1
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Rosati M, Barbieri L, Hlavac M, Kratzwald S, Lichtenecker RJ, Konrat R, Luchinat E, Banci L. Towards cost-effective side-chain isotope labelling of proteins expressed in human cells. JOURNAL OF BIOMOLECULAR NMR 2024; 78:237-247. [PMID: 39172315 PMCID: PMC11615012 DOI: 10.1007/s10858-024-00447-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/17/2024] [Indexed: 08/23/2024]
Abstract
Side chain isotope labelling is a powerful tool to study protein structure and interactions by NMR spectroscopy. 1H,13C labelling of side-chain methyl groups in a deuterated background allows studying large molecules, while side-chain aromatic groups are highly sensitive to the interaction with ligands, drugs, and other proteins. In E. coli, side chain labelling is performed by substituting amino acids with isotope-labelled precursors. However, proteins that can only be produced in mammalian cells require expensive isotope-labelled amino acids. Here we provide a simple and cost-effective method to label side chains in mammalian cells, which exploits the reversible reaction catalyzed by endogenous transaminases to convert isotope-labelled α-ketoacid precursors. We show by in-cell and in-lysate NMR spectroscopy that replacing an amino acid in the medium with its cognate precursor is sufficient to achieve selective labelling without scrambling, and how this approach allows monitoring conformational changes such as those arising from ligand binding.
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Affiliation(s)
- Martina Rosati
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine ─ CIRMMP, Sesto Fiorentino, Italy
| | | | | | - Roman J Lichtenecker
- MAG-LAB GmbH, Vienna, Austria
- Institute of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Robert Konrat
- MAG-LAB GmbH, Vienna, Austria
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Enrico Luchinat
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine ─ CIRMMP, Sesto Fiorentino, Italy.
- Dipartimento di Chimica, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
| | - Lucia Banci
- CERM ─ Magnetic Resonance Center, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine ─ CIRMMP, Sesto Fiorentino, Italy.
- Dipartimento di Chimica, Università degli Studi di Firenze, Sesto Fiorentino, Italy.
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2
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Ji YW, Wen XY, Tang HP, Jin ZS, Su WT, Zhou L, Xia ZY, Xia ZY, Lei SQ. DJ-1: Potential target for treatment of myocardial ischemia-reperfusion injury. Biomed Pharmacother 2024; 179:117383. [PMID: 39232383 DOI: 10.1016/j.biopha.2024.117383] [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: 06/21/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024] Open
Abstract
Ischemic heart disease (IHD) is a significant global health concern, resulting in high rates of mortality and disability among patients. Although coronary blood flow reperfusion is a key treatment for IHD, it often leads to acute myocardial ischemia-reperfusion injury (IRI). Current intervention strategies have limitations in providing adequate protection for the ischemic myocardium. DJ-1, originally known as a Parkinson's disease related protein, is a highly conserved cytoprotective protein. It is involved in enhancing mitochondrial function, scavenging reactive oxygen species (ROS), regulating autophagy, inhibiting apoptosis, modulating anaerobic metabolism, and exerting anti-inflammatory effects. DJ-1 is also required for protective strategies, such as ischemic preconditioning, ischemic postconditioning, remote ischemic preconditioning and pharmacological conditioning. Therefore, DJ-1 emerges as a potential target for the treatment of myocardial IRI. Our comprehensive review delves into its protective mechanisms in myocardial IRI and the structural foundations underlying its functions.
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Affiliation(s)
- Yan-Wei Ji
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xin-Yu Wen
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - He-Peng Tang
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhen-Shuai Jin
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wa-Ting Su
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lu Zhou
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhong-Yuan Xia
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zheng-Yuan Xia
- Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Shao-Qing Lei
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, China.
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3
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Costantino A, Pham LBT, Barbieri L, Calderone V, Ben‐Nissan G, Sharon M, Banci L, Luchinat E. Controlling the incorporation of fluorinated amino acids in human cells and its structural impact. Protein Sci 2024; 33:e4910. [PMID: 38358125 PMCID: PMC10868450 DOI: 10.1002/pro.4910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/16/2024]
Abstract
Fluorinated aromatic amino acids (FAAs) are promising tools when studying protein structure and dynamics by NMR spectroscopy. The incorporation FAAs in mammalian expression systems has been introduced only recently. Here, we investigate the effects of FAAs incorporation in proteins expressed in human cells, focusing on the probability of incorporation and its consequences on the 19 F NMR spectra. By combining 19 F NMR, direct MS and x-ray crystallography, we demonstrate that the probability of FAA incorporation is only a function of the FAA concentration in the expression medium and is a pure stochastic phenomenon. In contrast with the MS data, the x-ray structures of carbonic anhydrase II reveal that while the 3D structure is not affected, certain positions lack fluorine, suggesting that crystallization selectively excludes protein molecules featuring subtle conformational modifications. This study offers a predictive model of the FAA incorporation efficiency and provides a framework for controlling protein fluorination in mammalian expression systems.
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Affiliation(s)
- Azzurra Costantino
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Lan B. T. Pham
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Letizia Barbieri
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine – CIRMMPSesto FiorentinoItaly
| | - Vito Calderone
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Dipartimento di ChimicaUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Gili Ben‐Nissan
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Michal Sharon
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Lucia Banci
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine – CIRMMPSesto FiorentinoItaly
- Dipartimento di ChimicaUniversità degli Studi di FirenzeSesto FiorentinoItaly
| | - Enrico Luchinat
- CERM – Magnetic Resonance CenterUniversità degli Studi di FirenzeSesto FiorentinoItaly
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine – CIRMMPSesto FiorentinoItaly
- Dipartimento di ChimicaUniversità degli Studi di FirenzeSesto FiorentinoItaly
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4
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Sandrelli F, Bisaglia M. Molecular and Physiological Determinants of Amyotrophic Lateral Sclerosis: What the DJ-1 Protein Teaches Us. Int J Mol Sci 2023; 24:ijms24087674. [PMID: 37108835 PMCID: PMC10144135 DOI: 10.3390/ijms24087674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/12/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an adult-onset disease which causes the progressive degeneration of cortical and spinal motoneurons, leading to death a few years after the first symptom onset. ALS is mainly a sporadic disorder, and its causative mechanisms are mostly unclear. About 5-10% of cases have a genetic inheritance, and the study of ALS-associated genes has been fundamental in defining the pathological pathways likely also involved in the sporadic forms of the disease. Mutations affecting the DJ-1 gene appear to explain a subset of familial ALS forms. DJ-1 is involved in multiple molecular mechanisms, acting primarily as a protective agent against oxidative stress. Here, we focus on the involvement of DJ-1 in interconnected cellular functions related to mitochondrial homeostasis, reactive oxygen species (ROS) levels, energy metabolism, and hypoxia response, in both physiological and pathological conditions. We discuss the possibility that impairments in one of these pathways may affect the others, contributing to a pathological background in which additional environmental or genetic factors may act in favor of the onset and/or progression of ALS. These pathways may represent potential therapeutic targets to reduce the likelihood of developing ALS and/or slow disease progression.
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Affiliation(s)
| | - Marco Bisaglia
- Department of Biology, University of Padova, 35131 Padova, Italy
- Study Center for Neurodegeneration (CESNE), 35100 Padova, Italy
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5
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Pham LB, Costantino A, Barbieri L, Calderone V, Luchinat E, Banci L. Direct Expression of Fluorinated Proteins in Human Cells for 19F In-Cell NMR Spectroscopy. J Am Chem Soc 2023; 145:1389-1399. [PMID: 36604341 PMCID: PMC9853860 DOI: 10.1021/jacs.2c12086] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In-cell NMR spectroscopy is a powerful approach to study protein structure and function in the native cellular environment. It provides precious insights into the folding, maturation, interactions, and ligand binding of important pharmacological targets directly in human cells. However, its widespread application is hampered by the fact that soluble globular proteins often interact with large cellular components, causing severe line broadening in conventional heteronuclear NMR experiments. 19F NMR can overcome this issue, as fluorine atoms incorporated in proteins can be detected by simple background-free 1D NMR spectra. Here, we show that fluorinated amino acids can be easily incorporated in proteins expressed in human cells by employing a medium switch strategy. This straightforward approach allows the incorporation of different fluorinated amino acids in the protein of interest, reaching fluorination efficiencies up to 60%, as confirmed by mass spectrometry and X-ray crystallography. The versatility of the approach is shown by performing 19F in-cell NMR on several proteins, including those that would otherwise be invisible by 1H-15N in-cell NMR. We apply the approach to observe the interaction between an intracellular target, carbonic anhydrase 2, and its inhibitors, and to investigate how the formation of a complex between superoxide dismutase 1 and its chaperone CCS modulates the interaction of the chaperone subunit with the cellular environment.
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Affiliation(s)
- Lan B.
T. Pham
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy
| | - Azzurra Costantino
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy
| | - Letizia Barbieri
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, 50019Sesto Fiorentino, Italy
| | - Vito Calderone
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, 50019Sesto Fiorentino, Italy
| | - Enrico Luchinat
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum—Università di Bologna, Piazza Goidanich 60, 47521Cesena, Italy,
| | - Lucia Banci
- CERM—Magnetic
Resonance Center, Università degli
Studi di Firenze, Via
Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, 50019Sesto Fiorentino, Italy,Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, 50019Sesto Fiorentino, Italy,
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6
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Persulfidation of DJ-1: Mechanism and Consequences. Biomolecules 2022; 13:biom13010027. [PMID: 36671412 PMCID: PMC9856005 DOI: 10.3390/biom13010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
DJ-1 (also called PARK7) is a ubiquitously expressed protein involved in the etiology of Parkinson disease and cancers. At least one of its three cysteine residues is functionally essential, and its oxidation state determines the specific function of the enzyme. DJ-1 was recently reported to be persulfidated in mammalian cell lines, but the implications of this post-translational modification have not yet been analyzed. Here, we report that recombinant DJ-1 is reversibly persulfidated at cysteine 106 by reaction with various sulfane donors and subsequently inhibited. Strikingly, this reaction is orders of magnitude faster than C106 oxidation by H2O2, and persulfidated DJ-1 behaves differently than sulfinylated DJ-1. Both these PTMs most likely play a dedicated role in DJ-1 signaling or protective pathways.
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7
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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8
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De Lazzari F, Agostini F, Doni D, Malacrida S, Zordan MA, Costantini P, Bubacco L, Sandrelli F, Bisaglia M. DJ-1 and SOD1 Act Independently in the Protection against Anoxia in Drosophila melanogaster. Antioxidants (Basel) 2022; 11:antiox11081527. [PMID: 36009245 PMCID: PMC9405364 DOI: 10.3390/antiox11081527] [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: 07/13/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 12/01/2022] Open
Abstract
Redox homeostasis is a vital process the maintenance of which is assured by the presence of numerous antioxidant small molecules and enzymes and the alteration of which is involved in many pathologies, including several neurodegenerative disorders. Among the different enzymes involved in the antioxidant response, SOD1 and DJ-1 have both been associated with the pathogenesis of amyotrophic lateral sclerosis and Parkinson’s disease, suggesting a possible interplay in their mechanism of action. Copper deficiency in the SOD1-active site has been proposed as a central determinant in SOD1-related neurodegeneration. SOD1 maturation mainly relies on the presence of the protein copper chaperone for SOD1 (CCS), but a CCS-independent alternative pathway also exists and functions under anaerobic conditions. To explore the possible involvement of DJ-1 in such a pathway in vivo, we exposed Drosophila melanogaster to anoxia and evaluated the effect of DJ-1 on fly survival and SOD1 levels, in the presence or absence of CCS. Loss of DJ-1 negatively affects the fly response to the anoxic treatment, but our data indicate that the protective activity of DJ-1 is independent of SOD1 in Drosophila, indicating that the two proteins may act in different pathways.
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Affiliation(s)
- Federica De Lazzari
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
- Medical Research Council, Mitochondria Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Francesco Agostini
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Davide Doni
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Sandro Malacrida
- Institute of Mountain Emergency Medicine, Eurac Research, 39100 Bolzano, Italy
| | - Mauro A. Zordan
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Paola Costantini
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Luigi Bubacco
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
- Study Center for Neurodegeneration (CESNE), 35100 Padova, Italy
| | - Federica Sandrelli
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
- Correspondence: (F.S.); (M.B.)
| | - Marco Bisaglia
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
- Study Center for Neurodegeneration (CESNE), 35100 Padova, Italy
- Correspondence: (F.S.); (M.B.)
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9
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Luchinat E, Cremonini M, Banci L. Radio Signals from Live Cells: The Coming of Age of In-Cell Solution NMR. Chem Rev 2022; 122:9267-9306. [PMID: 35061391 PMCID: PMC9136931 DOI: 10.1021/acs.chemrev.1c00790] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Indexed: 12/12/2022]
Abstract
A detailed knowledge of the complex processes that make cells and organisms alive is fundamental in order to understand diseases and to develop novel drugs and therapeutic treatments. To this aim, biological macromolecules should ideally be characterized at atomic resolution directly within the cellular environment. Among the existing structural techniques, solution NMR stands out as the only one able to investigate at high resolution the structure and dynamic behavior of macromolecules directly in living cells. With the advent of more sensitive NMR hardware and new biotechnological tools, modern in-cell NMR approaches have been established since the early 2000s. At the coming of age of in-cell NMR, we provide a detailed overview of its developments and applications in the 20 years that followed its inception. We review the existing approaches for cell sample preparation and isotopic labeling, the application of in-cell NMR to important biological questions, and the development of NMR bioreactor devices, which greatly increase the lifetime of the cells allowing real-time monitoring of intracellular metabolites and proteins. Finally, we share our thoughts on the future perspectives of the in-cell NMR methodology.
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Affiliation(s)
- Enrico Luchinat
- Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum−Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Cremonini
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic
Resonance Center, Università degli
Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, 50019 Sesto Fiorentino, Italy
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10
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Zhang R, Zhong L, Sun K, Liu J, Wang Q, Mao D, Fang G, Long F. A Study on Curcumol Influencing Proliferation and Apoptosis of Hepatocellular Carcinoma Cells through DJ-1/PTEN/PI3K/AKT Pathway. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9912776. [PMID: 35647179 PMCID: PMC9142276 DOI: 10.1155/2022/9912776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/22/2021] [Indexed: 11/18/2022]
Abstract
Objective To study the mechanism of curcumol affecting the proliferation and apoptosis of liver cancer cells through the DJ-1/PTEN/PI3K/AKT pathway. Method HepG2 cells were cultured in vitro, treated with curcumol at concentrations of 10, 30, and 100 μg/mL, and DMSO was used as a control. The levels of cell proliferation and apoptosis were measured by CCK-8 and flow cytometry, respectively. RT-PCR and western blot were used to detect PTEN, p-AKT, DJ-1, and PI3K gene and protein expression changes. Result (1) Compared with the DMSO blank control group, the proliferation level of liver cancer cells in the 10 μg/mL curcumol group decreased, and the proportion of apoptosis increased (p <0.05). (2) Compared with the blank control group and the 10 and 30 μg/mL concentration groups, the proliferation level of liver cancer cells in the 100 μg/mL curcumol group was significantly reduced, and the proportion of cell apoptosis was significantly increased (p < 0.05). (3) Curcumol can significantly increase the expression of PTEN gene and protein in liver cancer cells and reduce the expression of DJ-1 and PI3K genes and protein in liver cancer cells (p < 0.05). Conclusion Curcumol can regulate DJ-1, PTEN, PI3K, and AKT signal transduction pathways, inhibit cell proliferation, and cause a significant increase in the proportion of cell apoptosis, and the pharmacodynamic effect of curcumol is dependent on the time and dose of action.
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Affiliation(s)
- Rongzhen Zhang
- Graduate School of Hunan University of Chinese Medicine, Hunan 410208, China
- Hepatology Department, First Affiliated Hospital, Guangxi University of Chinese Medicine, Guangxi 530023, China
| | - Lu Zhong
- Ruikang Clinical Faculty, Guangxi University of Chinese Medicine, Guangxi 530011, China
| | - Kewei Sun
- Hepatology Department, First Affiliated Hospital, Hunan University of Chinese Medicine, Hunan 10202, China
| | - Jiao Liu
- Graduate School, Guangxi University of Chinese Medicine, Guangxi 530001, China
| | - Qianna Wang
- Graduate School, Guangxi University of Chinese Medicine, Guangxi 530001, China
| | - Dewen Mao
- Hepatology Department, First Affiliated Hospital, Guangxi University of Chinese Medicine, Guangxi 530023, China
| | - Gang Fang
- Zhuang Medicine College, Guangxi University of Chinese Medicine, Guangxi 530001, China
| | - Fuli Long
- Hepatology Department, First Affiliated Hospital, Guangxi University of Chinese Medicine, Guangxi 530023, China
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11
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Wu Q, Liu X, Chai Z, Cheng K, Xu G, Jiang L, Liu M, Li C. Lanmodulin Remains Unfold and Fails to Interact with Lanthanide Ions in Escherichia coli Cells. Chem Commun (Camb) 2022; 58:8230-8233. [DOI: 10.1039/d2cc02038f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the conformation of a newly discovered specific lanthanide ions (Ln3+) binding protein, Lanmodulin (LanM), and its inteaction with Ln3+ in Escherichia coli cells using In-cell NMR. We found...
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12
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Molecular and pharmacological chaperones for SOD1. Biochem Soc Trans 2021; 48:1795-1806. [PMID: 32794552 PMCID: PMC7458393 DOI: 10.1042/bst20200318] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/25/2022]
Abstract
The efficacy of superoxide dismutase-1 (SOD1) folding impacts neuronal loss in motor system neurodegenerative diseases. Mutations can prevent SOD1 post-translational processing leading to misfolding and cytoplasmic aggregation in familial amyotrophic lateral sclerosis (ALS). Evidence of immature, wild-type SOD1 misfolding has also been observed in sporadic ALS, non-SOD1 familial ALS and Parkinson's disease. The copper chaperone for SOD1 (hCCS) is a dedicated and specific chaperone that assists SOD1 folding and maturation to produce the active enzyme. Misfolded or misfolding prone SOD1 also interacts with heat shock proteins and macrophage migration inhibitory factor to aid folding, refolding or degradation. Recognition of specific SOD1 structures by the molecular chaperone network and timely dissociation of SOD1-chaperone complexes are, therefore, important steps in SOD1 processing. Harnessing these interactions for therapeutic benefit is actively pursued as is the modulation of SOD1 behaviour with pharmacological and peptide chaperones. This review highlights the structural and mechanistic aspects of a selection of SOD1-chaperone interactions together with their impact on disease models.
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13
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Ma L, Gholam Azad M, Dharmasivam M, Richardson V, Quinn RJ, Feng Y, Pountney DL, Tonissen KF, Mellick GD, Yanatori I, Richardson DR. Parkinson's disease: Alterations in iron and redox biology as a key to unlock therapeutic strategies. Redox Biol 2021; 41:101896. [PMID: 33799121 PMCID: PMC8044696 DOI: 10.1016/j.redox.2021.101896] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022] Open
Abstract
A plethora of studies indicate that iron metabolism is dysregulated in Parkinson's disease (PD). The literature reveals well-documented alterations consistent with established dogma, but also intriguing paradoxical observations requiring mechanistic dissection. An important fact is the iron loading in dopaminergic neurons of the substantia nigra pars compacta (SNpc), which are the cells primarily affected in PD. Assessment of these changes reveal increased expression of proteins critical for iron uptake, namely transferrin receptor 1 and the divalent metal transporter 1 (DMT1), and decreased expression of the iron exporter, ferroportin-1 (FPN1). Consistent with this is the activation of iron regulator protein (IRP) RNA-binding activity, which is an important regulator of iron homeostasis, with its activation indicating cytosolic iron deficiency. In fact, IRPs bind to iron-responsive elements (IREs) in the 3ꞌ untranslated region (UTR) of certain mRNAs to stabilize their half-life, while binding to the 5ꞌ UTR prevents translation. Iron loading of dopaminergic neurons in PD may occur through these mechanisms, leading to increased neuronal iron and iron-mediated reactive oxygen species (ROS) generation. The "gold standard" histological marker of PD, Lewy bodies, are mainly composed of α-synuclein, the expression of which is markedly increased in PD. Of note, an atypical IRE exists in the α-synuclein 5ꞌ UTR that may explain its up-regulation by increased iron. This dysregulation could be impacted by the unique autonomous pacemaking of dopaminergic neurons of the SNpc that engages L-type Ca+2 channels, which imparts a bioenergetic energy deficit and mitochondrial redox stress. This dysfunction could then drive alterations in iron trafficking that attempt to rescue energy deficits such as the increased iron uptake to provide iron for key electron transport proteins. Considering the increased iron-loading in PD brains, therapies utilizing limited iron chelation have shown success. Greater therapeutic advancements should be possible once the exact molecular pathways of iron processing are dissected.
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Affiliation(s)
- L Ma
- School of Environment and Science, Griffith University Nathan, Brisbane, Queensland, Australia; Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia
| | - M Gholam Azad
- School of Environment and Science, Griffith University Nathan, Brisbane, Queensland, Australia; Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia; Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia
| | - M Dharmasivam
- School of Environment and Science, Griffith University Nathan, Brisbane, Queensland, Australia; Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia; Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia
| | - V Richardson
- School of Environment and Science, Griffith University Nathan, Brisbane, Queensland, Australia; Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia; Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia
| | - R J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia
| | - Y Feng
- School of Environment and Science, Griffith University Nathan, Brisbane, Queensland, Australia; Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia
| | - D L Pountney
- School of Medical Science, Griffith University, Gold Coast, Queensland, Australia
| | - K F Tonissen
- School of Environment and Science, Griffith University Nathan, Brisbane, Queensland, Australia; Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia
| | - G D Mellick
- School of Environment and Science, Griffith University Nathan, Brisbane, Queensland, Australia; Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia
| | - I Yanatori
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - D R Richardson
- School of Environment and Science, Griffith University Nathan, Brisbane, Queensland, Australia; Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia; Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia; Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
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14
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Trist BG, Hilton JB, Hare DJ, Crouch PJ, Double KL. Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic. Angew Chem Int Ed Engl 2021; 60:9215-9246. [PMID: 32144830 PMCID: PMC8247289 DOI: 10.1002/anie.202000451] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 12/11/2022]
Abstract
Cu/Zn superoxide dismutase (SOD1) is a frontline antioxidant enzyme catalysing superoxide breakdown and is important for most forms of eukaryotic life. The evolution of aerobic respiration by mitochondria increased cellular production of superoxide, resulting in an increased reliance upon SOD1. Consistent with the importance of SOD1 for cellular health, many human diseases of the central nervous system involve perturbations in SOD1 biology. But far from providing a simple demonstration of how disease arises from SOD1 loss-of-function, attempts to elucidate pathways by which atypical SOD1 biology leads to neurodegeneration have revealed unexpectedly complex molecular characteristics delineating healthy, functional SOD1 protein from that which likely contributes to central nervous system disease. This review summarises current understanding of SOD1 biology from SOD1 genetics through to protein function and stability.
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Affiliation(s)
- Benjamin G. Trist
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
| | - James B. Hilton
- Department of Pharmacology and TherapeuticsThe University of MelbourneParkvilleVictoria3052Australia
| | - Dominic J. Hare
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
- School of BioSciencesThe University of MelbourneParkvilleVictoria3052Australia
- Atomic Medicine InitiativeThe University of Technology SydneyBroadwayNew South Wales2007Australia
| | - Peter J. Crouch
- Department of Pharmacology and TherapeuticsThe University of MelbourneParkvilleVictoria3052Australia
| | - Kay L. Double
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
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15
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Hu Y, Cheng K, He L, Zhang X, Jiang B, Jiang L, Li C, Wang G, Yang Y, Liu M. NMR-Based Methods for Protein Analysis. Anal Chem 2021; 93:1866-1879. [PMID: 33439619 DOI: 10.1021/acs.analchem.0c03830] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a well-established method for analyzing protein structure, interaction, and dynamics at atomic resolution and in various sample states including solution state, solid state, and membranous environment. Thanks to rapid NMR methodology development, the past decade has witnessed a growing number of protein NMR studies in complex systems ranging from membrane mimetics to living cells, which pushes the research frontier further toward physiological environments and offers unique insights in elucidating protein functional mechanisms. In particular, in-cell NMR has become a method of choice for bridging the huge gap between structural biology and cell biology. Herein, we review the recent developments and applications of NMR methods for protein analysis in close-to-physiological environments, with special emphasis on in-cell protein structural determination and the analysis of protein dynamics, both difficult to be accessed by traditional methods.
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Affiliation(s)
- Yunfei Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China
| | - Lichun He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Bin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Guan Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
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16
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Chin TY, Wang CC, Ma KH, Kuo CW, Hu MK, Chueh SH. Antioxidative effect of DJ-1 is enhanced in NG108-15 cells by DPMQ-induced copper influx. Am J Physiol Cell Physiol 2020; 320:C635-C651. [PMID: 33356946 DOI: 10.1152/ajpcell.00515.2019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Disruption of copper homeostasis is closely involved in neurodegenerative disorders. This study examined whether a hybrid copper-binding compound, (E)-2-(4-(dimethylamino)phenylimino)methyl)quinolin-8-ol (DPMQ), is able to protect NG108-15 cells against oxidative stress. We found that treatment of cells with rotenone or hydrogen peroxide increased cellular oxidative stress and resulted in mitochondrial dysfunction and apoptosis. The cellular levels of Nrf2 and the Cu2+ chaperone DJ-1 were also decreased. These oxidative detrimental effects were all inhibited when cells were cotreated with DPMQ. DPMQ increased cellular Cu2+ content, DJ-1 protein level, superoxide dismutase (SOD) activity, and Nrf2 nuclear translocation under basal state. The activity of SOD decreased under redox imbalance and this decrease was blocked by DPMQ treatment, while the protein level of SOD1 remained unaltered regardless of the oxidative stress and DPMQ treatment. Using endogenous proteins, coimmunoprecipitation showed that DJ-1 bound with SOD1 and Nrf2 individually. The amount of Nrf2, bound to DJ-1, consistently reflected its cellular level, while the amount of SOD1, bound to DJ-1, was potentiated by DPMQ, being greater in the basal state than under redox imbalance. Simultaneous inclusion of nonpermeable Cu2+ chelator tetrathiomolybdate or triethylenetetramine during DPMQ treatment blocked all aforementioned effects of DPMQ, showing that the dependency of the effect of DPMQ on extracellular Cu2+. In addition, silencing of DJ-1 blocked the protection of DPMQ against oxidative stress. Taken all together, our results suggest that DPMQ stabilizes DJ-1 in a Cu2+-dependent manner, which then brings about SOD1 activation and Nrf2 nuclear translocation; these together alleviate cellular oxidative stress.
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Affiliation(s)
- Ting-Yu Chin
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli, Taiwan
| | - Che-Chuan Wang
- Department of Neurosurgery, Chi Mei Medical Center, Tainan, Taiwan.,Center for General Education, Southern Taiwan University of Science and Technology, Tainan, Taiwan
| | - Kuo-Hsing Ma
- Department of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan
| | - Chia-Wei Kuo
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Ming-Kuan Hu
- School of Pharmacy, National Defense Medical Center, Taipei, Taiwan
| | - Sheau-Huei Chueh
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
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17
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Trist BG, Hilton JB, Hare DJ, Crouch PJ, Double KL. Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Benjamin G. Trist
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
| | - James B. Hilton
- Department of Pharmacology and Therapeutics The University of Melbourne Parkville Victoria 3052 Australia
| | - Dominic J. Hare
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
- School of BioSciences The University of Melbourne Parkville Victoria 3052 Australia
- Atomic Medicine Initiative The University of Technology Sydney Broadway New South Wales 2007 Australia
| | - Peter J. Crouch
- Department of Pharmacology and Therapeutics The University of Melbourne Parkville Victoria 3052 Australia
| | - Kay L. Double
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
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18
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Luchinat E, Barbieri L, Campbell TF, Banci L. Real-Time Quantitative In-Cell NMR: Ligand Binding and Protein Oxidation Monitored in Human Cells Using Multivariate Curve Resolution. Anal Chem 2020; 92:9997-10006. [PMID: 32551584 PMCID: PMC7735651 DOI: 10.1021/acs.analchem.0c01677] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
In-cell NMR can investigate
protein conformational changes at atomic
resolution, such as those changes induced by drug binding or chemical
modifications, directly in living human cells, and therefore has great
potential in the context of drug development as it can provide an
early assessment of drug potency. NMR bioreactors can greatly improve
the cell sample stability over time and, more importantly, allow for
recording in-cell NMR data in real time to monitor the evolution of
intracellular processes, thus providing unique insights into the kinetics
of drug-target interactions. However, current implementations are
limited by low cell viability at >24 h times, the reduced sensitivity
compared to “static” experiments and the lack of protocols
for automated and quantitative analysis of large amounts of data.
Here, we report an improved bioreactor design which maintains human
cells alive and metabolically active for up to 72 h, and a semiautomated
workflow for quantitative analysis of real-time in-cell NMR data relying
on Multivariate Curve Resolution. We apply this setup to monitor protein–ligand
interactions and protein oxidation in real time. High-quality concentration
profiles can be obtained from noisy 1D and 2D NMR data with high temporal
resolution, allowing further analysis by fitting with kinetic models.
This unique approach can therefore be applied to investigate complex
kinetic behaviors of macromolecules in a cellular setting, and could
be extended in principle to any real-time NMR application in live
cells.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy.,Center for Colloids and Surface Science - CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence Italy
| | - Letizia Barbieri
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy.,Interuniversity Consortium for Magnetic Resonance of Metalloproteins - CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy
| | - Timothy F Campbell
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence Italy
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19
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Barbieri L, Luchinat E. Backbone resonance assignment of human DJ-1 in the reduced state and in the cysteine sulfinic acid state. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:371-376. [PMID: 31377986 DOI: 10.1007/s12104-019-09908-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
DJ-1 is a highly conserved soluble protein that is associated to several cellular pathways. In humans, DJ-1 has been implicated in several pathologies such as cancer, Parkinson's disease and amyotrophic lateral sclerosis. Several roles have been attributed to DJ-1, including defense against oxidative stress, chaperone activity and proteasome regulation. The recent finding that DJ-1 acts as a protein and DNA deglycase further confirms the protective function of DJ-1 and suggests a common mechanism of action in the various pathways in which DJ-1 is involved. Cysteine 106, located in the putative active site of DJ-1, is critical for the biological activity of DJ-1 and is easily oxidized to cysteine-sulfinate. While such oxidation modulates DJ-1 activity, the underlying molecular mechanism has not yet been elucidated. Cysteine oxidation does not perturb the protein structure, therefore changes in protein dynamics in solution could modulate its function. Here, we report a revised and completed (98%) backbone assignment of reduced DJ-1, together with the backbone assignment of oxidized DJ-1. Chemical shift perturbation is observed in several regions across the sequence, while no changes in secondary structure are observed. These data will provide the starting point for further characterization of the changes in the backbone dynamics of DJ-1 upon oxidation in solution at physiological temperature.
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Affiliation(s)
- Letizia Barbieri
- Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, Sesto Fiorentino, Italy
| | - Enrico Luchinat
- Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134, Florence, Italy.
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20
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van den Bedem H, Wilson MA. Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:958-966. [PMID: 31274417 PMCID: PMC6613112 DOI: 10.1107/s160057751900568x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/25/2019] [Indexed: 05/04/2023]
Abstract
Cysteine is a rare but functionally important amino acid that is often subject to covalent modification. Cysteine oxidation plays an important role in many human disease processes, and basal levels of cysteine oxidation are required for proper cellular function. Because reactive cysteine residues are typically ionized to the thiolate anion (Cys-S-), their formation of a covalent bond alters the electrostatic and steric environment of the active site. X-ray-induced photo-oxidation to sulfenic acids (Cys-SOH) can recapitulate some aspects of the changes that occur under physiological conditions. Here we propose how site-specific cysteine photo-oxidation can be used to interrogate ensuing changes in protein structure and dynamics at atomic resolution. Although this powerful approach can connect cysteine covalent modification to global protein conformational changes and function, careful biochemical validation must accompany all such studies to exclude misleading artifacts. New types of X-ray crystallography experiments and powerful computational methods are creating new opportunities to connect conformational dynamics to catalysis for the large class of systems that use covalently modified cysteine residues for catalysis or regulation.
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Affiliation(s)
- Henry van den Bedem
- Bioscience Division, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Mark A Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
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21
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Applications of In-Cell NMR in Structural Biology and Drug Discovery. Int J Mol Sci 2019; 20:ijms20010139. [PMID: 30609728 PMCID: PMC6337603 DOI: 10.3390/ijms20010139] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/24/2018] [Accepted: 12/29/2018] [Indexed: 01/23/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) is a method to provide the structural information of a target at an atomic level under physiological conditions and a full view of the conformational changes of a protein caused by ligand binding, post-translational modifications or protein⁻protein interactions in living cells. Previous in-cell NMR studies have focused on proteins that were overexpressed in bacterial cells and isotopically labeled proteins injected into oocytes of Xenopus laevis or delivered into human cells. Applications of in-cell NMR in probing protein modifications, conformational changes and ligand bindings have been carried out in mammalian cells by monitoring isotopically labeled proteins overexpressed in living cells. The available protocols and successful examples encourage wide applications of this technique in different fields such as drug discovery. Despite the challenges in this method, progress has been made in recent years. In this review, applications of in-cell NMR are summarized. The successful applications of this method in mammalian and bacterial cells make it feasible to play important roles in drug discovery, especially in the step of target engagement.
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22
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Bifunctional Chloroplastic DJ-1B from Arabidopsis thaliana is an Oxidation-Robust Holdase and a Glyoxalase Sensitive to H₂O₂. Antioxidants (Basel) 2019; 8:antiox8010008. [PMID: 30609642 PMCID: PMC6356872 DOI: 10.3390/antiox8010008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 12/15/2018] [Accepted: 12/22/2018] [Indexed: 01/04/2023] Open
Abstract
Members of the DJ-1 protein family are multifunctional enzymes whose loss increases the susceptibility of the cell to oxidative stress. However, little is known about the function of the plant DJ-1 homologs. Therefore, we analyzed the effect of oxidation on the structure and function of chloroplastic AtDJ-1B and studied the phenotype of T-DNA lines lacking the protein. In vitro oxidation of AtDJ-1B with H₂O₂ lowers its glyoxalase activity, but has no effect on its holdase chaperone function. Remarkably, upon oxidation, the thermostability of AtDJ-1B increases with no significant alteration of the overall secondary structure. Moreover, we found that AtDJ-1B transcript levels are invariable, and loss of AtDJ-1B does not affect plant viability, growth and stress response. All in all, two discrete functions of AtDJ-1B respond differently to H₂O₂, and AtDJ-1B is not essential for plant development under stress.
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23
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Luchinat E, Banci L. In-Cell NMR in Human Cells: Direct Protein Expression Allows Structural Studies of Protein Folding and Maturation. Acc Chem Res 2018; 51:1550-1557. [PMID: 29869502 DOI: 10.1021/acs.accounts.8b00147] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cellular structural biology methods are needed to characterize biological processes at atomic resolution in the physiological environment of the cell. Toward this goal, solution in-cell NMR is a powerful approach because it provides structural and dynamic data on macromolecules inside living cells. Several approaches have been developed for in-cell NMR in cultured human cells, which are needed to study processes related to human diseases that rely on the delivery of exogenous macromolecules to the cells. Such strategies, however, may not be applicable to proteins that are sensitive to the external environment or prone to aggregate and can introduce artifacts during protein purification or delivery. As a complementary approach, direct protein expression for in-cell NMR in human cells was developed. This strategy is especially useful when studying processes like protein folding, maturation, and post-translational modification, starting right after protein synthesis. Compared with the protein expression techniques in mammalian cells commonly used in cellular biology, the low sensitivity of NMR requires higher protein levels. Among the cell lines used for high-yield protein expression, the HEK293T cell line was chosen, as it can be efficiently transfected with a cost-effective reagent. A vector originally designed for secreted proteins allows high-level cytosolic protein expression. For isotopic labeling, commercially available or homemade labeled media are employed. Uniform or amino acid type-selective labeling strategies are possible. Protein expression can be targeted to specific organelles (e.g., mitochondria), allowing for in organello NMR applications. A variant of the approach was developed that allows the sequential expression of two or more proteins, with only one selectively labeled. Protein expression in HEK293T cells was applied to recapitulate the maturation steps of intracellular superoxide dismutase 1 (SOD1) and to study the effect of mutations linked to familial amyotrophic lateral sclerosis (fALS) by in-cell NMR. Intracellular wild-type SOD1 spontaneously binds zinc, while it needs the copper chaperone for superoxide dismutase (CCS) for copper delivery and disulfide bond formation. Some fALS-linked mutations impair zinc binding and cause SOD1 to irreversibly unfold, likely forming the precursor of cytotoxic aggregates. The SOD-like domain of CCS acts as a molecular chaperone toward mutant SOD1, stabilizing its folding and allowing zinc binding and correct maturation. Changes in protein redox state distributions can also be investigated by in-cell NMR. Mitochondrial proteins require the redox-regulating partners glutaredoxin 1 (Grx1) and thioredoxin (Trx) to remain in the reduced, import-competent state in the cytosol, whereas SOD1 requires CCS for disulfide bond formation. In both cases, the proteins do not equilibrate with the cytosolic redox pool. Cysteine oxidation in response to oxidative stress can also be monitored. In the near future, in-cell NMR in human cells will likely benefit from technological advancements in NMR hardware, the development of bioreactor systems for increased sample lifetime, the application of paramagnetic NMR to obtain structural restraints, and advanced tools for genome engineering and should be increasingly integrated with advanced cellular imaging techniques.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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24
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iNEXT: a European facility network to stimulate translational structural biology. FEBS Lett 2018; 592:1909-1917. [DOI: 10.1002/1873-3468.13062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Freisinger E, Sigel RKO. Celebrating Helmut Sigel. J Biol Inorg Chem 2017; 23:1-5. [PMID: 29218638 DOI: 10.1007/s00775-017-1523-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Eva Freisinger
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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