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Regev C, Jang H, Nussinov R. ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events. J Mol Biol 2025:169130. [PMID: 40216017 DOI: 10.1016/j.jmb.2025.169130] [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: 02/03/2025] [Revised: 03/19/2025] [Accepted: 04/01/2025] [Indexed: 04/26/2025]
Abstract
ERK, a coveted proliferation drug target, is a pivotal kinase in the Ras/ERK signaling cascade. Despite this, crucial questions about its activation have not been fully explored on the foundational, conformational level. Such questions include (i) Why ERK's activation demands dual phosphorylation; (ii) What is the role of each phosphorylation site in the activation loop; and (iii) Exactly how the (ordered) phosphorylation steps affect the conformational ensembles of the activation loop, their propensities and restriction to a narrower range favoring ERK's catalytic action. Here we used explicit molecular dynamics simulations to study ERK's stability and the conformational changes in different stages along the activation process. The initial monophosphorylation event elongates the activation loop to enable successive phosphorylations, which reintroduce stability/compactness through newly formed salt bridges. The interactions formed by monophosphorylation are site-dependent, with threonine's phosphorylation presenting stronger electrostatic interactions compared to tyrosine's. Dual phosphorylated ERKs revealed a compact kinase structure which allows the HRD catalytic motif to stabilize the ATP. We further observe that the hinge and the homodimerization binding site responded to a tri-state signaling code based solely on the phosphorylation degree (unphosphorylated, monophosphorylated, dual phosphorylated) of the activation loop, confirming that the activation loop can allosterically influence distant regions. Last, our findings indicate that threonine phosphorylation as the second step is necessary for ERK to become effectively activated and that activation depends on the phosphorylation order. Collectively, we offer ERK's dual allosteric phosphorylation code in activation and explain why the phosphorylation site order is crucial.
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Affiliation(s)
- Clil Regev
- Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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2
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Orand T, Delaforge E, Lee A, Kragelj J, Tengo M, Tengo L, Blackledge M, Boeri Erba E, Davis RJ, Palencia A, Jensen MR. Bipartite binding of the intrinsically disordered scaffold protein JIP1 to the kinase JNK1. Proc Natl Acad Sci U S A 2025; 122:e2419915122. [PMID: 39999166 PMCID: PMC11892650 DOI: 10.1073/pnas.2419915122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Accepted: 01/18/2025] [Indexed: 02/27/2025] Open
Abstract
Scaffold proteins are key players in many signaling pathways where they ensure spatial and temporal control of molecular interactions by simultaneous tethering of multiple signaling components. The protein JIP1 acts as a scaffold within the c-Jun N-terminal kinase (JNK) signaling pathway by assembling three kinases, MLK3, MKK7, and JNK, into a macromolecular complex that enables their specific activation. The recruitment of these kinases depends on the 450-amino acid intrinsically disordered tail of JIP1, however, the structural details of this tail and the molecular mechanisms by which it binds kinases have remained elusive. Here, we provide an atomic resolution structural description of the JIP1 tail, and we study its interaction with the kinase JNK1. Using NMR spectroscopy, we show that JNK1 not only engages with the well-known docking site motif (D-motif) of JIP1, but also interacts with a noncanonical F-motif. We determine the crystal structure of the JIP1-JNK1 complex at 2.35 Å resolution revealing a bipartite binding mode of JIP1. Our work provides insights into the sequence determinants of F-motifs suggesting that these motifs may be more prevalent in JNK substrates than previously recognized. More broadly, our study highlights the power of NMR spectroscopy in uncovering kinase interaction motifs within disordered scaffold proteins, and it paves the way for atomic-resolution interaction studies of JIP1 with its multitude of interaction partners.
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Affiliation(s)
- Thibault Orand
- Université Grenoble Alpes, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, CNRS, Institut de Biologie Structurale, Grenoble38044, France
| | - Elise Delaforge
- Université Grenoble Alpes, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, CNRS, Institut de Biologie Structurale, Grenoble38044, France
| | - Alexandra Lee
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA01655
| | - Jaka Kragelj
- Université Grenoble Alpes, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, CNRS, Institut de Biologie Structurale, Grenoble38044, France
| | - Maud Tengo
- Université Grenoble Alpes, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, CNRS, Institut de Biologie Structurale, Grenoble38044, France
| | - Laura Tengo
- Université Grenoble Alpes, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, CNRS, Institut de Biologie Structurale, Grenoble38044, France
| | - Martin Blackledge
- Université Grenoble Alpes, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, CNRS, Institut de Biologie Structurale, Grenoble38044, France
| | - Elisabetta Boeri Erba
- Université Grenoble Alpes, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, CNRS, Institut de Biologie Structurale, Grenoble38044, France
| | - Roger J. Davis
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA01655
| | - Andrés Palencia
- Institute for Advanced Biosciences, Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble38000, France
| | - Malene Ringkjøbing Jensen
- Université Grenoble Alpes, Commissariat à l’Énergie Atomique et aux Énergies Alternatives, CNRS, Institut de Biologie Structurale, Grenoble38044, France
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3
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Wu EJ, Kandalkar AT, Ehrmann JF, Tong AB, Zhang J, Cong Q, Wu H. A structural atlas of death domain fold proteins reveals their versatile roles in biology and function. Proc Natl Acad Sci U S A 2025; 122:e2426986122. [PMID: 39977327 PMCID: PMC11874512 DOI: 10.1073/pnas.2426986122] [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: 12/24/2024] [Accepted: 01/23/2025] [Indexed: 02/22/2025] Open
Abstract
Death domain fold (DDF) superfamily proteins are critically important players in pathways of cell death and inflammation. DDFs are often essential scaffolding domains in receptors, adaptors, or effectors of these pathways by mediating homo- and hetero-oligomerization including helical filament assembly. At the downstream ends of these pathways, effector oligomerization by DDFs brings the enzyme domains into proximity for their dimerization and activation. Hundreds of structures of these domains have been solved. However, a comprehensive understanding of DDFs is lacking. In this article, we report the curation of a DDF structural atlas as a public website (deathdomain.org) and deduce the common and distinct principles of DDF-mediated oligomerization among the four families (death domain or DD, death effector domain or DED, caspase recruitment domain or CARD, and pyrin domain or PYD). We further annotate DDFs genome-wide based on AlphaFold-predicted models and protein sequences. These studies reveal mechanistic rules for this widely distributed domain superfamily.
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Affiliation(s)
- Emily J. Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Saratoga High School, Saratoga, CA95070
| | - Ankita T. Kandalkar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Biology, College of Science, Northeastern University, Boston, MA02115
| | - Julian F. Ehrmann
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
| | - Alexander B. Tong
- Jason L. Choy Laboratory of Single-Molecule Biophysics, Institute for Quantitative Biosciences, Chemistry Graduate Group, University of California, Berkeley, CA94720
| | - Jing Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Eugene McDermott Center for Human Growth and Development, University of Texas, Southwestern Medical Center, Dallas, TX75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Qian Cong
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Eugene McDermott Center for Human Growth and Development, University of Texas, Southwestern Medical Center, Dallas, TX75390
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Biology, College of Science, Northeastern University, Boston, MA02115
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4
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Chou CL, Jayatissa NU, Kichula ET, Ou SM, Limbutara K, Knepper MA. Phosphoproteomic response to epidermal growth factor in native rat inner medullary collecting duct. Am J Physiol Renal Physiol 2025; 328:F29-F47. [PMID: 39508840 PMCID: PMC11918369 DOI: 10.1152/ajprenal.00182.2024] [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: 06/21/2024] [Revised: 09/25/2024] [Accepted: 11/01/2024] [Indexed: 12/18/2024] Open
Abstract
Epidermal growth factor (EGF) has important effects in the renal collecting duct to regulate salt and water transport. To identify elements of EGF-mediated signaling in the rat renal inner medullary collecting duct (IMCD), we carried out phosphoproteomic analysis. Biochemically isolated rat IMCD suspensions were treated with 1 µM of EGF or vehicle for 30 min. We performed comprehensive quantitative phosphoproteomics using tandem mass tag (TMT)-labeling of tryptic peptides followed by protein mass spectrometry. We present a data resource reporting all detected phosphorylation sites and their changes in response to EGF. For a total of 29,881 unique phosphorylation sites, 135 sites were increased and 119 sites were decreased based on stringent statistical analysis. The data are provided to users at https://esbl.nhlbi.nih.gov/Databases/EGF-phospho/. The analysis demonstrated that EGF signals through canonical EGF pathways in the renal IMCD. Analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in which EGF-regulated phosphoproteins are over-represented in native rat IMCD cells confirmed mapping to RAF-MEK-extracellular signal-regulated kinase (ERK) signaling but also pointed to a role for EGF in the regulation of protein translation. A large number of phosphoproteins regulated by EGF contained PDZ domains that are key elements of epithelial polarity determination. We also provide a collecting duct EGF-network map as a user-accessible web resource at https://esbl.nhlbi.nih.gov/Databases/EGF-network/. Overall, the phosphoproteomic data presented provide a useful resource for experimental design and modeling of signaling in the renal collecting duct.NEW & NOTEWORTHY EGF negatively regulates transepithelial water and salt transport across the kidney collecting duct. This study identified phosphoproteins affected by EGF stimulation in normal rat collecting ducts, providing insights into global cell signaling mechanisms. Bioinformatic analyses highlighted enhanced canonical ERK signaling alongside a diminished activity in the PI3K-Akt pathway, which is crucial for cell proliferation and survival. This EGF response differs somewhat from prior studies where both pathways were prominently activated.
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Affiliation(s)
- Chung-Lin Chou
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Nipun U Jayatissa
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Elena T Kichula
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Shuo-Ming Ou
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Kavee Limbutara
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
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5
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Mercurio I, D’Abrosca G, della Valle M, Malgieri G, Fattorusso R, Isernia C, Russo L, Di Gaetano S, Pedone EM, Pirone L, Del Gatto A, Zaccaro L, Alberga D, Saviano M, Mangiatordi GF. Molecular interactions between a diphenyl scaffold and PED/PEA15: Implications for type II diabetes therapeutics targeting PED/PEA15 - Phospholipase D1 interaction. Comput Struct Biotechnol J 2024; 23:2001-2010. [PMID: 38770160 PMCID: PMC11103223 DOI: 10.1016/j.csbj.2024.04.063] [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: 03/04/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
In a recent study, we have identified BPH03 as a promising scaffold for the development of compounds aimed at modulating the interaction between PED/PEA15 (Phosphoprotein Enriched in Diabetes/Phosphoprotein Enriched in Astrocytes 15) and PLD1 (phospholipase D1), with potential applications in type II diabetes therapy. PED/PEA15 is known to be overexpressed in certain forms of diabetes, where it binds to PLD1, thereby reducing insulin-stimulated glucose transport. The inhibition of this interaction reestablishes basal glucose transport, indicating PED as a potential target of ligands capable to recover glucose tolerance and insulin sensitivity. In this study, we employ computational methods to provide a detailed description of BPH03 interaction with PED, evidencing the presence of a hidden druggable pocket within its PLD1 binding surface. We also elucidate the conformational changes that occur during PED interaction with BPH03. Moreover, we report new NMR data supporting the in-silico findings and indicating that BPH03 disrupts the PED/PLD1 interface displacing PLD1 from its interaction with PED. Our study represents a significant advancement toward the development of potential therapeutics for the treatment of type II diabetes.
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Affiliation(s)
- Ivan Mercurio
- Institute of Crystallography, CNR, Via Amendola 122/o, 70126 Bari, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gianluca D’Abrosca
- Department of Clinical and Experimental Medicine, University of Foggia, Viale Pinto 1, 71122 Foggia, Italy
- Institute of Crystallography, CNR, Via Vivaldi 43, 81100, Caserta, Italy
| | - Maria della Valle
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | - Domenico Alberga
- Institute of Crystallography, CNR, Via Amendola 122/o, 70126 Bari, Italy
| | - Michele Saviano
- Institute of Crystallography, CNR, Via Vivaldi 43, 81100, Caserta, Italy
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6
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König C, Ivanisenko NV, Hillert-Richter LK, Namjoshi D, Natu K, Espe J, Reinhold D, Kolchanov NA, Ivanisenko VA, Kähne T, Bose K, Lavrik IN. Targeting type I DED interactions at the DED filament serves as a sensitive switch for cell fate decisions. Cell Chem Biol 2024; 31:1969-1985.e6. [PMID: 39053461 DOI: 10.1016/j.chembiol.2024.06.014] [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] [Received: 01/31/2024] [Revised: 03/22/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024]
Abstract
Activation of procaspase-8 in the death effector domain (DED) filaments of the death-inducing signaling complex (DISC) is a key step in apoptosis. In this study, a rationally designed cell-penetrating peptide, DEDid, was engineered to mimic the h2b helical region of procaspase-8-DED2 containing a highly conservative FL motif. Furthermore, mutations were introduced into the DEDid binding site of the procaspase-8 type I interface. Additionally, our data suggest that DEDid targets other type I DED interactions such as those of FADD. Both approaches of blocking type I DED interactions inhibited CD95L-induced DISC assembly, caspase activation and apoptosis. We showed that inhibition of procaspase-8 type I interactions by mutations not only diminished procaspase-8 recruitment to the DISC but also destabilized the FADD core of DED filaments. Taken together, this study offers insights to develop strategies to target DED proteins, which may be considered in diseases associated with cell death and inflammation.
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Affiliation(s)
- Corinna König
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, Magdeburg, Germany
| | - Nikita V Ivanisenko
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, Magdeburg, Germany
| | - Laura K Hillert-Richter
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, Magdeburg, Germany
| | - Deepti Namjoshi
- Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India
| | - Kalyani Natu
- Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India; Homi Bhabha National Institute, BARC Training School Complex, Mumbai, India
| | - Johannes Espe
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, Magdeburg, Germany
| | - Dirk Reinhold
- Institute of Molecular and Clinical immunology, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Nikolai A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia; Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Vladimir A Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia; Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia; State Novosibirsk University, Novosibirsk, Russia
| | - Thilo Kähne
- Institute of Experimental and Internal Medicine (iEIM), Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Kakoli Bose
- Integrated Biophysics and Structural Biology Lab, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Mumbai, India; Homi Bhabha National Institute, BARC Training School Complex, Mumbai, India
| | - Inna N Lavrik
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, Magdeburg, Germany.
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7
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Becker AE, Kochanowski P, Wu PK, Wątor E, Chen W, Guchhait K, Biela AP, Grudnik P, Park JI. ERK1/2 interaction with DHPS regulates eIF5A deoxyhypusination independently of ERK kinase activity. Cell Rep 2024; 43:114831. [PMID: 39392755 PMCID: PMC11544350 DOI: 10.1016/j.celrep.2024.114831] [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: 12/05/2023] [Revised: 08/20/2024] [Accepted: 09/19/2024] [Indexed: 10/13/2024] Open
Abstract
This study explores a non-kinase effect of extracellular regulated kinases 1/2 (ERK1/2) on the interaction between deoxyhypusine synthase (DHPS) and its substrate, eukaryotic translation initiation factor 5A (eIF5A). We report that Raf/MEK/ERK activation decreases the DHPS-ERK1/2 interaction while increasing DHPS-eIF5A association in cells. We determined the cryoelectron microscopy (cryo-EM) structure of the DHPS-ERK2 complex at 3.5 Å to show that ERK2 hinders substrate entrance to the DHPS active site, subsequently inhibiting deoxyhypusination in vitro. In cells, impairing the ERK2 activation loop, but not the catalytic site, prolongs the DHPS-ERK2 interaction irrespective of Raf/MEK signaling. The ERK2 Ser-Pro-Ser motif, but not the common docking or F-site recognition sites, also regulates this complex. These data suggest that ERK1/2 dynamically regulate the DHPS-eIF5A interaction in response to Raf/MEK activity, regardless of its kinase function. In contrast, ERK1/2 kinase activity is necessary to regulate the expression of DHPS and eIF5A. These findings highlight an ERK1/2-mediated dual kinase-dependent and -independent regulation of deoxyhypusination.
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Affiliation(s)
- Andrew E Becker
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Paweł Kochanowski
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Pui-Kei Wu
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Elżbieta Wątor
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Wenjing Chen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Koushik Guchhait
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Artur P Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Przemysław Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Jong-In Park
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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8
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Azmal M, Paul JK, Prima FS, Talukder OF, Ghosh A. An in silico molecular docking and simulation study to identify potential anticancer phytochemicals targeting the RAS signaling pathway. PLoS One 2024; 19:e0310637. [PMID: 39298437 PMCID: PMC11412525 DOI: 10.1371/journal.pone.0310637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Accepted: 09/02/2024] [Indexed: 09/21/2024] Open
Abstract
The dysregulation of the rat sarcoma (RAS) signaling pathway, particularly the MAPK/ERK cascade, is a hallmark of many cancers, leading to uncontrolled cellular proliferation and resistance to apoptosis-inducing treatments. Dysregulation of the MAPK/ERK pathway is common in various cancers including pancreatic, lung, and colon cancers, making it a critical target for therapeutic intervention. Natural compounds, especially phytochemicals, offer a promising avenue for developing new anticancer therapies due to their potential to interfere with these signaling pathways. This study investigates the potential of anticancer phytochemicals to inhibit the MAPK/ERK pathway through molecular docking and simulation techniques. A total of 26 phytochemicals were screened from an initial set of 340 phytochemicals which were retrieved from Dr. Duke's database using in silico methods for their binding affinity and stability. Molecular docking was performed to identify key interactions with ERK2, followed by molecular dynamics (MD) simulations to evaluate the stability of these interactions. The study identified several phytochemicals, including luteolin, hispidulin, and isorhamnetin with a binding score of -10.1±0 Kcal/mol, -9.86±0.15 Kcal/mol, -9.76±0.025 Kcal/mol, respectively as promising inhibitors of the ERK2 protein. These compounds demonstrated significant binding affinities and stable interactions with ERK2 in MD simulation studies up to 200ns, particularly at the active site. The radius of gyration analysis confirmed the stability of these phytochemical-protein complexes' compactness, indicating their potential to inhibit ERK activity. The stability and binding affinity of these compounds suggest that they can effectively inhibit ERK2 activity, potentially leading to more effective and less toxic cancer treatments. The findings underscore the therapeutic promise of these phytochemicals, which could serve as a basis for developing new cancer therapies.
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Affiliation(s)
- Mahir Azmal
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Jibon Kumar Paul
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Fatema Sultana Prima
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Omar Faruk Talukder
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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9
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Haller YA, Jiang J, Wan Z, Childress A, Wang S, Haydel SE. M. tuberculosis PrrA binds the dosR promoter and regulates mycobacterial adaptation to hypoxia. Tuberculosis (Edinb) 2024; 148:102531. [PMID: 38885567 DOI: 10.1016/j.tube.2024.102531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024]
Abstract
The PrrAB two-component system (TCS) is essential for Mycobacterium tuberculosis viability. Previously, it was demonstrated that PrrA binds DNA in the absence of PrrB-mediated transphosphorylation and that non-cognate serine/threonine-kinases phosphorylate PrrA threonine-6 (T6). Therefore, we investigated the differential binding affinity and regulatory properties of the M. tuberculosis-derived wild-type PrrA, PrrA phosphomimetic (D58E, T6E), and PrrA phosphoablative (D58A, T6A) proteins with the prrAMtb, dosRMtb, and cydAMtb genes. While we hypothesized greater DNA binding affinity and more pronounced regulation by PrrA phosphomimetic variants, recombinant, wild-type PrrAMtb bound DNA with greatest affinity. Collectively, wild-type PrrAMtb recombinant protein displayed the highest binding affinity to the dosRMtb promoter (KD 3.46 ± 2.09 nM), followed by the prrAMtb promoter (KD 9.00 ± 2.66 nM). To establish PrrAMtb regulatory activity, we constructed M. smegmatis ΔprrABMsmeg::prrAMtb strains with each of the PrrAMtb variants and extrachromosomal prrAMtb, dosRMtb, and cydAMtb promoter-mCherry reporter fusions. Our findings showed that PrrAMtb is autoregulatory and induces dosRMtb expression only during in vitro, hypoxic growth. Combined expression of prrABMtb in M. smegmatis ΔprrAB significantly induced cydAMtb promoter-mCherry expression. Our studies advanced the understanding of PrrA function and PrrAB phosphorylation-mediated regulatory mechanisms and control of mycobacterial dosR and cydA hypoxic and low-oxygen responsive genes.
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Affiliation(s)
- Yannik A Haller
- School of Life Sciences, Arizona State University, Tempe, AZ, USA; Biodesign Institute Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ, USA
| | - Jiapei Jiang
- Biodesign Institute Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Zijian Wan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA; School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA
| | - Alexia Childress
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Shaopeng Wang
- Biodesign Institute Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Shelley E Haydel
- School of Life Sciences, Arizona State University, Tempe, AZ, USA; Biodesign Institute Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ, USA.
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10
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Yang B, Lin Y, Huang Y, Shen YQ, Chen Q. Thioredoxin (Trx): A redox target and modulator of cellular senescence and aging-related diseases. Redox Biol 2024; 70:103032. [PMID: 38232457 PMCID: PMC10827563 DOI: 10.1016/j.redox.2024.103032] [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] [Received: 10/14/2023] [Revised: 12/03/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024] Open
Abstract
Thioredoxin (Trx) is a compact redox-regulatory protein that modulates cellular redox state by reducing oxidized proteins. Trx exhibits dual functionality as an antioxidant and a cofactor for diverse enzymes and transcription factors, thereby exerting influence over their activity and function. Trx has emerged as a pivotal biomarker for various diseases, particularly those associated with oxidative stress, inflammation, and aging. Recent clinical investigations have underscored the significance of Trx in disease diagnosis, treatment, and mechanistic elucidation. Despite its paramount importance, the intricate interplay between Trx and cellular senescence-a condition characterized by irreversible growth arrest induced by multiple aging stimuli-remains inadequately understood. In this review, our objective is to present a comprehensive and up-to-date overview of the structure and function of Trx, its involvement in redox signaling pathways and cellular senescence, its association with aging and age-related diseases, as well as its potential as a therapeutic target. Our review aims to elucidate the novel and extensive role of Trx in senescence while highlighting its implications for aging and age-related diseases.
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Affiliation(s)
- Bowen Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Yumeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Yibo Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Ying-Qiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
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11
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Anderson JW, Vaisar D, Jones DN, Pegram LM, Vigers GP, Chen H, Moffat JG, Ahn NG. Conformation selection by ATP-competitive inhibitors and allosteric communication in ERK2. eLife 2024; 12:RP91507. [PMID: 38537148 PMCID: PMC10972564 DOI: 10.7554/elife.91507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named 'L' and 'R,' where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here, we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
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Affiliation(s)
- Jake W Anderson
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - David Vaisar
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - David N Jones
- Department of Pharmacology, University of Colorado Anschutz Medical CenterBoulderUnited States
| | - Laurel M Pegram
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | | | - Huifen Chen
- Genentech, Inc.South San FranciscoUnited States
| | | | - Natalie G Ahn
- Department of Biochemistry, University of ColoradoBoulderUnited States
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12
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Pegram L, Riccardi D, Ahn N. Activation Loop Plasticity and Active Site Coupling in the MAP Kinase, ERK2. J Mol Biol 2023; 435:168309. [PMID: 37806554 PMCID: PMC10676806 DOI: 10.1016/j.jmb.2023.168309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 09/03/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
Previous studies of the protein kinase, ERK2, using NMR and hydrogen-exchange measurements have shown changes in dynamics accompanying its activation by phosphorylation. However, knowledge about the conformational motions involved is incomplete. Here, we examined ERK2 using long conventional molecular dynamics (MD) simulations starting from crystal structures of phosphorylated (2P) and unphosphorylated (0P) forms. Individual trajectories were run for (5 to 25) μs, totaling 727 μs. The results show unexpected flexibility of the A-loop, with multiple long-lived (>5 μs) conformational states in both 2P- and 0P-ERK2. Differential contact network and principal component analyses reveal coupling between the A-loop fold and active site dynamics, with evidence for conformational selection in the kinase core of 2P-ERK2 but not 0P-ERK2. Simulations of 2P-ERK2 show A-loop states corresponding to restrained dynamics within the N-lobe, including regions around catalytic residues. One A-loop conformer forms lasting interactions with the L16 segment, leading to reduced RMSF and greater compaction in the active site. By contrast, simulations of 0P-ERK2 reveal excursions of A-loop residues away from the C-lobe, leading to greater active site mobility. Thus, the A-loop in ERK2 switches between distinct conformations that reflect coupling with the active site, possibly via the L16 segment. Crystal packing interactions suggest that lattice contacts with the A-loop may restrain its structural variation in X-ray structures of ERK2. The novel conformational states identified by MD expand our understanding of ERK2 regulation, by linking the activated state of the kinase to reduced dynamics and greater compaction surrounding the catalytic site.
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Affiliation(s)
- Laurel Pegram
- Department of Biochemistry, University of Colorado, Boulder, CO 80305, USA
| | - Demian Riccardi
- Thermodynamics Research Center, Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO, USA
| | - Natalie Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO 80305, USA.
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13
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Anderson JW, Vaisar D, Jones DN, Pegram LM, Vigers GP, Chen H, Moffat JG, Ahn NG. Conformation Selection by ATP-competitive Inhibitors and Allosteric Communication in ERK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557258. [PMID: 37745518 PMCID: PMC10515847 DOI: 10.1101/2023.09.12.557258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named "L" and "R", where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
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Affiliation(s)
| | - David Vaisar
- Department of Biochemistry, University of Colorado, Boulder, CO
| | - David N. Jones
- Department of Pharmacology, University of Colorado Anschutz Medical Center, Aurora, CO
| | - Laurel M. Pegram
- Department of Biochemistry, University of Colorado, Boulder, CO
- Present address: Loxo Oncology, Louisville, CO 80027
| | - Guy P. Vigers
- Array BioPharma, Inc., Boulder, CO
- Present address: Allium Consulting LLC, Boulder, CO 80304
| | - Huifen Chen
- Genentech, Inc. South San Francisco, CA, USA
| | | | - Natalie G. Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO
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14
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Litowczenko J, Wychowaniec JK, Załęski K, Marczak Ł, Edwards-Gayle CJC, Tadyszak K, Maciejewska BM. Micro/nano-patterns for enhancing differentiation of human neural stem cells and fabrication of nerve conduits via soft lithography and 3D printing. BIOMATERIALS ADVANCES 2023; 154:213653. [PMID: 37862812 DOI: 10.1016/j.bioadv.2023.213653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023]
Abstract
Topographical cues on materials can manipulate cellular fate, particularly for neural cells that respond well to such cues. Utilizing biomaterial surfaces with topographical features can effectively influence neuronal differentiation and promote neurite outgrowth. This is crucial for improving the regeneration of damaged neural tissue after injury. Here, we utilized groove patterns to create neural conduits that promote neural differentiation and axonal growth. We investigated the differentiation of human neural stem cells (NSCs) on silicon dioxide groove patterns with varying height-to-width/spacing ratios. We hypothesize that NSCs can sense the microgrooves with nanoscale depth on different aspect ratio substrates and exhibit different morphologies and differentiation fate. A comprehensive approach was employed, analyzing cell morphology, neurite length, and cell-specific markers. These aspects provided insights into the behavior of the investigated NSCs and their response to the topographical cues. Three groove-pattern models were designed with varying height-to-width/spacing ratios of 80, 42, and 30 for groove pattern widths of 1 μm, 5 μm, and 10 μm and nanoheights of 80 nm, 210 nm, and 280 nm. Smaller groove patterns led to longer neurites and more effective differentiation towards neurons, whereas larger patterns promoted multidimensional differentiation towards both neurons and glia. We transferred these cues onto patterned polycaprolactone (PCL) and PCL-graphene oxide (PCL-GO) composite 'stamps' using simple soft lithography and reproducible extrusion 3D printing methods. The patterned scaffolds elicited a response from NSCs comparable to that of silicon dioxide groove patterns. The smallest pattern stimulated the highest neurite outgrowth, while the middle-sized grooves of PCL-GO induced effective synaptogenesis. We demonstrated the potential for such structures to be wrapped into tubes and used as grafts for peripheral nerve regeneration. Grooved PCL and PCL-GO conduits could be a promising alternative to nerve grafting.
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Affiliation(s)
- Jagoda Litowczenko
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, PL61614 Poznań, Poland.
| | - Jacek K Wychowaniec
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, PL61614 Poznań, Poland; AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Karol Załęski
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, PL61614 Poznań, Poland
| | - Łukasz Marczak
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | | | - Krzysztof Tadyszak
- Institute of Macromolecular Chemistry, CAS, Heyrovského nám. 2, 162 06 Prague 6, Czech Republic
| | - Barbara M Maciejewska
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, PL61614 Poznań, Poland
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15
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Postiglione AE, Adams LL, Ekhator ES, Odelade AE, Patwardhan S, Chaudhari M, Pardue AS, Kumari A, LeFever WA, Tornow OP, Kaoud TS, Neiswinger J, Jeong JS, Parsonage D, Nelson KJ, Kc DB, Furdui CM, Zhu H, Wommack AJ, Dalby KN, Dong M, Poole LB, Keyes JD, Newman RH. Hydrogen peroxide-dependent oxidation of ERK2 within its D-recruitment site alters its substrate selection. iScience 2023; 26:107817. [PMID: 37744034 PMCID: PMC10514464 DOI: 10.1016/j.isci.2023.107817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/11/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) are dysregulated in many pervasive diseases. Recently, we discovered that ERK1/2 is oxidized by signal-generated hydrogen peroxide in various cell types. Since the putative sites of oxidation lie within or near ERK1/2's ligand-binding surfaces, we investigated how oxidation of ERK2 regulates interactions with the model substrates Sub-D and Sub-F. These studies revealed that ERK2 undergoes sulfenylation at C159 on its D-recruitment site surface and that this modification modulates ERK2 activity differentially between substrates. Integrated biochemical, computational, and mutational analyses suggest a plausible mechanism for peroxide-dependent changes in ERK2-substrate interactions. Interestingly, oxidation decreased ERK2's affinity for some D-site ligands while increasing its affinity for others. Finally, oxidation by signal-generated peroxide enhanced ERK1/2's ability to phosphorylate ribosomal S6 kinase A1 (RSK1) in HeLa cells. Together, these studies lay the foundation for examining crosstalk between redox- and phosphorylation-dependent signaling at the level of kinase-substrate selection.
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Affiliation(s)
- Anthony E. Postiglione
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Biology, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Laquaundra L. Adams
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Ese S. Ekhator
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Anuoluwapo E. Odelade
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Supriya Patwardhan
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Meenal Chaudhari
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Computational Data Science and Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Mathematics and Computer Science, University of Virginia at Wise, Wise, VA 24293, USA
| | - Avery S. Pardue
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Anjali Kumari
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - William A. LeFever
- Department of Chemistry, High Point University, High Point, NC 27268, USA
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Olivia P. Tornow
- Department of Chemistry, High Point University, High Point, NC 27268, USA
| | - Tamer S. Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Johnathan Neiswinger
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biology, Belhaven University, Jackson, MS 39202, USA
| | - Jun Seop Jeong
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Kimberly J. Nelson
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Dukka B. Kc
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Cristina M. Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew J. Wommack
- Department of Chemistry, High Point University, High Point, NC 27268, USA
| | - Kevin N. Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ming Dong
- Department of Chemistry, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Jeremiah D. Keyes
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
- Department of Biology, Penn State University Behrend, Erie, PA 16563, USA
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
| | - Robert H. Newman
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
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16
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Martin-Vega A, Cobb MH. Navigating the ERK1/2 MAPK Cascade. Biomolecules 2023; 13:1555. [PMID: 37892237 PMCID: PMC10605237 DOI: 10.3390/biom13101555] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological processes including proliferation, cell cycle control, growth, and survival; common across all cell types. Notably, ERK1/2 are implicated in specific processes in a context-dependent manner as in stem cells and pancreatic β-cells. Alterations in the different components of this cascade result in dysregulation of the effector kinases ERK1/2 which communicate with hundreds of substrates. Aberrant activation of the pathway contributes to a range of disorders, including cancer. This review provides an overview of the structure, activation, regulation, and mutational frequency of the different tiers of the cascade; with a particular focus on ERK1/2. We highlight the importance of scaffold proteins that contribute to kinase localization and coordinate interaction dynamics of the kinases with substrates, activators, and inhibitors. Additionally, we explore innovative therapeutic approaches emphasizing promising avenues in this field.
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Affiliation(s)
- Ana Martin-Vega
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
| | - Melanie H. Cobb
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA
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17
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Pegram L, Riccardi D, Ahn N. Activation loop plasticity and active site coupling in the MAP kinase, ERK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.537040. [PMID: 37090603 PMCID: PMC10120733 DOI: 10.1101/2023.04.15.537040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Changes in the dynamics of the protein kinase, ERK2, have been shown to accompany its activation by dual phosphorylation. However, our knowledge about the conformational changes represented by these motions is incomplete. Previous NMR relaxation dispersion studies showed that active, dual-phosphorylated ERK2 undergoes global exchange between at least two energetically similar conformations. These findings, combined with measurements by hydrogen exchange mass spectrometry (HX-MS), suggested that the global conformational exchange involves motions of the activation loop (A-loop) that are coupled to regions surrounding the kinase active site. In order to better understand the contribution of dynamics to the activation of ERK2, we applied long conventional molecular dynamics (MD) simulations starting from crystal structures of active, phosphorylated (2P), and inactive, unphosphorylated (0P) ERK2. Individual trajectories were run for (5 to 25) µ s and totaled 727 µ s. The results showed that the A-loop is unexpectedly flexible in both 2P- and 0P-ERK2, and able to adopt multiple long-lived (>5 µ s) conformational states. Simulations starting from the X-ray structure of 2P-ERK2 (2ERK) revealed A-loop states corresponding to restrained dynamics within the N-lobe, including regions surrounding catalytic residues. One A-loop conformer forms lasting interactions with the C-terminal L16 segment and shows reduced RMSF and greater compaction in the active site. By contrast, simulations starting from the most common X-ray conformation of 0P-ERK2 (5UMO) reveal frequent excursions of A-loop residues away from a C-lobe docking site pocket and towards a new state that shows greater dynamics in the N-lobe and disorganization around the active site. Thus, the A-loop in ERK2 appears to switch between distinct conformational states that reflect allosteric coupling with the active site, likely occurring via the L16 segment. Analyses of crystal packing interactions across many structural datasets suggest that the A-loop observed in X-ray structures of ERK2 may be driven by lattice contacts and less representative of the solution structure. The novel conformational states identified by MD expand our understanding of ERK2 regulation, by linking the activated state of the kinase to reduced dynamics and greater compaction surrounding the catalytic site.
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18
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O’Shaughnessy WJ, Dewangan PS, Paiz EA, Reese ML. Not your Mother's MAPKs: Apicomplexan MAPK function in daughter cell budding. PLoS Pathog 2022; 18:e1010849. [PMID: 36227859 PMCID: PMC9560070 DOI: 10.1371/journal.ppat.1010849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Reversible phosphorylation by protein kinases is one of the core mechanisms by which biological signals are propagated and processed. Mitogen-activated protein kinases, or MAPKs, are conserved throughout eukaryotes where they regulate cell cycle, development, and stress response. Here, we review advances in our understanding of the function and biochemistry of MAPK signaling in apicomplexan parasites. As expected for well-conserved signaling modules, MAPKs have been found to have multiple essential roles regulating both Toxoplasma tachyzoite replication and sexual differentiation in Plasmodium. However, apicomplexan MAPK signaling is notable for the lack of the canonical kinase cascade that normally regulates the networks, and therefore must be regulated by a distinct mechanism. We highlight what few regulatory relationships have been established to date, and discuss the challenges to the field in elucidating the complete MAPK signaling networks in these parasites.
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Affiliation(s)
- William J. O’Shaughnessy
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, Texas, United States of America
| | - Pravin S. Dewangan
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, Texas, United States of America
| | - E. Ariana Paiz
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michael L. Reese
- Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas, Southwestern Medical Center, Dallas, Texas, United States of America
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19
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Ikedife J, He J, Wei Y. PEA-15 engages in allosteric interactions using a common scaffold in a phosphorylation-dependent manner. Sci Rep 2022; 12:116. [PMID: 34997083 PMCID: PMC8742051 DOI: 10.1038/s41598-021-04099-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/15/2021] [Indexed: 11/10/2022] Open
Abstract
Phosphoprotein enriched in astrocytes, 15 kDa (PEA-15) is a death-effector domain (DED) containing protein involved in regulating mitogen-activated protein kinase and apoptosis pathways. In this molecular dynamics study, we examined how phosphorylation of the PEA-15 C-terminal tail residues, Ser-104 and Ser-116, allosterically mediates conformational changes of the DED and alters the binding specificity from extracellular-regulated kinase (ERK) to Fas-associated death domain (FADD) protein. We delineated that the binding interfaces between the unphosphorylated PEA-15 and ERK2 and between the doubly phosphorylated PEA-15 and FADD are similarly composed of a scaffold that includes both the DED and the C-terminal tail residues of PEA-15. While the unphosphorylated serine residues do not directly interact with ERK2, the phosphorylated Ser-116 engages in strong electrostatic interactions with arginine residues on FADD DED. Upon PEA-15 binding, FADD repositions its death domain (DD) relative to the DED, an essential conformational change to allow the death-inducing signaling complex (DISC) assembly.
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Affiliation(s)
- Joyce Ikedife
- Department of Chemistry, New Jersey City University, Jersey City, NJ, 07305, USA
| | - Jianlin He
- Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005, Fujian, China
| | - Yufeng Wei
- Department of Chemistry, New Jersey City University, Jersey City, NJ, 07305, USA.
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20
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Cotton TR, Cobbold SA, Bernardini JP, Richardson LW, Wang XS, Lechtenberg BC. Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216. Mol Cell 2021; 82:598-615.e8. [PMID: 34998453 DOI: 10.1016/j.molcel.2021.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 10/11/2021] [Accepted: 12/08/2021] [Indexed: 12/13/2022]
Abstract
An increasing number of genetic diseases are linked to deregulation of E3 ubiquitin ligases. Loss-of-function mutations in the RING-between-RING (RBR) family E3 ligase RNF216 (TRIAD3) cause Gordon-Holmes syndrome (GHS) and related neurodegenerative diseases. Functionally, RNF216 assembles K63-linked ubiquitin chains and has been implicated in regulation of innate immunity signaling pathways and synaptic plasticity. Here, we report crystal structures of key RNF216 reaction states including RNF216 in complex with ubiquitin and its reaction product, K63 di-ubiquitin. Our data provide a molecular explanation for chain-type specificity and reveal the molecular basis for disruption of RNF216 function by pathogenic GHS mutations. Furthermore, we demonstrate how RNF216 activity and chain-type specificity are regulated by phosphorylation and that RNF216 is allosterically activated by K63-linked di-ubiquitin. These molecular insights expand our understanding of RNF216 function and its role in disease and further define the mechanistic diversity of the RBR E3 ligase family.
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Affiliation(s)
- Thomas R Cotton
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Simon A Cobbold
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jonathan P Bernardini
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Lachlan W Richardson
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Xiangyi S Wang
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Bernhard C Lechtenberg
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia.
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21
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Li D, Liu Y, Yi P, Zhu Z, Li W, Zhang QC, Li JB, Ou G. RNA editing restricts hyperactive ciliary kinases. Science 2021; 373:984-991. [PMID: 34446600 DOI: 10.1126/science.abd8971] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/01/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
Protein kinase activity must be precisely regulated, but how a cell governs hyperactive kinases remains unclear. In this study, we generated a constitutively active mitogen-activated protein kinase DYF-5 (DYF-5CA) in Caenorhabditis elegans that disrupted sensory cilia. Genetic suppressor screens identified that mutations of ADR-2, an RNA adenosine deaminase, rescued ciliary phenotypes of dyf-5CA We found that dyf-5CA animals abnormally transcribed antisense RNAs that pair with dyf-5CA messenger RNA (mRNA) to form double-stranded RNA, recruiting ADR-2 to edit the region ectopically. RNA editing impaired dyf-5CA mRNA splicing, and the resultant intron retentions blocked DYF-5CA protein translation and activated nonsense-mediated dyf-5CA mRNA decay. The kinase RNA editing requires kinase hyperactivity. The similar RNA editing-dependent feedback regulation restricted the other ciliary kinases NEKL-4/NEK10 and DYF-18/CCRK, which suggests a widespread mechanism that underlies kinase regulation.
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Affiliation(s)
- Dongdong Li
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Yufan Liu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Peishan Yi
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Zhiwen Zhu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
| | - Wei Li
- School of Medicine, Tsinghua University, Beijing, China
| | - Qiangfeng Cliff Zhang
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China. .,Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.,McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing, China
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22
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Lee S, Kim J, Jo J, Chang JW, Sim J, Yun H. Recent advances in development of hetero-bivalent kinase inhibitors. Eur J Med Chem 2021; 216:113318. [PMID: 33730624 DOI: 10.1016/j.ejmech.2021.113318] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022]
Abstract
Identifying a pharmacological agent that targets only one of more than 500 kinases present in humans is an important challenge. One potential solution to this problem is the development of bivalent kinase inhibitors, which consist of two connected fragments, each bind to a dissimilar binding site of the bisubstrate enzyme. The main advantage of bivalent (type V) kinase inhibitors is generating more interactions with target enzymes that can enhance the molecules' selectivity and affinity compared to single-site inhibitors. Earlier type V inhibitors were not suitable for the cellular environment and were mostly used in in vitro studies. However, recently developed bivalent compounds have high kinase affinity, high biological and chemical stability in vivo. This review summarized the hetero-bivalent kinase inhibitors described in the literature from 2014 to the present. We attempted to classify the molecules by serine/threonine and tyrosine kinase inhibitors, and then each target kinase and its hetero-bivalent inhibitor was assessed in depth. In addition, we discussed the analysis of advantages, limitations, and perspectives of bivalent kinase inhibitors compared with the monovalent kinase inhibitors.
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Affiliation(s)
- Seungbeom Lee
- College of Pharmacy, CHA University, Pocheon-si, Gyeonggi-do, 11160, Republic of Korea
| | - Jisu Kim
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Jeyun Jo
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea
| | - Jae Won Chang
- Department of Pharmacology & Chemical Biology, School of Medicine, Emory University, Atlanta, GA, USA; Department of Hematology & Medical Oncology, School of Medicine, Emory University, Atlanta, GA, USA; Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Jaehoon Sim
- College of Pharmacy, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Hwayoung Yun
- College of Pharmacy, Pusan National University, Busan, 46241, Republic of Korea.
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23
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Wu Y, Li X, Chen M, Liu Z, Zhang X, Zheng S, Xu X. Phosphorylation of PED/PEA-15 at Ser116 and phosphorylation of p27 at Thr187 indicates a poor prognosis in hepatocellular carcinoma. Oncol Lett 2021; 21:177. [PMID: 33574916 PMCID: PMC7816284 DOI: 10.3892/ol.2021.12438] [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: 12/24/2019] [Accepted: 11/24/2020] [Indexed: 11/06/2022] Open
Abstract
Hepatocellular carcinoma (HCC) constitutes a deadly cancer with a high rate of recurrence and metastasis. Phosphoprotein enriched in diabetes/phosphoprotein enriched in astrocytes-15 (PED/PEA-15) is a protein involved in the metabolism of glucose that regulates numerous cellular processes, including cell division, apoptosis and migration in numerous types of cancer. However, PED/PEA-15 may act as a tumor-promotor or a tumor-suppressor depending on its phosphorylation status. In the present study, the association between the phosphorylation of PED/PEA-15 at Ser116 [PED/PEA-15(S116)], the phosphorylation of P27 at Thr187 [P-p27(T187)] and the clinicopathological features and prognosis of patients with HCC was assessed. The levels of PED/PEA-15(S116) and P-p27(T187) were determined using immunohistochemistry and western blotting analysis in resected liver tumor tissues and adjacent non-cancerous tissues obtained from 60 patients with HCC as well as normal liver tissues from 12 patients with benign lesions. The association between the expression levels of these two markers and the clinicopathological features of patients with HCC was explored. Using the Kaplan-Meier method, the prognostic value of PED/PEA-15(S116) and P-p27(T187) expression levels was determined. The results demonstrated that the levels of PED/PEA-15(S116) and P-p27(T187) proteins were remarkably higher in the HCC group compared with those in the adjacent and normal tissue groups (both P<0.05). In addition, a moderate positive correlation was observed between the levels of PED/PEA-15(S116) and P-p27(T187) (r=0.434; P<0.05). The levels of these two proteins were associated with the Edmondson grade, Tumor-Node-Metastasis (TNM) stage, vascular invasion and tumor multiplicity (all P<0.05). Furthermore, the Kaplan-Meier analysis results demonstrated that patients with HCC that presented with positive expression of PED/PEA-15(S116) and P-p27(T187) exhibited a dismal prognosis compared with that in patients with negative expression regarding the overall survival (OS), as well as disease-free survival (both P<0.05). Multivariate Cox analysis revealed that the TNM stage (P<0.05), vascular invasion (P<0.05), PED/PEA-15(S116) levels (P<0.001) and P-p27(T187) levels (P<0.05) were independent prognostic factors for OS in patients with HCC. In conclusion the results of the present study demonstrated that PED/PEA-15(S116) and P-p27(T187) levels were upregulated in HCC tissues compared with those in the adjacent and normal tissues; PED/PEA-15(S116) and P-p27(T187) expression may serve as an indicator of a poor prognosis in patients with HCC, suggesting that these proteins may be prospective therapeutic targets for HCC.
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Affiliation(s)
- Yifeng Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China.,Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang 310006, P.R. China.,Division of Hepatobiliary and Pancreatic Surgery, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo, Zhejiang 315040, P.R. China
| | - Xianpeng Li
- Division of Hepatobiliary and Pancreatic Surgery, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo, Zhejiang 315040, P.R. China
| | - Mingliang Chen
- Division of Hepatobiliary and Pancreatic Surgery, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo, Zhejiang 315040, P.R. China
| | - Zhikun Liu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China.,Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang 310006, P.R. China
| | - Xuanyu Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China.,Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang 310006, P.R. China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China.,Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang 310006, P.R. China
| | - Xiao Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China.,Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang 310006, P.R. China
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24
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PEA15 loss of function and defective cerebral development in the domestic cat. PLoS Genet 2020; 16:e1008671. [PMID: 33290415 DOI: 10.1371/journal.pgen.1008671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Cerebral cortical size and organization are critical features of neurodevelopment and human evolution, for which genetic investigation in model organisms can provide insight into developmental mechanisms and the causes of cerebral malformations. However, some abnormalities in cerebral cortical proliferation and folding are challenging to study in laboratory mice due to the absence of gyri and sulci in rodents. We report an autosomal recessive allele in domestic cats associated with impaired cerebral cortical expansion and folding, giving rise to a smooth, lissencephalic brain, and that appears to be caused by homozygosity for a frameshift in PEA15 (phosphoprotein expressed in astrocytes-15). Notably, previous studies of a Pea15 targeted mutation in mice did not reveal structural brain abnormalities. Affected cats, however, present with a non-progressive hypermetric gait and tremors, develop dissociative behavioral defects and aggression with age, and exhibit profound malformation of the cerebrum, with a 45% average decrease in overall brain weight, and reduction or absence of the ectosylvian, sylvian and anterior cingulate gyrus. Histologically, the cerebral cortical layers are disorganized, there is substantial loss of white matter in tracts such as the corona radiata and internal capsule, but the cerebellum is relatively spared. RNA-seq and immunohistochemical analysis reveal astrocytosis. Fibroblasts cultured from affected cats exhibit increased TNFα-mediated apoptosis, and increased FGFb-induced proliferation, consistent with previous studies implicating PEA15 as an intracellular adapter protein, and suggesting an underlying pathophysiology in which increased death of neurons accompanied by increased proliferation of astrocytes gives rise to abnormal organization of neuronal layers and loss of white matter. Taken together, our work points to a new role for PEA15 in development of a complex cerebral cortex that is only apparent in gyrencephalic species.
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25
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Wang S, Wang C, Hu Y, Li X, Jin S, Liu O, Gou R, Zhuang Y, Guo Q, Nie X, Zhu L, Liu J, Lin B. ZNF703 promotes tumor progression in ovarian cancer by interacting with HE4 and epigenetically regulating PEA15. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:264. [PMID: 33246486 PMCID: PMC7693506 DOI: 10.1186/s13046-020-01770-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/08/2020] [Indexed: 12/11/2022]
Abstract
Background It is known that the transcription factor zinc finger protein 703 (ZNF703) plays an important role in physiological functions and the occurrence and development of various tumors. However, the role and mechanism of ZNF703 in ovarian cancer are unclear. Materials and methods Immunohistochemistry was used to analyze the expression of ZNF703 in ovarian cancer patients and to assess the effect of ZNF703 expression on the survival and prognosis of ovarian cancer patients. ZNF703 overexpression and suppression expression experiments were used to evaluate the effect of ZNF703 on malignant biological behavior of ovarian cancer cells in vitro. Detecting the interaction between HE4 and ZNF703 by immunofluorescence colocalization and coprecipitation, and nuclear translocation. Chromatin immunoprecipitation-sequencing (ChIP-Seq), dual luciferase reporter assay, ChIP-PCR, in vivo model were applied to study the molecular mechanism of ZNF703 affecting the development of ovarian cancer. Results ZNF703 was highly expressed in ovarian cancer tissues, and its expression level is related to the prognosis of ovarian cancer patients. In vivo and in vitro experiments confirmed that ZNF703 overexpression/inhibition expression will promoted/inhibited the malignant biological behavior of ovarian cancer. Mechanically, ZNF703 interacted with HE4, and HE4 promoted nuclear translocation of ZNF703. ChIP-Seq identified multiple regulatory targets of ZNF703, of which ZNF703 directly binds to the enhancer region of PEA15 to promote the transcription of PEA15 and thereby promoted the proliferation of cancer cells. Conclusion The results showed that ZNF703 as an oncogene played an important role in the epigenetic modification of ovarian cancer proliferation, and suggested that ZNF703 as a transcription factor may become a prognostic factor and a potential therapeutic target for ovarian cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-020-01770-0.
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Affiliation(s)
- Shuang Wang
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China
| | - Caixia Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yuexin Hu
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China
| | - Xiao Li
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China
| | - Shan Jin
- Department of Obstetrics and Gynaecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, China
| | - Ouxuan Liu
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China
| | - Rui Gou
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China
| | - Yuan Zhuang
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China
| | - Qian Guo
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China
| | - Xin Nie
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China
| | - Liancheng Zhu
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China
| | - Juanjuan Liu
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China
| | - Bei Lin
- Department of Obstetrics and Gynaecology, Shengjing Hospital Affiliated to China Medical University, No. 36, Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China. .,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, Liaoning, China.
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26
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ERK signalling: a master regulator of cell behaviour, life and fate. Nat Rev Mol Cell Biol 2020; 21:607-632. [PMID: 32576977 DOI: 10.1038/s41580-020-0255-7] [Citation(s) in RCA: 643] [Impact Index Per Article: 128.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2020] [Indexed: 12/13/2022]
Abstract
The proteins extracellular signal-regulated kinase 1 (ERK1) and ERK2 are the downstream components of a phosphorelay pathway that conveys growth and mitogenic signals largely channelled by the small RAS GTPases. By phosphorylating widely diverse substrates, ERK proteins govern a variety of evolutionarily conserved cellular processes in metazoans, the dysregulation of which contributes to the cause of distinct human diseases. The mechanisms underlying the regulation of ERK1 and ERK2, their mode of action and their impact on the development and homeostasis of various organisms have been the focus of much attention for nearly three decades. In this Review, we discuss the current understanding of this important class of kinases. We begin with a brief overview of the structure, regulation, substrate recognition and subcellular localization of ERK1 and ERK2. We then systematically discuss how ERK signalling regulates six fundamental cellular processes in response to extracellular cues. These processes are cell proliferation, cell survival, cell growth, cell metabolism, cell migration and cell differentiation.
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27
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Ancient MAPK ERK7 is regulated by an unusual inhibitory scaffold required for Toxoplasma apical complex biogenesis. Proc Natl Acad Sci U S A 2020; 117:12164-12173. [PMID: 32409604 PMCID: PMC7275706 DOI: 10.1073/pnas.1921245117] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Apicomplexan parasites include organisms that cause widespread and devastating human diseases such as malaria, cryptosporidiosis, and toxoplasmosis. These parasites are named for a structure, called the “apical complex,” that organizes their invasion and secretory machinery. We found that two proteins, apical cap protein 9 (AC9) and an enzyme called ERK7, work together to facilitate apical complex assembly. Intriguingly, ERK7 is an ancient molecule that is found throughout Eukaryota, though its regulation and function are poorly understood. AC9 is a scaffold that concentrates ERK7 at the base of the developing apical complex. In addition, AC9 binding likely confers substrate selectivity upon ERK7. This simple competitive regulatory model may be a powerful but largely overlooked mechanism throughout biology. Apicomplexan parasites use a specialized cilium structure called the apical complex to organize their secretory organelles and invasion machinery. The apical complex is integrally associated with both the parasite plasma membrane and an intermediate filament cytoskeleton called the inner-membrane complex (IMC). While the apical complex is essential to the parasitic lifestyle, little is known about the regulation of apical complex biogenesis. Here, we identify AC9 (apical cap protein 9), a largely intrinsically disordered component of the Toxoplasma gondii IMC, as essential for apical complex development, and therefore for host cell invasion and egress. Parasites lacking AC9 fail to successfully assemble the tubulin-rich core of their apical complex, called the conoid. We use proximity biotinylation to identify the AC9 interaction network, which includes the kinase extracellular signal-regulated kinase 7 (ERK7). Like AC9, ERK7 is required for apical complex biogenesis. We demonstrate that AC9 directly binds ERK7 through a conserved C-terminal motif and that this interaction is essential for ERK7 localization and function at the apical cap. The crystal structure of the ERK7–AC9 complex reveals that AC9 is not only a scaffold but also inhibits ERK7 through an unusual set of contacts that displaces nucleotide from the kinase active site. ERK7 is an ancient and autoactivating member of the mitogen-activated kinase (MAPK) family and its regulation is poorly understood in all organisms. We propose that AC9 dually regulates ERK7 by scaffolding and concentrating it at its site of action while maintaining it in an “off” state until the specific binding of a true substrate.
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28
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Ohkubo T, Kameyama A, Kamiya K, Kondo M, Hara M. F-segments of Arabidopsis dehydrins show cryoprotective activities for lactate dehydrogenase depending on the hydrophobic residues. PHYTOCHEMISTRY 2020; 173:112300. [PMID: 32087435 DOI: 10.1016/j.phytochem.2020.112300] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 05/26/2023]
Abstract
Although dehydrins show cryoprotective activities for freeze-sensitive enzymes, the underlying mechanism is still under investigation. Here, we report that F-segments conserved in some dehydrins cryoprotected lactate dehydrogenase (LDH) as well as K-segments, which were previously identified as cryoprotective segments of dehydrins. The cryoprotective activity levels of four F-segments of Arabidopsis dehydrins were similar to that of a typical K-segment. Amino acid substitution experiments indicated that the activity of the F-segment of Arabidopsis COR47 (designated as Fseg) depended on the hydrophobic residues (L, F, and V). Intriguingly, when all the amino acids other than the hydrophobic residues were changed to glycine, the cryoprotective activity did not change, suggesting that the hydrophobic amino acids were sufficient for Fseg activity. Circular dichroism analysis indicated that Fseg was mainly disordered in aqueous solution as well as Fseg_Φ/T, in which the hydrophobic residues of Fseg were changed to T. This suggested that the hydrophobic interaction might be related to the cryoprotective activities of Fseg.
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Affiliation(s)
- Tomohiro Ohkubo
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka, Shizuoka, 422-8529, Japan
| | - Ayuko Kameyama
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka, Shizuoka, 422-8529, Japan
| | - Keita Kamiya
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka, Shizuoka, 422-8529, Japan
| | - Mitsuru Kondo
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka, Shizuoka, 422-8529, Japan; Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Shizuoka, Shizuoka, 422-8529, Japan
| | - Masakazu Hara
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka, Shizuoka, 422-8529, Japan.
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29
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Fenn K, Wong CT, Darbari VC. Mycobacterium tuberculosis Uses Mce Proteins to Interfere With Host Cell Signaling. Front Mol Biosci 2020; 6:149. [PMID: 31998747 PMCID: PMC6961568 DOI: 10.3389/fmolb.2019.00149] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis continues to be the main cause for mortality by an infectious agent, making Mycobacterium tuberculosis one of the most successful pathogens to survive for long durations within human cells. In order to survive against host defenses, M. tuberculosis modulates host cell signaling. It employs many proteins to achieve this and the Mce proteins are emerging as one group that play a role in host cell signaling in addition to their primary role as lipid/sterol transporters. Mce proteins belong to the conserved Mce/MlaD superfamily ubiquitous in diderm bacteria and chloroplasts. In mycobacteria, mce operons, encode for six different Mce proteins that assemble with inner membrane permeases into complexes that span across the mycobacterial cell wall. Their involvement in signaling modulation is varied and they have been shown to bind ERK1/2 to alter host cytokine expression; eEF1A1 to promote host cell proliferation and integrins for host cell adherence and entry. Recently, structures of prokaryotic Mce/MlaD proteins have been determined, giving an insight into the conserved domain. In this mini-review, we discuss current evidence for the role of mycobacterial Mce proteins in host cell signaling and structural characteristics of the protein-protein interactions coordinated by the human proteins to modulate the host signaling.
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Affiliation(s)
- Katherine Fenn
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Chi Tung Wong
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Vidya Chandran Darbari
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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30
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Crespo-Flores SL, Cabezas A, Hassan S, Wei Y. PEA-15 C-Terminal Tail Allosterically Modulates Death-Effector Domain Conformation and Facilitates Protein-Protein Interactions. Int J Mol Sci 2019; 20:ijms20133335. [PMID: 31284641 PMCID: PMC6651876 DOI: 10.3390/ijms20133335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/28/2019] [Accepted: 07/05/2019] [Indexed: 11/16/2022] Open
Abstract
Phosphoprotein enriched in astrocytes, 15 kDa (PEA-15) exerts its regulatory roles on several critical cellular pathways through protein–protein interactions depending on its phosphorylation states. It can either inhibit the extracellular signal-regulated kinase (ERK) activities when it is dephosphorylated or block the assembly of death-inducing signaling complex (DISC) and the subsequent activation of apoptotic initiator, caspase-8, when it is phosphorylated. Due to the important roles of PEA-15 in regulating these pathways that lead to opposite cellular outcomes (cell proliferation vs. cell death), we proposed a phosphostasis (phosphorylation homeostasis) model, in which the phosphorylation states of the protein are vigorously controlled and regulated to maintain a delicate balance. The phosphostasis gives rise to the protective cellular functions of PEA-15 to preserve optimum cellular conditions. In this article, using advanced multidimensional nuclear magnetic resonance (NMR) techniques combined with a novel chemical shift (CS)-Rosetta algorithm for de novo protein structural determination, we report a novel conformation of PEA-15 death-effector domain (DED) upon interacting with ERK2. This new conformation is modulated by the irregularly structured C-terminal tail when it first recognizes and binds to ERK2 at the d-peptide recruitment site (DRS) in an allosteric manner, and is facilitated by the rearrangement of the surface electrostatic and hydrogen-bonding interactions on the DED. In this ERK2-bound conformation, three of the six helices (α2, α3, and α4) comprising the DED reorient substantially in comparison to the free-form structure, exposing key residues on the other three helices that directly interact with ERK2 at the DEF-docking site (docking site for ERK, FxF) and the activation loop. Additionally, we provide evidence that the phosphorylation of the C-terminal tail leads to a distinct conformation of DED, allowing efficient interactions with Fas-associated death domain (FADD) protein at the DISC. Our results substantiate the allosteric regulatory roles of the C-terminal tail in modulating DED conformation and facilitating protein–protein interactions of PEA-15.
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Affiliation(s)
| | - Andres Cabezas
- Department of Chemistry, New Jersey City University, Jersey City, NJ 07305-1596, USA
| | - Sherouk Hassan
- Department of Chemistry, New Jersey City University, Jersey City, NJ 07305-1596, USA
| | - Yufeng Wei
- Department of Chemistry, New Jersey City University, Jersey City, NJ 07305-1596, USA.
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31
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Olea-Flores M, Zuñiga-Eulogio MD, Mendoza-Catalán MA, Rodríguez-Ruiz HA, Castañeda-Saucedo E, Ortuño-Pineda C, Padilla-Benavides T, Navarro-Tito N. Extracellular-Signal Regulated Kinase: A Central Molecule Driving Epithelial-Mesenchymal Transition in Cancer. Int J Mol Sci 2019; 20:E2885. [PMID: 31200510 PMCID: PMC6627365 DOI: 10.3390/ijms20122885] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a reversible cellular process, characterized by changes in gene expression and activation of proteins, favoring the trans-differentiation of the epithelial phenotype to a mesenchymal phenotype. This process increases cell migration and invasion of tumor cells, progression of the cell cycle, and resistance to apoptosis and chemotherapy, all of which support tumor progression. One of the signaling pathways involved in tumor progression is the MAPK pathway. Within this family, the ERK subfamily of proteins is known for its contributions to EMT. The ERK subfamily is divided into typical (ERK 1/2/5), and atypical (ERK 3/4/7/8) members. These kinases are overexpressed and hyperactive in various types of cancer. They regulate diverse cellular processes such as proliferation, migration, metastasis, resistance to chemotherapy, and EMT. In this context, in vitro and in vivo assays, as well as studies in human patients, have shown that ERK favors the expression, function, and subcellular relocalization of various proteins that regulate EMT, thus promoting tumor progression. In this review, we discuss the mechanistic roles of the ERK subfamily members in EMT and tumor progression in diverse biological systems.
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Affiliation(s)
- Monserrat Olea-Flores
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Miriam Daniela Zuñiga-Eulogio
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Miguel Angel Mendoza-Catalán
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Hugo Alberto Rodríguez-Ruiz
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Eduardo Castañeda-Saucedo
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Carlos Ortuño-Pineda
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
| | - Teresita Padilla-Benavides
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
| | - Napoleón Navarro-Tito
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas s/n Chilpancingo, Gro. 39090, Mexico.
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32
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Sammons RM, Ghose R, Tsai KY, Dalby KN. Targeting ERK beyond the boundaries of the kinase active site in melanoma. Mol Carcinog 2019; 58:1551-1570. [PMID: 31190430 DOI: 10.1002/mc.23047] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022]
Abstract
Extracellular signal-regulated kinase 1/2 (ERK1/2) constitute a point of convergence for complex signaling events that regulate essential cellular processes, including proliferation and survival. As such, dysregulation of the ERK signaling pathway is prevalent in many cancers. In the case of BRAF-V600E mutant melanoma, ERK inhibition has emerged as a viable clinical approach to abrogate signaling through the ERK pathway, even in cases where MEK and Raf inhibitor treatments fail to induce tumor regression due to resistance mechanisms. Several ERK inhibitors that target the active site of ERK have reached clinical trials, however, many critical ERK interactions occur at other potentially druggable sites on the protein. Here we discuss the role of ERK signaling in cell fate, in driving melanoma, and in resistance mechanisms to current BRAF-V600E melanoma treatments. We explore targeting ERK via a distinct site of protein-protein interaction, known as the D-recruitment site (DRS), as an alternative or supplementary mode of ERK pathway inhibition in BRAF-V600E melanoma. Targeting the DRS with inhibitors in melanoma has the potential to not only disrupt the catalytic apparatus of ERK but also its noncatalytic functions, which have significant impacts on spatiotemporal signaling dynamics and cell fate.
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Affiliation(s)
- Rachel M Sammons
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York
| | - Kenneth Y Tsai
- Departments of Anatomic Pathology and Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas.,Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
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33
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Zaballos MA, Acuña-Ruiz A, Morante M, Crespo P, Santisteban P. Regulators of the RAS-ERK pathway as therapeutic targets in thyroid cancer. Endocr Relat Cancer 2019; 26:R319-R344. [PMID: 30978703 DOI: 10.1530/erc-19-0098] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/30/2022]
Abstract
Thyroid cancer is mostly an ERK-driven carcinoma, as up to 70% of thyroid carcinomas are caused by mutations that activate the RAS/ERK mitogenic signaling pathway. The incidence of thyroid cancer has been steadily increasing for the last four decades; yet, there is still no effective treatment for advanced thyroid carcinomas. Current research efforts are focused on impairing ERK signaling with small-molecule inhibitors, mainly at the level of BRAF and MEK. However, despite initial promising results in animal models, the clinical success of these inhibitors has been limited by the emergence of tumor resistance and relapse. The RAS/ERK pathway is an extremely complex signaling cascade with multiple points of control, offering many potential therapeutic targets: from the modulatory proteins regulating the activation state of RAS proteins to the scaffolding proteins of the pathway that provide spatial specificity to the signals, and finally, the negative feedbacks and phosphatases responsible for inactivating the pathway. The aim of this review is to give an overview of the biology of RAS/ERK regulators in human cancer highlighting relevant information on thyroid cancer and future areas of research.
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Affiliation(s)
- Miguel A Zaballos
- Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Adrián Acuña-Ruiz
- Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Morante
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Cantabria, Santander, Spain
| | - Piero Crespo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Cantabria, Santander, Spain
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
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34
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Wagner T, André-Leroux G, Hindie V, Barilone N, Lisa MN, Hoos S, Raynal B, Vulliez-Le Normand B, O'Hare HM, Bellinzoni M, Alzari PM. Structural insights into the functional versatility of an FHA domain protein in mycobacterial signaling. Sci Signal 2019; 12:12/580/eaav9504. [PMID: 31064884 DOI: 10.1126/scisignal.aav9504] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Forkhead-associated (FHA) domains are modules that bind to phosphothreonine (pThr) residues in signaling cascades. The FHA-containing mycobacterial protein GarA is a central element of a phosphorylation-dependent signaling pathway that redirects metabolic flux in response to amino acid starvation or cell growth requirements. GarA acts as a phosphorylation-dependent ON/OFF molecular switch. In its nonphosphorylated ON state, the GarA FHA domain engages in phosphorylation-independent interactions with various metabolic enzymes that orchestrate nitrogen flow, such as 2-oxoglutarate decarboxylase (KGD). However, phosphorylation at the GarA N-terminal region by the protein kinase PknB or PknG triggers autoinhibition through the intramolecular association of the N-terminal domain with the FHA domain, thus blocking all downstream interactions. To investigate these different FHA binding modes, we solved the crystal structures of the mycobacterial upstream (phosphorylation-dependent) complex PknB-GarA and the downstream (phosphorylation-independent) complex GarA-KGD. Our results show that the phosphorylated activation loop of PknB serves as a docking site to recruit GarA through canonical FHA-pThr interactions. However, the same GarA FHA-binding pocket targets an allosteric site on nonphosphorylated KGD, where a key element of recognition is a phosphomimetic aspartate. Further enzymatic and mutagenesis studies revealed that GarA acted as a dynamic allosteric inhibitor of KGD by preventing crucial motions in KGD that are necessary for catalysis. Our results provide evidence for physiological phosphomimetics, supporting numerous mutagenesis studies using such approaches, and illustrate how evolution can shape a single FHA-binding pocket to specifically interact with multiple phosphorylated and nonphosphorylated protein partners.
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Affiliation(s)
- Tristan Wagner
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Gwénaëlle André-Leroux
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Valérie Hindie
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Nathalie Barilone
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - María-Natalia Lisa
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Sylviane Hoos
- Institut Pasteur, Plateforme de Biophysique Moléculaire, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Bertrand Raynal
- Institut Pasteur, Plateforme de Biophysique Moléculaire, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Brigitte Vulliez-Le Normand
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Helen M O'Hare
- Leicester Tuberculosis Research Group (LTBRG) and Leicester Institute of Structural and Chemical Biology (LISCB), Department of Respiratory Science & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Marco Bellinzoni
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | - Pedro M Alzari
- Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.
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Baig MH, Kausar MA, Husain FM, Shakil S, Ahmad I, Yadav BS, Saeed M. Interfering PLD1-PED/PEA15 interaction using self-inhibitory peptides: An in silico study to discover novel therapeutic candidates against type 2 diabetes. Saudi J Biol Sci 2019; 26:160-164. [PMID: 30622421 PMCID: PMC6319087 DOI: 10.1016/j.sjbs.2018.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/13/2018] [Accepted: 08/20/2018] [Indexed: 11/25/2022] Open
Abstract
Diabetes type 2 (T2D) is a very complex disorder with a large number of cases reported worldwide. There are several reported molecular targets which are being used towards drug design. In spite of extensive research efforts, there is no sure shot treatment available. One of the major reasons for this failure or restricted success in T2D research is the identification of a major/breakthrough therapeutic target responsible for the progression of T2D. It has been well documented that one of the major causes mediating the insulin resistance is the interaction of PLD1 with PED/PEA15. Herein, we have performed in silico experiments to investigate the interaction between PLD1 with PED/PEA15. Furthermore, this study has explored pertinent molecular interactions involving the self-derived peptides. The peptides identified in this study are found to be capable of restricting the interaction of these two proteins. Accordingly, the study suggests that the “self-derived peptides” could be used as promising therapeutic candidate(s) against T2D.
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Affiliation(s)
- Mohammad Hassan Baig
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
- Corresponding author.
| | - Mohd Adnan Kausar
- Department of Biochemistry, College of Medicine, University of Hail, Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, Saudi Arabia
| | - Shazi Shakil
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- Research center for advanced materials science, King Khalid university, Abha, Saudi Arabia
| | - Brijesh S. Yadav
- Department of Bioengineering, University of Information Science and Technology, The Former Yugolav Republic of Macedonia
| | - Mohd Saeed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Saudi Arabia
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36
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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: 1.4] [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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37
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Zou J, Lei T, Guo P, Yu J, Xu Q, Luo Y, Ke R, Huang D. Mechanisms shaping the role of ERK1/2 in cellular senescence (Review). Mol Med Rep 2018; 19:759-770. [PMID: 30535440 PMCID: PMC6323238 DOI: 10.3892/mmr.2018.9712] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/10/2018] [Indexed: 01/19/2023] Open
Abstract
Senescence is a result of cellular stress and is a potential mechanism for regulating cancer. As a member of the mitogen-activated protein kinase family, ERK1/2 (extracellular signal-regulated protein kinase) has an important role in delivering extracellular signals to the nucleus, and these signals regulate the cell cycle, cell proliferation and cell development. Previous studies demonstrated that ERK1/2 is closely associated with cell aging; however other previous studies suggested that ERK1/2 exerts an opposite effect on aging models and target proteins, even within the same cell model. Recent studies demonstrated that the effect of ERK1/2 on aging is likely associated with its target proteins and regulators, negative feedback loops, phosphorylated ERK1/2 factors and ERK1/2 translocation from the cytoplasm to the nucleus. The present review aims to examine the mechanism of ERK1/2 and discuss its role in cellular outcomes and novel drug development.
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Affiliation(s)
- Junrong Zou
- Research Institute of Digestive Diseases, Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Tingting Lei
- Research Institute of Digestive Diseases, Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Pei Guo
- Department of Pathology, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong 518110, P.R. China
| | - Jason Yu
- Department of Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Qichao Xu
- Department of Pharmacology, The People's Hospital of Xinyu City, Xinyu, Jiangxi 338025, P.R. China
| | - Yunfei Luo
- Jiangxi Provincial Key Laboratory of Tumor Pathogenesis and Molecular Pathology, Department of Pathophysiology, School of Basic Medical Sciences, Medical College of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Rong Ke
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, IL 60612, USA
| | - Deqiang Huang
- Research Institute of Digestive Diseases, Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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38
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Salort G, Álvaro-Bartolomé M, García-Sevilla JA. Pentobarbital and other anesthetic agents induce opposite regulations of MAP kinases p-MEK and p-ERK, and upregulate p-FADD/FADD neuroplastic index in brain during hypnotic states in mice. Neurochem Int 2018; 122:59-72. [PMID: 30423425 DOI: 10.1016/j.neuint.2018.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/30/2018] [Accepted: 11/09/2018] [Indexed: 01/07/2023]
Abstract
Midazolam and ketamine-induced anesthesia were recently shown to induce a disruption of MEK/ERK sequential phosphorylation with parallel upregulation of p-FADD in the mouse brain. The present study was designed to assess whether other structurally diverse anesthetic agents (pentobarbital, ethanol, chloral hydrate, isoflurane) also impair brain p-MEK to p-ERK signal and increase p-FADD during the particular time course of 'sleep' in mice. Pentobarbital (50 mg/kg)-, ethanol (4000 mg/kg)-, chloral hydrate (400 mg/kg)-, and isoflurane (2% in O2)-induced anesthesia (range: 24-60 min) were associated with unaltered or increased p-MEK1/2 (up to +155%) and decreased p-ERK1/2 (up to -60%) contents, revealing disruption of MEK to ERK activation in mouse brain cortex. These anesthetic agents also upregulated cortical p-FADD (up to +110%), but not total FADD (moderately decreased), which resulted in increased neuroplastic/survival p-FADD/FADD ratios (up to +2.8 fold). The inhibition of pentobarbital metabolism with SKF525-A (a cytochrome P450 inhibitor) augmented barbiturate anesthesia (2.6 times) and induced a greater and sustained upregulation of p-MEK with p-ERK downregulation, as well as prolonged increases of p-FADD content and p-FADD/FADD ratio (effects lasting for more than 240 min). Pentobarbital also upregulated significantly the cortical contents of other markers of neuroplasticity such as the ERK inhibitor p-PEA-15 (up to +46%), the transcription factor NF-κB (up to +27%) and the synaptic density protein PSD-95 (up to +20%) during 'sleep'. The results reveal a paradoxical stimulation of p-MEK without the concomitant (canonical) activation of p-ERK (e.g. with pentobarbital and isoflurane), for which various molecular mechanisms are discussed. The downregulation of brain p-ERK may participate in the manifestations of adverse effects displayed by most hypnotic/anesthetic agents in clinical use (e.g. amnesia).
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Affiliation(s)
- Glòria Salort
- Laboratory of Neuropharmacology, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), University of the Balearic Islands (UIB), Institut d'investigació Sanitària Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - María Álvaro-Bartolomé
- Laboratory of Neuropharmacology, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), University of the Balearic Islands (UIB), Institut d'investigació Sanitària Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Jesús A García-Sevilla
- Laboratory of Neuropharmacology, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), University of the Balearic Islands (UIB), Institut d'investigació Sanitària Illes Balears (IdISBa), Palma de Mallorca, Spain.
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39
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Tang B, Liang W, Liao Y, Li Z, Wang Y, Yan C. PEA15 promotes liver metastasis of colorectal cancer by upregulating the ERK/MAPK signaling pathway. Oncol Rep 2018; 41:43-56. [PMID: 30365128 PMCID: PMC6278416 DOI: 10.3892/or.2018.6825] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022] Open
Abstract
Liver metastasis is one of the major causes of death in patients with colorectal cancer, and although treatment has improved recently, the long‑term survival rate of patients has not improved significantly. In the present study, we used immunohistochemistry to determine that phosphoprotein enriched in astrocytes‑15 kDa (PEA15) was highly expressed in colorectal cancer tissues and liver metastatic cancer tissues. It was also highly expressed in metastatic colorectal cancer patients compared to non‑metastatic patients. Through clinicopathological data of patients with liver metastasis of colorectal cancer, we found that high expression of PEA15 was positively correlated with TNM staging, liver metastasis and poor prognosis of colorectal cancer patients. Using confocal immunofluorescence microscopy, western blotting and cell proliferation, migration and invasion assays, we also determined that PEA15 could promote cancer cell proliferation in vitro and in vivo, epithelial mesenchymal transition (EMT) and the characteristics of cancer stem cells in vitro, thus promoting the abilities of invasion and migration. In addition, we revealed that PEA15 promoted the liver metastasis of colorectal cancer cells in a xenograft tumor metastasis model. In addition, concerning the mechanism, we used gene chip analysis to determine that PEA15 upregulated the ERK/MAPK signaling pathway in colorectal cancer cells. Therefore, we concluded that PEA15 may be a potential biomarker for liver metastasis of colorectal cancer therapy. Collectively, PEA15 promoted the development of liver metastasis of colorectal cancer through the ERK/MAPK signaling pathway.
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Affiliation(s)
- Bo Tang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Wenjin Liang
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi 541004, P.R. China
| | - Yong Liao
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi 541004, P.R. China
| | - Zeming Li
- Department of Hepatobiliary Surgery, Guilin Medical University, Affiliated Hospital, Guilin, Guangxi 541004, P.R. China
| | - Yan Wang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Chao Yan
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
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40
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Chen J, Wang J, Lu Y, Zhao S, Yu Q, Wang X, Tu P, Zeng K, Jiang Y. Uncovering potential anti-neuroinflammatory components of Modified Wuziyanzong Prescription through a target-directed molecular docking fingerprint strategy. J Pharm Biomed Anal 2018; 156:328-339. [DOI: 10.1016/j.jpba.2018.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/23/2018] [Accepted: 05/01/2018] [Indexed: 12/18/2022]
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41
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Wheaton K, Aten S, Queiroz LS, Sullivan K, Oberdick J, Hoyt KR, Obrietan K. Circadian expression and functional characterization of PEA-15 within the mouse suprachiasmatic nucleus. Eur J Neurosci 2018; 47:845-857. [PMID: 29383758 DOI: 10.1111/ejn.13850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/15/2017] [Accepted: 01/15/2018] [Indexed: 12/14/2022]
Abstract
The circadian timing system influences the functional properties of most, if not all, physiological processes. Central to the mammalian timing system is the suprachiasmatic nucleus (SCN) of the hypothalamus. The SCN functions as a 'master clock' that sets the phasing of ancillary circadian oscillator populations found throughout the body. Further, via an entraining input from the retina, the SCN ensures that the clock oscillators are synchronized to the daily light/dark cycle. A critical component of the SCN timing and entrainment systems is the p44/42 mitogen-activated protein kinase (ERK/MAPK) pathway. Here, we examined the expression and function of phosphoprotein-enriched in astrocytes (PEA-15), an ERK scaffold protein that serves as a key regulator of MAPK signaling. A combination of immunolabeling and Western blotting approaches revealed high levels of PEA-15 within the SCN. PEA-15 expression was enriched in distinct subpopulations of SCN neurons, including arginine vasopressin (AVP)-positive neurons of the SCN shell region. Further, expression profiling detected a significant circadian oscillation in PEA-15 expression within the SCN. Brief photic stimulation during the early subjective night led to a significant increase in PEA-15 phosphorylation, an event that can trigger ERK/PEA-15 dissociation. Consistent with this, co-immunoprecipitation assays revealed that PEA-15 is directly bound to ERK in the SCN and that photic stimulation leads to their dissociation. Finally, we show that PEA-15 regulates ERK/MAPK-dependent activation of the core clock gene period1. Together, these data raise the prospect that PEA-15 functions as a key regulator of the SCN timing system.
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Affiliation(s)
- Kelin Wheaton
- Division of Pharmacology, Ohio State University, Columbus, OH, 43210, USA
| | - Sydney Aten
- Department of Neuroscience, Ohio State University, Columbus, OH, 43210, USA
| | | | - Kyle Sullivan
- Department of Neuroscience, Ohio State University, Columbus, OH, 43210, USA
| | - John Oberdick
- Department of Neuroscience, Ohio State University, Columbus, OH, 43210, USA
| | - Kari R Hoyt
- Division of Pharmacology, Ohio State University, Columbus, OH, 43210, USA
| | - Karl Obrietan
- Department of Neuroscience, Ohio State University, Columbus, OH, 43210, USA
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42
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Ryou JH, Sohn YK, Kim DG, Kyeong HH, Kim HS. Engineering and cytosolic delivery of a native regulatory protein and its variants for modulation of ERK2 signaling pathway. Biotechnol Bioeng 2018; 115:839-849. [PMID: 29240226 DOI: 10.1002/bit.26516] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/30/2017] [Accepted: 12/04/2017] [Indexed: 12/24/2022]
Abstract
The modulation of a cell signaling process using a molecular binder followed by an analysis of the cellular response is crucial for understanding its role in the cellular function and developing pharmaceuticals. Herein, we present the modulation of the ERK2-mediated signaling pathway through the cytosolic delivery of a native regulatory protein for ERK2, that is, PEA-15 (phosphoprotein enriched in astrocytes, 15 kDa), and its engineered variants using a bacterial toxin-based delivery system. Based on biochemical and structural analyses, PEA-15 variants with different phosphorylation sites and a high affinity for ERK2 were designed. Semi-rational approach led to about an 830-fold increase in the binding affinity of PEA-15, resulting in more effective modulation of the ERK2-mediated signaling. Our approach enabled an understanding of the cellular function of the ERK2-mediated signaling process and the effect of PEA-15 phosphorylation on its action as an ERK2 blocker. We demonstrated the utility and potential of our approach by showing an efficient cytosolic delivery of these PEA-15 variants and the effective suppression of cell proliferation through the inhibition of the ERK2 function. The present approach can be used broadly for modulating the cell signaling processes and understanding their roles in cellular function, as well as for the development of therapeutics.
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Affiliation(s)
- Jeong-Hyun Ryou
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Yoo-Kyoung Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Dong-Gun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Hyun-Ho Kyeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Hak-Sung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
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43
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Simões ICM, Coimbra JTS, Neves RPP, Costa IPD, Ramos MJ, Fernandes PA. Properties that rank protein:protein docking poses with high accuracy. Phys Chem Chem Phys 2018; 20:20927-20942. [DOI: 10.1039/c8cp03888k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The development of docking algorithms to predict near-native structures of protein:protein complexes from the structure of the isolated monomers is of paramount importance for molecular biology and drug discovery.
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Affiliation(s)
- Inês C. M. Simões
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - João T. S. Coimbra
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Rui P. P. Neves
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Inês P. D. Costa
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Maria J. Ramos
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
| | - Pedro A. Fernandes
- UCIBIO
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
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44
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Kawakami M, Mustachio LM, Rodriguez-Canales J, Mino B, Roszik J, Tong P, Wang J, Lee JJ, Myung JH, Heymach JV, Johnson FM, Hong S, Zheng L, Hu S, Villalobos PA, Behrens C, Wistuba I, Freemantle S, Liu X, Dmitrovsky E. Next-Generation CDK2/9 Inhibitors and Anaphase Catastrophe in Lung Cancer. J Natl Cancer Inst 2017; 109:2982387. [PMID: 28376145 DOI: 10.1093/jnci/djw297] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 11/08/2016] [Indexed: 12/30/2022] Open
Abstract
Background The first generation CDK2/7/9 inhibitor seliciclib (CYC202) causes multipolar anaphase and apoptosis in lung cancer cells with supernumerary centrosomes (known as anaphase catastrophe). We investigated a new and potent CDK2/9 inhibitor, CCT68127 (Cyclacel). Methods CCT68127 was studied in lung cancer cells (three murine and five human) and control murine pulmonary epithelial and human immortalized bronchial epithelial cells. Robotic CCT68127 cell-based proliferation screens were used. Cells undergoing multipolar anaphase and inhibited centrosome clustering were scored. Reverse phase protein arrays (RPPAs) assessed CCT68127 effects on signaling pathways. The function of PEA15, a growth regulator highlighted by RPPAs, was analyzed. Syngeneic murine lung cancer xenografts (n = 4/group) determined CCT68127 effects on tumorigenicity and circulating tumor cell levels. All statistical tests were two-sided. Results CCT68127 inhibited growth up to 88.5% (SD = 6.4%, P < .003) at 1 μM, induced apoptosis up to 42.6% (SD = 5.5%, P < .001) at 2 μM, and caused G1 or G2/M arrest in lung cancer cells with minimal effects on control cells (growth inhibition at 1 μM: 10.6%, SD = 3.6%, P = .32; apoptosis at 2 μM: 8.2%, SD = 1.0%, P = .22). A robotic screen found that lung cancer cells with KRAS mutation were particularly sensitive to CCT68127 ( P = .02 for IC 50 ). CCT68127 inhibited supernumerary centrosome clustering and caused anaphase catastrophe by 14.1% (SD = 3.6%, P < .009 at 1 μM). CCT68127 reduced PEA15 phosphorylation by 70% (SD = 3.0%, P = .003). The gain of PEA15 expression antagonized and its loss enhanced CCT68127-mediated growth inhibition. CCT68127 reduced lung cancer growth in vivo ( P < .001) and circulating tumor cells ( P = .004). Findings were confirmed with another CDK2/9 inhibitor, CYC065. Conclusions Next-generation CDK2/9 inhibition elicits marked antineoplastic effects in lung cancer via anaphase catastrophe and reduced PEA15 phosphorylation.
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Affiliation(s)
- Masanori Kawakami
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lisa Maria Mustachio
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaime Rodriguez-Canales
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Mino
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Roszik
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pan Tong
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ja Hye Myung
- Department of Biopharmaceutical Sciences, College of Pharmacy, The University of Illinois, Chicago, IL, USA
| | - John V Heymach
- Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Faye M Johnson
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Seungpyo Hong
- Department of Biopharmaceutical Sciences, College of Pharmacy, The University of Illinois, Chicago, IL, USA
| | - Lin Zheng
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shanhu Hu
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Pamela Andrea Villalobos
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio Wistuba
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah Freemantle
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Xi Liu
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ethan Dmitrovsky
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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45
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Monteiro HP, Ogata FT, Stern A. Thioredoxin promotes survival signaling events under nitrosative/oxidative stress associated with cancer development. Biomed J 2017; 40:189-199. [PMID: 28918907 PMCID: PMC6136292 DOI: 10.1016/j.bj.2017.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/05/2017] [Accepted: 06/05/2017] [Indexed: 02/07/2023] Open
Abstract
Accumulating mutations may drive cells into the acquisition of abnormal phenotypes that are characteristic of cancer cells. Cancer cells feature profound alterations in proliferation programs that result in a new population of cells that overrides normal tissue construction and maintenance programs. To achieve this goal, cancer cells are endowed with up regulated survival signaling pathways. They also must counteract the cytotoxic effects of high levels of nitric oxide (NO) and of reactive oxygen species (ROS), which are by products of cancer cell growth. Accumulating experimental evidence associates cancer cell survival with their capacity to up-regulate antioxidant systems. Elevated expression of the antioxidant protein thioredoxin-1 (Trx1) has been correlated with cancer development. Trx1 has been characterized as a multifunctional protein, playing different roles in different cell compartments. Trx1 migrates to the nucleus in cells exposed to nitrosative/oxidative stress conditions. Trx1 nuclear migration has been related to the activation of transcription factors associated with cell survival and cell proliferation. There is a direct association between the p21Ras-ERK1/2 MAP Kinases survival signaling pathway and Trx1 nuclear migration under nitrosative stress. The expression of the cytoplasmic protein, the thioredoxin-interacting protein (Txnip), determines the change in Trx1 cellular compartmentalization. The anti-apoptotic actions of Trx1 and its denitrosylase activity occur in the cytoplasm and serve as important regulators of cell survival. Within this context, this review focuses on the participation of Trx1 in cells under nitrosative/oxidative stress in survival signaling pathways associated with cancer development.
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Affiliation(s)
- Hugo P Monteiro
- Department of Biochemistry, Center for Cellular and Molecular Therapy - CTCMol, Paulista Medical School/Federal University of São Paulo, SP, Brazil
| | - Fernando T Ogata
- Department of Biochemistry, Center for Cellular and Molecular Therapy - CTCMol, Paulista Medical School/Federal University of São Paulo, SP, Brazil; Division of Biochemistry, Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Arnold Stern
- New York University School of Medicine, New York, NY, USA.
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46
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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: 2.3] [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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47
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Lechtenberg BC, Mace PD, Sessions EH, Williamson R, Stalder R, Wallez Y, Roth GP, Riedl SJ, Pasquale EB. Structure-Guided Strategy for the Development of Potent Bivalent ERK Inhibitors. ACS Med Chem Lett 2017; 8:726-731. [PMID: 28740606 DOI: 10.1021/acsmedchemlett.7b00127] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/12/2017] [Indexed: 12/19/2022] Open
Abstract
ERK is the effector kinase of the RAS-RAF-MEK-ERK signaling cascade, which promotes cell transformation and malignancy in many cancers and is thus a major drug target in oncology. Kinase inhibitors targeting RAF or MEK are already used for the treatment of certain cancers, such as melanoma. Although the initial response to these drugs can be dramatic, development of drug resistance is a major challenge, even with combination therapies targeting both RAF and MEK. Importantly, most resistance mechanisms still rely on activation of the downstream effector kinase ERK, making it a promising target for drug development efforts. Here, we report the design and structural/functional characterization of a set of bivalent ERK inhibitors that combine a small molecule inhibitor that binds to the ATP-binding pocket with a peptide that selectively binds to an ERK protein interaction surface, the D-site recruitment site (DRS). Our studies show that the lead bivalent inhibitor, SBP3, has markedly improved potency compared to the small molecule inhibitor alone. Unexpectedly, we found that SBP3 also binds to several ERK-related kinases that contain a DRS, highlighting the importance of experimentally verifying the predicted specificity of bivalent inhibitors. However, SBP3 does not target any other kinases belonging to the same CMGC branch of the kinome. Additionally, our modular click chemistry inhibitor design facilitates the generation of different combinations of small molecule inhibitors with ERK-targeting peptides.
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Affiliation(s)
- Bernhard C. Lechtenberg
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Peter D. Mace
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - E. Hampton Sessions
- Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, Florida 32827, United States
| | - Robert Williamson
- Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, Florida 32827, United States
| | - Romain Stalder
- Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, Florida 32827, United States
| | - Yann Wallez
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Gregory P. Roth
- Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, Florida 32827, United States
| | - Stefan J. Riedl
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Elena B. Pasquale
- Cancer
Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
- Pathology
Department, University of California San Diego, La Jolla, California 92093, United States
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48
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Völgyi K, Gulyássy P, Todorov MI, Puska G, Badics K, Hlatky D, Kékesi KA, Nyitrai G, Czurkó A, Drahos L, Dobolyi A. Chronic Cerebral Hypoperfusion Induced Synaptic Proteome Changes in the rat Cerebral Cortex. Mol Neurobiol 2017; 55:4253-4266. [PMID: 28620701 DOI: 10.1007/s12035-017-0641-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/29/2017] [Indexed: 12/23/2022]
Abstract
Chronic cerebral hypoperfusion (CCH) evokes mild cognitive impairment (MCI) and contributes to the progression of vascular dementia and Alzheimer's disease (AD). How CCH induces these neurodegenerative processes that may spread along the synaptic network and whether they are detectable at the synaptic proteome level of the cerebral cortex remains to be established. In the present study, we report the synaptic protein changes in the cerebral cortex after stepwise bilateral common carotid artery occlusion (BCCAO) induced CCH in the rat. The occlusions were confirmed with magnetic resonance angiography 5 weeks after the surgery. Synaptosome fractions were prepared using sucrose gradient centrifugation from cerebral cortex dissected 7 weeks after the occlusion. The synaptic protein differences between the sham operated and CCH groups were analyzed with label-free nanoUHPLC-MS/MS. We identified 46 proteins showing altered abundance due to CCH. In particular, synaptic protein and lipid metabolism, as well as GABA shunt-related proteins showed increased while neurotransmission and synaptic assembly-related proteins showed decreased protein level changes in CCH rats. Protein network analysis of CCH-induced protein alterations suggested the importance of increased synaptic apolipoprotein E (APOE) level as a consequence of CCH. Therefore, the change in APOE level was confirmed with Western blotting. The identified synaptic protein changes would precede the onset of dementia-like symptoms in the CCH model, suggesting their importance in the development of vascular dementia.
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Affiliation(s)
- Katalin Völgyi
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and Eötvös Loránd University, Pázmány Péter sétány 1C, Budapest, H-1117, Hungary.
| | - Péter Gulyássy
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Mihail Ivilinov Todorov
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and Eötvös Loránd University, Pázmány Péter sétány 1C, Budapest, H-1117, Hungary.,Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gina Puska
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Kata Badics
- Laboratory of Proteomics, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Dávid Hlatky
- Preclinical Imaging and Biomarker Laboratory, Pharmacology and Drug Safety Research, Richter Gedeon Plc, Budapest, Hungary
| | - Katalin Adrienna Kékesi
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Physiology and Neurobiology, Eötvös Loránd University, Budapest, Hungary
| | - Gabriella Nyitrai
- Preclinical Imaging and Biomarker Laboratory, Pharmacology and Drug Safety Research, Richter Gedeon Plc, Budapest, Hungary
| | - András Czurkó
- Preclinical Imaging and Biomarker Laboratory, Pharmacology and Drug Safety Research, Richter Gedeon Plc, Budapest, Hungary
| | - László Drahos
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Arpád Dobolyi
- MTA-ELTE NAP B Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and Eötvös Loránd University, Pázmány Péter sétány 1C, Budapest, H-1117, Hungary
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49
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Fiory F, Spinelli R, Raciti GA, Parrillo L, D'esposito V, Formisano P, Miele C, Beguinot F. Targetting PED/PEA-15 for diabetes treatment. Expert Opin Ther Targets 2017; 21:571-581. [PMID: 28395542 DOI: 10.1080/14728222.2017.1317749] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION PED/PEA-15 is an ubiquitously expressed protein, involved in the regulation of proliferation and apoptosis. It is commonly overexpressed in Type 2 Diabetes (T2D) and in different T2D-associated comorbidities, including cancer and certain neurodegenerative disorders. Areas covered: In mice, Ped/Pea-15 overexpression impairs glucose tolerance and, in combination with high fat diets, further promotes insulin resistance and T2D. It also controls β-cell mass, altering caspase-3 activation and the expression of pro- and antiapoptotic genes. These changes are mediated by PED/PEA-15-PLD1 binding. Overexpression of PLD1 D4 domain specifically blocks Ped/Pea-15-PLD1 interaction, reverting the effect of Ped/Pea-15 in vivo. D4α, a D4 N-terminal peptide, is able to displace Ped/Pea-15-PLD1 binding, but features greater stability in vivo compared to the entire D4 peptide. Here, we review early mechanistic studies on PED/PEA-15 relevance in apoptosis before focusing on its role in cancer and T2D. Finally, we describe potential therapeutic opportunities for T2D based on PED/PEA-15 targeting. Expert opinion: T2D is a major problem for public health and economy. Thus, the identification of new molecules with pharmacological activity for T2D represents an urgent need. Further studies with D4α will help to identify smaller pharmacologically active peptides and innovative molecules of potential pharmacological interest for T2D treatment.
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Affiliation(s)
- Francesca Fiory
- a National Council of Research , URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore" , Naples , Italy.,b Department of Translational Medical Sciences , University of Naples "Federico II" , Naples , Italy
| | - Rosa Spinelli
- a National Council of Research , URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore" , Naples , Italy.,b Department of Translational Medical Sciences , University of Naples "Federico II" , Naples , Italy
| | - Gregory Alexander Raciti
- a National Council of Research , URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore" , Naples , Italy.,b Department of Translational Medical Sciences , University of Naples "Federico II" , Naples , Italy
| | - Luca Parrillo
- a National Council of Research , URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore" , Naples , Italy.,b Department of Translational Medical Sciences , University of Naples "Federico II" , Naples , Italy
| | - Vittoria D'esposito
- a National Council of Research , URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore" , Naples , Italy.,b Department of Translational Medical Sciences , University of Naples "Federico II" , Naples , Italy
| | - Pietro Formisano
- a National Council of Research , URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore" , Naples , Italy.,b Department of Translational Medical Sciences , University of Naples "Federico II" , Naples , Italy
| | - Claudia Miele
- a National Council of Research , URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore" , Naples , Italy.,b Department of Translational Medical Sciences , University of Naples "Federico II" , Naples , Italy
| | - Francesco Beguinot
- a National Council of Research , URT of the Institute of Experimental Endocrinology and Oncology "G. Salvatore" , Naples , Italy.,b Department of Translational Medical Sciences , University of Naples "Federico II" , Naples , Italy
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Müller I. Guidelines for the successful generation of protein-ligand complex crystals. Acta Crystallogr D Struct Biol 2017; 73:79-92. [PMID: 28177304 PMCID: PMC5297911 DOI: 10.1107/s2059798316020271] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/21/2016] [Indexed: 11/23/2022] Open
Abstract
With continuous technical improvements at synchrotron facilities, data-collection rates have increased dramatically. This makes it possible to collect diffraction data for hundreds of protein-ligand complexes within a day, provided that a suitable crystal system is at hand. However, developing a suitable crystal system can prove challenging, exceeding the timescale of data collection by several orders of magnitude. Firstly, a useful crystallization construct of the protein of interest needs to be chosen and its expression and purification optimized, before screening for suitable crystallization and soaking conditions can start. This article reviews recent publications analysing large data sets of crystallization trials, with the aim of identifying factors that do or do not make a good crystallization construct, and gives guidance in the design of an expression construct. It provides an overview of common protein-expression systems, addresses how ligand binding can be both help and hindrance for protein purification, and describes ligand co-crystallization and soaking, with an emphasis on troubleshooting.
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Affiliation(s)
- Ilka Müller
- Structural Biology, Discovery from Charles River, Chesterford Research Park, Saffron Walden CB10 1XL, England
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