (often referred to as kinase docking) may govern a more complex activation pattern. Kinase docking is indispensable for many signaling disease-relevant Ser/Thr kinases and it is mediated by a dedicated surface groove on the kinase domain which is distinct from the substrate-binding pocket. Thus, interfering with kinase docking provides an alternative strategy to control kinases. We describe activity sensors developed for p90 ribosomal S6 kinase (RSK) and mitogen-activated protein kinases (MAPKs: ERK, p38, and JNK) whose substrate phosphorylation is known to depend on kinase-docking-groove-mediated protein-protein binding. The in vitro assays were based on fragment complementation of the NanoBit luciferase, which is facilitated upon substrate motif phosphorylation. The new phosphorylation-assisted luciferase complementation (PhALC) sensors are highly selective and the PhALC assay is a useful tool for the quantitative analysis of kinase activity or kinase docking, and even for high-throughput screening of academic compound collections.
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Affiliation(s)
- Ádám L. Póti
- Biomolecular Interactions Research Group, HUN-REN Research Center for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary
- Doctoral School of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Laura Dénes
- Biomolecular Interactions Research Group, HUN-REN Research Center for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary
| | - Kinga Papp
- Biomolecular Interactions Research Group, HUN-REN Research Center for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary
| | - Csaba Bató
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Attila Reményi
- Biomolecular Interactions Research Group, HUN-REN Research Center for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary
| | - Anita Alexa
- Biomolecular Interactions Research Group, HUN-REN Research Center for Natural Sciences, Institute of Organic Chemistry, 1117 Budapest, Hungary
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2
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Ghorbel M, Haddaji N, Feki K, Tounsi S, Chihaoui M, Alghamdi A, Mseddi K, Brini F. Identification of a putative kinase interacting domain in the durum wheat catalase 1 (TdCAT1) protein. Heliyon 2023; 9:e18916. [PMID: 37609422 PMCID: PMC10440534 DOI: 10.1016/j.heliyon.2023.e18916] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023] Open
Abstract
Catalases are crucial antioxidant enzymes that regulate plants responses to different biotic and abiotic stresses. It has been previously shown that the activities of durum wheat catalase proteins (TdCAT1) were stimulated in the presence of divalent cations Mn2+, Mg2+, Fe2+, Zn2+, and Ca2+. In addition, TdCAT1s can interact with calmodulins in calcium-independent manner, and this interaction stimulates its catalytic activity in a calcium-dependent manner. Moreover, this activity is further enhanced by Mn2+ cations. The current study showed that wheat catalase presents different phosphorylation targets. Besides, we demonstrated that catalase is able to interact with Mitogen Activated Proteins kinases via a conserved domain. This interaction activates wheat catalase independently of its phosphorylation status but is more promoted by Mn2+, Fe2+ and Ca2+ divalent cations. Interestingly, we have demonstrated that durum wheat catalase activity is differentially regulated by Mitogen Activated Proteins kinases and Calmodulins in the presence of calcium. Moreover, the V0 of the reaction increase gradually following the increasing quantities of Mn2+ divalent cations. Such results have never been described before and suggest i) complex regulatory mechanisms exerted on wheat catalase, ii) divalent cations (Mn2+; Mg2+; Ca2+ and Fe2+) act as key cofactors in these regulatory mechanisms.
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Affiliation(s)
- Mouna Ghorbel
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha'il City, 81451, Saudi Arabia
| | - Najla Haddaji
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha'il City, 81451, Saudi Arabia
| | - Kaouthar Feki
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax, 3018, Tunisia
| | - Sana Tounsi
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax, 3018, Tunisia
| | - Mejda Chihaoui
- Computer Science Departement, Applied College- University of Ha'il, P.O. Box 2440, Ha'il City, 81451, Saudi Arabia
| | - Ahmad Alghamdi
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha'il City, 81451, Saudi Arabia
| | - Khalil Mseddi
- Department of Biology, Faculty of Science of Sfax, University of Sfax, Sfax, 3000, Tunisia
| | - Faiçal Brini
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax, 3018, Tunisia
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3
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Bardwell L, Thorner J. Mitogen-activated protein kinase (MAPK) cascades-A yeast perspective. Enzymes 2023; 54:137-170. [PMID: 37945169 DOI: 10.1016/bs.enz.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Discovery of the class of protein kinase now dubbed a mitogen (or messenger)-activated protein kinase (MAPK) is an illustrative example of how disparate lines of investigation can converge and reveal an enzyme family universally conserved among eukaryotes, from single-celled microbes to humans. Moreover, elucidation of the circuitry controlling MAPK function defined a now overarching principle in enzyme regulation-the concept of an activation cascade mediated by sequential phosphorylation events. Particularly ground-breaking for this field of exploration were the contributions of genetic approaches conducted using several model organisms, but especially the budding yeast Saccharomyces cerevisiae. Notably, examination of how haploid yeast cells respond to their secreted peptide mating pheromones was crucial in pinpointing genes encoding MAPKs and their upstream activators. Fully contemporaneous biochemical analysis of the activities elicited upon stimulation of mammalian cells by insulin and other growth- and differentiation-inducing factors lead eventually to the demonstration that components homologous to those in yeast were involved. Continued studies of these pathways in yeast were integral to other foundational discoveries in MAPK signaling, including the roles of tethering, scaffolding and docking interactions.
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Affiliation(s)
- Lee Bardwell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, College of Letters and Science, University of California, Berkeley, Berkeley, CA, United States.
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4
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Sacerdoti M, Gross LZF, Riley AM, Zehnder K, Ghode A, Klinke S, Anand GS, Paris K, Winkel A, Herbrand AK, Godage HY, Cozier GE, Süß E, Schulze JO, Pastor-Flores D, Bollini M, Cappellari MV, Svergun D, Gräwert MA, Aramendia PF, Leroux AE, Potter BVL, Camacho CJ, Biondi RM. Modulation of the substrate specificity of the kinase PDK1 by distinct conformations of the full-length protein. Sci Signal 2023; 16:eadd3184. [PMID: 37311034 DOI: 10.1126/scisignal.add3184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 05/19/2023] [Indexed: 06/15/2023]
Abstract
The activation of at least 23 different mammalian kinases requires the phosphorylation of their hydrophobic motifs by the kinase PDK1. A linker connects the phosphoinositide-binding PH domain to the catalytic domain, which contains a docking site for substrates called the PIF pocket. Here, we used a chemical biology approach to show that PDK1 existed in equilibrium between at least three distinct conformations with differing substrate specificities. The inositol polyphosphate derivative HYG8 bound to the PH domain and disrupted PDK1 dimerization by stabilizing a monomeric conformation in which the PH domain associated with the catalytic domain and the PIF pocket was accessible. In the absence of lipids, HYG8 potently inhibited the phosphorylation of Akt (also termed PKB) but did not affect the intrinsic activity of PDK1 or the phosphorylation of SGK, which requires docking to the PIF pocket. In contrast, the small-molecule valsartan bound to the PIF pocket and stabilized a second distinct monomeric conformation. Our study reveals dynamic conformations of full-length PDK1 in which the location of the linker and the PH domain relative to the catalytic domain determines the selective phosphorylation of PDK1 substrates. The study further suggests new approaches for the design of drugs to selectively modulate signaling downstream of PDK1.
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Affiliation(s)
- Mariana Sacerdoti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Lissy Z F Gross
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Andrew M Riley
- Medicinal Chemistry and Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Karin Zehnder
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Abhijeet Ghode
- Biological Sciences, National University of Singapore, Singapore 119077, Singapore
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires C1405BWE, Argentina
| | - Ganesh Srinivasan Anand
- Biological Sciences, National University of Singapore, Singapore 119077, Singapore
- Department of Chemistry, Huck Institutes of the Life Sciences, Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802, USA
| | - Kristina Paris
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Statistics, University of Pittsburgh, WWPH 1821, Pittsburgh, PA 15213, USA
| | - Angelika Winkel
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Amanda K Herbrand
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - H Yasmin Godage
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Gyles E Cozier
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Evelyn Süß
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Jörg O Schulze
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Daniel Pastor-Flores
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- KBI Biopharma, Technologielaan 8, B-3001 Leuven, Belgium
| | - Mariela Bollini
- Centro de Investigaciones en Bionanociencias 'Elizabeth Jares-Erijman' CIBION, CONICET, Buenos Aires C1425FQD, Argentina
| | - María Victoria Cappellari
- Centro de Investigaciones en Bionanociencias 'Elizabeth Jares-Erijman' CIBION, CONICET, Buenos Aires C1425FQD, Argentina
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
| | - Melissa A Gräwert
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, 22607 Hamburg, Germany
| | - Pedro F Aramendia
- Centro de Investigaciones en Bionanociencias 'Elizabeth Jares-Erijman' CIBION, CONICET, Buenos Aires C1425FQD, Argentina
- Departamento de Química Inorgánica, Analítica y Química Física, FCEN, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
| | - Barry V L Potter
- Medicinal Chemistry and Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- DKTK German Cancer Consortium (DKTK), Frankfurt, Germany
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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5
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Li Z, Chen R, Li Y, Zhou Q, Zhao H, Zeng K, Zhao B, Lu Z. A comprehensive overview of PPM1B: From biological functions to diseases. Eur J Pharmacol 2023; 947:175633. [PMID: 36863552 DOI: 10.1016/j.ejphar.2023.175633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/08/2023] [Accepted: 02/28/2023] [Indexed: 03/04/2023]
Abstract
Reversible phosphorylation of proteins is an important mechanism that regulates cellular processes, which are precisely regulated by protein kinases and phosphatases. PPM1B is a metal ion-dependent serine/threonine protein phosphatase, which regulates multiple biological functions by targeting substrate dephosphorylation, such as cell cycle, energy metabolism, inflammatory responses. In this review, we summarized the occurrent understandings of PPM1B focused on its regulation of signaling pathways, related diseases, and small-molecular inhibitors, which may provide new insights for the identification of PPM1B inhibitors and the treatment of PPM1B-related diseases.
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Affiliation(s)
- Zhongyao Li
- School of Pharmacy and Pharmaceutical Sciences, Institute of Materia Medica, Shandong First Medical University, Shandong Academy of Medical Sciences, NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Ji'nan, 250117, Shandong, China
| | - Ruoyu Chen
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, Shandong, China
| | - Yanxia Li
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, Shandong, China
| | - Qian Zhou
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, Shandong, China
| | - Huanxin Zhao
- School of Pharmacy and Pharmaceutical Sciences, Institute of Materia Medica, Shandong First Medical University, Shandong Academy of Medical Sciences, NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Ji'nan, 250117, Shandong, China
| | - Kewu Zeng
- School of Pharmacy and Pharmaceutical Sciences, Institute of Materia Medica, Shandong First Medical University, Shandong Academy of Medical Sciences, NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Ji'nan, 250117, Shandong, China.
| | - Baobing Zhao
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, Shandong, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, Shandong, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, 250012, Shandong, China.
| | - Zhiyuan Lu
- School of Pharmacy and Pharmaceutical Sciences, Institute of Materia Medica, Shandong First Medical University, Shandong Academy of Medical Sciences, NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Ji'nan, 250117, Shandong, China.
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6
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Spiliotopoulos A, Maurer SK, Tsoumpeli MT, Bonfante JAF, Owen JP, Gough KC, Dreveny I. Next-Generation Phage Display to Identify Peptide Ligands of Deubiquitinases. Methods Mol Biol 2023; 2591:189-218. [PMID: 36350550 DOI: 10.1007/978-1-0716-2803-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phage display (PD) is a powerful method and has been extensively used to generate monoclonal antibodies and identify epitopes, mimotopes, and protein interactions. More recently, the combination of next-generation sequencing (NGS) with PD (NGPD) has revolutionized the capabilities of the method by creating large data sets of sequences from affinity selection-based approaches (biopanning) otherwise challenging to obtain. NGPD can monitor motif enrichment, allow tracking of the selection process over consecutive rounds, and highlight unspecific binders. To tackle the wealth of data obtained, bioinformatics tools have been developed that allow for identifying specific binding sequences (binders) that can then be validated. Here, we provide a detailed account of the use of NGPD experiments to identify ubiquitin-specific protease peptide ligands.
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Affiliation(s)
- Anastasios Spiliotopoulos
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
- Vertex Pharmaceuticals, Abingdon, Oxfordshire, UK
| | - Sigrun K Maurer
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Maria T Tsoumpeli
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
| | - Juan A F Bonfante
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK
| | - Jonathan P Owen
- ADAS UK, School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington, Loughborough, Leicestershire, UK
| | - Kevin C Gough
- School of Veterinary Medicine and Science, Sutton Bonington Campus, Sutton Bonington, Leicestershire, UK.
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK.
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7
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Tartaglia M, Aoki Y, Gelb BD. The molecular genetics of RASopathies: An update on novel disease genes and new disorders. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:425-439. [PMID: 36394128 PMCID: PMC10100036 DOI: 10.1002/ajmg.c.32012] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/31/2022] [Accepted: 11/05/2022] [Indexed: 11/18/2022]
Abstract
Enhanced signaling through RAS and the mitogen-associated protein kinase (MAPK) cascade underlies the RASopathies, a family of clinically related disorders affecting development and growth. In RASopathies, increased RAS-MAPK signaling can result from the upregulated activity of various RAS GTPases, enhanced function of proteins positively controlling RAS function or favoring the efficient transmission of RAS signaling to downstream transducers, functional upregulation of RAS effectors belonging to the MAPK cascade, or inefficient signaling switch-off operated by feedback mechanisms acting at different levels. The massive effort in RASopathy gene discovery performed in the last 20 years has identified more than 20 genes implicated in these disorders. It has also facilitated the characterization of several molecular activating mechanisms that had remained unappreciated due to their minor impact in oncogenesis. Here, we provide an overview on the discoveries collected during the last 5 years that have delivered unexpected insights (e.g., Noonan syndrome as a recessive disease) and allowed to profile new RASopathies, novel disease genes and new molecular circuits contributing to the control of RAS-MAPK signaling.
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Affiliation(s)
- Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pediatrics and Genetics, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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8
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Sang D, Shu T, Pantoja CF, Ibáñez de Opakua A, Zweckstetter M, Holt LJ. Condensed-phase signaling can expand kinase specificity and respond to macromolecular crowding. Mol Cell 2022; 82:3693-3711.e10. [PMID: 36108633 PMCID: PMC10101210 DOI: 10.1016/j.molcel.2022.08.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/18/2022] [Accepted: 08/12/2022] [Indexed: 10/14/2022]
Abstract
Phase separation can concentrate biomolecules and accelerate reactions. However, the mechanisms and principles connecting this mesoscale organization to signaling dynamics are difficult to dissect because of the pleiotropic effects associated with disrupting endogenous condensates. To address this limitation, we engineered new phosphorylation reactions within synthetic condensates. We generally found increased activity and broadened kinase specificity. Phosphorylation dynamics within condensates were rapid and could drive cell-cycle-dependent localization changes. High client concentration within condensates was important but not the main factor for efficient phosphorylation. Rather, the availability of many excess client-binding sites together with a flexible scaffold was crucial. Phosphorylation within condensates was also modulated by changes in macromolecular crowding. Finally, the phosphorylation of the Alzheimer's-disease-associated protein Tau by cyclin-dependent kinase 2 was accelerated within condensates. Thus, condensates enable new signaling connections and can create sensors that respond to the biophysical properties of the cytoplasm.
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Affiliation(s)
- Dajun Sang
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10010, USA
| | - Tong Shu
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10010, USA
| | - Christian F Pantoja
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Alain Ibáñez de Opakua
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10010, USA.
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9
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Energetic determinants of animal cell polarity regulator Par-3 interaction with the Par complex. J Biol Chem 2022; 298:102223. [PMID: 35787373 PMCID: PMC9352551 DOI: 10.1016/j.jbc.2022.102223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 12/03/2022] Open
Abstract
The animal cell polarity regulator Par-3 recruits the Par complex (consisting of Par-6 and atypical PKC, aPKC) to specific sites on the cell membrane. Although numerous physical interactions have been reported between Par-3 and the Par complex, it is unclear how each of these interactions contributes to the overall binding. Using a purified, intact Par complex and a quantitative binding assay, here, we found that the energy required for this interaction is provided by the second and third PDZ protein interaction domains of Par-3. We show that both Par-3 PDZ domains bind to the PDZ-binding motif of aPKC in the Par complex, with additional binding energy contributed from the adjacent catalytic domain of aPKC. In addition to highlighting the role of Par-3 PDZ domain interactions with the aPKC kinase domain and PDZ-binding motif in stabilizing Par-3–Par complex assembly, our results indicate that each Par-3 molecule can potentially recruit two Par complexes to the membrane during cell polarization. These results provide new insights into the energetic determinants and structural stoichiometry of the Par-3–Par complex assembly.
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10
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Iwanov I, Rossi A, Montesi M, Doytchinova I, Sargsyan A, Momekov G, Panseri S, Naydenova E. Peptide-based targeted cancer therapeutics: design, synthesis and biological evaluation. Eur J Pharm Sci 2022; 176:106249. [PMID: 35779821 DOI: 10.1016/j.ejps.2022.106249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/17/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022]
Abstract
Cancer is the leading cause for human mortality together with cardiovascular diseases. Abl (Abelson) tyrosine kinases play a fundamental role in transducing various signals that control proliferation, survival, migration and invasion in several cancers such as Chronic Myeloid Leukemia (CML), breast cancer and brain cancer. For these reasons Abl tyrosine kinases are considered important biological targets in drug discovery. In this study a series of lysine-based oligopeptides with expected Abl inhibitory activity were designed resembling the binding of FDA-approved drugs (i.e. of Imatinib and Nilotinib), synthesized, purified by High Performance Liquid Chromatography (HPLC), analyzed by mass spectrometry (MS) and biologically tested in vitro in CML (AR-230 and K-562), breast cancers (MDA-MB 231 and MDA-MB 468) and glioblastoma cell lines (U87 and U118). The solid-phase peptide synthesis (SPPS) by Fmoc (9-fluorenylmethoxycarbonyl) chemistry was used to synthesize target compounds. AutoDock Vina was applied for simulation binding to Abl. The biological activities were measured evaluating cytotoxic effect, induction of apoptosis and inhibition of cancer cells migration. The new peptides exhibited different concentration-dependent antiproliferative effect against the tumor cell lines after 72 h treatment. The most promising results were obtained with the U87 glioblastoma cell line where a significant reduction of the migration ability was detected with one compound (H-Lys1-Lys2-Lys3-NH2).
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Affiliation(s)
- Iwan Iwanov
- University of Chemical Technology and Metallurgy, 8 Blvd. Kliment Ohridski, 1756, Sofia, Bulgaria
| | - Arianna Rossi
- Institute of Science and Technology for Ceramics, National Research Council of Italy, via Granarolo 64, Faenza (RA), Italy; University of Messina, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Piazza Pugliatti 1, Messina (ME), Italy
| | - Monica Montesi
- Institute of Science and Technology for Ceramics, National Research Council of Italy, via Granarolo 64, Faenza (RA), Italy
| | | | - Armen Sargsyan
- Scientific and Production Center "Armbiotechnology" NAS RA, 14 Gyurjyan str., Yerevan, 0056, Armenia
| | - Georgi Momekov
- Medical University of Sofia, 2 Dunav st., Sofia, 1000, Bulgaria
| | - Silvia Panseri
- Institute of Science and Technology for Ceramics, National Research Council of Italy, via Granarolo 64, Faenza (RA), Italy.
| | - Emilia Naydenova
- University of Chemical Technology and Metallurgy, 8 Blvd. Kliment Ohridski, 1756, Sofia, Bulgaria.
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11
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Zhang R, Dong Q, Zhao P, Eickelkamp A, Ma C, He G, Li F, Wallrad L, Becker T, Li Z, Kudla J, Tian X. The potassium channel GhAKT2bD is regulated by CBL-CIPK calcium signaling complexes and facilitates K + allocation in cotton. FEBS Lett 2022; 596:1904-1920. [PMID: 35561107 DOI: 10.1002/1873-3468.14377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 11/12/2022]
Abstract
Efficient allocation of the essential nutrient potassium (K+ ) is a central determinant of plant ion homeostasis and involves AKT2 K+ channels. Here, we characterize four AKT2 K+ channels from cotton and report that xylem and phloem expressed GhAKT2bD facilitates K+ allocation and that AKT2-silencing impairs plant growth and development. We uncover kinase activity-dependent activation of GhAKT2bD-mediated K+ uptake by AtCBL4-GhCIPK1 calcium signaling complexes in HEK293T cells. Moreover, AtCBL4-AtCIPK6 complexes known to convey activation of AtAKT2 in Arabidopsis also activate cotton GhAKT2bD in HEK293T cells. Collectively, these findings reveal an essential role for AKT2 in the source-sink allocation of K+ in cotton and identify GhAKT2bD as subject to complex regulation by CBL-CIPK Ca2+ sensor-kinase complexes.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.,Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| | - Qiuyan Dong
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| | - Panpan Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Anna Eickelkamp
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| | - Chunmin Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Gefeng He
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| | - Fangjun Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Lukas Wallrad
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| | - Tobias Becker
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| | - Zhaohu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| | - Xiaoli Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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12
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Kocik RA, Gasch AP. Breadth and Specificity in Pleiotropic Protein Kinase A Activity and Environmental Responses. Front Cell Dev Biol 2022; 10:803392. [PMID: 35252178 PMCID: PMC8888911 DOI: 10.3389/fcell.2022.803392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Protein Kinase A (PKA) is an essential kinase that is conserved across eukaryotes and plays fundamental roles in a wide range of organismal processes, including growth control, learning and memory, cardiovascular health, and development. PKA mediates these responses through the direct phosphorylation of hundreds of proteins-however, which proteins are phosphorylated can vary widely across cell types and environmental cues, even within the same organism. A major question is how cells enact specificity and precision in PKA activity to mount the proper response, especially during environmental changes in which only a subset of PKA-controlled processes must respond. Research over the years has uncovered multiple strategies that cells use to modulate PKA activity and specificity. This review highlights recent advances in our understanding of PKA signaling control including subcellular targeting, phase separation, feedback control, and standing waves of allosteric regulation. We discuss how the complex inputs and outputs to the PKA network simultaneously pose challenges and solutions in signaling integration and insulation. PKA serves as a model for how the same regulatory factors can serve broad pleiotropic functions but maintain specificity in localized control.
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Affiliation(s)
- Rachel A Kocik
- Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, United States.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States.,Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, United States
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13
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Seo SY, Yang JH, Kim S, Sohn S, Oh JH, Mao L, Wang JQ, Choe ES. Interaction of JNK and mGluR5 in the regulation of psychomotor behaviours after repeated cocaine administration. Addict Biol 2022; 27:e13127. [PMID: 35229936 DOI: 10.1111/adb.13127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 11/30/2022]
Abstract
Activation of protein kinases after cocaine administration controls psychomotor behaviours by interacting with metabotropic receptors in the brain. This study identified how c-Jun N-terminal kinase (JNK) interacts with metabotropic glutamate receptor 5 (mGluR5) in vitro and in the caudate and putamen (CPu). The potential role of this interaction in the regulation of psychomotor behaviour was also evaluated after administration of cocaine. Active JNK phosphorylates a threonine residue at position 1055 in the carboxyl terminus (CT) of mGluR5 in vitro. The binding of active JNK to the D-motif within CT2 is necessary for that phosphorylation. Interaction of phosphorylated JNK and mGluR5 occurs in the CPu. Unilateral interference of the interaction decreases the repeated cocaine-induced increases in locomotor activity and conditioned place preference. These findings suggest that activation of JNK has the capability to interact with mGluR5 in the CPu. Phosphorylation of mGluR5 following the JNK-mGluR5 interaction may be responsible for the potentiation of behavioural sensitisation and cocaine-wanting behaviour in response to cocaine administration.
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Affiliation(s)
- Su Yeon Seo
- Department of Biological Sciences Pusan National University Busan South Korea
| | - Ju Hwan Yang
- Department of Biological Sciences Pusan National University Busan South Korea
| | - Sunghyun Kim
- Department of Biological Sciences Pusan National University Busan South Korea
| | - Sumin Sohn
- Department of Biological Sciences Pusan National University Busan South Korea
| | - Jeong Hwan Oh
- Department of Biological Sciences Pusan National University Busan South Korea
| | - Li‐Min Mao
- Department of Anesthesiology and Basic Medical Science University of Missouri–Kansas City Kansas City Missouri USA
| | - John Q. Wang
- Department of Anesthesiology and Basic Medical Science University of Missouri–Kansas City Kansas City Missouri USA
| | - Eun Sang Choe
- Department of Biological Sciences Pusan National University Busan South Korea
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14
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Alexa A, Sok P, Gross F, Albert K, Kobori E, Póti ÁL, Gógl G, Bento I, Kuang E, Taylor SS, Zhu F, Ciliberto A, Reményi A. A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host. Nat Commun 2022; 13:472. [PMID: 35078976 PMCID: PMC8789800 DOI: 10.1038/s41467-022-28109-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/07/2022] [Indexed: 12/16/2022] Open
Abstract
The Kaposi's sarcoma associated herpesvirus protein ORF45 binds the extracellular signal-regulated kinase (ERK) and the p90 Ribosomal S6 kinase (RSK). ORF45 was shown to be a kinase activator in cells but a kinase inhibitor in vitro, and its effects on the ERK-RSK complex are unknown. Here, we demonstrate that ORF45 binds ERK and RSK using optimized linear binding motifs. The crystal structure of the ORF45-ERK2 complex shows how kinase docking motifs recognize the activated form of ERK. The crystal structure of the ORF45-RSK2 complex reveals an AGC kinase docking system, for which we provide evidence that it is functional in the host. We find that ORF45 manipulates ERK-RSK signaling by favoring the formation of a complex, in which activated kinases are better protected from phosphatases and docking motif-independent RSK substrate phosphorylation is selectively up-regulated. As such, our data suggest that ORF45 interferes with the natural design of kinase docking systems in the host.
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Affiliation(s)
- Anita Alexa
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Péter Sok
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Fridolin Gross
- IFOM, Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy
| | - Krisztián Albert
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Evan Kobori
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0654, USA
| | - Ádám L Póti
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Gergő Gógl
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Isabel Bento
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Ersheng Kuang
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4370, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0654, USA
| | - Fanxiu Zhu
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4370, USA
| | - Andrea Ciliberto
- IFOM, Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy
| | - Attila Reményi
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary.
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15
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Dynamic equilibria in protein kinases. Curr Opin Struct Biol 2021; 71:215-222. [PMID: 34425481 DOI: 10.1016/j.sbi.2021.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/15/2021] [Accepted: 07/14/2021] [Indexed: 12/14/2022]
Abstract
Structural changes involved in protein kinase activation and ligand binding have been determined from a wealth of X-ray crystallographic evidence. Recent solution studies using NMR, EPR, HX-MS, and fluorescence techniques have deepened this understanding by highlighting the underlying energetics and dynamics of multistate conformational ensembles. This new research is showing how activation mechanisms and ligand binding alter the internal motions of kinases and enable allosteric coupling between distal regulatory regions and the active site.
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16
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Alexa A, Ember O, Szabó I, Mo'ath Y, Póti ÁL, Reményi A, Bánóczi Z. Peptide Based Inhibitors of Protein Binding to the Mitogen-Activated Protein Kinase Docking Groove. Front Mol Biosci 2021; 8:690429. [PMID: 34277705 PMCID: PMC8281026 DOI: 10.3389/fmolb.2021.690429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/18/2021] [Indexed: 11/21/2022] Open
Abstract
Mitogen-activated protein kinases (MAPK) are important regulatory units in cells and they take part in the regulation of many cellular functions such as cell division, differentiation or apoptosis. All MAPKs have a shallow docking groove that interacts with linear binding motifs of their substrate proteins and their regulatory proteins such as kinases, phosphatases, scaffolds. Inhibition of these protein–protein interactions may reduce or abolish the activity of the targeted kinase. Based on the wide range of their biological activity, this kind of inhibition can be useful in the treatment of many disorders like tumors, inflammation or undesired cell apoptosis. In this study a linear binding motif from the RHDF1 protein—a 15 amino acids long peptide—was selected for optimization to increase its cellular uptake but retaining its low micromolar binding affinity. First, we synthesized an octaarginine conjugate that showed efficient cellular uptake. Next, we set out to reduce the size of this construct. We were able to decrease the length of the original peptide, and to increase its cellular uptake with specific chemical modifications. These new constructs bound better to ERK2 and p38 kinases than the original peptide and they showed markedly increased cellular uptake. The new octaarginine conjugate and one of the minimized bicyclic derivatives could inhibit the phosphorylation of intracellular ERK or p38. However, the modulation of MAPK phosphorylation levels by these cell-penetrating peptides were complex, despite that in biochemical assays they all inhibited MAPK-substrate binding as well as phosphorylation. The optimized peptides depending on the applied concentration caused an expected decrease, but also some unexpected increase in MAPK phosphorylation patterns in the cell. This possibly reflects the complexity of MAPK docking groove mediated protein–protein interactions including bone fide MAPK clients such activator kinases, deactivating phosphatases or regulatory scaffolds. Thus, our findings with optimized cell-penetrating “inhibitory” peptides highlight the opportunities but also the pitfalls of docking peptide based MAPK activity regulation and call for a better quantitative understanding of MAPK mediated protein–protein interactions in cells.
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Affiliation(s)
- Anita Alexa
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Orsolya Ember
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary.,Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ildikó Szabó
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Eötvös L. University, Budapest, Hungary
| | - Yousef Mo'ath
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ádám L Póti
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Attila Reményi
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
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17
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Clemens L, Kutuzov M, Bayer KV, Goyette J, Allard J, Dushek O. Determination of the molecular reach of the protein tyrosine phosphatase SHP-1. Biophys J 2021; 120:2054-2066. [PMID: 33781765 PMCID: PMC8204385 DOI: 10.1016/j.bpj.2021.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/05/2021] [Accepted: 03/23/2021] [Indexed: 12/26/2022] Open
Abstract
Immune receptors signal by recruiting (or tethering) enzymes to their cytoplasmic tails to catalyze reactions on substrates within reach. This is the case for the phosphatase SHP-1, which, upon tethering to inhibitory receptors, dephosphorylates diverse substrates to control T cell activation. Precisely how tethering regulates SHP-1 activity is incompletely understood. Here, we measure binding, catalysis, and molecular reach for tethered SHP-1 reactions. We determine the molecular reach of SHP-1 to be 13.0 nm, which is longer than the estimate from the allosterically active structure (5.3 nm), suggesting that SHP-1 can achieve a longer reach by exploring multiple active conformations. Using modeling, we show that when uniformly distributed, receptor-SHP-1 complexes can only reach 15% of substrates, but this increases to 90% when they are coclustered. When within reach, we show that membrane recruitment increases the activity of SHP-1 by a 1000-fold increase in local concentration. The work highlights how molecular reach regulates the activity of membrane-recruited SHP-1 with insights applicable to other membrane-tethered reactions.
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Affiliation(s)
- Lara Clemens
- Center for Complex Biological Systems, University of California Irvine, Irvine, California
| | - Mikhail Kutuzov
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences University of New South Wales, Sydney, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Jun Allard
- Center for Complex Biological Systems, University of California Irvine, Irvine, California.
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom.
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18
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Ali K, Li W, Qin Y, Wang S, Feng L, Wei Q, Bai Q, Zheng B, Li G, Ren H, Wu G. Kinase Function of Brassinosteroid Receptor Specified by Two Allosterically Regulated Subdomains. FRONTIERS IN PLANT SCIENCE 2021; 12:802924. [PMID: 35095975 PMCID: PMC8792736 DOI: 10.3389/fpls.2021.802924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/13/2021] [Indexed: 05/07/2023]
Abstract
Plants acquire the ability to adapt to the environment using transmembrane receptor-like kinases (RLKs) to sense the challenges from their surroundings and respond appropriately. RLKs perceive a variety of ligands through their variable extracellular domains (ECDs) that activate the highly conserved intracellular kinase domains (KDs) to control distinct biological functions through a well-developed downstream signaling cascade. A new study has emerged that brassinosteroid-insensitive 1 (BRI1) family and excess microsporocytes 1 (EMS1) but not GASSHO1 (GSO1) and other RLKs control distinct biological functions through the same signaling pathway, raising a question how the signaling pathway represented by BRI1 is specified. Here, we confirm that BRI1-KD is not functionally replaceable by GSO1-KD since the chimeric BRI1-GSO1 cannot rescue bri1 mutants. We then identify two subdomains S1 and S2. BRI1 with its S1 and S2 substituted by that of GSO1 cannot rescue bri1 mutants. Conversely, chimeric BRI1-GSO1 with its S1 and S2 substituted by that of BRI1 can rescue bri1 mutants, suggesting that S1 and S2 are the sufficient requirements to specify the signaling function of BRI1. Consequently, all the other subdomains in the KD of BRI1 are functionally replaceable by that of GSO1 although the in vitro kinase activities vary after replacements, suggesting their functional robustness and mutational plasticity with diverse kinase activity. Interestingly, S1 contains αC-β4 loop as an allosteric hotspot and S2 includes kinase activation loop, proposedly regulating kinase activities. Further analysis reveals that this specific function requires β4 and β5 in addition to αC-β4 loop in S1. We, therefore, suggest that BRI1 specifies its kinase function through an allosteric regulation of these two subdomains to control its distinct biological functions, providing a new insight into the kinase evolution.
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19
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Ma M, Bordignon P, Dotto GP, Pelet S. Visualizing cellular heterogeneity by quantifying the dynamics of MAPK activity in live mammalian cells with synthetic fluorescent biosensors. Heliyon 2020; 6:e05574. [PMID: 33319088 PMCID: PMC7723811 DOI: 10.1016/j.heliyon.2020.e05574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/26/2020] [Accepted: 11/18/2020] [Indexed: 01/19/2023] Open
Abstract
Mitogen-Activated Protein Kinases (MAPKs) control a wide array of cellular functions by transducing extracellular information into defined biological responses. In order to understand how these pathways are regulated, dynamic single cell measurements are highly needed. Fluorescence microscopy is well suited to perform these measurements. However, more dynamic and sensitive biosensors that allow the quantification of signaling activity in living mammalian cells are required. We have engineered a synthetic fluorescent substrate for human MAPKs (ERK, JNK and p38) that relocates from the nucleus to the cytoplasm when phosphorylated by the kinases. We demonstrate that this reporter displays an improved response compared to other relocation biosensors. This assay allows to monitor the heterogeneity in the MAPK response in a population of isogenic cells, revealing pulses of ERK activity upon a physiological EGFR stimulation. We show applicability of this approach to the analysis of multiple cancer cell lines and primary cells as well as its application in vivo to developing tumors. Using this ERK biosensor, dynamic single cell measurements with high temporal resolution can be obtained. These MAPK reporters can be widely applied to the analysis of molecular mechanisms of MAPK signaling in healthy and diseased state, in cell culture assays or in vivo.
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Affiliation(s)
- Min Ma
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
- Department of Biochemistry, University of Lausanne, Switzerland
| | - Pino Bordignon
- Department of Biochemistry, University of Lausanne, Switzerland
| | | | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
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20
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Bandyopadhyay S, Bhaduri S, Örd M, Davey NE, Loog M, Pryciak PM. Comprehensive Analysis of G1 Cyclin Docking Motif Sequences that Control CDK Regulatory Potency In Vivo. Curr Biol 2020; 30:4454-4466.e5. [PMID: 32976810 PMCID: PMC8009629 DOI: 10.1016/j.cub.2020.08.099] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 11/17/2022]
Abstract
Many protein-modifying enzymes recognize their substrates via docking motifs, but the range of functionally permissible motif sequences is often poorly defined. During eukaryotic cell division, cyclin-specific docking motifs help cyclin-dependent kinases (CDKs) phosphorylate different substrates at different stages, thus enforcing a temporally ordered series of events. In budding yeast, CDK substrates with Leu/Pro-rich (LP) docking motifs are recognized by Cln1/2 cyclins in late G1 phase, yet the key sequence features of these motifs were unknown. Here, we comprehensively analyze LP motif requirements in vivo by combining a competitive growth assay with deep mutational scanning. We quantified the effect of all single-residue replacements in five different LP motifs by using six distinct G1 cyclins from diverse fungi including medical and agricultural pathogens. The results uncover substantial tolerance for deviations from the consensus sequence, plus requirements at some positions that are contingent on the favorability of other motif residues. They also reveal the basis for variations in functional potency among wild-type motifs, and allow derivation of a quantitative matrix that predicts the strength of other candidate motif sequences. Finally, we find that variation in docking motif potency can advance or delay the time at which CDK substrate phosphorylation occurs, and thereby control the temporal ordering of cell cycle regulation. The overall results provide a general method for surveying viable docking motif sequences and quantifying their potency in vivo, and they reveal how variations in docking strength can tune the degree and timing of regulatory modifications.
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Affiliation(s)
- Sushobhana Bandyopadhyay
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Samyabrata Bhaduri
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Peter M Pryciak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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21
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Lu Z, Xiao P, Zhou Y, Li Z, Yu X, Sun J, Shen Y, Zhao B. Identification of HN252 as a potent inhibitor of protein phosphatase PPM1B. J Cell Mol Med 2020; 24:13463-13471. [PMID: 33048454 PMCID: PMC7701510 DOI: 10.1111/jcmm.15975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 08/20/2020] [Accepted: 09/20/2020] [Indexed: 12/25/2022] Open
Abstract
Protein phosphatase 1B (PPM1B), a member of metal-dependent protein serine/threonine phosphatase family, is involved in the regulation of several signalling pathways. However, our understanding of its substrate interaction and physiological functions is still largely limited. There is no reported PPM1B inhibitor to date. In this study, we identified HN252, a p-terphenyl derivative, as a potent PPM1B inhibitor (Ki = 0.52 ± 0.06 µM). HN252 binding to PPM1B displayed remarkable and specific inhibition of PPM1B in both in vitro and ex vivo. With the aid of this small molecular inhibitor, we identified 30 proteins' serine/threonine phosphorylation as potential substrates of PPM1B, 5 of which were demonstrated by immunoprecipitation, including one known (CDK2) and 4 novel ones (AKT1, HSP90B, β-catenin and BRCA1). Furthermore, GO and KEGG analysis of dramatically phosphorylated proteins by PPM1B inhibition indicated that PPM1B plays roles in the regulation of multiple cellular processes and signalling pathways, such as gene transcription, inflammatory regulation, ageing and tumorigenesis. Our work provides novel insights into further investigation of molecular mechanisms of PPM1B.
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Affiliation(s)
- Zhiyuan Lu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Peng Xiao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuan Zhou
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhenyu Li
- Department of Pharmacy, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jinpeng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Baobing Zhao
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
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22
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Lv X, Cui S, Gu Y, Li J, Du G, Liu L. Enzyme Assembly for Compartmentalized Metabolic Flux Control. Metabolites 2020; 10:E125. [PMID: 32224973 PMCID: PMC7241084 DOI: 10.3390/metabo10040125] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/16/2022] Open
Abstract
Enzyme assembly by ligand binding or physically sequestrating enzymes, substrates, or metabolites into isolated compartments can bring key molecules closer to enhance the flux of a metabolic pathway. The emergence of enzyme assembly has provided both opportunities and challenges for metabolic engineering. At present, with the development of synthetic biology and systems biology, a variety of enzyme assembly strategies have been proposed, from the initial direct enzyme fusion to scaffold-free assembly, as well as artificial scaffolds, such as nucleic acid/protein scaffolds, and even some more complex physical compartments. These assembly strategies have been explored and applied to the synthesis of various important bio-based products, and have achieved different degrees of success. Despite some achievements, enzyme assembly, especially in vivo, still has many problems that have attracted significant attention from researchers. Here, we focus on some selected examples to review recent research on scaffold-free strategies, synthetic artificial scaffolds, and physical compartments for enzyme assembly or pathway sequestration, and we discuss their notable advances. In addition, the potential applications and challenges in the applications are highlighted.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shixiu Cui
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yang Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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Mustafa S, Mobashir M. LC–MS and docking profiling reveals potential difference between the pure and crude fucoidan metabolites. Int J Biol Macromol 2020; 143:11-29. [DOI: 10.1016/j.ijbiomac.2019.11.232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/24/2019] [Accepted: 11/29/2019] [Indexed: 12/19/2022]
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24
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Lopez ED, Burastero O, Arcon JP, Defelipe LA, Ahn NG, Marti MA, Turjanski AG. Kinase Activation by Small Conformational Changes. J Chem Inf Model 2019; 60:821-832. [PMID: 31714778 DOI: 10.1021/acs.jcim.9b00782] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein kinases (PKs) are allosteric enzymes that play an essential role in signal transduction by regulating a variety of key cellular processes. Most PKs suffer conformational rearrangements upon phosphorylation that strongly enhance the catalytic activity. Generally, it involves the movement of the phosphorylated loop toward the active site and the rotation of the whole C-terminal lobe. However, not all kinases undergo such a large configurational change: The MAPK extracellular signal-regulated protein kinases ERK1 and ERK2 achieve a 50 000 fold increase in kinase activity with only a small motion of the C-terminal region. In the present work, we used a combination of molecular simulation tools to characterize the conformational landscape of ERK2 in the active (phosphorylated) and inactive (unphosphorylated) states in solution in agreement with NMR experiments. We show that the chemical reaction barrier is strongly dependent on ATP conformation and that the "active" low-barrier configuration is subtly regulated by phosphorylation, which stabilizes a key salt bridge between the conserved Lys52 and Glu69 belonging to helix-C and promotes binding of a second Mg ion. Our study highlights that the on-off switch embedded in the kinase fold can be regulated by small, medium, and large conformational changes.
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Affiliation(s)
- Elias D Lopez
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
| | - Osvaldo Burastero
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
| | - Juan P Arcon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
| | - Lucas A Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
| | - Natalie G Ahn
- Department of Chemistry and Biochemistry , University of Colorado , Boulder , Colorado 80309 , United States
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
| | - Adrian G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
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25
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Mining for protein S-sulfenylation in Arabidopsis uncovers redox-sensitive sites. Proc Natl Acad Sci U S A 2019; 116:21256-21261. [PMID: 31578252 DOI: 10.1073/pnas.1906768116] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hydrogen peroxide (H2O2) is an important messenger molecule for diverse cellular processes. H2O2 oxidizes proteinaceous cysteinyl thiols to sulfenic acid, also known as S-sulfenylation, thereby affecting the protein conformation and functionality. Although many proteins have been identified as S-sulfenylation targets in plants, site-specific mapping and quantification remain largely unexplored. By means of a peptide-centric chemoproteomics approach, we mapped 1,537 S-sulfenylated sites on more than 1,000 proteins in Arabidopsis thaliana cells. Proteins involved in RNA homeostasis and metabolism were identified as hotspots for S-sulfenylation. Moreover, S-sulfenylation frequently occurred on cysteines located at catalytic sites of enzymes or on cysteines involved in metal binding, hinting at a direct mode of action for redox regulation. Comparison of human and Arabidopsis S-sulfenylation datasets provided 155 conserved S-sulfenylated cysteines, including Cys181 of the Arabidopsis MITOGEN-ACTIVATED PROTEIN KINASE4 (AtMAPK4) that corresponds to Cys161 in the human MAPK1, which has been identified previously as being S-sulfenylated. We show that, by replacing Cys181 of recombinant AtMAPK4 by a redox-insensitive serine residue, the kinase activity decreased, indicating the importance of this noncatalytic cysteine for the kinase mechanism. Altogether, we quantitatively mapped the S-sulfenylated cysteines in Arabidopsis cells under H2O2 stress and thereby generated a comprehensive view on the S-sulfenylation landscape that will facilitate downstream plant redox studies.
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26
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Mitchell DC, Menon A, Garner AL. Chemoproteomic Profiling Uncovers CDK4-Mediated Phosphorylation of the Translational Suppressor 4E-BP1. Cell Chem Biol 2019; 26:980-990.e8. [PMID: 31056462 DOI: 10.1016/j.chembiol.2019.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/04/2019] [Accepted: 03/25/2019] [Indexed: 01/03/2023]
Abstract
Recent estimates of the human proteome suggest there are ∼20,000 protein-coding genes, the protein products of which contain >145,000 phosphosites. Unfortunately, in-depth examination of the human phosphoproteome has outpaced the ability to annotate the kinases that mediate these post-translational modifications. To obtain actionable information about phosphorylation-driven signaling cascades, it is essential to identify the kinases responsible for phosphorylating sites that differ across disease states. To fill in these gaps we have developed an unbiased, chemoproteomic approach for identifying high-confidence kinase-substrate interactions with phosphosite specificity. Using this assay, we uncovered the role of cyclin-dependent kinase 4 (CDK4), a clinically validated kinase important for cell-cycle progression, in regulating cap-dependent translation via phosphorylation of the tumor suppressor 4E-BP1. The discovery of this signaling axis sheds light on the mechanisms by which CDK4/6 inhibitors control cell proliferation and constitutes a successful example of kinase discovery using an activity-based, kinase-directed probe.
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Affiliation(s)
- Dylan C Mitchell
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arya Menon
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amanda L Garner
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
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27
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Winters MJ, Pryciak PM. MAPK modulation of yeast pheromone signaling output and the role of phosphorylation sites in the scaffold protein Ste5. Mol Biol Cell 2019; 30:1037-1049. [PMID: 30726174 PMCID: PMC6589907 DOI: 10.1091/mbc.e18-12-0793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Mitogen-activated protein kinases (MAPKs) mediate numerous eukaryotic signaling responses. They also can modulate their own signaling output via positive or negative feedback loops. In the yeast pheromone response pathway, the MAPK Fus3 triggers negative feedback that dampens its own activity. One target of this feedback is Ste5, a scaffold protein that promotes Fus3 activation. Binding of Fus3 to a docking motif (D motif) in Ste5 causes signal dampening, which was proposed to involve a central cluster of phosphorylation sites in Ste5. Here, we reanalyzed the role of these central sites. Contrary to prior claims, phosphorylation-mimicking mutations at these sites did not impair signaling. Also, the hyperactive signaling previously observed when these sites were mutated to nonphosphorylatable residues arose from their replacement with valine residues and was not observed with other substitutes. Instead, a cluster of N-terminal sites in Ste5, not the central sites, is required for the rapid dampening of initial responses. Further results suggest that the role of the Fus3 D motif is most simply explained by a tethering effect that promotes Ste5 phosphorylation, rather than an allosteric effect proposed to regulate Fus3 activity. These findings substantially revise our understanding of how MAPK feedback attenuates scaffold-mediated signaling in this model pathway.
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Affiliation(s)
- Matthew J Winters
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Peter M Pryciak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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28
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Ghorbel M, Zaidi I, Ebel C, Hanin M. Differential regulation of the durum wheat MAPK phosphatase 1 by calmodulin, bivalent cations and possibly mitogen activated protein kinase 3. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:242-252. [PMID: 30584966 DOI: 10.1016/j.plaphy.2018.12.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
MAPK phosphatases (MKPs) are relevant negative regulators of MAPKs in eukaryotes as they mediate the feedback control of MAPK cascades in multiple cellular processes. Despite their relevance, our knowledge on the role of cereal MKPs in stress tolerance is scarce and TMKP1 remains today the only studied MKP in wheat. TMKP1 was previously reported to be involved in plant salt stress tolerance. Moreover, TMKP1 was shown to interact with calmodulin (CaM), 14-3-3 and TMPK3/TMPK6 proteins, which regulate its catalytic activity. To further understand the functional properties of TMKP1, we investigate here the contribution of its phosphorylation status, and of TMPK3 together with CaM and bivalent cations on the catalytic activity. In-gel kinase assays revealed that TMKP1 can be phosphorylated by similar wheat and Arabidopsis MAPKs, including most likely MPK3 and MPK6. In addition, we provide evidence for the capacity of wheat TMPK3 to bind to TMKP1 via a conserved Kinase Interacting Domain (KID) located on its C-terminal part. This interaction leads to a stimulation of TMKP1 activity in the presence of Mn2+ or Mg2+ ions, but to its inhibition in the presence of Ca2+ ions. However, the phosphorylation status of TMKP1 seems to be dispensable for TMKP1 activation by TMPK3. Remarkably, in assays combining TMPK3 with CaM/Ca2+ complex, we registered rather an inhibition of TMKP1 activity which however can be suppressed by Mn2+ cations. Our data are in favor of complex differential regulation of TMKP1 by its MPK substrates, metallic cations that might help in fine-tuning the plant cellular responses to various stresses.
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Affiliation(s)
- Mouna Ghorbel
- Laboratoire de Biotechnologie et Amélioration des Plantes, Centre de Biotechnologie de Sfax, BP "1177", 3018, Sfax, Tunisia; Unité de Génomique Fonctionnelle et Physiologie des Plantes, Institut Supérieur de Biotechnologie, Université de Sfax, BP "1175", 3038, Sfax, Tunisia
| | - Ikram Zaidi
- Laboratoire de Biotechnologie et Amélioration des Plantes, Centre de Biotechnologie de Sfax, BP "1177", 3018, Sfax, Tunisia
| | - Chantal Ebel
- Unité de Génomique Fonctionnelle et Physiologie des Plantes, Institut Supérieur de Biotechnologie, Université de Sfax, BP "1175", 3038, Sfax, Tunisia
| | - Moez Hanin
- Unité de Génomique Fonctionnelle et Physiologie des Plantes, Institut Supérieur de Biotechnologie, Université de Sfax, BP "1175", 3038, Sfax, Tunisia.
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29
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Ghose R. Nature of the Pre-Chemistry Ensemble in Mitogen-Activated Protein Kinases. J Mol Biol 2018; 431:145-157. [PMID: 30562484 DOI: 10.1016/j.jmb.2018.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
Abstract
In spite of the availability of a significant amount of structural detail on docking interactions involving mitogen-activated protein kinases (MAPKs) and their substrates, the mechanism by which the disordered phospho-acceptor on the substrate transiently interacts with the kinase catalytic elements and is phosphorylated, often with high efficiency, remains poorly understood. Here, this dynamic interaction is analyzed in the context of available biophysical and biochemical data for ERK2, an archetypal MAPK. A hypothesis about the nature of the ternary complex involving a MAPK, its substrate, and ATP immediately prior to the chemical step (the pre-chemistry complex) is proposed. It is postulated that the solution ensemble (the pre-chemistry ensemble) representing the pre-chemistry complex comprises several conformations that are linked by dynamics on multiple timescales. These individual conformations possess different intrinsic abilities to proceed through the chemical step. The overall rate of chemistry is therefore related to the microscopic nature of the pre-chemistry ensemble, its constituent conformational microstates, and their intrinsic abilities to yield a phosphorylated product. While characterizing these microstates within the pre-chemistry ensemble in atomic or near-atomic detail is an extremely challenging proposition, recent developments in hybrid methodologies that employ computational approaches driven by experimental data appear to provide the most promising path forward toward achieving this goal.
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Affiliation(s)
- Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Physics, The Graduate Center of CUNY, New York, NY 10016, USA
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30
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Yang JH, Seo SY, Oh JH, Ryu IS, Kim J, Lee DK, Ryu Y, Choe ES. Activation of Protein Kinase G After Repeated Cocaine Administration Is Necessary for the Phosphorylation of α-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid Receptor GluA1 at Serine 831 in the Rat Nucleus Accumbens. Front Mol Neurosci 2018; 11:263. [PMID: 30104957 PMCID: PMC6077228 DOI: 10.3389/fnmol.2018.00263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 07/12/2018] [Indexed: 12/16/2022] Open
Abstract
Phosphorylation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors in the striatum plays a crucial role in regulating the receptor-coupled signaling cascades leading to behavioral changes associated with psychostimulant exposure. The present study determined if activation of protein kinase G (PKG) contributes to the phosphorylation of AMPA receptor GluA1 subunit at the position of serine 831 (GluA1-S831) in the rat nucleus accumbens (NAc) after repeated cocaine administration. The results demonstrated that repeated intraperitoneal (i.p.) injections of cocaine (20 mg/kg) once a day for seven consecutive days significantly increased the level of phosphorylated (p)GluA1-S831. This increase was decreased by the intra-NAc infusion of either the cyclic guanosine monophosphate (cGMP) analog, Rp-8-Br-PET-cGMPS (5 nmol/1 μL), or the PKG inhibitor, KT5823 (2 nmol/1 μL). Repeated cocaine administration increased PKG binding activity to GluA1. This increase in GluA1-S831 phosphorylation after repeated cocaine administration was decreased by the intra-NAc infusion of the synthetic peptide (Tat-tagged interfering peptide (Tat-GluA1-i)), that interferes with the binding of PKG to GluA1. Intra-NAc infusion of the interfering peptide also reduced the repeated cocaine-induced increase in locomotor activity. These findings suggest that activated PKG, after repeated exposure to cocaine, binds to AMPA receptor GluA1 and is required for the phosphorylation of S831, contributing to behavioral changes.
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Affiliation(s)
- Ju Hwan Yang
- Department of Biological Sciences, Pusan National University, Busan, South Korea
| | - Su Yeon Seo
- Department of Biological Sciences, Pusan National University, Busan, South Korea.,Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Jeong Hwan Oh
- Department of Biological Sciences, Pusan National University, Busan, South Korea.,Institute of Fisheries Sciences, Pukyong National University, Busan, South Korea
| | - In Soo Ryu
- Department of Biological Sciences, Pusan National University, Busan, South Korea.,Substance Abuse Pharmacology Group, Korea Institute of Toxicology, Daejeon, South Korea
| | - Jieun Kim
- Department of Biological Sciences, Pusan National University, Busan, South Korea
| | - Dong Kun Lee
- Department of Physiology, School of Medicine and Institution of Health Sciences, Gyeongsang National University, Jinju, South Korea
| | - Yeonhee Ryu
- Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Eun Sang Choe
- Department of Biological Sciences, Pusan National University, Busan, South Korea
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31
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Hussain M, Angus SP, Kuhlman B. Engineering a Protein Binder Specific for p38α with Interface Expansion. Biochemistry 2018; 57:4526-4535. [PMID: 29975520 DOI: 10.1021/acs.biochem.8b00408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein binding specificities can be manipulated by redesigning contacts that already exist at an interface or by expanding the interface to allow interactions with residues adjacent to the original binding site. Previously, we developed a strategy, called AnchorDesign, for expanding interfaces around linear binding epitopes. The epitope is embedded in a loop of a scaffold protein, in our case a monobody, and then surrounding residues on the monobody are optimized for binding using directed evolution or computational design. Using this strategy, we have increased binding affinities by >100-fold, but we have not tested whether it can be used to control protein binding specificities. Here, we test whether AnchorDesign can be used to engineer a monobody that binds specifically to the mitogen-activated protein kinase (MAPK) p38α but not to the related MAPKs ERK2 and JNK. To anchor the binding interaction, we used a small (D) docking motif from the mitogen-activated protein kinase kinase (MAP2K) MKK6 that interacts with similar affinity with p38α and ERK2. Our hypothesis was that by embedding the motif in a larger protein that we could expand the interface and create contacts with residues that are not conserved between p38α and ERK2. Molecular modeling was used to inform insertion of the D motif into the monobody, and a combination of phage and yeast display were used to optimize the interface. Binding experiments demonstrate that the engineered monobody binds to the target surface on p38α and does not exhibit detectable binding to ERK2 or JNK.
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32
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Petrides A, Vinnicombe G. Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains. PLoS Comput Biol 2018; 14:e1006107. [PMID: 29771922 PMCID: PMC5976211 DOI: 10.1371/journal.pcbi.1006107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 05/30/2018] [Accepted: 03/26/2018] [Indexed: 11/19/2022] Open
Abstract
This paper is concerned with the potential multistability of protein concentrations in the cell. That is, situations where one, or a family of, proteins may sit at one of two or more different steady state concentrations in otherwise identical cells, and in spite of them being in the same environment. For models of multisite protein phosphorylation for example, in the presence of excess substrate, it has been shown that the achievable number of stable steady states can increase linearly with the number of phosphosites available. In this paper, we analyse the consequences of adding enzyme docking to these and similar models, with the resultant sequestration of phosphatase and kinase by the fully unphosphorylated and by the fully phosphorylated substrates respectively. In the large molecule numbers limit, where deterministic analysis is applicable, we prove that there are always values for these rates of sequestration which, when exceeded, limit the extent of multistability. For the models considered here, these numbers are much smaller than the affinity of the enzymes to the substrate when it is in a modifiable state. As substrate enzyme-sequestration is increased, we further prove that the number of steady states will inevitably be reduced to one. For smaller molecule numbers a stochastic analysis is more appropriate, where multistability in the large molecule numbers limit can manifest itself as multimodality of the probability distribution; the system spending periods of time in the vicinity of one mode before jumping to another. Here, we find that substrate enzyme sequestration can induce bimodality even in systems where only a single steady state can exist at large numbers. To facilitate this analysis, we develop a weakly chained diagonally dominant M-matrix formulation of the Chemical Master Equation, allowing greater insights in the way particular mechanisms, like enzyme sequestration, can shape probability distributions and therefore exhibit different behaviour across different regimes.
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Affiliation(s)
- Andreas Petrides
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Glenn Vinnicombe
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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33
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MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PLoS Comput Biol 2018; 13:e1006088. [PMID: 29738528 PMCID: PMC5940180 DOI: 10.1371/journal.pcbi.1006088] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae, the upstream regulatory network controlling protein phosphorylation is less well dissected. Here, we developed a computational approach to infer the signaling network that regulates phosphorylation changes in response to salt stress. We developed an approach to link predicted regulators to groups of likely co-regulated phospho-peptides responding to stress, thereby creating new edges in a background protein interaction network. We then use integer linear programming (ILP) to integrate wild type and mutant phospho-proteomic data and predict the network controlling stress-activated phospho-proteomic changes. The network we inferred predicted new regulatory connections between stress-activated and growth-regulating pathways and suggested mechanisms coordinating metabolism, cell-cycle progression, and growth during stress. We confirmed several network predictions with co-immunoprecipitations coupled with mass-spectrometry protein identification and mutant phospho-proteomic analysis. Results show that the cAMP-phosphodiesterase Pde2 physically interacts with many stress-regulated transcription factors targeted by PKA, and that reduced phosphorylation of those factors during stress requires the Rck2 kinase that we show physically interacts with Pde2. Together, our work shows how a high-quality computational network model can facilitate discovery of new pathway interactions during osmotic stress. Cells sense and respond to stressful environments by utilizing complex signaling networks that integrate diverse signals to coordinate a multi-faceted physiological response. Much of this response is controlled by post-translational protein phosphorylation. Although many regulators that mediate changes in protein phosphorylation are known, how these regulators inter-connect in a single regulatory network that can transmit cellular signals is not known. It is also unclear how regulators that promote growth and regulators that activate the stress response interconnect to reorganize resource allocation during stress. Here, we developed an integrated experimental and computational workflow to infer the signaling network that regulates phosphorylation changes during osmotic stress in the budding yeast Saccharomyces cerevisiae. The workflow integrates data measuring protein phosphorylation changes in response to osmotic stress with known physical interactions between yeast proteins from large-scale datasets, along with other information about how regulators recognize their targets. The resulting network suggested new signaling connections between regulators and pathways, including those involved in regulating growth and defense, and predicted new regulators involved in stress defense. Our work highlights the power of using network inference to deliver new insight on how cells coordinate a diverse adaptive strategy to stress.
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Affiliation(s)
- Matthew E. MacGilvray
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin -Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, Madison, WI, United States of America
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- * E-mail:
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34
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The present and the future of motif-mediated protein-protein interactions. Curr Opin Struct Biol 2018; 50:162-170. [PMID: 29730529 DOI: 10.1016/j.sbi.2018.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/07/2018] [Accepted: 04/11/2018] [Indexed: 01/14/2023]
Abstract
Protein-protein interactions (PPIs) are essential to governing virtually all cellular processes. Of particular importance are the versatile motif-mediated interactions (MMIs), which are thus far underrepresented in available interaction data. This is largely due to technical difficulties inherent in the properties of MMIs, but due to the increasing recognition of the vital roles of MMIs in biology, several systematic approaches have recently been developed to detect novel MMIs. Consequently, rapidly growing numbers of motifs are being identified and pursued further for therapeutic applications. In this review, we discuss the current understanding on the diverse functions and disease-relevance of MMIs, the key methodologies for detection of MMIs, and the potential of MMIs for drug development.
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35
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O'Kane PT, Mrksich M. An Assay Based on SAMDI Mass Spectrometry for Profiling Protein Interaction Domains. J Am Chem Soc 2017; 139:10320-10327. [PMID: 28689418 DOI: 10.1021/jacs.7b03805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This paper describes an assay that can profile the binding of a protein to ligands and can rank the affinities of a library of ligands. The method is based on the enhanced rate of an enzyme-mediated reaction that follows from colocalization of the enzyme and substrate by a protein-ligand interaction. This assay uses a self-assembled monolayer that presents a candidate peptide ligand for a receptor and a peptide substrate for an enzyme. The receptor is prepared as a fusion to the relevant enzyme so that binding of the receptor to the immobilized ligand brings the enzyme to the surface, where it can more rapidly modify its substrate. The extent of conversion of the substrate to product is therefore a measure of the average time the ligand-receptor complex is present and is quantified using the SAMDI mass spectrometry technique. The approach is used to profile the binding of chromodomain proteins to methylated lysine peptides derived from the histone 3 protein. The relative affinities for the peptide ligands found in this work agreed with results from prior studies. Additionally, this work revealed cross-talk interactions whereby phosphorylation of certain residues impaired binding of chromodomains to the peptide ligands. The method presented here, which we term protein interaction by SAMDI (PI-SAMDI), has the advantages that it is applicable to low-affinity interactions because the complexes are not observed directly, but rather leave a "covalent record" of the interaction that is measured with mass spectrometry and because it is compatible with laboratory automation for high-throughput analysis.
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Affiliation(s)
- Patrick T O'Kane
- Department of Chemistry, Department of Biomedical Engineering, and Department of Cell & Molecular Biology, Northwestern University , Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department of Chemistry, Department of Biomedical Engineering, and Department of Cell & Molecular Biology, Northwestern University , Evanston, Illinois 60208, United States
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Local destabilization, rigid body, and fuzzy docking facilitate the phosphorylation of the transcription factor Ets-1 by the mitogen-activated protein kinase ERK2. Proc Natl Acad Sci U S A 2017; 114:E6287-E6296. [PMID: 28716922 DOI: 10.1073/pnas.1702973114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mitogen-activated protein (MAP) kinase substrates are believed to require consensus docking motifs (D-site, F-site) to engage and facilitate efficient site-specific phosphorylation at specific serine/threonine-proline sequences by their cognate kinases. In contrast to other MAP kinase substrates, the transcription factor Ets-1 has no canonical docking motifs, yet it is efficiently phosphorylated by the MAP kinase ERK2 at a consensus threonine site (T38). Using NMR methodology, we demonstrate that this phosphorylation is enabled by a unique bipartite mode of ERK2 engagement by Ets-1 and involves two suboptimal noncanonical docking interactions instead of a single canonical docking motif. The N terminus of Ets-1 interacts with a part of the ERK2 D-recruitment site that normally accommodates the hydrophobic sidechains of a canonical D-site, retaining a significant degree of disorder in its ERK2-bound state. In contrast, the C-terminal region of Ets-1, including its Pointed (PNT) domain, engages in a largely rigid body interaction with a section of the ERK2 F-recruitment site through a binding mode that deviates significantly from that of a canonical F-site. This latter interaction is notable for the destabilization of a flexible helix that bridges the phospho-acceptor site to the rigid PNT domain. These two spatially distinct, individually weak docking interactions facilitate the highly specific recognition of ERK2 by Ets-1, and enable the optimal localization of its dynamic phospho-acceptor T38 at the kinase active site to enable efficient phosphorylation.
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Plain F, Congreve SD, Yee RSZ, Kennedy J, Howie J, Kuo CW, Fraser NJ, Fuller W. An amphipathic α-helix directs palmitoylation of the large intracellular loop of the sodium/calcium exchanger. J Biol Chem 2017; 292:10745-10752. [PMID: 28432123 PMCID: PMC5481580 DOI: 10.1074/jbc.m116.773945] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/19/2017] [Indexed: 11/06/2022] Open
Abstract
The electrogenic sodium/calcium exchanger (NCX) mediates bidirectional calcium transport controlled by the transmembrane sodium gradient. NCX inactivation occurs in the absence of phosphatidylinositol 4,5-bisphosphate and is facilitated by palmitoylation of a single cysteine at position 739 within the large intracellular loop of NCX. The aim of this investigation was to identify the structural determinants of NCX1 palmitoylation. Full-length NCX1 (FL-NCX1) and a YFP fusion protein of the NCX1 large intracellular loop (YFP-NCX1) were expressed in HEK cells. Single amino acid changes around Cys-739 in FL-NCX1 and deletions on the N-terminal side of Cys-739 in YFP-NCX1 did not affect NCX1 palmitoylation, with the exception of the rare human polymorphism S738F, which enhanced FL-NCX1 palmitoylation, and D741A, which modestly reduced it. In contrast, deletion of a 21-amino acid segment enriched in aromatic amino acids on the C-terminal side of Cys-739 abolished YFP-NCX1 palmitoylation. We hypothesized that this segment forms an amphipathic α-helix whose properties facilitate Cys-739 palmitoylation. Introduction of negatively charged amino acids to the hydrophobic face or of helix-breaking prolines impaired palmitoylation of both YFP-NCX1 and FL-NCX1. Alanine mutations on the hydrophilic face of the helix significantly reduced FL-NCX1 palmitoylation. Of note, when the helix-containing segment was introduced adjacent to cysteines that are not normally palmitoylated, they became palmitoylation sites. In conclusion, we have identified an amphipathic α-helix in the NCX1 large intracellular loop that controls NCX1 palmitoylation. NCX1 palmitoylation is governed by a distal secondary structure element rather than by local primary sequence.
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Affiliation(s)
- Fiona Plain
- From the Division of Molecular and Clinical Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
| | - Samitha Dilini Congreve
- From the Division of Molecular and Clinical Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
| | - Rachel Sue Zhen Yee
- From the Division of Molecular and Clinical Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
| | - Jennifer Kennedy
- From the Division of Molecular and Clinical Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
| | - Jacqueline Howie
- From the Division of Molecular and Clinical Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
| | - Chien-Wen Kuo
- From the Division of Molecular and Clinical Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
| | - Niall J Fraser
- From the Division of Molecular and Clinical Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
| | - William Fuller
- From the Division of Molecular and Clinical Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland, United Kingdom
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38
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Thompson JA, Carlson GM. The regulatory α and β subunits of phosphorylase kinase directly interact with its substrate, glycogen phosphorylase. Biochem Biophys Res Commun 2017; 482:221-225. [PMID: 27845042 DOI: 10.1016/j.bbrc.2016.11.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 11/08/2016] [Indexed: 11/17/2022]
Abstract
The selective phosphorylation of glycogen phosphorylase (GP) by its only known kinase, phosphorylase kinase (PhK), keeps glycogen catabolism tightly regulated. In addition to the obligatory interaction between the catalytic γ subunit of PhK and the phosphorylatable region of GP, previous studies have suggested additional sites of interaction between this kinase and its protein substrate. Using short chemical crosslinkers, we have identified direct interactions of GP with the large regulatory α and β subunits of PhK. These newfound interactions were found to be sensitive to ligands that bind PhK.
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Affiliation(s)
- Jackie A Thompson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Gerald M Carlson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Arrington JV, Hsu CC, Tao WA. Kinase Assay-Linked Phosphoproteomics: Discovery of Direct Kinase Substrates. Methods Enzymol 2016; 586:453-471. [PMID: 28137576 DOI: 10.1016/bs.mie.2016.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dissection of direct kinase-substrate relationships provides invaluable information about phosphorylation pathways and can highlight both pathogenic mechanisms and possible drug targets for diseases in which abnormal kinase activity is linked to onset and progression. Here, we describe a mass spectrometry-based strategy to define the direct substrates of a kinase of interest. The kinase assay-linked phosphoproteomics approach examines putative kinase substrates both in vitro and in vivo to produce a list of highly confident substrates.
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Affiliation(s)
- J V Arrington
- Purdue University, West Lafayette, IN, United States; Purdue University Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, United States
| | - C-C Hsu
- Purdue University, West Lafayette, IN, United States
| | - W A Tao
- Purdue University, West Lafayette, IN, United States; Purdue University Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, United States; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States.
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40
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Gordley RM, Williams RE, Bashor CJ, Toettcher JE, Yan S, Lim WA. Engineering dynamical control of cell fate switching using synthetic phospho-regulons. Proc Natl Acad Sci U S A 2016; 113:13528-13533. [PMID: 27821768 PMCID: PMC5127309 DOI: 10.1073/pnas.1610973113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Many cells can sense and respond to time-varying stimuli, selectively triggering changes in cell fate only in response to inputs of a particular duration or frequency. A common motif in dynamically controlled cells is a dual-timescale regulatory network: although long-term fate decisions are ultimately controlled by a slow-timescale switch (e.g., gene expression), input signals are first processed by a fast-timescale signaling layer, which is hypothesized to filter what dynamic information is efficiently relayed downstream. Directly testing the design principles of how dual-timescale circuits control dynamic sensing, however, has been challenging, because most synthetic biology methods have focused solely on rewiring transcriptional circuits, which operate at a single slow timescale. Here, we report the development of a modular approach for flexibly engineering phosphorylation circuits using designed phospho-regulon motifs. By then linking rapid phospho-feedback with slower downstream transcription-based bistable switches, we can construct synthetic dual-timescale circuits in yeast in which the triggering dynamics and the end-state properties of the ON state can be selectively tuned. These phospho-regulon tools thus open up the possibility to engineer cells with customized dynamical control.
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Affiliation(s)
- Russell M Gordley
- Howard Hughes Medical Institute, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Reid E Williams
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Graduate Group in Biophysics, University of California, San Francisco, CA 94158
| | - Caleb J Bashor
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
- Graduate Group in Biophysics, University of California, San Francisco, CA 94158
| | | | - Shude Yan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Wendell A Lim
- Howard Hughes Medical Institute, San Francisco, CA 94158;
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
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41
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Misiura MM, Kolomeisky AB. Theoretical Investigation of the Mechanisms of ERK2 Enzymatic Catalysis. J Phys Chem B 2016; 120:10508-10514. [PMID: 27649451 DOI: 10.1021/acs.jpcb.6b08435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ERK2 are protein kinases that during the enzymatic catalysis, in contrast to traditional enzymes, utilize additional interactions with substrates outside of the active sites. It is widely believed that these docking interactions outside of the enzymatic pockets enhance the specificity of these proteins. However, the molecular mechanisms of how the docking interactions affect the catalysis remain not well understood. Here, we develop a simple theoretical approach to analyze the enzymatic catalysis in ERK2 proteins. Our method is based on first-passage process analysis, and it provides explicit expressions for all dynamic properties of the system. It is found that there are specific binding energies for substrates in docking and catalytic domains that lead to maximal enzymatic reaction rates. Thus, we propose that the role of the docking interactions is not only to increase the enzymatic specificity but also to optimize the dynamics of the catalytic process. Our theoretical results are utilized to describe experimental observations on ERK2 enzymatic activities.
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Affiliation(s)
- Mikita M Misiura
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
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42
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Guo M, Wei J, Zhou Y, Qin Q. MKK7 confers different activities to viral infection of Singapore grouper iridovirus (SGIV) and nervous necrosis virus (NNV) in grouper. FISH & SHELLFISH IMMUNOLOGY 2016; 57:419-427. [PMID: 27601297 DOI: 10.1016/j.fsi.2016.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/13/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
Mitogen-activated protein kinase 7 (MKK7) is one of the major stress-activated protein kinase (SAPK)-activating kinases in response to environmental or physiological stimuli. Here a MKK7 named as Ec-MKK7 was identified from orange-spotted grouper, Epinephelus coioides. The full-length cDNA of Ec-MKK7 was 1853 bp, with an open reading frame (ORF) of 1272 bp encoding a putative protein of 423 amino acids. A characteristic S-K-A-K-T motif was contained in the domain of dual-specificity protein kinase, mitogen-activated protein kinase kinase 7 (PKc_MKK7). Intracellular localization showed that Ec-MKK7 was localized in both the cytoplasm and the nucleus of grouper spleen (GS) and/or grouper brain (EAGB) cells. Moreover, Ec-MKK7 was universally expressed in all examined tissues and showed expression modulation to challenges of lipopolysacchride (LPS), Singapore grouper iridovirus (SGIV) and polyriboinosinic polyribocytidylic acid (poly I:C) in vivo. A gene targeting strategy over-expressing Ec-MKK7 was performed to examine the activities of MKK7 to viral infection in vitro. Our data showed that Ec-MKK7 was involved in the evasion and replication of SGIV but played an antiviral role to the infection of nervous necrosis virus (NNV). All results demonstrated that Ec-MKK7 could play important roles in grouper innate immunity and show distinct functions on virus infection.
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Affiliation(s)
- Minglan Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Jingguang Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Yongcan Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Marine Science, Hainan University, Haikou, 570228, PR China.
| | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China; College of Marine Sciences, South China Agricultural University, Guangzhou 510301, PR China.
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43
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Groves B, Khakhar A, Nadel CM, Gardner RG, Seelig G. Rewiring MAP kinases in Saccharomyces cerevisiae to regulate novel targets through ubiquitination. eLife 2016; 5. [PMID: 27525484 PMCID: PMC5019841 DOI: 10.7554/elife.15200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 08/14/2016] [Indexed: 12/18/2022] Open
Abstract
Evolution has often copied and repurposed the mitogen-activated protein kinase (MAPK) signaling module. Understanding how connections form during evolution, in disease and across individuals requires knowledge of the basic tenets that govern kinase-substrate interactions. We identify criteria sufficient for establishing regulatory links between a MAPK and a non-native substrate. The yeast MAPK Fus3 and human MAPK ERK2 can be functionally redirected if only two conditions are met: the kinase and substrate contain matching interaction domains and the substrate includes a phospho-motif that can be phosphorylated by the kinase and recruit a downstream effector. We used a panel of interaction domains and phosphorylation-activated degradation motifs to demonstrate modular and scalable retargeting. We applied our approach to reshape the signaling behavior of an existing kinase pathway. Together, our results demonstrate that a MAPK can be largely defined by its interaction domains and compatible phospho-motifs and provide insight into how MAPK-substrate connections form. DOI:http://dx.doi.org/10.7554/eLife.15200.001 Nature has evolved a number of ways to link signals from a cell’s environment, like the concentration of a hormone, to the behavior of that cell. These new connections often form by reusing certain common signaling components, such as mitogen-activated protein kinases. These enzymes – referred to as MAPKs for short – are activated by specific signals and alter the activity of target proteins in the cell by adding a phosphate group to them: a process called phosphorylation. These connections thus dictate how cells respond to their environments – and consequently, disruptions to the connections are a common source of disease. Groves, Khakhar et al. set out to understand how connections can be made between a MAPK and a new target protein to gain insights into how these links emerge through evolution and how they might break in disease. Their approach focused on one of the ways that phosphorylation can alter the activity of a target protein: marking it for degradation. Experiments with budding yeast showed that a MAPK could only achieve this if two conditions are met. First, the target protein and kinase need to bind to each other. Second, the target needs to contain a site that when phosphorylated is subsequently recognized by the cell’s protein degradation machinery. By engineering proteins so that they fulfilled these two criteria, Groves, Khakhar et al. created new connections between a yeast MAPK called Fus3 or a human MAPK called ERK2 and a variety of targets. The results showed that the parts of the proteins involved in the interaction step could be completely separate from the parts that are involved in the phosphorylation step. This suggests that connections between kinases and their targets can be rewired simple by mixing together parts of other existing proteins. Finally, Groves, Khakhar et al. confirmed that engineered connections between kinases and targets could predictably change how yeast cells responded to a hormone that normally controls the yeast’s reproductive cycle. Together these results bring us one step closer to understanding how cells assemble the signaling pathways that they use to process information. However further work is needed to see if these findings can be generalized to other signaling components, and if so, to explore if new connections can be built to yield more complicated cellular behaviors. DOI:http://dx.doi.org/10.7554/eLife.15200.002
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Affiliation(s)
- Benjamin Groves
- Department of Electrical Engineering, University of Washington, Seattle, United States
| | - Arjun Khakhar
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Cory M Nadel
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Richard G Gardner
- Department of Pharmacology, University of Washington, Seattle, United States
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, United States.,Department of Computer Science and Engineering, University of Washington, Seattle, United States
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Qvit N, Disatnik MH, Sho J, Mochly-Rosen D. Selective Phosphorylation Inhibitor of Delta Protein Kinase C-Pyruvate Dehydrogenase Kinase Protein-Protein Interactions: Application for Myocardial Injury in Vivo. J Am Chem Soc 2016; 138:7626-35. [PMID: 27218445 PMCID: PMC5065007 DOI: 10.1021/jacs.6b02724] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein kinases regulate numerous cellular processes, including cell growth, metabolism, and cell death. Because the primary sequence and the three-dimensional structure of many kinases are highly similar, the development of selective inhibitors for only one kinase is challenging. Furthermore, many protein kinases are pleiotropic, mediating diverse and sometimes even opposing functions by phosphorylating multiple protein substrates. Here, we set out to develop an inhibitor of a selective protein kinase phosphorylation of only one of its substrates. Focusing on the pleiotropic delta protein kinase C (δPKC), we used a rational approach to identify a distal docking site on δPKC for its substrate, pyruvate dehydrogenase kinase (PDK). We reasoned that an inhibitor of PDK's docking should selectively inhibit the phosphorylation of only PDK without affecting phosphorylation of the other δPKC substrates. Our approach identified a selective inhibitor of PDK docking to δPKC with an in vitro Kd of ∼50 nM and reducing cardiac injury IC50 of ∼5 nM. This inhibitor, which did not affect the phosphorylation of other δPKC substrates even at 1 μM, demonstrated that PDK phosphorylation alone is critical for δPKC-mediated injury by heart attack. The approach we describe is likely applicable for the identification of other substrate-specific kinase inhibitors.
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Affiliation(s)
- Nir Qvit
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford CA 94305-5174 USA
| | - Marie-Hélène Disatnik
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford CA 94305-5174 USA
| | - Jie Sho
- Kunming Biomed International Chenggong, Kunming, P.R. China
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford CA 94305-5174 USA
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45
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Hamill S, Lou HJ, Turk BE, Boggon TJ. Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases. Mol Cell 2016; 62:397-408. [PMID: 27153537 PMCID: PMC4860616 DOI: 10.1016/j.molcel.2016.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 01/07/2023]
Abstract
Cofilin/actin-depolymerizing factor (ADF) proteins are critical nodes that relay signals from protein kinase cascades to the actin cytoskeleton, in particular through site-specific phosphorylation at residue Ser3. This is important for regulation of the roles of cofilin in severing and stabilizing actin filaments. Consequently, cofilin/ADF Ser3 phosphorylation is tightly controlled as an almost exclusive substrate for LIM kinases. Here we determine the LIMK1:cofilin-1 co-crystal structure. We find an interface that is distinct from canonical kinase-substrate interactions. We validate this previously unobserved mechanism for high-fidelity kinase-substrate recognition by in vitro kinase assays, examination of cofilin phosphorylation in mammalian cells, and functional analysis in S. cerevisiae. The interface is conserved across all LIM kinases. Remarkably, we also observe both pre- and postphosphotransfer states in the same crystal lattice. This study therefore provides a molecular understanding of how kinase-substrate recognition acts as a gatekeeper to regulate actin cytoskeletal dynamics.
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Affiliation(s)
- Stephanie Hamill
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520,Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520
| | - Titus J. Boggon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520,Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520,Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520,To who correspondence should be addressed:
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46
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Qvit N, Joshi AU, Cunningham AD, Ferreira JCB, Mochly-Rosen D. Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) Protein-Protein Interaction Inhibitor Reveals a Non-catalytic Role for GAPDH Oligomerization in Cell Death. J Biol Chem 2016; 291:13608-21. [PMID: 27129213 DOI: 10.1074/jbc.m115.711630] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 12/16/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an important glycolytic enzyme, has a non-catalytic (thus a non-canonical) role in inducing mitochondrial elimination under oxidative stress. We recently demonstrated that phosphorylation of GAPDH by δ protein kinase C (δPKC) inhibits this GAPDH-dependent mitochondrial elimination. δPKC phosphorylation of GAPDH correlates with increased cell injury following oxidative stress, suggesting that inhibiting GAPDH phosphorylation should decrease cell injury. Using rational design, we identified pseudo-GAPDH (ψGAPDH) peptide, an inhibitor of δPKC-mediated GAPDH phosphorylation that does not inhibit the phosphorylation of other δPKC substrates. Unexpectedly, ψGAPDH decreased mitochondrial elimination and increased cardiac damage in an animal model of heart attack. Either treatment with ψGAPDH or direct phosphorylation of GAPDH by δPKC decreased GAPDH tetramerization, which corresponded to reduced GAPDH glycolytic activity in vitro and ex vivo Taken together, our study identified the potential mechanism by which oxidative stress inhibits the protective GAPDH-mediated elimination of damaged mitochondria. Our study also identified a pharmacological tool, ψGAPDH peptide, with interesting properties. ψGAPDH peptide is an inhibitor of the interaction between δPKC and GAPDH and of the resulting phosphorylation of GAPDH by δPKC. ψGAPDH peptide is also an inhibitor of GAPDH oligomerization and thus an inhibitor of GAPDH glycolytic activity. Finally, we found that ψGAPDH peptide is an inhibitor of the elimination of damaged mitochondria. We discuss how this unique property of increasing cell damage following oxidative stress suggests a potential use for ψGAPDH peptide-based therapy.
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Affiliation(s)
- Nir Qvit
- From the Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305-5174 and
| | - Amit U Joshi
- From the Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305-5174 and
| | - Anna D Cunningham
- From the Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305-5174 and
| | - Julio C B Ferreira
- the Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Daria Mochly-Rosen
- From the Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305-5174 and
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47
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de Oliveira PSL, Ferraz FAN, Pena DA, Pramio DT, Morais FA, Schechtman D. Revisiting protein kinase-substrate interactions: Toward therapeutic development. Sci Signal 2016; 9:re3. [PMID: 27016527 DOI: 10.1126/scisignal.aad4016] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite the efforts of pharmaceutical companies to develop specific kinase modulators, few drugs targeting kinases have been completely successful in the clinic. This is primarily due to the conserved nature of kinases, especially in the catalytic domains. Consequently, many currently available inhibitors lack sufficient selectivity for effective clinical application. Kinases phosphorylate their substrates to modulate their activity. One of the important steps in the catalytic reaction of protein phosphorylation is the correct positioning of the target residue within the catalytic site. This positioning is mediated by several regions in the substrate binding site, which is typically a shallow crevice that has critical subpockets that anchor and orient the substrate. The structural characterization of this protein-protein interaction can aid in the elucidation of the roles of distinct kinases in different cellular processes, the identification of substrates, and the development of specific inhibitors. Because the region of the substrate that is recognized by the kinase can be part of a linear consensus motif or a nonlinear motif, advances in technology beyond simple linear sequence scanning for consensus motifs were needed. Cost-effective bioinformatics tools are already frequently used to predict kinase-substrate interactions for linear consensus motifs, and new tools based on the structural data of these interactions improve the accuracy of these predictions and enable the identification of phosphorylation sites within nonlinear motifs. In this Review, we revisit kinase-substrate interactions and discuss the various approaches that can be used to identify them and analyze their binding structures for targeted drug development.
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Affiliation(s)
- Paulo Sérgio L de Oliveira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | - Felipe Augusto N Ferraz
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-970, Brazil
| | - Darlene A Pena
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Dimitrius T Pramio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Felipe A Morais
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil
| | - Deborah Schechtman
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508000, Brazil.
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48
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Zeke A, Bastys T, Alexa A, Garai Á, Mészáros B, Kirsch K, Dosztányi Z, Kalinina OV, Reményi A. Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases. Mol Syst Biol 2015; 11:837. [PMID: 26538579 PMCID: PMC4670726 DOI: 10.15252/msb.20156269] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Mitogen‐activated protein kinases (MAPK) are broadly used regulators of cellular signaling. However, how these enzymes can be involved in such a broad spectrum of physiological functions is not understood. Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less‐characterized disordered regions. We used a structurally consistent model on kinase‐docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under‐explored part of the human proteome and applied experimental tools specifically tailored to detect low‐affinity protein–protein interactions for their validation in vitro and in cell‐based assays. The combined computational and experimental approach enabled the identification of many novel MAPK‐docking motifs that were elusive for other large‐scale protein–protein interaction screens. The analysis produced an extensive list of independently evolved linear binding motifs from a functionally diverse set of proteins. These all target, with characteristic binding specificity, an ancient protein interaction surface on evolutionarily related but physiologically clearly distinct three MAPKs (JNK, ERK, and p38). This inventory of human protein kinase binding sites was compared with that of other organisms to examine how kinase‐mediated partnerships evolved over time. The analysis suggests that most human MAPK‐binding motifs are surprisingly new evolutionarily inventions and newly found links highlight (previously hidden) roles of MAPKs. We propose that short MAPK‐binding stretches are created in disordered protein segments through a variety of ways and they represent a major resource for ancient signaling enzymes to acquire new regulatory roles.
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Affiliation(s)
- András Zeke
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Tomas Bastys
- Max Planck Institute for Informatics, Saarbrücken, Germany Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | - Anita Alexa
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Ágnes Garai
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Bálint Mészáros
- Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Klára Kirsch
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | | | - Attila Reményi
- Lendület Protein Interaction Group, Institute of Enzymology Research Center for Natural Sciences Hungarian Academy of Sciences, Budapest, Hungary
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49
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Bardwell AJ, Bardwell L. Two hydrophobic residues can determine the specificity of mitogen-activated protein kinase docking interactions. J Biol Chem 2015; 290:26661-74. [PMID: 26370088 DOI: 10.1074/jbc.m115.691436] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 11/06/2022] Open
Abstract
MAPKs bind to many of their upstream regulators and downstream substrates via a short docking motif (the D-site) on their binding partner. MAPKs that are in different families (e.g. ERK, JNK, and p38) can bind selectively to D-sites in their authentic substrates and regulators while discriminating against D-sites in other pathways. Here we demonstrate that the short hydrophobic region at the distal end of the D-site plays a critical role in determining the high selectivity of JNK MAPKs for docking sites in their cognate MAPK kinases. Changing just 1 or 2 key hydrophobic residues in this submotif is sufficient to turn a weak JNK-binding D-site into a strong one, or vice versa. These specificity-determining differences are also found in the D-sites of the ETS family transcription factors Elk-1 and Net. Moreover, swapping two hydrophobic residues between these D-sites switches the relative efficiency of Elk-1 and Net as substrates for ERK versus JNK, as predicted. These results provide new insights into docking specificity and suggest that this specificity can evolve rapidly by changes to just 1 or 2 amino acids.
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Affiliation(s)
- A Jane Bardwell
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
| | - Lee Bardwell
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
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50
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Assis DM, Juliano L, Paschoalin T, Kouyoumdjian M, Calixto JB, Santos RAS, Pertinhez TA, Gauthier F, Moreau T, Blaber M, Juliano MA. Pharmacological Activities and Hydrolysis by Peptidases of [Phospho-Ser(6)]-Bradykinin (pS(6)-BK). Biochem Pharmacol 2015; 97:203-14. [PMID: 26235942 DOI: 10.1016/j.bcp.2015.07.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/27/2015] [Indexed: 12/27/2022]
Abstract
Phosphorylated kininogen and some of its fragments containing serine phosphorylated bradykinin ([pS(6)]-Bk) were identified in human serum and plasma by a phosphoproteomic approach. We report the kininogenase ability of human tissue and plasma kallikreins and tryptase to generate [pS(6)]-Bk or Lys-[pS(6)]-Bk having as substrate the synthetic human kininogen fluorescent fragment Abz-MISLMKRPPGF[pS(386)]PFRSSRI-NH2. The pharmacological assays of [pS(6)]-Bk showed it as a full B2 bradykinin receptor agonist in smooth muscle, it produces a portal liver hypertensive response in rat and mouse paw edema that lasts longer than Bk. The rat hypotensive response to infusions of Bk is greater than that of [pS(6)]Bk, both if injected through femoral vein or aorta. [pS(6)]-Bk was more resistant than Bk to kininase digestion performed with angiotensin converting enzyme, neprilysin, thimet oligopeptidase, aminopeptidase P and carboxypeptidase M. (1)H-NMR experiments indicated that [pS(6)]-Bk has lower flexibility, with the pS(6)-P(7) bond restricted to the trans conformation, and can explain [pS(6)]-Bk resistance to hydrolysis. In conclusion, [pS(6)]-Bk presenting lower activity than Bk, with longer lasting effects and being slowly released by kininogenases from synthetic Abz-MISLMKRPPGF[pS(386)]PFRSSRI-NH2, suggests that phosphorylation of the kininogens can be an efficient kallikrein-kinin system regulator.
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Affiliation(s)
- Diego M Assis
- Department of Biophysics, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo/SP, Brazil
| | - Luiz Juliano
- Department of Biophysics, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo/SP, Brazil.
| | - Thaysa Paschoalin
- Department of Biophysics, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo/SP, Brazil
| | - Maria Kouyoumdjian
- Department of Biochemistry, Biophysics and Medicine, São Paulo Federal University, São Paulo/SP, Brazil
| | - Joao B Calixto
- Department of Pharmacology, Federal University of Santa Catarina, Florianópolis/SC, Brazil
| | - Robson A S Santos
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte/MG, Brazil
| | - Thelma A Pertinhez
- Transfusion Medicine Unit, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Italy
| | | | | | - Michael Blaber
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Maria A Juliano
- Department of Biophysics, Escola Paulista de Medicina, Federal University of São Paulo, São Paulo/SP, Brazil.
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