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Łuczkowski M, Leszczyńska W, Wątły J, Clemens S, Krężel A. Phytochelatins Bind Zn(II) with Micro- to Picomolar Affinities without the Formation of Binuclear Complexes, Exhibiting Zinc Buffering and Muffling Rather than Storing Functions. Inorg Chem 2024; 63:10915-10931. [PMID: 38845098 DOI: 10.1021/acs.inorgchem.4c01707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Phytochelatins (PCs) are poly-Cys peptides containing a repeating γ-Glu-Cys motif synthesized in plants, algae, certain fungi, and worms by PC synthase from reduced glutathione. It has been shown that an excess of toxic metal ions induces their biosynthesis and that they are responsible for the detoxification process. Little is known about their participation in essential metal binding under nontoxic, basal conditions under which PC synthase is active. This study presents spectroscopic and thermodynamic interactions with the PC2-PC5 series, mainly focusing on the relations between Zn(II) complex stability and cellular Zn(II) availability. The investigations employed mass spectrometry, UV-vis spectroscopy, potentiometry, competition assays with zinc probes, and isothermal titration calorimetry (ITC). All peptides form ZnL complexes, while ZnL2 was found only for PC2, containing two to four sulfur donors in the coordination sphere. Binuclear species typical of Cd(II)-PC complexes are not formed in the case of Zn(II). Results demonstrate that the affinity for Zn(II) increases linearly from PC2 to PC4, ranging from micro- to low-picomolar. Further elongation does not significantly increase the stability. Stability elevation is driven mainly by entropic factors related to the chelate effect and conformational restriction rather than enthalpic factors related to the increasing number of sulfur donors. The affinity of the investigated PCs falls within the range of exchangeable Zn(II) concentrations (hundreds of pM) observed in plants, supporting for the first time a role of PCs both in buffering and in muffling cytosolic Zn(II) concentrations under normal conditions, not exposed to zinc excess, where short PCs have been identified in numerous studies. Furthermore, we found that Cd(II)-PC complexes demonstrate significantly higher metal capacities due to the formation of polynuclear species, which are lacking for Zn(II), supporting the role of PCs in Cd(II) storage (detoxification) and Zn(II) buffering and muffling. Our results on phytochelatins' coordination chemistry and thermodynamics are important for zinc biology and understanding the molecular basis of cadmium toxicity, leaving room for future studies.
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Affiliation(s)
- Marek Łuczkowski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Weronika Leszczyńska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Joanna Wątły
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Stephan Clemens
- Department of Plant Physiology, Faculty of Biology, Chemistry and Earth Sciences, University of Bayreuth, 95440 Bayreuth, Germany
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
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2
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Holtzen SE, Rakshit A, Palmer AE. Protocol for measuring labile cytosolic Zn 2+ using an in situ calibration of a genetically encoded FRET sensor. STAR Protoc 2024; 5:103130. [PMID: 38870018 DOI: 10.1016/j.xpro.2024.103130] [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: 03/08/2024] [Revised: 04/15/2024] [Accepted: 05/24/2024] [Indexed: 06/15/2024] Open
Abstract
Zinc (Zn2+) plays roles in structure, catalysis, and signaling. The majority of cellular Zn2+ is bound by proteins, but a fraction of total Zn2+ exists in a labile form. Here, we present a protocol for measuring labile cytosolic Zn2+ using an in situ calibration of a genetically encoded Förster resonance energy transfer (FRET) sensor. We describe steps for producing buffered Zn2+ solutions for performing an imaging-based calibration and analyzing the imaging data generated to determine labile Zn2+ concentration in single cells. For complete details on the use and execution of this protocol, please refer to Rakshit and Holtzen et al.1.
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Affiliation(s)
- Samuel E Holtzen
- BioFrontiers Institute and Department of Biochemistry, 3415 Colorado Avenue, University of Colorado Boulder, Boulder, CO 80303, USA; Department of Molecular Cellular Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Ananya Rakshit
- BioFrontiers Institute and Department of Biochemistry, 3415 Colorado Avenue, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Amy E Palmer
- BioFrontiers Institute and Department of Biochemistry, 3415 Colorado Avenue, University of Colorado Boulder, Boulder, CO 80303, USA.
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3
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Rua AJ, Alexandrescu AT. Formerly degenerate seventh zinc finger domain from transcription factor ZNF711 rehabilitated by experimental NMR structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.588434. [PMID: 38645208 PMCID: PMC11030341 DOI: 10.1101/2024.04.06.588434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Domain Z7 of nuclear transcription factor ZNF711 has the consensus last metal-ligand H23 found in odd-numbered zinc-fingers of this protein replaced by a phenylalanine. Ever since the discovery of ZNF711 it has been thought that Z7 is probably non-functional because of the H23F substitution. The presence of H26 three positions downstream prompted us to examine if this histidine could substitute as the last metal ligand. The Z7 domain adopts a stable tertiary structure upon metal binding. The NMR structure of Zn2+-bound Z7 shows the classical ββα-fold of CCHH zinc fingers. Mutagenesis and pH titration experiments indicate that H26 is not involved in metal binding and that Z7 has a tridentate metal-binding site comprised of only residues C3, C6, and H19. By contrast, an F23H mutation that introduces a histidine in the consensus position forms a tetradentate ligand. The structure of the WT Z7 is stable causing restricted ring-flipping of phenyalanines 10 and 23. Dynamics are increased with either the H26A or F23H substitutions and aromatic ring rotation is no longer hindered in the two mutants. The mutations have only small effects on the Kd values for Zn2+ and Co2+ and retain the high thermal stability of the WT domain above 80 °C. Like two previously reported designed zinc fingers with the last ligand replaced by water, the WT Z7 domain is catalytically active, hydrolyzing 4-nitophenyl acetate. We discuss the implications of naturally occurring tridentate zinc fingers for cancer mutations and drug targeting of notoriously undruggable transcription factors. Our findings that Z7 can fold with only a subset of three metal ligands suggests the recent view that most everything about protein structure can be predicted through homology modeling might be premature for at least the resilient and versatile zinc-finger motif.
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Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut
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4
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Shao X, Xing F, Zhang Y, Lok CN, Che CM. Integrative chemoproteomics reveals anticancer mechanisms of silver(i) targeting the proteasome regulatory complex. Chem Sci 2024; 15:5349-5359. [PMID: 38577372 PMCID: PMC10988589 DOI: 10.1039/d3sc04834a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/27/2024] [Indexed: 04/06/2024] Open
Abstract
Silver compounds have favorable properties as promising anticancer drug candidates, such as low side effects, anti-inflammatory properties, and high potential to overcome drug resistance. However, the exact mechanism by which Ag(i) confers anticancer activity remains unclear, which hinders further development of anticancer applications of silver compounds. Here, we combine thermal proteome profiling, cysteine profiling, and ubiquitome profiling to study the molecular mechanisms of silver(i) complexes supported by non-toxic thiourea (TU) ligands. Through the formation of AgTU complexes, TU ligands deliver Ag+ ions to cancer cells and tumour xenografts to elicit inhibitory potency. Our chemical proteomics studies show that AgTU acts on the ubiquitin-proteasome system (UPS) and disrupts protein homeostasis, which has been identified as a main anticancer mechanism. Specifically, Ag+ ions are released from AgTU in the cellular environment, directly target the 19S proteasome regulatory complex, and may oxidize its cysteine residues, thereby inhibiting proteasomal activity and accumulating ubiquitinated proteins. After AgTU treatment, proteasome subunits are massively ubiquitinated and aberrantly aggregated, leading to impaired protein homeostasis and paraptotic death of cancer cells. This work reveals the unique anticancer mechanism of Ag(i) targeting the 19S proteasome regulatory complex and opens up new avenues for optimizing silver-based anticancer efficacy.
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Affiliation(s)
- Xiaojian Shao
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F., Building 17W, Hong Kong Science Park, New Territories Hong Kong P. R. China
| | - Fangrong Xing
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F., Building 17W, Hong Kong Science Park, New Territories Hong Kong P. R. China
| | - Yiwei Zhang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F., Building 17W, Hong Kong Science Park, New Territories Hong Kong P. R. China
| | - Chun-Nam Lok
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F., Building 17W, Hong Kong Science Park, New Territories Hong Kong P. R. China
| | - Chi-Ming Che
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited Units 1503-1511, 15/F., Building 17W, Hong Kong Science Park, New Territories Hong Kong P. R. China
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5
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Szarszoń K, Mikołajczyk A, Grelich-Mucha M, Wieczorek R, Matera-Witkiewicz A, Olesiak-Bańska J, Rowińska-Żyrek M, Wątły J. Bioinorganic chemistry of shepherin II complexes helps to fight Candida albicans? J Inorg Biochem 2024; 253:112476. [PMID: 38171045 DOI: 10.1016/j.jinorgbio.2023.112476] [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: 10/30/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
The fungal cell wall and cell membrane are an important target for antifungal therapies, and a needle-like cell wall or membrane disruption may be an entirely novel antifungal mode of action. In this work, we show how the coordination of Zn(II) triggers the antifungal properties of shepherin II, a glycine- and histidine-rich antimicrobial peptide from the root of Capsella bursa-pastoris. We analyze Cu(II) and Zn(II) complexes of this peptide using experimental and theoretical methods, such as: mass spectrometry, potentiometry, UV-Vis and CD spectroscopies, AFM imaging, biological activity tests and DFT calculations in order to understand the correlation between their metal binding mode, structure, morphology and biological activity. We observe that Zn(II) coordinates to Shep II and causes a structural change, resulting in fibril formation, what has a pronounced biological consequence - a strong anticandidal activity. This phenomenon was observed neither for the peptide itself, nor for its copper(II) complex. The Zn(II) - shepherin II complex can be considered as a starting point for further anticandidal drug discovery, which is extremely important in the era of increasing antifungal drug resistance.
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Affiliation(s)
- Klaudia Szarszoń
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aleksandra Mikołajczyk
- Screening of Biological Activity Assays and Collection of Biological Material Laboratory, Wrocław Medical University Biobank, Faculty of Pharmacy, Wrocław Medical University, 50-556 Wrocław, Poland
| | - Manuela Grelich-Mucha
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Agnieszka Matera-Witkiewicz
- Screening of Biological Activity Assays and Collection of Biological Material Laboratory, Wrocław Medical University Biobank, Faculty of Pharmacy, Wrocław Medical University, 50-556 Wrocław, Poland
| | - Joanna Olesiak-Bańska
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | | | - Joanna Wątły
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
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6
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Yi B, Tanaka YL, Cornish D, Kosako H, Butlertanaka EP, Sengupta P, Lippincott-Schwartz J, Hultquist JF, Saito A, Yoshimura SH. Host ZCCHC3 blocks HIV-1 infection and production through a dual mechanism. iScience 2024; 27:109107. [PMID: 38384847 PMCID: PMC10879702 DOI: 10.1016/j.isci.2024.109107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/12/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Most mammalian cells prevent viral infection and proliferation by expressing various restriction factors and sensors that activate the immune system. Several host restriction factors that inhibit human immunodeficiency virus type 1 (HIV-1) have been identified, but most of them are antagonized by viral proteins. Here, we describe CCHC-type zinc-finger-containing protein 3 (ZCCHC3) as a novel HIV-1 restriction factor that suppresses the production of HIV-1 and other retroviruses, but does not appear to be directly antagonized by viral proteins. It acts by binding to Gag nucleocapsid (GagNC) via zinc-finger motifs, which inhibits viral genome recruitment and results in genome-deficient virion production. ZCCHC3 also binds to the long terminal repeat on the viral genome via the middle-folded domain, sequestering the viral genome to P-bodies, which leads to decreased viral replication and production. This distinct, dual-acting antiviral mechanism makes upregulation of ZCCHC3 a novel potential therapeutic strategy.
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Affiliation(s)
- Binbin Yi
- Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-Cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuri L. Tanaka
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Daphne Cornish
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Erika P. Butlertanaka
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Prabuddha Sengupta
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | | | - Judd F. Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
- Center for Animal Disease Control, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki, Miyazaki 889-2192, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, 5200 Kiyotakecho Kihara, Miyazaki, Miyazaki 889-1692, Japan
| | - Shige H. Yoshimura
- Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-Cho, Sakyo-ku, Kyoto 606-8501, Japan
- Center for Living Systems Information Science (CeLiSIS), Kyoto University, Yoshida-Konoe-Cho, Sakyo-ku, Kyoto 606-8501, Japan
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7
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Kocyła AM, Czogalla A, Wessels I, Rink L, Krężel A. A combined biochemical and cellular approach reveals Zn 2+-dependent hetero- and homodimeric CD4 and Lck assemblies in T cells. Structure 2024; 32:292-303.e7. [PMID: 38157858 DOI: 10.1016/j.str.2023.11.013] [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: 07/12/2023] [Revised: 10/25/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
The CD4 or CD8 co-receptors' interaction with the protein-tyrosine kinase Lck initiates the tyrosine phosphorylation cascade leading to T cell activation. A critical question is: to what extent are co-receptors and Lck coupled? Our contribution concerns Zn2+, indispensable for CD4- and CD8-Lck formation. We combined biochemical and cellular approaches to show that dynamic fluctuations of free Zn2+ in physiological ranges influence Zn(CD4)2 and Zn(CD4)(Lck) species formation and their ratio, although the same Zn(Cys)2(Cys)2 cores. Moreover, we demonstrated that the affinity of Zn2+ to CD4 and CD4-Lck species differs significantly. Increased intracellular free Zn2+ concentration in T cells causes higher CD4 partitioning in the plasma membrane. We additionally found that CD4 palmitoylation decreases the specificity of CD4-Lck formation in the reconstituted membrane model. Our findings help elucidate co-receptor-Lck coupling stoichiometry and demonstrate that intracellular free Zn2+ has a major role in the interplay between CD4 dimers and CD4-Lck assembly.
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Affiliation(s)
- Anna M Kocyła
- Department of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Aleksander Czogalla
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Inga Wessels
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Lothar Rink
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland.
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8
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Pham TL, Conde González MR, Fazliev S, Kishore A, Comba P, Thomas F. Relationship of Thermostability and Binding Affinity in Metal-binding WW-Domain Minireceptors. Chembiochem 2024; 25:e202300715. [PMID: 38127995 DOI: 10.1002/cbic.202300715] [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: 10/18/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023]
Abstract
The design of metallo-miniproteins advances our understanding of the structural and functional roles of metals in proteins. We recently designed a metal-binding WW domain, WW-CA-Nle, which displays three histidine residues on its surface for coordination of divalent metals Ni(II), Zn(II) and Cu(II). However, WW-CA-Nle is a molten globule in the apo state and thus showed only moderate binding affinities with Kd values in the μM regime. In this report, we hypothesize that improved thermal stability of the apo state of the metal binding WW-domain scaffold should lead to improved preorganization of the metal-binding site and consequently to higher metal-binding affinities. By redesigning WW-CA-Nle, we obtained WW-CA variants, WW-CA-min and WW-CA-ANG, which were fully folded in the apo states and displayed moderate to excellent thermostabilities in the apo and holo states. We were able to show that the improved thermal stabilities led to improved metal binding, which was reflected in Kd values that were at least one order of magnitude lower compared to WW-CA-Nle. EPR spectroscopy and ITC measurements revealed a better defined and predisposed metal binding site in WW-CA-ANG.
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Affiliation(s)
- Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Marcos R Conde González
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Max Planck School Matter to Life
| | - Sunnatullo Fazliev
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Max Planck School Matter to Life
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Agi Kishore
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Max Planck School Matter to Life
- Institute of Inorganic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Peter Comba
- Institute of Inorganic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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9
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Hwang Y, Mohammad Mydul Islam AK, Park S, Kang HG, Lee C, Lim MH, Lee SJ. Decoding the Parkinson's Symphony: PARIS, Maestro of Transcriptional Regulation and Metal Coordination for Dopamine Release. ACS Chem Neurosci 2024; 15:447-455. [PMID: 38241020 DOI: 10.1021/acschemneuro.3c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024] Open
Abstract
Parkin interacting substrate (PARIS) is a pivotal transcriptional regulator in the brain that orchestrates the activity of various enzymes through its intricate interactions with biomolecules, including nucleic acids. Notably, the binding of PARIS to insulin response sequences (IRSs) triggers a cascade of events that results in the functional loss in the substantia nigra, which impairs dopamine release and, subsequently, exacerbates the relentless neurodegeneration. Here, we report the details of the interactions of PARIS with IRSs via classical zinc finger (ZF) domains in PARIS, namely, PARIS(ZF2-4). Our biophysical studies with purified PARIS(ZF2-4) elucidated the binding partner of PARIS, which generates specific interactions with the IRS1 (5'-TATTTTT, Kd = 38.9 ± 2.4 nM) that is positioned in the promoter region of peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α). Mutational and metal-substitution studies demonstrated that Zn(II)-PARIS(ZF2-4) could recognize its binding partner selectively. Overall, our work provides submolecular details regarding PARIS and shows that it is a transcriptional factor that regulates dopamine release. Thus, PARIS could be a crucial target for therapeutic applications.
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Affiliation(s)
- Yunha Hwang
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | | | - Seongmin Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyun Goo Kang
- Department of Neurology and Research Institute of Clinical Medicine, Jeonbuk National University Hospital, Jeonju 54896, Republic of Korea
| | - Chaemin Lee
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seung Jae Lee
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Institute of Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
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10
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Rogowska A, Król-Górniak A, Railean V, Kanawati B, Schmitt-Kopplin P, Michalke B, Sugajski M, Pomastowski P, Buszewski B. Deciphering the complexes of zinc ions and hen egg white lysozyme: Instrumental analysis, molecular docking, and antimicrobial assessment. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123490. [PMID: 37816265 DOI: 10.1016/j.saa.2023.123490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/12/2023]
Abstract
In the research presented in this manuscript, an intricate study has been carried out on the interaction of zinc ions with the hen egg white lysozyme (HEWL) protein. Utilizing a spectroscopic technique, the alterations that arise due to the binding of Zn2+ to the HEWL were scrutinized, underscoring the paramount significance of deprotonated carboxyl and thiol groups in the process of binding. The binding phenomena were substantiated using capillary electrophoresis integrated with inductively coupled plasma mass spectrometry (CE-ICP-MS). Further spectrometric assessments (MALDI-TOF MS and FT-ICR-MS) shed light on the direct interaction of zinc ions with the functional groups of the protein. Importantly, high-resolution FT-ICR-MS techniques elucidated the capability of a single protein molecule to bind to multiple zinc ions. The empirically derived spectroscopic data received additional confirmation via a molecular docking study of the Zn2+ binding process, which highlighted a substantial affinity between the predicted 3D model of zinc-lysozyme complexes. Predominantly, the interaction between the bound entities was observed at the cysteine residues. Lastly, the conducted antimicrobial tests revealed that the zinc-lysozyme complexes manifest an inhibitory effect against bacterial (E. coli and S. aureus) and yeast (C. albicans) strains.
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Affiliation(s)
- Agnieszka Rogowska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland; Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Anna Król-Górniak
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland; Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Viorica Railean
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland; Department of Infectious, Invasive Diseases and Veterinary Administration, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Toruń, Poland.
| | - Basem Kanawati
- Research Unit Analytical BioGeoChemistry, Helmholtz Center Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany.
| | - Phillipe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Center Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Bernhard Michalke
- Research Unit Analytical BioGeoChemistry, Helmholtz Center Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Mateusz Sugajski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, Wileńska 4, 87-100 Torun, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Torun, Poland
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11
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Lin H, Suzuki K, Smith N, Li X, Nalbach L, Fuentes S, Spigelman AF, Dai XQ, Bautista A, Ferdaoussi M, Aggarwal S, Pepper AR, Roma LP, Ampofo E, Li WH, MacDonald PE. A role and mechanism for redox sensing by SENP1 in β-cell responses to high fat feeding. Nat Commun 2024; 15:334. [PMID: 38184650 PMCID: PMC10771529 DOI: 10.1038/s41467-023-44589-x] [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: 02/23/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024] Open
Abstract
Pancreatic β-cells respond to metabolic stress by upregulating insulin secretion, however the underlying mechanisms remain unclear. Here we show, in β-cells from overweight humans without diabetes and mice fed a high-fat diet for 2 days, insulin exocytosis and secretion are enhanced without increased Ca2+ influx. RNA-seq of sorted β-cells suggests altered metabolic pathways early following high fat diet, where we find increased basal oxygen consumption and proton leak, but a more reduced cytosolic redox state. Increased β-cell exocytosis after 2-day high fat diet is dependent on this reduced intracellular redox state and requires the sentrin-specific SUMO-protease-1. Mice with either pancreas- or β-cell-specific deletion of this fail to up-regulate exocytosis and become rapidly glucose intolerant after 2-day high fat diet. Mechanistically, redox-sensing by the SUMO-protease requires a thiol group at C535 which together with Zn+-binding suppresses basal protease activity and unrestrained β-cell exocytosis, and increases enzyme sensitivity to regulation by redox signals.
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Affiliation(s)
- Haopeng Lin
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Guangzhou Laboratory, Guangzhou, 510005, Guangdong, China
| | - Kunimasa Suzuki
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Nancy Smith
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Xi Li
- Departments of Cell Biology and Biochemistry, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390-9039, USA
| | - Lisa Nalbach
- Institute for Clinical & Experimental Surgery, Saarland University, Homburg/Saar, Germany
- Biophysics Department, Center for Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Sonia Fuentes
- Departments of Cell Biology and Biochemistry, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390-9039, USA
| | - Aliya F Spigelman
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Xiao-Qing Dai
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Austin Bautista
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Mourad Ferdaoussi
- Faculty Saint-Jean, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Saloni Aggarwal
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Andrew R Pepper
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Leticia P Roma
- Biophysics Department, Center for Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Emmanuel Ampofo
- Institute for Clinical & Experimental Surgery, Saarland University, Homburg/Saar, Germany
| | - Wen-Hong Li
- Departments of Cell Biology and Biochemistry, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390-9039, USA
| | - Patrick E MacDonald
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
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12
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Almeida NMS, Bali SK, James D, Wang C, Wilson AK. Binding of Per- and Polyfluoroalkyl Substances (PFAS) to the PPARγ/RXRα-DNA Complex. J Chem Inf Model 2023; 63:7423-7443. [PMID: 37990410 DOI: 10.1021/acs.jcim.3c01384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Nuclear receptors are the fundamental building blocks of gene expression regulation and the focus of many drug targets. While binding to DNA, nuclear receptors act as transcription factors, governing a multitude of functions in the human body. Peroxisome proliferator-activator receptor γ (PPARγ) and the retinoid X receptor α (RXRα) form heterodimers with unique properties and have a primordial role in insulin sensitization. This PPARγ/RXRα heterodimer has been shown to be impacted by per- and polyfluoroalkyl substances (PFAS) and linked to a variety of significant health conditions in humans. Herein, a selection of the most common PFAS (legacy and emerging) was studied utilizing molecular dynamics simulations for PPARγ/RXRα. The local and global structural effects of PFAS binding on the known ligand binding pockets of PPARγ and RXRα as well as the DNA binding domain (DBD) of RXRα were inspected. The binding free energies were predicted computationally and were compared between the different binding pockets. In addition, two electronic structure approaches were utilized to model the interaction of PFAS within the DNA binding domain, density functional theory (DFT) and domain-based pair natural orbital coupled cluster with perturbative triples (DLPNO-CCSD(T)) approaches, with implicit solvation. Residue decomposition and hydrogen-bonding analysis were also performed, detailing the role of prominent residues in molecular recognition. The role of l-carnitine is explored as a potential in vivo remediation strategy for PFAS interaction with the PPARγ/RXRα heterodimer. In this work, it was found that PFAS can bind and act as agonists for all of the investigated pockets. For the first time in the literature, PFAS are postulated to bind to the DNA binding domain in a nonspecific manner. In addition, for the PPARγ ligand binding domain, l-carnitine shows promise in replacing smaller PFAS from the pocket.
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Affiliation(s)
- Nuno M S Almeida
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Semiha Kevser Bali
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Deepak James
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Cong Wang
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
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13
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Rua AJ, Whitehead RD, Alexandrescu AT. NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol X 2023; 8:100093. [PMID: 37655311 PMCID: PMC10465944 DOI: 10.1016/j.yjsbx.2023.100093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
ZNF750 is a nuclear transcription factor that activates skin differentiation and has tumor suppressor roles in several cancers. Unusually, ZNF750 has only a single zinc-finger (ZNF) domain, Z*, with an amino acid sequence that differs markedly from the CCHH family consensus. Because of its sequence differences Z* is classified as degenerate, presumed to have lost the ability to bind the zinc ion required for folding. AlphaFold predicts an irregular structure for Z* with low confidence. Low confidence predictions are often inferred to be intrinsically disordered regions of proteins, which would be the case if Z* did not bind Zn2+. We use NMR and CD spectroscopy to show that a 25-51 segment of ZNF750 corresponding to the Z* domain folds into a well-defined antiparallel ββα tertiary structure with a pM dissociation constant for Zn2+ and a thermal stability >80 °C. Of three alternative Zn2+ ligand sets, Z* uses a CCHC rather than the expected CCHH ligating motif. The switch in the last ligand maintains the folding topology and hydrophobic core of the classical ZNF motif. CCHC ZNFs are typically associated with protein-protein interactions, raising the possibility that ZNF750 interacts with DNA through other proteins rather than directly. The structure of Z* provides context for understanding the function of the domain and its cancer-associated mutations. We expect other ZNFs currently classified as degenerate could be CCHC-type structures like Z*.
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Affiliation(s)
- Antonio J. Rua
- Department of Molecular and Cellular Biology, University of Connecticut, United States
| | - Richard D. Whitehead
- Department of Molecular and Cellular Biology, University of Connecticut, United States
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14
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Potok P, Kola A, Valensin D, Capdevila M, Potocki S. Copper Forms a PPII Helix-Like Structure with the Catalytic Domains of Bacterial Zinc Metalloproteases. Inorg Chem 2023; 62:18425-18439. [PMID: 37909295 PMCID: PMC10647932 DOI: 10.1021/acs.inorgchem.3c02391] [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: 07/13/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/03/2023]
Abstract
The rapid spread of antibiotic-resistant bacteria continuously raises concerns about the future ineffectiveness of current antimicrobial treatments against infectious diseases. To address this problem, new therapeutic strategies and antimicrobial drugs with unique modes of action are urgently needed. Inhibition of metalloproteases, bacterial virulence factors, is a promising target for the development of antibacterial treatments. In this study, the interaction among Zn(II), Cu(II), and the metal-binding domains of two metalloproteases, AprA (Pseudomonas aureginosa) and CpaA (Acinetobacter baumanii), was investigated. The objective was to determine the coordination sphere of Zn(II) with a peptide model of two zinc-dependent metalloproteases. Additionally, the study explored the formation of Cu(II) complexes with the domains, as Cu(II) has been shown to inhibit metalloproteases. The third aim was to understand the role of nonbinding amino acids in stabilizing the metal complexes formed by these proteases. This work identified specific coordination patterns (HExxHxxxxxH) for both Zn(II) and Cu(II) complexes, with AprA and CpaA exhibiting a higher affinity for Cu(II) compared to Zn(II). The study also found that the CpaA domain has greater stability for both Zn(II) and Cu(II) complexes compared to AprA. The nonbinding amino acids of CpaA surrounding the metal ion contribute to the increased thermodynamic stability of the metal-peptide complex through various intramolecular interactions. These interactions can also influence the secondary structures of the peptides. The presence of certain amino acids, such as tyrosine, arginine, and glutamic acid, and their interactions contribute to the stability and, only in the case of Cu(II) complexes, the formation of a rare protein structure called a left-handed polyproline II helix (PPII), which is known to play a role in the stability and function of various proteins. These findings provide valuable insights into the coordination chemistry of bacterial metalloproteases and expand our understanding of potential mechanisms for inhibiting these enzymes.
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Affiliation(s)
- Paulina Potok
- Faculty
of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Arian Kola
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Daniela Valensin
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Merce Capdevila
- Departament
de Química, Universitat Autònoma
de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Sławomir Potocki
- Faculty
of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland
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15
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Flores BM, Uppalapati CK, Pascual AS, Vong A, Baatz MA, Harrison AM, Leyva KJ, Hull EE. Biological Effects of HDAC Inhibitors Vary with Zinc Binding Group: Differential Effects on Zinc Bioavailability, ROS Production, and R175H p53 Mutant Protein Reactivation. Biomolecules 2023; 13:1588. [PMID: 38002270 PMCID: PMC10669723 DOI: 10.3390/biom13111588] [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: 09/21/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
The coordination of zinc by histone deacetylase inhibitors (HDACi), altering the bioavailability of zinc to histone deacetylases (HDACs), is key to HDAC enzyme inhibition. However, the ability of zinc binding groups (ZBGs) to alter intracellular free Zn+2 levels, which may have far-reaching effects, has not been explored. Using two HDACis with different ZBGs, we documented shifts in intracellular free Zn+2 concentrations that correlate with subsequent ROS production. Next, we assayed refolding and reactivation of the R175H mutant p53 protein in vitro to provide greater biological context as the activity of this mutant depends on cellular zinc concentration. The data presented demonstrates the differential activity of HDACi in promoting R175H response element (RE) binding. After cells are treated with HDACi, there are differences in R175H mutant p53 refolding and reactivation, which may be related to treatments. Collectively, we show that HDACis with distinct ZBGs differentially impact the intracellular free Zn+2 concentration, ROS levels, and activity of R175H; therefore, HDACis may have significant activity independent of their ability to alter acetylation levels. Our results suggest a framework for reevaluating the role of zinc in the variable or off-target effects of HDACi, suggesting that the ZBGs of HDAC inhibitors may provide bioavailable zinc without the toxicity associated with zinc metallochaperones such as ZMC1.
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Affiliation(s)
- Brianna M. Flores
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
- Arizona College of Osteopathic Medicine, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA
| | - Chandana K. Uppalapati
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (C.K.U.); (K.J.L.)
| | - Agnes S. Pascual
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
| | - Alan Vong
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
| | - Margaux A. Baatz
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
| | - Alisha M. Harrison
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
| | - Kathryn J. Leyva
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (C.K.U.); (K.J.L.)
| | - Elizabeth E. Hull
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, 19555 N 59th Avenue, Glendale, AZ 85308, USA; (B.M.F.); (A.S.P.); (M.A.B.)
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16
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Bregnard TA, Fairchild D, Erlandsen H, Semenova IV, Szczepaniak R, Ahmed A, Weller SK, Korzhnev DM, Bezsonova I. Conformational exchange at a C 2H 2 zinc-binding site facilitates redox sensing by the PML protein. Structure 2023; 31:1086-1099.e6. [PMID: 37473756 PMCID: PMC10528520 DOI: 10.1016/j.str.2023.06.014] [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: 12/20/2022] [Revised: 05/12/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023]
Abstract
The promyelocytic leukemia protein, PML, plays a vital role in the cellular response to oxidative stress; however, the molecular mechanism of its action remains poorly understood. Here, we identify redox-sensitive sites of PML. A molecule of PML is cysteine-rich and contains three zinc-binding domains including RING, B-box1, and B-box2. Using in vitro assays, we have compared the sensitivity of the isolated RING and B-box1 domains and shown that B-box1 is more sensitive to oxidation. NMR studies of PML dynamics showed that one of the Zn-coordination sites within the B-box1 undergoes significant conformational exchange, revealing a hotspot for exposure of reactive cysteines. In agreement with the in vitro data, enhancement of the B-box1 Zn-coordination dynamics led to more efficient recruitment of PML into PML nuclear bodies in cells. Overall, our results suggest that the increased sensitivity of B-box1 to oxidative stress makes this domain an important redox-sensing component of PML.
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Affiliation(s)
- Thomas A Bregnard
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Daniel Fairchild
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Heidi Erlandsen
- Center for Open Research Resources & Equipment, UCONN, Storrs, CT 06269, USA
| | - Irina V Semenova
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Renata Szczepaniak
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Affrin Ahmed
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Sandra K Weller
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA.
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17
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Álamo P, Parladé E, Favaro MTP, Gallardo A, Mendoza R, Ferreira LC, Roher N, Mangues R, Villaverde A, Vázquez E. Probing the Biosafety of Implantable Artificial Secretory Granules for the Sustained Release of Bioactive Proteins. ACS APPLIED MATERIALS & INTERFACES 2023; 15:39167-39175. [PMID: 37614001 PMCID: PMC10450642 DOI: 10.1021/acsami.3c08643] [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: 06/15/2023] [Accepted: 07/27/2023] [Indexed: 08/25/2023]
Abstract
Among bio-inspired protein materials, secretory protein microparticles are of clinical interest as self-contained, slow protein delivery platforms that mimic secretory granules of the human endocrine system, in which the protein is both the drug and the scaffold. Upon subcutaneous injection, their progressive disintegration results in the sustained release of the building block polypeptides, which reach the bloodstream for systemic distribution and subsequent biological effects. Such entities are easily fabricated in vitro by Zn-assisted cross-molecular coordination of histidine residues. Using cationic Zn for the assembly of selected pure protein species and in the absence of any heterologous holding material, these granules are expected to be nontoxic and therefore adequate for different clinical uses. However, such presumed biosafety has not been so far confirmed and the potential protein dosage threshold not probed yet. By selecting the receptor binding domain (RBD) from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein as a model protein and using a mouse lab model, we have explored the toxicity of RBD-made secretory granules at increasing doses up to ∼100 mg/kg of animal weight. By monitoring body weight and biochemical blood markers and through the histological scrutiny of main tissues and organs, we have not observed systemic toxicity. Otherwise, the bioavailability of the material was demonstrated by the induction of specific antibody responses. The presented data confirm the intrinsic biosafety of artificial secretory granules made by recombinant proteins and prompt their further clinical development as self-contained and dynamic protein reservoirs.
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Affiliation(s)
- Patricia Álamo
- Institut
d’Investigació Biomèdica Sant Pau (IIB SANT PAU), 08041 Barcelona, Spain
- Josep
Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
| | - Eloi Parladé
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marianna T. P. Favaro
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
- Instituto
de Ciências Biomédicas, Universidade
de São Paulo, São
Paulo 05508-000, Brazil
| | - Alberto Gallardo
- Institut
d’Investigació Biomèdica Sant Pau (IIB SANT PAU), 08041 Barcelona, Spain
- Department
of Pathology, Hospital de la Santa Creu
i Sant Pau, 08025 Barcelona, Spain
| | - Rosa Mendoza
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Luís C.
S. Ferreira
- Instituto
de Ciências Biomédicas, Universidade
de São Paulo, São
Paulo 05508-000, Brazil
| | - Nerea Roher
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
- Department
of Cell Biology, Animal Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ramón Mangues
- Institut
d’Investigació Biomèdica Sant Pau (IIB SANT PAU), 08041 Barcelona, Spain
- Josep
Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
| | - Antonio Villaverde
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Esther Vázquez
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
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18
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Yoo J, Han J, Lim MH. Transition metal ions and neurotransmitters: coordination chemistry and implications for neurodegeneration. RSC Chem Biol 2023; 4:548-563. [PMID: 37547459 PMCID: PMC10398360 DOI: 10.1039/d3cb00052d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/26/2023] [Indexed: 08/08/2023] Open
Abstract
Neurodegeneration is characterized by a disturbance in neurotransmitter-mediated signaling pathways. Recent studies have highlighted the significant role of transition metal ions, including Cu(i/ii), Zn(ii), and Fe(ii/iii), in neurotransmission, thereby making the coordination chemistry of neurotransmitters a growing field of interest in understanding signal dysfunction. This review outlines the physiological functions of transition metal ions and neurotransmitters, with the metal-binding properties of small molecule-based neurotransmitters and neuropeptides. Additionally, we discuss the structural and conformational changes of neurotransmitters induced by redox-active metal ions, such as Cu(i/ii) and Fe(ii/iii), and briefly describe the outcomes arising from their oxidation, polymerization, and aggregation. These observations have important implications for neurodegeneration and emphasize the need for further research to develop potential therapeutic strategies.
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Affiliation(s)
- Jeasang Yoo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Jiyeon Han
- Department of Applied Chemistry, University of Seoul Seoul 02504 Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
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19
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Rua AJ, Whitehead Iii RD, Alexandrescu AT. WITHDRAWN: NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750. J Struct Biol 2023:108003. [PMID: 37487847 DOI: 10.1016/j.jsb.2023.108003] [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: 06/21/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
This article was initially published in the Journal of Structural Biology, instead of the Journal of Structural Biology: X, due to a publisher error. We regret the inconvenience. The link to the article published in Journal of Structural Biology: X is presented below: https://www.sciencedirect.com/science/article/pii/S2590152423000090. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/policies/article-withdrawal.
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Affiliation(s)
- Antonio J Rua
- Department of Molecular and Cellular Biology, University of Connecticut
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20
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Camp OG, Bembenek JN, Goud PT, Awonuga AO, Abu-Soud HM. The Implications of Insufficient Zinc on the Generation of Oxidative Stress Leading to Decreased Oocyte Quality. Reprod Sci 2023; 30:2069-2078. [PMID: 36920672 PMCID: PMC11047769 DOI: 10.1007/s43032-023-01212-0] [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: 12/12/2022] [Accepted: 03/07/2023] [Indexed: 03/16/2023]
Abstract
Zinc is a transition metal that displays wide physiological implications ranging from participation in hundreds of enzymes and proteins to normal growth and development. In the reproductive tract of both sexes, zinc maintains a functional role in spermatogenesis, ovulation, fertilization, normal pregnancy, fetal development, and parturition. In this work, we review evidence to date regarding the importance of zinc in oocyte maturation and development, with emphasis on the role of key zinc-binding proteins, as well as examine the effects of zinc and reactive oxygen species (ROS) on oocyte quality and female fertility. We summarize our current knowledge about the participation of zinc in the developing oocyte bound to zinc finger proteins as well as loosely bound zinc ion in the intracellular and extracellular environments. These include aspects related to (1) the impact of zinc deficiency and overwhelming production of ROS under inflammatory conditions on the offset of the physiological antioxidant machinery disturbing biomolecules, proteins, and cellular processes, and their role in contributing to further oxidative stress; (2) the role of ROS in modulating damage to proteins containing zinc, such as zinc finger proteins and nitric oxide synthases (NOS), and expelling the zinc resulting in loss of protein function; and (3) clarify the different role of oxidative stress and zinc deficiency in the pathophysiology of infertility diseases with special emphasis on endometriosis-associated infertility.
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Affiliation(s)
- Olivia G Camp
- Departments of Obstetrics and Gynecology and Biochemistry and Molecular Biology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, 48201, USA
| | - Joshua N Bembenek
- Departments of Obstetrics and Gynecology and Biochemistry and Molecular Biology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, 48201, USA
| | - Pravin T Goud
- Division of Reproductive Endocrinology and Infertility & California IVF Fertility Center, Department of Obstetrics and Gynecology, University of California Davis, Sacramento, CA, 95833, USA
- Laurel Fertility Care, San Francisco, CA, 94109, USA
- California Northstate University Medical College, Elk Grove, CA, 95757, USA
| | - Awoniyi O Awonuga
- Departments of Obstetrics and Gynecology and Biochemistry and Molecular Biology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, 48201, USA
| | - Husam M Abu-Soud
- Departments of Obstetrics and Gynecology and Biochemistry and Molecular Biology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, 48201, USA.
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
- Department of Microbiology, Immunology and Biochemistry, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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21
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Song H, Ding G, Zhao C, Li Y. Genome-Wide Identification of B-Box Gene Family and Expression Analysis Suggest Its Roles in Responses to Cercospora Leaf Spot in Sugar Beet ( Beta Vulgaris L.). Genes (Basel) 2023; 14:1248. [PMID: 37372426 DOI: 10.3390/genes14061248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The B-box (BBX) protein, which is a zinc-finger protein containing one or two B-box domains, plays a crucial role in the growth and development of plants. Plant B-box genes are generally involved in morphogenesis, the growth of floral organs, and various life activities in response to stress. In this study, the sugar beet B-box genes (hereafter referred to as BvBBXs) were identified by searching the homologous sequences of the Arabidopsis thaliana B-box gene family. The gene structure, protein physicochemical properties, and phylogenetic analysis of these genes were systematically analyzed. In this study, 17 B-box gene family members were identified from the sugar beet genome. A B-box domain can be found in all sugar beet BBX proteins. BvBBXs encode 135 to 517 amino acids with a theoretical isoelectric point of 4.12 to 6.70. Chromosome localization studies revealed that BvBBXs were dispersed across nine sugar beet chromosomes except chromosomes 5 and 7. The sugar beet BBX gene family was divided into five subfamilies using phylogenetic analysis. The gene architectures of subfamily members on the same evolutionary tree branch are quite similar. Light, hormonal, and stress-related cis-acting elements can be found in the promoter region of BvBBXs. The BvBBX gene family was differently expressed in sugar beet following Cercospora leaf spot infection, according to RT-qPCR data. It is shown that the BvBBX gene family may influence how the plant reacts to a pathogen infection.
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Affiliation(s)
- He Song
- College of Modern Agriculture and Ecological Environment, Heilongjiang University, Harbin 150080, China
| | - Guangzhou Ding
- Sugar Beet Engineering Research Center of Heilongjiang Province, Harbin 150080, China
| | - Chunlei Zhao
- Sugar Beet Engineering Research Center of Heilongjiang Province, Harbin 150080, China
| | - Yanli Li
- Sugar Beet Engineering Research Center of Heilongjiang Province, Harbin 150080, China
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22
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Singh AK, Pomorski A, Wu S, Peris-Díaz MD, Czepczyńska-Krężel H, Krężel A. The connection of α- and β-domains in mammalian metallothionein-2 differentiates Zn(II) binding affinities, affects folding, and determines zinc buffering properties. Metallomics 2023; 15:mfad029. [PMID: 37147085 PMCID: PMC10243857 DOI: 10.1093/mtomcs/mfad029] [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: 03/25/2023] [Accepted: 05/03/2023] [Indexed: 05/07/2023]
Abstract
Mammalian metallothioneins (MTs) are small Cys-rich proteins involved in Zn(II) and Cu(I) homeostasis. They bind seven Zn(II) ions in two distinct β- and α-domains, forming Zn3Cys9 and Zn4Cys11 clusters, respectively. After six decades of research, their role in cellular buffering of Zn(II) ions has begun to be understood recently. This is because of different affinities of bound ions and the proteins' coexistence in variously Zn(II)-loaded Zn4-7MT species in the cell. To date, it has remained unclear how these mechanisms of action occur and how the affinities are differentiated despite the Zn(S-Cys)4 coordination environment being the same. Here, we dissect the molecular basis of these phenomena by using several MT2 mutants, hybrid protein, and isolated domains. Through a combination of spectroscopic and stability studies, thiol(ate) reactivity, and steered molecular dynamics, we demonstrate that both protein folding and thermodynamics of Zn(II) ion (un)binding significantly differ between isolated domains and the whole protein. Close proximity reduces the degrees of freedom of separated domains, making them less dynamic. It is caused by the formation of intra- and interdomain electrostatic interactions. The energetic consequence of domains connection has a critical impact on the role of MTs in the cellular environment, where they function not only as a zinc sponge but also as a zinc buffering system keeping free Zn(II) in the right concentrations. Any change of that subtle system affects the folding mechanism, zinc site stabilities, and cellular zinc buffer components.
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Affiliation(s)
- Avinash Kumar Singh
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Adam Pomorski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Sylwia Wu
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Manuel D Peris-Díaz
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Hanna Czepczyńska-Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
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23
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Shi G, Ai K, Yan X, Zhou Z, Cai F, Bao M, Zhang J. Genome-Wide Analysis of the BBX Genes in Platanus × acerifolia and Their Relationship with Flowering and/or Dormancy. Int J Mol Sci 2023; 24:ijms24108576. [PMID: 37239923 DOI: 10.3390/ijms24108576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The B-BOX (BBX) gene family is widely distributed in animals and plants and is involved in the regulation of their growth and development. In plants, BBX genes play important roles in hormone signaling, biotic and abiotic stress, light-regulated photomorphogenesis, flowering, shade response, and pigment accumulation. However, there has been no systematic analysis of the BBX family in Platanus × acerifolia. In this study, we identified 39 BBX genes from the P. × acerifolia genome, and used TBtools, MEGA, MEME, NCBI CCD, PLANTCARE and other tools for gene collinearity analysis, phylogenetic analysis, gene structure, conserved domain analysis, and promoter cis-element analysis, and used the qRT-PCR and transcriptome data for analyzing expression pattern of the PaBBX genes. Collinearity analysis indicated segmental duplication was the main driver of the BBX family in P. × acerifolia, and phylogenetic analysis showed that the PaBBX family was divided into five subfamilies: I, II, III, IV and V. Gene structure analysis showed that some PaBBX genes contained super-long introns that may regulate their own expression. Moreover, the promoter of PaBBX genes contained a significant number of cis-acting elements that are associated with plant growth and development, as well as hormone and stress responses. The qRT-PCR results and transcriptome data indicated that certain PaBBX genes exhibited tissue-specific and stage-specific expression patterns, suggesting that these genes may have distinct regulatory roles in P. × acerifolia growth and development. In addition, some PaBBX genes were regularly expressed during the annual growth of P. × acerifolia, corresponding to different stages of flower transition, dormancy, and bud break, indicating that these genes may be involved in the regulation of flowering and/or dormancy of P. × acerifolia. This article provided new ideas for the study of dormancy regulation and annual growth patterns in perennial deciduous plants.
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Affiliation(s)
- Gehui Shi
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Afairs, Wuhan 430070, China
| | - Kangyu Ai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Afairs, Wuhan 430070, China
| | - Xu Yan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Afairs, Wuhan 430070, China
| | - Zheng Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Afairs, Wuhan 430070, China
| | - Fangfang Cai
- Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Afairs, Wuhan 430070, China
| | - Jiaqi Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Afairs, Wuhan 430070, China
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24
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Pinto ÉSM, Krause MJ, Dorn M, Feltes BC. The nucleotide excision repair proteins through the lens of molecular dynamics simulations. DNA Repair (Amst) 2023; 127:103510. [PMID: 37148846 DOI: 10.1016/j.dnarep.2023.103510] [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: 10/26/2022] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Mutations that affect the proteins responsible for the nucleotide excision repair (NER) pathway can lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, Cockayne syndrome, and Cerebro-oculo-facio-skeletal syndrome. Hence, understanding their molecular behavior is needed to elucidate these diseases' phenotypes and how the NER pathway is organized and coordinated. Molecular dynamics techniques enable the study of different protein conformations, adaptable to any research question, shedding light on the dynamics of biomolecules. However, as important as they are, molecular dynamics studies focused on DNA repair pathways are still becoming more widespread. Currently, there are no review articles compiling the advancements made in molecular dynamics approaches applied to NER and discussing: (i) how this technique is currently employed in the field of DNA repair, focusing on NER proteins; (ii) which technical setups are being employed, their strengths and limitations; (iii) which insights or information are they providing to understand the NER pathway or NER-associated proteins; (iv) which open questions would be suited for this technique to answer; and (v) where can we go from here. These questions become even more crucial considering the numerous 3D structures published regarding the NER pathway's proteins in recent years. In this work, we tackle each one of these questions, revising and critically discussing the results published in the context of the NER pathway.
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Affiliation(s)
| | - Mathias J Krause
- Institute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Márcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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25
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Hajdu B, Hunyadi-Gulyás É, Kato K, Kawaguchi A, Nagata K, Gyurcsik B. Zinc binding of a Cys2His2-type zinc finger protein is enhanced by the interaction with DNA. J Biol Inorg Chem 2023; 28:301-315. [PMID: 36820987 PMCID: PMC10036435 DOI: 10.1007/s00775-023-01988-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023]
Abstract
Zinc finger proteins specifically recognize DNA sequences and, therefore, play a crucial role in living organisms. In this study the Zn(II)-, and DNA-binding of 1MEY#, an artificial zinc finger protein consisting of three finger units was characterized by multiple methods. Fluorimetric, circular dichroism and isothermal calorimetric titrations were applied to determine the accurate stability constant of a zinc finger protein. Assuming that all three zinc finger subunits behave identically, the obtained thermodynamic data for the Zn(II) binding were ΔHbinding site = - (23.5 - 28.0) kcal/mol (depending on the applied protonation state of the cysteines) and logβ'pH 7.4 = 12.2 ± 0.1, being similar to those of the CP1 consensus zinc finger peptide. The specific DNA binding of the protein can be characterized by logβ'pH 7.4 = 8.20 ± 0.08, which is comparable to the affinity of the natural zinc finger proteins (Sp1, WT1, TFIIIA) toward DNA. This value is ~ 1.9 logβ' unit higher than those determined for semi- or nonspecific DNA binding. Competitive circular dichroism and electrophoretic mobility shift measurements revealed that the conditional stability constant characteristic for Zn(II) binding of 1MEY# protein increased by 3.4 orders of magnitude in the presence of its target DNA sequence.
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Affiliation(s)
- Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm Tér 7, 6720, Szeged, Hungary
| | - Éva Hunyadi-Gulyás
- Laboratory of Proteomics Research, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Temesvári Krt. 62, 6726, Szeged, Hungary
| | - Kohsuke Kato
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm Tér 7, 6720, Szeged, Hungary.
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26
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Negi S, Imanishi M, Hamori M, Kawahara-Nakagawa Y, Nomura W, Kishi K, Shibata N, Sugiura Y. The past, present, and future of artificial zinc finger proteins: design strategies and chemical and biological applications. J Biol Inorg Chem 2023; 28:249-261. [PMID: 36749405 PMCID: PMC9903285 DOI: 10.1007/s00775-023-01991-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/25/2023] [Indexed: 02/08/2023]
Abstract
Zinc finger proteins are abundant in the human proteome and are responsible for a variety of functions. The domains that constitute zinc finger proteins are compact spherical structures, each comprising approximately 30 amino acid residues, but they also have precise molecular factor functions: zinc binding and DNA recognition. Due to the biological importance of zinc finger proteins and their unique structural and functional properties, many artificial zinc finger proteins have been created and are expected to improve their functions and biological applications. In this study, we review previous studies on the redesign and application of artificial zinc finger proteins, focusing on the experimental results obtained by our research group. In addition, we systematically review various design strategies used to construct artificial zinc finger proteins and discuss in detail their potential biological applications, including gene editing. This review will provide relevant information to researchers involved or interested in the field of artificial zinc finger proteins as a potential new treatment for various diseases.
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Affiliation(s)
- Shigeru Negi
- Faculty of Pharmaceutical Science, Doshisha Women's University Kyotanabe, Kyoto, 610-0395, Japan.
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Mami Hamori
- Faculty of Pharmaceutical Science, Doshisha Women's University Kyotanabe, Kyoto, 610-0395, Japan
| | - Yuka Kawahara-Nakagawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-Cho, Ako-Gun, Hyogo, 678-1297, Japan
| | - Wataru Nomura
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-Ku, Hiroshima, 734-8553, Japan
| | - Kanae Kishi
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-Ku, Hiroshima, 734-8553, Japan
| | - Nobuhito Shibata
- Faculty of Pharmaceutical Science, Doshisha Women's University Kyotanabe, Kyoto, 610-0395, Japan
| | - Yukio Sugiura
- Faculty of Pharmaceutical Science, Doshisha Women's University Kyotanabe, Kyoto, 610-0395, Japan
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27
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Antonenko A, Singh AK, Mosna K, Krężel A. OaAEP1 Ligase-Assisted Chemoenzymatic Synthesis of Full Cysteine-Rich Metal-Binding Cyanobacterial Metallothionein SmtA. Bioconjug Chem 2023. [PMID: 36921066 PMCID: PMC10119931 DOI: 10.1021/acs.bioconjchem.3c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Among all approaches used for the semisynthesis of natural or chemically modified products, enzyme-assisted ligation is among the most promising and dynamically developing approaches. Applying an efficient C247A mutant of Oldenlandia affinis plant ligase OaAEP1 and solid-phase peptide synthesis chemistry, we present the chemoenzymatic synthesis of a complete sequence of the cysteine-rich and metal-binding cyanobacterial metallothionein Synechococcus metallothionein A (SmtA). Zn(II) and Cd(II) binding to the newly synthesized SmtA showed identical properties to the protein expressed in Escherichia coli. The presented approach is the first example of the use of OaAEP1 mutant for total protein synthesis of metallothionein, which occurs in mild conditions preventing cysteine thiol oxidation. The recognition motif of the applied enzyme could naturally occur in the protein structure or be synthetically or genetically incorporated in some loops or secondary structure elements. Therefore, we envision that this strategy can be used for efficiently obtaining SmtA and for a wide range of proteins and their derivatives.
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Affiliation(s)
- Anastasiia Antonenko
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Avinash Kumar Singh
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Karolina Mosna
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław 50-383, Poland
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28
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Kerber O, Tran J, Misiaszek A, Chorążewska A, Bal W, Krężel A. Zn(II) to Ag(I) Swap in Rad50 Zinc Hook Domain Leads to Interprotein Complex Disruption through the Formation of Highly Stable Ag x(Cys) y Cores. Inorg Chem 2023; 62:4076-4087. [PMID: 36863010 PMCID: PMC10015552 DOI: 10.1021/acs.inorgchem.2c03767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The widespread application of silver nanoparticles in medicinal and daily life products increases the exposure to Ag(I) of thiol-rich biological environments, which help control the cellular metallome. A displacement of native metal cofactors from their cognate protein sites is a known phenomenon for carcinogenic and otherwise toxic metal ions. Here, we examined the interaction of Ag(I) with the peptide model of the interprotein zinc hook (Hk) domain of Rad50 protein from Pyrococcus furiosus, a key player in DNA double-strand break (DSB) repair. The binding of Ag(I) to 14 and 45 amino acid long peptide models of apo- and Zn(Hk)2 was experimentally investigated by UV-vis spectroscopy, circular dichroism, isothermal titration calorimetry, and mass spectrometry. The Ag(I) binding to the Hk domain was found to disrupt its structure via the replacement of the structural Zn(II) ion by multinuclear Agx(Cys)y complexes. The ITC analysis indicated that the formed Ag(I)-Hk species are at least 5 orders of magnitude stronger than the otherwise extremely stable native Zn(Hk)2 domain. These results show that Ag(I) ions may easily disrupt the interprotein zinc binding sites as an element of silver toxicity at the cellular level.
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Affiliation(s)
- Olga Kerber
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Józef Tran
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Alicja Misiaszek
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Aleksandra Chorążewska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
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29
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A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data. Int J Mol Sci 2023; 24:ijms24065440. [PMID: 36982515 PMCID: PMC10055966 DOI: 10.3390/ijms24065440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been developed to represent zinc(II) sites, with the bonded and nonbonded models being the most used. In the present work, we tested the well-known zinc AMBER force field (ZAFF) and a recently developed nonbonded force field (NBFF) to assess how accurately they reproduce the dynamic behavior of zinc(II)-proteins. For this, we selected as benchmark six zinc-fingers. This superfamily is extremely heterogenous in terms of architecture, binding mode, function, and reactivity. From repeated MD simulations, we computed the order parameter (S2) of all backbone N-H bond vectors in each system. These data were superimposed to heteronuclear Overhauser effect measurements taken by NMR spectroscopy. This provides a quantitative estimate of the accuracy of the FFs in reproducing protein dynamics, leveraging the information about the protein backbone mobility contained in the NMR data. The correlation between the MD-computed S2 and the experimental data indicated that both tested FFs reproduce well the dynamic behavior of zinc(II)-proteins, with comparable accuracy. Thus, along with ZAFF, NBFF represents a useful tool to simulate metalloproteins with the advantage of being extensible to diverse systems such as those bearing dinuclear metal sites.
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30
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Cho YL, Tzou YM, Wang CC, Lee YC, Hsu LC, Liu SL, Assakinah A, Chen YH, Thi Than NA, Liu YT, Rinklebe J. Removal and concurrent reduction of Cr(VI) by thermoacidophilic Cyanidiales: a novel extreme biomaterial enlightened for acidic and neutral conditions. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130334. [PMID: 36462243 DOI: 10.1016/j.jhazmat.2022.130334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/26/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Thermoacidophilic Cyanidiales maintain a competitive edge in inhabiting extreme environments enriched with metals. Here, species of Cyanidioschyzon merolae (Cm), Cyanidium caldarium (Cc), and Galdieria partita (Gp) were exploited to remove hexavalent chromium [Cr(VI)]. Cm and Gp could remove 168.1 and 93.7 mg g-1 of Cr(VI) at pH 2.0 and 7.0, respectively, wherein 89% and 62% of sorbed Cr on Cm and Gp occurred as trivalent chromium [Cr(III)]. Apart from surface-sorbed Cr(VI), the in vitro Cr(III) bound with polysaccharide and in vivo chromium(III) hydroxide [Cr(OH)3] attested to the reduction capability of Cyanidiales. The distribution of Cr species varied as a function of sorbed Cr amount, yet a relatively consistent proportion of Cr(OH)3, irrespective of Cr sorption capacity, was found only on Cm and Cc at pH 2.0. In conjunction with TXM (transmission X-ray microscopy) images that showed less impaired cell integrity and possible intracellular Cr distribution on Cm and Cc at pH 2.0, the in vivo Cr(OH)3 might be the key to promoting the Cr sorption capacity (≥ 152 mg g-1). Cyanidiales are promising candidates for the green and sustainable remediation of Cr(VI) due to their great removal capacity, the spontaneous reduction under oxic conditions, and in vivo accumulation.
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Affiliation(s)
- Yen-Lin Cho
- Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Min Tzou
- Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 40227, Taiwan; Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chun-Chieh Wang
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Yao-Chang Lee
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Liang-Ching Hsu
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Shao-Lun Liu
- Department of Life Science, Tunghai University, Taichung 40704, Taiwan
| | - Afifah Assakinah
- Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Hsien Chen
- Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Nhu Anh Thi Than
- Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Ting Liu
- Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 40227, Taiwan; Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Jörg Rinklebe
- Laboratory of Soil, and Groundwater-Management, Institute of Foundation Engineering, Water, and Waste, Management, School of Architecture and Civil Engineering, University of Wuppertal, Wuppertal 42285, Germany
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Gou Q, Luo H, Zhang Q, Deng J, Zhao R, Odunmbaku O, Wang L, Li L, Zheng Y, Li J, Chao D, Li M. Electrolyte Regulation of Bio-Inspired Zincophilic Additive toward High-Performance Dendrite-Free Aqueous Zinc-Ion Batteries. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207502. [PMID: 36650991 DOI: 10.1002/smll.202207502] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Aqueous zinc-ion batteries hold attractive potential for large-scale energy storage devices owing to their prominent electrochemical performance and high security. Nevertheless, the applications of aqueous electrolytes have generated various challenges, including uncontrolled dendrite growth and parasitic reactions, thereby deteriorating the Zn anode's stability. Herein, inspired by the superior affinity between Zn2+ and amino acid chains in the zinc finger protein, a cost-effective and green glycine additive is incorporated into aqueous electrolytes to stabilize the Zn anode. As confirmed by experimental characterizations and theoretical calculations, the glycine additives can not only reorganize the solvation sheaths of hydrated Zn2+ via partial substitution of coordinated H2 O but also preferentially adsorb onto the Zn anode, thereby significantly restraining dendrite growth and interfacial side reactions. Accordingly, the Zn anode could realize a long lifespan of over 2000 h and enhanced reversibility (98.8%) in the glycine-containing electrolyte. Furthermore, the assembled Zn||α-MnO2 full cells with glycine-modified electrolyte also delivers substantial capacity retention (82.3% after 1000 cycles at 2 A g-1 ), showing promising application prospects. This innovative bio-inspired design concept would inject new vitality into the development of aqueous electrolytes.
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Affiliation(s)
- Qianzhi Gou
- MOE Key Laboratory of Low-grade Energy Utilization Technologies and Systems, CQU-NUS Renewable Energy Materials & Devices Joint Laboratory, School of Energy & Power Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Haoran Luo
- MOE Key Laboratory of Low-grade Energy Utilization Technologies and Systems, CQU-NUS Renewable Energy Materials & Devices Joint Laboratory, School of Energy & Power Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Qi Zhang
- MOE Key Laboratory of Low-grade Energy Utilization Technologies and Systems, CQU-NUS Renewable Energy Materials & Devices Joint Laboratory, School of Energy & Power Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Jiangbin Deng
- MOE Key Laboratory of Low-grade Energy Utilization Technologies and Systems, CQU-NUS Renewable Energy Materials & Devices Joint Laboratory, School of Energy & Power Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Ruizheng Zhao
- Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, School of Chemistry and Materials, Fudan University, Shanghai, 200433, P. R. China
| | - Omololu Odunmbaku
- MOE Key Laboratory of Low-grade Energy Utilization Technologies and Systems, CQU-NUS Renewable Energy Materials & Devices Joint Laboratory, School of Energy & Power Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Lei Wang
- MOE Key Laboratory of Low-grade Energy Utilization Technologies and Systems, CQU-NUS Renewable Energy Materials & Devices Joint Laboratory, School of Energy & Power Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Lingjie Li
- Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Yujie Zheng
- MOE Key Laboratory of Low-grade Energy Utilization Technologies and Systems, CQU-NUS Renewable Energy Materials & Devices Joint Laboratory, School of Energy & Power Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Jun Li
- MOE Key Laboratory of Low-grade Energy Utilization Technologies and Systems, CQU-NUS Renewable Energy Materials & Devices Joint Laboratory, School of Energy & Power Engineering, Chongqing University, Chongqing, 400044, P. R. China
| | - Dongliang Chao
- Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, School of Chemistry and Materials, Fudan University, Shanghai, 200433, P. R. China
| | - Meng Li
- MOE Key Laboratory of Low-grade Energy Utilization Technologies and Systems, CQU-NUS Renewable Energy Materials & Devices Joint Laboratory, School of Energy & Power Engineering, Chongqing University, Chongqing, 400044, P. R. China
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32
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Donaghy C, Javellana JG, Hong YJ, Djoko K, Angeles-Boza AM. The Synergy between Zinc and Antimicrobial Peptides: An Insight into Unique Bioinorganic Interactions. Molecules 2023; 28:molecules28052156. [PMID: 36903402 PMCID: PMC10004757 DOI: 10.3390/molecules28052156] [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: 01/05/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 03/02/2023] Open
Abstract
Antimicrobial peptides (AMPs) are essential components of innate immunity across all species. AMPs have become the focus of attention in recent years, as scientists are addressing antibiotic resistance, a public health crisis that has reached epidemic proportions. This family of peptides represents a promising alternative to current antibiotics due to their broad-spectrum antimicrobial activity and tendency to avoid resistance development. A subfamily of AMPs interacts with metal ions to potentiate antimicrobial effectiveness, and, as such, they have been termed metalloAMPs. In this work, we review the scientific literature on metalloAMPs that enhance their antimicrobial efficacy when combined with the essential metal ion zinc(II). Beyond the role played by Zn(II) as a cofactor in different systems, it is well-known that this metal ion plays an important role in innate immunity. Here, we classify the different types of synergistic interactions between AMPs and Zn(II) into three distinct classes. By better understanding how each class of metalloAMPs uses Zn(II) to potentiate its activity, researchers can begin to exploit these interactions in the development of new antimicrobial agents and accelerate their use as therapeutics.
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Affiliation(s)
- Caroline Donaghy
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | | | - Young-Jin Hong
- Department of Chemistry, Durham University, Durham DH1 3LE, UK
| | - Karrera Djoko
- Department of Chemistry, Durham University, Durham DH1 3LE, UK
- Correspondence: (K.D.); (A.M.A.-B.)
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
- Institute of Materials Sciences, University of Connecticut, Storrs, CT 06269, USA
- Correspondence: (K.D.); (A.M.A.-B.)
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Rogowska A, Pryshchepa O, Som NN, Śpiewak P, Gołębiowski A, Rafińska K, Dobrucka R, Kurzydłowski K, Buszewski B, Pomastowski P. Study On The Zinc Ions Binding To Human Lactoferrin. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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Stoltzfus AT, Campbell CJ, Worth MM, Hom K, Stemmler TL, Michel SLJ. Pb(II) coordination to the nonclassical zinc finger tristetraprolin: retained function with an altered fold. J Biol Inorg Chem 2023; 28:85-100. [PMID: 36478265 DOI: 10.1007/s00775-022-01980-1] [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: 06/06/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022]
Abstract
Tristetraprolin (TTP) is a nonclassical CCCH zinc finger (ZF) that plays a crucial role in regulating inflammation. TTP regulates cytokine mRNAs by specific binding of its two conserved ZF domains (CysX8CysX5CysX3His) to adenylate-uridylate-rich sequences (AREs) at the 3'-untranslated region, leading to degradation of the RNA. Dysregulation of TTP in animal models has demonstrated several cytokine-related syndromes, including chronic inflammation and autoimmune disorders. Exposure to Pb(II), a prevalent environmental toxin, is known to contribute to similar pathologies, in part by disruption of and/or competition with cysteine-rich metalloproteins. TTP's role during stress as a ubiquitous translational regulator of cell signaling (and dysfunction), which may underpin various phenotypes of Pb(II) toxicity, highlights the importance of understanding the interaction between TTP and Pb(II). The impact of Pb(II) binding on TTP's fold and RNA-binding function was analyzed via UV-Vis spectroscopy, circular dichroism, X-ray absorption spectroscopy, nuclear magnetic resonance spectroscopy, and fluorescence anisotropy. A construct containing the two ZF domains of TTP (TTP-2D) bound to Pb(II) with nanomolar affinity and exhibited a different geometry and fold in comparison to Zn2-TTP-2D. Despite the altered secondary structure, Pb(II)-substituted TTP-2D bound a canonical ARE sequence more selectively than Zn2-TTP-2D. Taken together, these data suggest that Pb(II) may interfere with proper TTP regulation and hinder the cell's ability to respond to inflammation.
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Affiliation(s)
- Andrew T Stoltzfus
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Courtney J Campbell
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Madison M Worth
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA.
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Dadgar Z, Shariatzadeh SMA, Mehranjani MS, Kheirolahi A. The therapeutic effect of co-administration of pentoxifylline and zinc in men with idiopathic infertility. Ir J Med Sci 2023; 192:431-439. [PMID: 35182288 DOI: 10.1007/s11845-022-02931-0] [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: 12/18/2021] [Accepted: 01/19/2022] [Indexed: 02/04/2023]
Abstract
Pentoxifylline is a derivative of methylxanthine that affects sperm motility. Also, zinc is an antioxidant that is involved in the activation of antioxidant enzymes. This study aimed to evaluate the effect of co-administration of pentoxifylline, and zinc in men with idiopathic infertility. In the present study, men with idiopathic infertility were identified and randomly divided into four groups: pentoxifylline, zinc, pentoxifylline + zinc, and placebo. According to the grouping, the patients received pentoxifylline and zinc for 3 months. Then, sperm parameters, biochemical factors, reproductive hormones, inflammatory factors, and DNA damage were evaluated before and after intervention. Data analysis was performed using SPSS software. Pentoxifylline and zinc were significantly effective in improving biochemical parameters, inflammatory factors, concentration, and motility of sperm. Pentoxifylline did not affect sperm morphology and reproductive hormones. However, in the zinc and zinc + pentoxifylline groups, a significant increase in normal morphology and reproductive hormones was observed. In the pentoxifylline group, sperm DNA fragmentation increased significantly, while in the zinc and zinc + pentoxifylline group, DNA fragmentation reduced significantly. Because of the role of zinc in protecting sperm chromatin, it is recommended that zinc and pentoxifyllinebe prescribed simultaneously. Clinical trial code: NCT05156684.
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Affiliation(s)
- Zeynab Dadgar
- Department of Biology, Faculty of Science, Arak University, Arak, Iran
| | | | | | - Abdolreza Kheirolahi
- Department of Urology, Lorestan University of Medical Sciences, Khorramabad, Iran
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36
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Interactions of an Artificial Zinc Finger Protein with Cd(II) and Hg(II): Competition and Metal and DNA Binding. INORGANICS 2023. [DOI: 10.3390/inorganics11020064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cys2His2 zinc finger proteins are important for living organisms, as they—among other functions—specifically recognise DNA when Zn(II) is coordinated to the proteins, stabilising their ββα secondary structure. Therefore, competition with other metal ions may alter their original function. Toxic metal ions such as Cd(II) or Hg(II) might be especially dangerous because of their similar chemical properties to Zn(II). Most competition studies carried out so far have involved small zinc finger peptides. Therefore, we have investigated the interactions of toxic metal ions with a zinc finger proteins consisting of three finger units and the consequences on the DNA binding properties of the protein. Binding of one Cd(II) per finger subunit of the protein was shown by circular dichroism spectroscopy, fluorimetry and electrospray ionisation mass spectrometry. Cd(II) stabilised a similar secondary structure to that of the Zn(II)-bound protein but with a slightly lower affinity. In contrast, Hg(II) could displace Zn(II) quantitatively (logβ′ ≥ 16.7), demolishing the secondary structure, and further Hg(II) binding was also observed. Based on electrophoretic gel mobility shift assays, the Cd(II)-bound zinc finger protein could recognise the specific DNA target sequence similarly to the Zn(II)-loaded form but with a ~0.6 log units lower stability constant, while Hg(II) could destroy DNA binding completely.
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37
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Liu S, Morihiro K, Takeuchi F, Li Y, Okamoto A. Interstrand crosslinking oligonucleotides elucidate the effect of metal ions on the methylation status of repetitive DNA elements. Front Chem 2023; 11:1122474. [PMID: 36711237 PMCID: PMC9881727 DOI: 10.3389/fchem.2023.1122474] [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: 12/13/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
DNA methylation plays an important physiological function in cells, and environmental changes result in fluctuations in DNA methylation levels. Metal ions have become both environmental and health concerns, as they have the potential to disrupt the genomic DNA methylation status, even on specific sequences. In the current research, the methylation status of two typical repetitive DNA elements, i.e., long-interspersed nuclear element-1 (LINE-1) and alpha satellite (α-sat), was imaged and assessed using methylation-specific fluorescence in situ hybridization (MeFISH). This technique elucidated the effect of several metal ions on the methylation levels of repetitive DNA sequences. The upregulation and downregulation of the methylation levels of repetitive DNA elements by various metal ions were confirmed and depended on their concentration. This is the first example to investigate the effects of metal ions on DNA methylation in a sequence-specific manner.
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Affiliation(s)
- Shan Liu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kunihiko Morihiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Fumika Takeuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Yufeng Li
- The Key Laboratory of Molecular Oncology of Hebei Province, Tangshan People’s Hospital, Tangshan, Hebei, China
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan,*Correspondence: Akimitsu Okamoto,
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Félix SS, Laurents DV, Oroz J, Cabrita EJ. Fused in sarcoma undergoes cold denaturation: Implications for phase separation. Protein Sci 2023; 32:e4521. [PMID: 36453011 PMCID: PMC9793971 DOI: 10.1002/pro.4521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022]
Abstract
The mediation of liquid-liquid phase separation (LLPS) for fused in sarcoma (FUS) protein is generally attributed to the low-complexity, disordered domains and is enhanced at low temperature. The role of FUS folded domains on the LLPS process remains relatively unknown since most studies are mainly based on fragmented FUS domains. Here, we investigate the effect of metabolites on full-length (FL) FUS LLPS using turbidity assays and differential interference contrast (DIC) microscopy, and explore the behavior of the folded domains by nuclear magnetic resonance (NMR) spectroscopy. FL FUS LLPS is maximal at low concentrations of glucose and glutamate, moderate concentrations of NaCl, Zn2+ , and Ca2+ and at the isoelectric pH. The FUS RNA recognition motif (RRM) and zinc-finger (ZnF) domains are found to undergo cold denaturation above 0°C at a temperature that is determined by the conformational stability of the ZnF domain. Cold unfolding exposes buried nonpolar residues that can participate in LLPS-promoting hydrophobic interactions. Therefore, these findings constitute the first evidence that FUS globular domains may have an active role in LLPS under cold stress conditions and in the assembly of stress granules, providing further insight into the environmental regulation of LLPS.
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Affiliation(s)
- Sara S. Félix
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | | | - Javier Oroz
- Instituto de Química Física Rocasolano (IQFR), CSICMadridSpain
| | - Eurico J. Cabrita
- UCIBIO, Department of ChemistryNOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal,Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de LisboaCaparicaPortugal
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Nagarajan H, Vetrivel U. Deciphering the structural and functional impact of missense mutations in Egr1-DNA interacting interface: an integrative computational approach. J Biomol Struct Dyn 2022; 40:11758-11770. [PMID: 34402752 DOI: 10.1080/07391102.2021.1965030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Early growth response-1 (Egr1) is a zinc-finger transcription factor that plays a critical role in controlling cell growth, proliferation, differentiation, angiogenesis, and apoptosis. Egr1 is induced by many growth factors, cytokines, and stress signals and is also known to be involved in several pathological conditions like cancer, neurological and ocular disorders. The DNA binding domain of Egr1 is a highly conserved Cys2His2 (C2H2) zinc finger (ZNF) domain which specifically binds to GC-rich consensus sequence GcG (G/T) GGGCG and activates transcription. As the C2H2 domain specifically recognizes its DNA target, the mutations spanning this region shall perturb DNA recognition and may hinder transcription of target genes. Therefore, in this study, the missense mutations occurring specifically at the DNA binding domain (DBD) of Egr1 were probed by computational approaches involving in silico screening of pathogenic and functional mutants coupled with extensive molecular dynamics simulations, to determine the mutants that affect its structural stability and interactions with DNA. From the pathogenicity analysis of 38 missense mutations spanning Egr1-DBD, 17 were predicted as pathogenic, and 7 amongst these were found to have functional impact on Egr1. On combined analysis of molecular dynamics simulation, Residue interaction analysis and Egr1-DNA interaction analysis results, the mutants R371C and R375C showed least impact, whilst, H382R tend to increase the structural stability, whereas R360H, H390R, E393V, and H414Y conferred greater impact by altering the structural stability and DNA interactions. Hence, this study exposes the prospects of considering these 4 deleterious mutations for clinical significance, but needs further experimental validation.HighlightsEgr1's DNA binding domain is a highly conserved Cys2His2 (C2H2) zinc finger domain that specifically recognizes its DNA target.Mutations spanning in the DNA binding domain shall perturb DNA recognition and may hinder transcription.Among the missense mutations, mutants R360H, H390R, E393V, and H414Y were inferred to have a greater impact on Egr1 by altering the structural stability and DNA interactions.
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Affiliation(s)
- Hemavathy Nagarajan
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India.,National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research (Govt. of India), Belagavi, Karnataka, India
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40
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New TEMPO-Appended 2,2'-Bipyridine-Based Eu(III), Tb(III), Gd(III) and Sm(III) Complexes: Synthesis, Photophysical Studies and Testing Photoluminescence-Based Bioimaging Abilities. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238414. [PMID: 36500504 PMCID: PMC9739109 DOI: 10.3390/molecules27238414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Linked to Alzheimer's disease (AD), amyloids and tau-protein are known to contain a large number of cysteine (Cys) residues. In addition, certain levels of some common biogenic thiols (cysteine (Cys), homocysteine (Hcy), glutathione (GSH), etc.) in biological fluids are closely related to AD as well as other diseases. Therefore, probes with a selective interaction with the above-mentioned thiols can be used for the monitoring and visualizing changes of (bio)thiols in the biological fluids as well as in the brain of animal models of Alzheimer's disease. In this study, new Eu(III), Tb(III), Gd(III) and Sm(III) complexes of 2,2'-bipyridine ligands containing TEMPO fragments as receptor units for (bio)thiols are reported. The presence of free radical fragments of the ligand in the complexes was proved by using the electronic paramagnetic resonance (EPR) method. Among all the complexes, the Eu(III) complex turned out to be the most promising one as luminescence- and spin-probe for the detection of biogenic thiols. The EPR and fluorescent titration methods showed the interaction of the resulting complex with free Cys and GSH in solution. To study the practical applicability of the probes for the monitoring of AD in-vivo, by using the above-mentioned Eu(III)-based probe, the staining of the brain of mice with amyloidosis and Vero cell cultures supplemented with the cysteine-enriched medium was studied as well as the fluorescence titration of Bovine Serum Albumin, BSA (as the model for the thiol moieties containing protein), was carried out. Based on the results of fluorescence titration, the formation of a non-covalent inclusion complex between the above-mentioned Eu(III) complex and BSA was suggested.
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Leipart V, Enger Ø, Turcu DC, Dobrovolska O, Drabløs F, Halskau Ø, Amdam GV. Resolving the zinc binding capacity of honey bee vitellogenin and locating its putative binding sites. INSECT MOLECULAR BIOLOGY 2022; 31:810-820. [PMID: 36054587 PMCID: PMC9804912 DOI: 10.1111/imb.12807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
The protein vitellogenin (Vg) plays a central role in lipid transportation in most egg-laying animals. High Vg levels correlate with stress resistance and lifespan potential in honey bees (Apis mellifera). Vg is the primary circulating zinc-carrying protein in honey bees. Zinc is an essential metal ion in numerous biological processes, including the function and structure of many proteins. Measurements of Zn2+ suggest a variable number of ions per Vg molecule in different animal species, but the molecular implications of zinc-binding by this protein are not well-understood. We used inductively coupled plasma mass spectrometry to determine that, on average, each honey bee Vg molecule binds 3 Zn2+ -ions. Our full-length protein structure and sequence analysis revealed seven potential zinc-binding sites. These are located in the β-barrel and α-helical subdomains of the N-terminal domain, the lipid binding site, and the cysteine-rich C-terminal region of unknown function. Interestingly, two potential zinc-binding sites in the β-barrel can support a proposed role for this structure in DNA-binding. Overall, our findings suggest that honey bee Vg bind zinc at several functional regions, indicating that Zn2+ -ions are important for many of the activities of this protein. In addition to being potentially relevant for other egg-laying species, these insights provide a platform for studies of metal ions in bee health, which is of global interest due to recent declines in pollinator numbers.
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Affiliation(s)
- Vilde Leipart
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesAasNorway
| | - Øyvind Enger
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesAasNorway
| | | | | | - Finn Drabløs
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health SciencesNTNU – Norwegian University of Science and TechnologyTrondheimNorway
| | - Øyvind Halskau
- Department of Biological SciencesUniversity of BergenBergenNorway
| | - Gro V. Amdam
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesAasNorway
- School of Life SciencesArizona State UniversityTempeArizonaUSA
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Łuczkowski M, Padjasek M, Ba Tran J, Hemmingsen L, Kerber O, Habjanič J, Freisinger E, Krężel A. An Extremely Stable Interprotein Tetrahedral Hg(Cys) 4 Core Forms in the Zinc Hook Domain of Rad50 Protein at Physiological pH. Chemistry 2022; 28:e202202738. [PMID: 36222310 PMCID: PMC9828754 DOI: 10.1002/chem.202202738] [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: 09/01/2022] [Indexed: 11/09/2022]
Abstract
In nature, thiolate-based systems are the primary targets of divalent mercury (HgII ) toxicity. The formation of Hg(Cys)x cores in catalytic and structural protein centers mediates mercury's toxic effects and ultimately leads to cellular damage. Multiple studies have revealed distinct HgII -thiolate coordination preferences, among which linear HgII complexes are the most commonly observed in solution at physiological pH. Trigonal or tetrahedral geometries are formed at basic pH or in tight intraprotein Cys-rich metal sites. So far, no interprotein tetrahedral HgII complex formed at neutral pH has been reported. Rad50 protein is a part of the multiprotein MRN complex, a major player in DNA damage-repair processes. Its central region consists of a conserved CXXC motif that enables dimerization of two Rad50 molecules by coordinating ZnII . Dimerized motifs form a unique interprotein zinc hook domain (Hk) that is critical for the biological activity of the MRN. Using a series of length-differentiated peptide models of the Pyrococcus furiosus zinc hook domain, we investigated its interaction with HgII . Using UV-Vis, CD, PAC, and 199 Hg NMR spectroscopies as well as anisotropy decay, we discovered that all Rad50 fragments preferentially form homodimeric Hg(Hk)2 species with a distorted tetrahedral HgS4 coordination environment at physiological pH; this is the first example of an interprotein mercury site displaying tetrahedral geometry in solution. At higher HgII content, monomeric HgHk complexes with linear geometry are formed. The Hg(Cys)4 core of Rad50 is extremely stable and does not compete with cyanides, NAC, or DTT. Applying ITC, we found that the stability constant of the Rad50 Hg(Hk)2 complex is approximately three orders of magnitude higher than those of the strongest HgII complexes known to date.
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Affiliation(s)
- Marek Łuczkowski
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| | - Michał Padjasek
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| | - Józef Ba Tran
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| | - Lars Hemmingsen
- Department of ChemistryUniversity of CopenhagenUniversitetsparken 52100København ØDenmark
| | - Olga Kerber
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| | - Jelena Habjanič
- Department of ChemistryUniversity of ZurichWinterthurerstrasse 1908057ZürichSwitzerland
| | - Eva Freisinger
- Department of ChemistryUniversity of ZurichWinterthurerstrasse 1908057ZürichSwitzerland
| | - Artur Krężel
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
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Kluska K, Chorążewska A, Peris-Díaz MD, Adamczyk J, Krężel A. Non-Conserved Amino Acid Residues Modulate the Thermodynamics of Zn(II) Binding to Classical ββα Zinc Finger Domains. Int J Mol Sci 2022; 23:ijms232314602. [PMID: 36498928 PMCID: PMC9735795 DOI: 10.3390/ijms232314602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Classical zinc fingers domains (ZFs) bind Zn(II) ion by a pair of cysteine and histidine residues to adopt a characteristic and stable ββα fold containing a small hydrophobic core. As a component of transcription factors, they recognize specific DNA sequences to transcript particular genes. The loss of Zn(II) disrupts the unique structure and function of the whole protein. It has been shown that the saturation of ZFs under cellular conditions is strictly related to their affinity for Zn(II). High affinity warrants their constant saturation, while medium affinity results in their transient structurization depending on cellular zinc availability. Therefore, there must be factors hidden in the sequence and structure of ZFs that impact Zn(II)-to-protein affinities to control their function. Using molecular dynamics simulations and experimental spectroscopic and calorimetric approaches, we showed that particular non-conserved residues derived from ZF sequences impact hydrogen bond formation. Our in silico and in vitro studies show that non-conserved residues can alter metal-coupled folding mechanisms and overall ZF stability. Furthermore, we show that Zn(II) binding to ZFs can also be entropically driven. This preference does not correlate either with Zn(II) binding site or with the extent of the secondary structure but is strictly related to a reservoir of interactions within the second coordination shell, which may loosen or tighten up the structure. Our findings shed new light on how the functionality of ZFs is modulated by non-coordinating residues diversity under cellular conditions. Moreover, they can be helpful for systematic backbone alteration of native ZF ββα scaffold to create artificial foldamers and proteins with improved stability.
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Coordination Chemistry of Phosphate Groups in Systems Including Copper(II) Ions, Phosphoethanolamine and Pyrimidine Nucleotides. Int J Mol Sci 2022; 23:ijms232213718. [PMID: 36430195 PMCID: PMC9691210 DOI: 10.3390/ijms232213718] [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: 10/10/2022] [Revised: 10/29/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
The activity of phosphate groups of phosphoethanolamine and pyrimidine nucleotides (thymidine 5-monophosphate, cytidine 5-monophosphate and uridine 5'monophosphate) in the process of complexation metal ions in aqueous solution was studied. Using the potentiometric method with computer calculation of the data and spectroscopic methods such as UV-Vis, EPR, 13C and 31P NMR as well as FT-IR, the overall stability constants of the complexes as well as coordination modes were obtained. At lower pH, copper(II) ions are complexed only by phosphate groups, whereas the endocyclic nitrogen atom of nucleotides has been identified as a negative center interacting with the -NH3+ groups of phosphoethanolamine.
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Rodzik A, Railean V, Pomastowski P, Žuvela P, Wong MW, Buszewski B. The influence of zinc ions concentration on β-lactoglobulin structure – physicochemical properties of Zn–β-lactoglobulin complexes. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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46
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Hosseinzadeh B, Ahmadi M. Coordination geometry in metallo-supramolecular polymer networks. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214733] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Zhao P, Wang Z, Xie X, Jiang T, Chun‐Him Lai N, Yang B, Yi B, Fu H, Zhang K, Li G, Wang Y, Bian L. Directed Conformational Switching of a Zinc Finger Analogue Regulates the Mechanosensing and Differentiation of Stem Cells. Angew Chem Int Ed Engl 2022; 61:e202203847. [DOI: 10.1002/anie.202203847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Pengchao Zhao
- School of Biomedical Sciences and Engineering Guangzhou International Campus South China University of Technology Guangzhou 511442 P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction South China University of Technology Guangzhou 510006 P. R. China
- Department of Biomedical Engineering The Chinese University of Hong Kong Hong Kong 999077 P. R. China
| | - Ziqi Wang
- Department of Physics The Chinese University of Hong Kong Hong Kong 999077 P. R. China
| | - Xian Xie
- Department of Biomedical Engineering The Chinese University of Hong Kong Hong Kong 999077 P. R. China
| | - Tianshen Jiang
- School of Biomedical Sciences and Engineering Guangzhou International Campus South China University of Technology Guangzhou 511442 P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction South China University of Technology Guangzhou 510006 P. R. China
| | - Nathanael Chun‐Him Lai
- Department of Biomedical Engineering The Chinese University of Hong Kong Hong Kong 999077 P. R. China
| | - Boguang Yang
- Department of Biomedical Engineering The Chinese University of Hong Kong Hong Kong 999077 P. R. China
| | - Bo Yi
- School of Biomedical Sciences and Engineering Guangzhou International Campus South China University of Technology Guangzhou 511442 P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction South China University of Technology Guangzhou 510006 P. R. China
| | - Hao Fu
- School of Biomedical Sciences and Engineering Guangzhou International Campus South China University of Technology Guangzhou 511442 P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction South China University of Technology Guangzhou 510006 P. R. China
| | - Kunyu Zhang
- School of Biomedical Sciences and Engineering Guangzhou International Campus South China University of Technology Guangzhou 511442 P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction South China University of Technology Guangzhou 510006 P. R. China
| | - Gang Li
- Department of Orthopaedics and Traumatology Faculty of Medicine The Chinese University of Hong Kong Hong Kong 999077 P. R. China
| | - Yi Wang
- Department of Physics The Chinese University of Hong Kong Hong Kong 999077 P. R. China
| | - Liming Bian
- School of Biomedical Sciences and Engineering Guangzhou International Campus South China University of Technology Guangzhou 511442 P. R. China
- National Engineering Research Center for Tissue Restoration and Reconstruction South China University of Technology Guangzhou 510006 P. R. China
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Choi TS, Tezcan FA. Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior. J Am Chem Soc 2022; 144:18090-18100. [PMID: 36154053 PMCID: PMC9949983 DOI: 10.1021/jacs.2c08050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Selective metal binding is a key requirement not only for the functions of natural metalloproteins but also for the potential applications of artificial metalloproteins in heterogeneous environments such as cells and environmental samples. The selection of transition-metal ions through protein design can, in principle, be achieved through the appropriate choice and the precise positioning of amino acids that comprise the primary metal coordination sphere. However, this task is made difficult by the intrinsic flexibility of proteins and the fact that protein design approaches generally lack the sub-Å precision required for the steric selection of metal ions. We recently introduced a flexible/probabilistic protein design strategy (MASCoT) that allows metal ions to search for optimal coordination geometry within a flexible, yet covalently constrained dimer interface. In an earlier proof-of-principle study, we used MASCoT to generate an artificial metalloprotein dimer, (AB)2, which selectively bound CoII and NiII over CuII (as well as other first-row transition-metal ions) through the imposition of a rigid octahedral coordination geometry, thus countering the Irving-Williams trend. In this study, we set out to redesign (AB)2 to examine the applicability of MASCoT to the selective binding of other metal ions. We report here the design and characterization of a new flexible protein dimer, B2, which displays ZnII selectivity over all other tested metal ions including CuII both in vitro and in cellulo. Selective, anti-Irving-Williams ZnII binding by B2 is achieved through the formation of a unique trinuclear Zn coordination motif in which His and Glu residues are rigidly placed in a tetrahedral geometry. These results highlight the utility of protein flexibility in the design and discovery of selective binding motifs.
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49
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Relations between Structure and Zn(II) Binding Affinity Shed Light on the Mechanisms of Rad50 Hook Domain Functioning and Its Phosphorylation. Int J Mol Sci 2022; 23:ijms231911140. [PMID: 36232441 PMCID: PMC9569753 DOI: 10.3390/ijms231911140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
The metal binding at protein–protein interfaces is still uncharted territory in intermolecular interactions. To date, only a few protein complexes binding Zn(II) in an intermolecular manner have been deeply investigated. The most notable example of such interfaces is located in the highly conserved Rad50 protein, part of the Mre11-Rad50-Nbs1 (MRN) complex, where Zn(II) is required for homodimerization (Zn(Rad50)2). The high stability of Zn(Rad50)2 is conserved not only for the protein derived from the thermophilic archaeon Pyrococcus furiosus (logK12 = 20.95 for 130-amino-acid-long fragment), which was the first one studied, but also for the human paralog studied here (logK12 = 19.52 for a 183-amino-acid-long fragment). As we reported previously, the extremely high stability results from the metal-coupled folding process where particular Rad50 protein fragments play a critical role. The sequence–structure–stability analysis based on human Rad50 presented here separates the individual structural components that increase the stability of the complex, pointing to amino acid residues far away from the Zn(II) binding site as being largely responsible for the complex stabilization. The influence of the individual components is very well reflected by the previously published crystal structure of the human Rad50 zinc hook (PDB: 5GOX). In addition, we hereby report the effect of phosphorylation of the zinc hook domain, which exerts a destabilizing effect on the domain. This study identifies factors governing the stability of metal-mediated protein–protein interactions and illuminates their molecular basis.
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50
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Bulathge AW, Villones RLE, Herbert FC, Gassensmith JJ, Meloni G. Comparative cisplatin reactivity towards human Zn7-metallothionein-2 and MTF-1 zinc fingers: potential implications in anticancer drug resistance. Metallomics 2022; 14:mfac061. [PMID: 36026541 PMCID: PMC9477119 DOI: 10.1093/mtomcs/mfac061] [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: 03/25/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022]
Abstract
Cis-diamminedichloroplatinum(II) (cisplatin) is a widely used metal-based chemotherapeutic drug for the treatment of cancers. However, intrinsic and acquired drug resistance limit the efficacy of cisplatin-based treatments. Increased production of intracellular thiol-rich molecules, in particular metallothioneins (MTs), which form stable coordination complexes with the electrophilic cisplatin, results in cisplatin sequestration leading to pre-target resistance. MT-1/-2 are overexpressed in cancer cells, and their expression is controlled by the metal response element (MRE)-binding transcription factor-1 (MTF-1), featuring six Cys2His2-type zinc fingers which, upon zinc metalation, recognize specific MRE sequences in the promoter region of MT genes triggering their expression. Cisplatin can efficiently react with protein metal binding sites featuring nucleophilic cysteine and/or histidine residues, including MTs and zinc fingers proteins, but the preferential reactivity towards specific targets with competing binding sites cannot be easily predicted. In this work, by in vitro competition reactions, we investigated the thermodynamic and kinetic preferential reactivity of cisplatin towards human Zn7MT-2, each of the six MTF-1 zinc fingers, and the entire human MTF-1 zinc finger domain. By spectroscopic, spectrometric, and electrophoretic mobility shift assays (EMSA), we demonstrated that cisplatin preferentially reacts with Zn7MT-2 to form Cys4-Pt(II) complexes, resulting in zinc release from MT-2. Zinc transfer from MT-2 to the MTF-1 triggers MTF-1 metalation, activation, and binding to target MRE sequences, as demonstrated by EMSA with DNA oligonucleotides. The cisplatin-dependent MT-mediated MTF-1 activation leading to apo-MT overexpression potentially establishes one of the molecular mechanisms underlying the development and potentiation of MT-mediated pre-target resistance.
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Affiliation(s)
- Anjala W Bulathge
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX-75080, USA
| | - Rhiza Lyne E Villones
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX-75080, USA
| | - Fabian C Herbert
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX-75080, USA
| | - Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX-75080, USA
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX-75080, USA
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