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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 PMCID: PMC11191002 DOI: 10.1021/acs.inorgchem.4c01707] [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: 04/26/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [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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Kolonko-Adamska M, Zawadzka-Kazimierczuk A, Bartosińska-Marzec P, Koźmiński W, Popowicz G, Krężel A, Ożyhar A, Greb-Markiewicz B. Interaction patterns of methoprene-tolerant and germ cell-expressed Drosophila JH receptors suggest significant differences in their functioning. Front Mol Biosci 2023; 10:1215550. [PMID: 37654797 PMCID: PMC10465699 DOI: 10.3389/fmolb.2023.1215550] [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: 05/02/2023] [Accepted: 07/17/2023] [Indexed: 09/02/2023] Open
Abstract
Methoprene-tolerant (Met) and germ cell-expressed (Gce) proteins were shown to be juvenile hormone (JH) receptors of Drosophila melanogaster with partially redundant functions. We raised the question of where the functional differentiation of paralogs comes from. Therefore, we tested Met and Gce interaction patterns with selected partners. In this study, we showed the ability of Gce and its C-terminus (GceC) to interact with 14-3-3 in the absence of JH. In contrast, Met or Met C-terminus (MetC) interactions with 14-3-3 were not observed. We also performed a detailed structural analysis of Met/Gce interactions with the nuclear receptor fushi tarazu factor-1 (Ftz-F1) ligand-binding domain. We showed that GceC comprising an Ftz-F1-binding site and full-length protein interacts with Ftz-F1. In contrast to Gce, only MetC (not full-length Met) can interact with Ftz-F1 in the absence of JH. We propose that the described differences result from the distinct tertiary structure and accessibility of binding sites in the full-length Met/Gce. Moreover, we hypothesize that each interacting partner can force disordered MetC and GceC to change the structure in a partner-specific manner. The observed interactions seem to determine the subcellular localization of Met/Gce by forcing their translocation between the nucleus and the cytoplasm, which may affect the activity of the proteins. The presented differences between Met and Gce can be crucial for their functional differentiation during D. melanogaster development and indicate Gce as a more universal and more active paralog. It is consistent with the theory indicating gce as an ancestor gene.
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Affiliation(s)
- M. Kolonko-Adamska
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - A. Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - P. Bartosińska-Marzec
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - W. Koźmiński
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - G. Popowicz
- Helmholtz Zentrum München, Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, Germany
| | - A. Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - A. Ożyhar
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - B. Greb-Markiewicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wroclaw, Poland
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3
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Azatian SB, Canny MD, Latham MP. Three segment ligation of a 104 kDa multi-domain protein by SrtA and OaAEP1. JOURNAL OF BIOMOLECULAR NMR 2023; 77:25-37. [PMID: 36539644 PMCID: PMC10149453 DOI: 10.1007/s10858-022-00409-w] [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: 09/23/2022] [Accepted: 11/28/2022] [Indexed: 05/03/2023]
Abstract
NMR spectroscopy is an excellent tool for studying protein structure and dynamics which provides a deeper understanding of biological function. As the size of the biomolecule of interest increases, it can become advantageous to dilute the number of observed signals in the NMR spectrum to decrease spectral overlap and increase resolution. One way to limit the number of resonances in the NMR data is by selectively labeling a smaller domain within the larger macromolecule, a process called segmental isotopic labeling. Many examples of segmental isotopic labeling have been described where two segments of a protein are ligated together by chemical or enzymatic means, but there are far fewer descriptions of a three or more segment ligation reaction. Herein, we describe an enzymatic segmental labeling scheme that combines the widely used Sortase A and more recently described OaAEP1 for a two site ligation strategy. In preparation to study proposed long-range allostery in the 104 kDa DNA damage repair protein Rad50, we ligated side-chain methyl group labeled Zn Hook domain between two long segments of otherwise unlabeled P.furiosus Rad50. Enzymatic activity data demonstrated that the scars resulting from the ligation reactions did not affect Rad50 function within the Mre11-Rad50 DNA double strand break repair complex. Finally, methyl-based NMR spectroscopy confirmed the formation of the full-length ligated protein. Our strategy highlights the strengths of OaAEP1 for segmental labeling, namely faster reaction times and a smaller recognition sequence, and provides a straightforward template for using these two enzymes in multisite segmental labeling reactions.
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Affiliation(s)
- Stephan B Azatian
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Marella D Canny
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael P Latham
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
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4
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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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5
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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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6
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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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7
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Cadmium hijacks the high zinc response by binding and activating the HIZR-1 nuclear receptor. Proc Natl Acad Sci U S A 2021; 118:2022649118. [PMID: 34649987 DOI: 10.1073/pnas.2022649118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2021] [Indexed: 11/18/2022] Open
Abstract
Cadmium is an environmental pollutant and significant health hazard that is similar to the physiological metal zinc. In Caenorhabditis elegans, high zinc homeostasis is regulated by the high zinc activated nuclear receptor (HIZR-1) transcription factor. To define relationships between the responses to high zinc and cadmium, we analyzed transcription. Many genes were activated by both high zinc and cadmium, and hizr-1 was necessary for activation of a subset of these genes; in addition, many genes activated by cadmium did not require hizr-1, indicating there are at least two mechanisms of cadmium-regulated transcription. Cadmium directly bound HIZR-1, promoted nuclear accumulation of HIZR-1 in intestinal cells, and activated HIZR-1-mediated transcription via the high zinc activation (HZA) enhancer. Thus, cadmium binding promotes HIZR-1 activity, indicating that cadmium acts as a zinc mimetic to hijack the high zinc response. To elucidate the relationships between high zinc and cadmium detoxification, we analyzed genes that function in three pathways: the pcs-1/phytochelatin pathway strongly promoted cadmium resistance but not high zinc resistance, the hizr-1/HZA pathway strongly promoted high zinc resistance but not cadmium resistance, and the mek-1/sek-1/kinase signaling pathway promoted resistance to high zinc and cadmium. These studies identify resistance pathways that are specific for high zinc and cadmium, as well as a shared pathway.
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8
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Brandis JEP, Zalesak SM, Kane MA, Michel SLJ. Cadmium Exchange with Zinc in the Non-Classical Zinc Finger Protein Tristetraprolin. Inorg Chem 2021; 60:7697-7707. [PMID: 33999622 PMCID: PMC8501473 DOI: 10.1021/acs.inorgchem.0c03808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Tristetraprolin (TTP) is a nonclassical CCCH zinc finger protein that regulates inflammation. TTP targets AU-rich RNA sequences of cytokine mRNAs forming a TTP/mRNA complex. This complex is then degraded, switching off the inflammatory response. Cadmium, a known carcinogen, triggers proinflammatory effects, and there is evidence that Cd increases TTP expression in cells, suggesting that Zn-TTP may be a target for cadmium toxicity. We sought to determine whether Cd exchanges with Zn in the TTP active site and measure the effect of RNA binding on this exchange. A construct of TTP that contains the two CCCH domains (TTP-2D) was employed to investigate these interactions. A spin-filter ICP-MS experiment to quantify the metal that is bound to the ZF after metal exchange was performed, and it was determined that Cd exchanges with Zn in Zn2-TTP-2D and that Zn exchanges with Cd in Cd2-TTP-2D. A native ESI-MS experiment to identify the metal-ZF complexes formed after metal exchange was performed, and M-TTP-2D complexes with singular and double metal exchange were observed. Metal exchange was measured in both the absence and presence of TTP's partner RNA, with retention of RNA binding. These data show that Cd can exchange with Zn in TTP without affecting function.
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Affiliation(s)
- Joel E P Brandis
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Stephanie M Zalesak
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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9
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Wątły J, Łuczkowski M, Padjasek M, Krężel A. Phytochelatins as a Dynamic System for Cd(II) Buffering from the Micro- to Femtomolar Range. Inorg Chem 2021; 60:4657-4675. [PMID: 33736430 PMCID: PMC8041291 DOI: 10.1021/acs.inorgchem.0c03639] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Indexed: 01/30/2023]
Abstract
Phytochelatins (PCs) are short Cys-rich peptides with repeating γ-Glu-Cys motifs found in plants, algae, certain fungi, and worms. Their biosynthesis has been found to be induced by heavy metals-both biogenic and toxic. Among all metal inducers, Cd(II) has been the most explored from a biological and chemical point of view. Although Cd(II)-induced PC biosynthesis has been widely examined, still little is known about the structure of Cd(II) complexes and their thermodynamic stability. Here, we systematically investigated glutathione (GSH) and PC2-PC6 systems, with regard to their complex stoichiometries and spectroscopic and thermodynamic properties. We paid special attention to the determination of stability constants using several complementary techniques. All peptides form CdL complexes, but CdL2 was found for GSH, PC2, and partially for PC3. Moreover, binuclear species CdxLy were identified for the series PC3-PC6 in an excess of Cd(II). Potentiometric and competition spectroscopic studies showed that the affinity of Cd(II) complexes increases from GSH to PC4 almost linearly from micromolar (log K7.4GSH = 5.93) to the femtomolar range (log K7.4PC4 = 13.39) and additional chain elongation does not increase the stability significantly. Data show that PCs form an efficient system which buffers free Cd(II) ions in the pico- to femtomolar range under cellular conditions, avoiding significant interference with Zn(II) complexes. Our study confirms that the favorable entropy change is the factor governing the elevation of phytochelatins' stability and illuminates the importance of the chelate effect in shifting the free Gibbs energy.
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Affiliation(s)
| | | | - Michał Padjasek
- 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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10
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Tran JB, Krężel A. InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information. J Proteome Res 2021; 20:1889-1901. [PMID: 33502860 PMCID: PMC8023803 DOI: 10.1021/acs.jproteome.0c00906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
InterMetalDB is a
free-of-charge database and browser of intermolecular
metal binding sites that are present on the interfaces of macromolecules
forming larger assemblies based on structural information deposited
in Protein Data Bank (PDB). It can be found and freely used at https://intermetaldb.biotech.uni.wroc.pl/. InterMetalDB collects the interfacial binding sites with involvement
of metal ions and clusters them on the basis of 50% sequence similarity
and the nearest metal environment (5 Å radius). The data are
available through the web interface where they can be queried, viewed,
and downloaded. Complexity of the query depends on the user, because
the questions in the query are connected with each other by a logical
AND. InterMetalDB offers several useful options for filtering records
including searching for structures by particular parameters such as
structure resolution, structure description, and date of deposition.
Records can be filtered by coordinated metal ion, number of bound
amino acid residues, coordination sphere, and other features. InterMetalDB
is regularly updated and will continue to be regularly updated with
new content in the future. InterMetalDB is a useful tool for all researchers
interested in metalloproteins, protein engineering, and metal-driven
oligomerization.
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Affiliation(s)
- Józef Ba Tran
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
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11
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Kocyła A, Tran JB, Krężel A. Galvanization of Protein-Protein Interactions in a Dynamic Zinc Interactome. Trends Biochem Sci 2020; 46:64-79. [PMID: 32958327 DOI: 10.1016/j.tibs.2020.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023]
Abstract
The presence of Zn2+ at protein-protein interfaces modulates complex function, stability, and introduces structural flexibility/complexity, chemical selectivity, and reversibility driven in a Zn2+-dependent manner. Recent studies have demonstrated that dynamically changing Zn2+ affects numerous cellular processes, including protein-protein communication and protein complex assembly. How Zn2+-involved protein-protein interactions (ZPPIs) are formed and dissociate and how their stability and reactivity are driven in a zinc interactome remain poorly understood, mostly due to experimental obstacles. Here, we review recent research advances on the role of Zn2+ in the formation of interprotein sites, their architecture, function, and stability. Moreover, we underline the importance of zinc networks in intersystemic communication and highlight bioinformatic and experimental challenges required for the identification and investigation of ZPPIs.
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Affiliation(s)
- Anna Kocyła
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Józef Ba Tran
- 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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12
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Padjasek M, Maciejczyk M, Nowakowski M, Kerber O, Pyrka M, Koźmiński W, Krężel A. Metal Exchange in the Interprotein Zn II -Binding Site of the Rad50 Hook Domain: Structural Insights into Cd II -Induced DNA-Repair Inhibition. Chemistry 2020; 26:3297-3313. [PMID: 31846102 PMCID: PMC7155053 DOI: 10.1002/chem.201904942] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/12/2019] [Indexed: 11/17/2022]
Abstract
CdII is a major genotoxic agent that readily displaces ZnII in a multitude of zinc proteins, abrogates redox homeostasis, and deregulates cellular metalloproteome. To date, this displacement has been described mostly for cysteine(Cys)-rich intraprotein binding sites in certain zinc finger domains and metallothioneins. To visualize how a ZnII -to-CdII swap can affect the target protein's status and thus understand the molecular basis of CdII -induced genotoxicity an intermolecular ZnII -binding site from the crucial DNA repair protein Rad50 and its zinc hook domain were examined. By using a length-varied peptide base, ZnII -to-CdII displacement in Rad50's hook domain is demonstrated to alter it in a bimodal fashion: 1) CdII induces around a two-orders-of-magnitude stabilization effect (log K 12 Zn II =20.8 vs. log K 12 Cd II =22.7), which defines an extremely high affinity of a peptide towards a metal ion, and 2) the displacement disrupts the overall assembly of the domain, as shown by NMR spectroscopic and anisotropy decay data. Based on the results, a new model explaining the molecular mechanism of CdII genotoxicity that underlines CdII 's impact on Rad50's dimer stability and quaternary structure that could potentially result in abrogation of the major DNA damage response pathway is proposed.
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Affiliation(s)
- Michał Padjasek
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| | - Maciej Maciejczyk
- Department of Physics and BiophysicsFaculty of Food ScienceUniversity of Warmia and Mazury in OlsztynOczapowskiego 410-719OlsztynPoland
| | - Michał Nowakowski
- Faculty of ChemistryBiological and Chemical Research CenterUniversity of WarsawŻwirki i Wigury 10102-089WarsawPoland
| | - Olga Kerber
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
| | - Maciej Pyrka
- Department of Physics and BiophysicsFaculty of Food ScienceUniversity of Warmia and Mazury in OlsztynOczapowskiego 410-719OlsztynPoland
| | - Wiktor Koźmiński
- Faculty of ChemistryBiological and Chemical Research CenterUniversity of WarsawŻwirki i Wigury 10102-089WarsawPoland
| | - Artur Krężel
- Department of Chemical BiologyFaculty of BiotechnologyUniversity of WrocławJoliot-Curie 14a50-383WrocławPoland
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Kluska K, Peris-Díaz MD, Płonka D, Moysa A, Dadlez M, Deniaud A, Bal W, Krężel A. Formation of highly stable multinuclear Ag nS n clusters in zinc fingers disrupts their structure and function. Chem Commun (Camb) 2020; 56:1329-1332. [PMID: 31912071 DOI: 10.1039/c9cc09418k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Silver (Ag(i)) binding to consensus zinc fingers (ZFs) causes Zn(ii) release inducing a gradual disruption of the hydrophobic core, followed by an overall conformational change and formation of highly stable AgnSn clusters. A compact eight-membered Ag4S4 structure formed by a CCCC ZF is the first cluster example reported for a single biological molecule. Ag(i)-induced conformational changes of ZFs can, as a consequence, affect transcriptional regulation and other cellular processes.
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Affiliation(s)
- Katarzyna Kluska
- 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.
| | - Dawid Płonka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Alexander Moysa
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Aurélien Deniaud
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, F-38000 Grenoble, France
| | - 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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