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Chargui A. Lysine-63-linked polyubiquitination: a principal target of cadmium carcinogenesis. Toxicol Res 2024; 40:349-360. [PMID: 38911543 PMCID: PMC11187039 DOI: 10.1007/s43188-024-00236-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/13/2024] [Accepted: 03/27/2024] [Indexed: 06/25/2024] Open
Abstract
Cadmium is an environmental pollutant that constitutes a major danger to human health. It is considered a definite human carcinogen. The lung and kidney are the most sensitive organs for cancer development, and we recently provided the first evidence of direct upregulation of lysine-63-linked polyubiquitination by cadmium, particularly in response to environmentally relevant concentrations. Investigations of K63 polyubiquitination have greatly progressed, and various strategies have been reported for studying this molecular process in different biological systems under both physiological and stress conditions. Furthermore, the mechanisms underlying cadmium-induced accumulation of K63-polyubiquitinated proteins in lung and renal cells continue to be of interest given the unknown mechanism involved in the carcinogenesis of this metal. Cadmium is persistent within the cytosol and induces oxidative stress, which continuously damages proteins and causes K63 polyubiquitination, leading to the regulation/activation of different cellular signaling pathways. The aim of this review was to perform a critical analysis of the knowledge about K63 polyubiquitination induced by cadmium and its effect on selective autophagy, CYLD, the NF-KB pathway and Hif-1α. We also report data obtained in different experimental studies using cadmium, highlighting similarities in the induction of the ubiquitination system. A more detailed discussion will concern the role of K63 polyubiquitination in cadmium-exposed renal proximal convoluted tubules and lung cells since they are suitable model systems that are extremely sensitive to environmental stress, and cadmium is one of the most carcinogenic metals to which humans are exposed. We ultimately concluded that K63 polyubiquitination may be the origin of cadmium carcinogenesis in the lung and kidney. Graphical Abstract Pathways of cadmium carcinogenesis: Cadmium mimics zinc and induces Lysine-63-linked polyubiquitination, which promotes three intracellular processes: (1) accumulation of ubiquitinated proteins, (2) stabilization of hypoxic inducible factor-1α and (3) activation of the nuclear factor-kappaB pathway, which results in the blockade of selective autophagy, angiogenesis, inflammation and cell proliferation.
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Affiliation(s)
- Abderrahmen Chargui
- Université de Jendouba, Ecole Supérieure d’Agriculture du Kef (ESAK), LR: Appui à la Durabilité des Systèmes de Production Agricoles du Nord-Ouest, 7119 Le Kef, Tunisie
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Bokor M, Tantos Á. General Characterization of Properties of Ordered and Disordered Proteins by Wide-Line 1H NMR. ACS OMEGA 2024; 9:23468-23475. [PMID: 38854569 PMCID: PMC11154930 DOI: 10.1021/acsomega.4c00517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Wide-line 1H NMR is an efficient spectroscopic method to determine the disorder tendency of a protein. It directly measures the properties of the hydration shell of proteins, delivering exact and measurable values of their disorder/order content. A comparison is performed between several globular and disordered proteins. The common properties of the subzero mobile hydration water of these two groups were investigated. The amount of the mobile hydration water and the shape of the melting diagram at subzero temperatures together provide a possibility to distinguish globular proteins from disordered proteins. The shape of the melting diagram also gives information about the presence of secondary structural elements. The disordered and globular protein regions' fundamentally different structures are reflected in their melting diagrams, allowing one to directly determine the level of disorder in a specific protein structure. Intrinsically disordered proteins bind water more strongly than globular proteins, which is shown by the somewhat higher temperature values where mobile hydration water first appears but with a significantly higher heterogeneity in the energy distributions of protein-water interactions.
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Affiliation(s)
- Mónika Bokor
- Institute
for Solid State Physics and Optics, HUN-REN
Wigner Research Centre for Physics, 1121 Budapest, Hungary
| | - Ágnes Tantos
- HUN-REN
Research Centre for Natural Sciences, Institute
of Enzymology, 1117 Budapest, Hungary
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Gorrec F, Bellini D. The FUSION protein crystallization screen. J Appl Crystallogr 2022; 55:310-319. [PMID: 35497656 PMCID: PMC8985600 DOI: 10.1107/s1600576722001765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/15/2022] [Indexed: 11/16/2022] Open
Abstract
The success and speed of atomic structure determination of biological macromolecules by X-ray crystallography depends critically on the availability of diffraction-quality crystals. However, the process of screening crystallization conditions often consumes large amounts of sample and time. An innovative protein crystallization screen formulation called FUSION has been developed to help with the production of useful crystals. The concept behind the formulation of FUSION was to combine the most efficient components from the three MORPHEUS screens into a single screen using a systematic approach. The resulting formulation integrates 96 unique combinations of crystallization additives. Most of these additives are small molecules and ions frequently found in crystal structures of the Protein Data Bank (PDB), where they bind proteins and complexes. The efficiency of FUSION is demonstrated by obtaining high yields of diffraction-quality crystals for seven different test proteins. In the process, two crystal forms not currently in the PDB for the proteins α-amylase and avidin were discovered.
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Affiliation(s)
- Fabrice Gorrec
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, Cambridgeshire CB2 0QH, United Kingdom
- Correspondence e-mail:
| | - Dom Bellini
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, Cambridgeshire CB2 0QH, United Kingdom
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Chargui A, Belaid A, Ndiaye PD, Imbert V, Samson M, Guigonis JM, Tauc M, Peyron JF, Poujeol P, Brest P, Hofman P, Mograbi B. The Carcinogen Cadmium Activates Lysine 63 (K63)-Linked Ubiquitin-Dependent Signaling and Inhibits Selective Autophagy. Cancers (Basel) 2021; 13:2490. [PMID: 34065348 PMCID: PMC8161291 DOI: 10.3390/cancers13102490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 01/18/2023] Open
Abstract
Signaling, proliferation, and inflammation are dependent on K63-linked ubiquitination-conjugation of a chain of ubiquitin molecules linked via lysine 63. However, very little information is currently available about how K63-linked ubiquitination is subverted in cancer. The present study provides, for the first time, evidence that cadmium (Cd), a widespread environmental carcinogen, is a potent activator of K63-linked ubiquitination, independently of oxidative damage, activation of ubiquitin ligase, or proteasome impairment. We show that Cd induces the formation of protein aggregates that sequester and inactivate cylindromatosis (CYLD) and selective autophagy, two tumor suppressors that deubiquitinate and degrade K63-ubiquitinated proteins, respectively. The aggregates are constituted of substrates of selective autophagy-SQSTM1, K63-ubiquitinated proteins, and mitochondria. These protein aggregates also cluster double-membrane remnants, which suggests an impairment in autophagosome maturation. However, failure to eliminate these selective cargos is not due to alterations in the general autophagy process, as degradation of long-lived proteins occurs normally. We propose that the simultaneous disruption of CYLD and selective autophagy by Cd feeds a vicious cycle that further amplifies K63-linked ubiquitination and downstream activation of the NF-κB pathway, processes that support cancer progression. These novel findings link together impairment of selective autophagy, K63-linked ubiquitination, and carcinogenesis.
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Affiliation(s)
- Abderrahman Chargui
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
- Higher School of Agriculture of Kef, University Jendouba, Le Kef and Laboratory of Histology, Embryology and Cell Biology, Faculty of Medicine Tunis, 7110 Le Kef, Tunisia
| | - Amine Belaid
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Papa Diogop Ndiaye
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Véronique Imbert
- Université Côte d’Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Institut National de la Santé et de la Recherche Médicale (INSERM), F-06204 Nice, France; (V.I.); (J.-F.P.)
| | - Michel Samson
- Université Côte d’Azur, Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des sciences du vivant Fréderic Joliot, Commissariat à l’Energie Atomique et aux énergies alternatives (CEA), F-06107 Nice, France; (M.S.); (J.-M.G.)
| | - Jean-Marie Guigonis
- Université Côte d’Azur, Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des sciences du vivant Fréderic Joliot, Commissariat à l’Energie Atomique et aux énergies alternatives (CEA), F-06107 Nice, France; (M.S.); (J.-M.G.)
| | - Michel Tauc
- Université Côte d’Azur, Laboratoire de Physiomédecine Moléculaire, LP2M, Labex ICST, Centre National de la Recherche Scientifique (CNRS), F-06107 Nice, France; (M.T.); (P.P.)
| | - Jean-François Peyron
- Université Côte d’Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Institut National de la Santé et de la Recherche Médicale (INSERM), F-06204 Nice, France; (V.I.); (J.-F.P.)
| | - Philippe Poujeol
- Université Côte d’Azur, Laboratoire de Physiomédecine Moléculaire, LP2M, Labex ICST, Centre National de la Recherche Scientifique (CNRS), F-06107 Nice, France; (M.T.); (P.P.)
| | - Patrick Brest
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Paul Hofman
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
- Université Côte d’Azur, Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Hospital-Integrated Biobank (BB-0033-00025), Centre Hospitalier Universitaire (CHU) de Nice, F-06001 Nice, France
| | - Baharia Mograbi
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
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Lin YW. Uranyl Binding to Proteins and Structural-Functional Impacts. Biomolecules 2020; 10:biom10030457. [PMID: 32187982 PMCID: PMC7175365 DOI: 10.3390/biom10030457] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/08/2020] [Accepted: 03/13/2020] [Indexed: 01/29/2023] Open
Abstract
The widespread use of uranium for civilian purposes causes a worldwide concern of its threat to human health due to the long-lived radioactivity of uranium and the high toxicity of uranyl ion (UO22+). Although uranyl–protein/DNA interactions have been known for decades, fewer advances are made in understanding their structural-functional impacts. Instead of focusing only on the structural information, this article aims to review the recent advances in understanding the binding of uranyl to proteins in either potential, native, or artificial metal-binding sites, and the structural-functional impacts of uranyl–protein interactions, such as inducing conformational changes and disrupting protein-protein/DNA/ligand interactions. Photo-induced protein/DNA cleavages, as well as other impacts, are also highlighted. These advances shed light on the structure-function relationship of proteins, especially for metalloproteins, as impacted by uranyl–protein interactions. It is desired to seek approaches for biological remediation of uranyl ions, and ultimately make a full use of the double-edged sword of uranium.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; ; Tel.: +86-734-8578079
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
- Hunan Key Laboratory for the Design and Application of Actinide Complexes, University of South China, Hengyang 421001, China
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Dutta S, Ghosh M, Karmakar R, Chakrabarti J. Dynamic signature of ligand binding over a protein surface. Phys Rev E 2019; 100:062411. [PMID: 31962438 DOI: 10.1103/physreve.100.062411] [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: 10/18/2019] [Indexed: 06/10/2023]
Abstract
We study the motion of Zn^{2+} in the presence of ubiquitin by all-atom molecular-dynamics simulations. We observe that unlike normal diffusive liquid, metal ions show an exponential tail in the self-van Hove function (self-vHf). Moreover, the metal ions are trapped strongly by acidic residues which form a binding pocket over the protein surface. The exponential tail disappears by mutation of trapping residues, suggesting that the tail appears due to trapped motion of the ions. The mean-squared displacements, however, in all the cases show linear dependence on time. Our model establishes that ligand binding generically results in an exponential tail of self-vHf. The self-vHf may give an approach to find binding pockets over a protein surface.
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Affiliation(s)
- Sutapa Dutta
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - Mahua Ghosh
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - Rahul Karmakar
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
| | - J Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
- Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata 700106, India
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