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Hecel A, Garstka K, Kozłowski H, Rowińska-Żyrek M. -HH and -HAAAH motifs act as fishing nets for biologically relevant metal ions in metallopeptides. J Inorg Biochem 2024; 252:112456. [PMID: 38154408 DOI: 10.1016/j.jinorgbio.2023.112456] [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: 10/26/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/30/2023]
Abstract
Histidine are one of the most common residues involved in transition metal ion binding in the active sites of metalloenzymes. In order to mimic enzymatic metal binding sites, it is crucial to understand the basic coordination modes of histidine residues, distributed at different positions in the peptide sequence. We show that: (i) the separation of two histidines has a large effect on complex stability - a sequence with adjusting histidine residues forms more stable complexes with Zn(II) than the one in which the residues are separated, while the contrary is observed for Cu(II) complexes, in which amide nitrogens participate in metal binding. No pronounced effect is observed for Ni(II) complexes, where the amides participate in binding at higher pH; (ii) non-coordinating amino acid residues (basic, acidic and aromatic ones) have a significant impact on complex stability; charged and aromatic residues may enhance Zn(II) binding, while the contrary is observed for the amide-binding Cu(II); (iii) cysteine containing sequences are much more effective Zn(II) and Ni(II) binding motifs at pH above 8, while histidine containing ligands are more suitable for effective Zn(II) and Ni(II) binding at lower pH.
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Affiliation(s)
- Aleksandra Hecel
- Faculty of Chemistry, University of Wrocław, 50-383 Wrocław, Poland.
| | - Kinga Garstka
- Faculty of Chemistry, University of Wrocław, 50-383 Wrocław, Poland
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wrocław, 50-383 Wrocław, Poland; Faculty of Health Sciences, University of Opole, 68 Katowicka St., 45-060 Opole, Poland
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2
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Hu X, Amin KS, Schneider M, Lim C, Salahub D, Baldauf C. System-Specific Parameter Optimization for Nonpolarizable and Polarizable Force Fields. J Chem Theory Comput 2024; 20:1448-1464. [PMID: 38279917 PMCID: PMC10867808 DOI: 10.1021/acs.jctc.3c01141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/29/2024]
Abstract
The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer (CT) and polarization (POL) effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding CT and POL. Furthermore, we present an open-source parametrization tool, called FFAFFURR, that enables the (system-specific) parametrization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a zinc-finger protein.
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Affiliation(s)
- Xiaojuan Hu
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kazi S. Amin
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Markus Schneider
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Carmay Lim
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Dennis Salahub
- Centre
for Molecular Simulation and Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Carsten Baldauf
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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3
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Fatima A, Zaheer T, Pal K, Abbas RZ, Akhtar T, Ali S, Mahmood MS. Zinc Oxide Nanoparticles Significant Role in Poultry and Novel Toxicological Mechanisms. Biol Trace Elem Res 2024; 202:268-290. [PMID: 37060542 DOI: 10.1007/s12011-023-03651-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/27/2023] [Indexed: 04/16/2023]
Abstract
Zinc oxide nanoparticles (ZnO NPs) have involved a lot of consideration owing to their distinctive features. The ZnO NPs can be described as particularly synthesized mineral salts via nanotechnology, varying in size from 1 to 100 nm, while zinc oxide (ZnO), it is an inorganic substrate of zinc (Zn). The Zn is a critical trace element necessary for various biological and physiological processes in the body. Studies have revealed ZnO NPs' efficient immuno-modulatory, growth-promoting, and antimicrobial properties in poultry birds. They offer increased bioavailability as compared to their traditional sources, producing better results in terms of productivity and welfare and consequently reducing ecological harm in the poultry sector. However, they have also been reported for their toxicological effects, which are size, shape, concentration, and exposure route dependent. The investigations done so far have yielded inconsistent results, therefore, a lot of additional studies and research are required to clarify the harmful consequences of ZnO NPs and to bring them to a logical end. This review explores an overview of efficient possible role of ZnO NPs, while comparing them with other nutritional Zn sources, in the poultry industry, primarily as dietary supplements that effect the growth, health, and performance of the birds. In addition to the anti-bacterial mechanisms of ZnO NPs and their promising role as antifungal, and anti-colloidal agent, this paper also covers the toxicological mechanisms of ZnO NPs and their consequent toxicological hazards to vital organs and the reproductive system of poultry birds.
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Affiliation(s)
- Arjmand Fatima
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Tean Zaheer
- Institute of Parasitology, University of Agriculture, Faisalabad, Pakistan
| | - Kaushik Pal
- University Center for Research and Development (UCRD), Department of Physics, Chandigarh University, Mohali, Gharuan, Punjab, 140413, India.
| | - Rao Zahid Abbas
- Institute of Parasitology, University of Agriculture, Faisalabad, Pakistan.
| | - Tayyaba Akhtar
- KBCMA College of Veterinary and Animal Sciences, Sub-Campus UVAS-Lahore, Narowal, Pakistan
| | - Sultan Ali
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
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Zhang L, Braynen J, Fahey A, Chopra K, Cifani P, Tadesse D, Regulski M, Hu F, van Dam HJJ, Xie M, Ware D, Blaby-Haas CE. Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1237722. [PMID: 37965006 PMCID: PMC10642216 DOI: 10.3389/fpls.2023.1237722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023]
Abstract
Metal homeostasis has evolved to tightly modulate the availability of metals within the cell, avoiding cytotoxic interactions due to excess and protein inactivity due to deficiency. Even in the presence of homeostatic processes, however, low bioavailability of these essential metal nutrients in soils can negatively impact crop health and yield. While research has largely focused on how plants assimilate metals, acclimation to metal-limited environments requires a suite of strategies that are not necessarily involved in metal transport across membranes. The identification of these mechanisms provides a new opportunity to improve metal-use efficiency and develop plant foodstuffs with increased concentrations of bioavailable metal nutrients. Here, we investigate the function of two distinct subfamilies of the nucleotide-dependent metallochaperones (NMCs), named ZNG1 and ZNG2, that are found in plants, using Arabidopsis thaliana as a reference organism. AtZNG1 (AT1G26520) is an ortholog of human and fungal ZNG1, and like its previously characterized eukaryotic relatives, localizes to the cytosol and physically interacts with methionine aminopeptidase type I (AtMAP1A). Analysis of AtZNG1, AtMAP1A, AtMAP2A, and AtMAP2B transgenic mutants are consistent with the role of Arabidopsis ZNG1 as a Zn transferase for AtMAP1A, as previously described in yeast and zebrafish. Structural modeling reveals a flexible cysteine-rich loop that we hypothesize enables direct transfer of Zn from AtZNG1 to AtMAP1A during GTP hydrolysis. Based on proteomics and transcriptomics, loss of this ancient and conserved mechanism has pleiotropic consequences impacting the expression of hundreds of genes, including those involved in photosynthesis and vesicle transport. Members of the plant-specific family of NMCs, ZNG2A1 (AT1G80480) and ZNG2A2 (AT1G15730), are also required during Zn deficiency, but their target protein(s) remain to be discovered. RNA-seq analyses reveal wide-ranging impacts across the cell when the genes encoding these plastid-localized NMCs are disrupted.
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Affiliation(s)
- Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Janeen Braynen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Audrey Fahey
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, United States
| | - Paolo Cifani
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Fangle Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Hubertus J. J. van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, United States
| | - Crysten E. Blaby-Haas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Fatouros PR, Roy U, Sur S. Implications of SARS-CoV-2 spike protein interactions with Zn-bound form of ACE2: a computational structural study. Biometals 2023:10.1007/s10534-023-00491-z. [PMID: 36725769 PMCID: PMC9891659 DOI: 10.1007/s10534-023-00491-z] [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: 07/13/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023]
Abstract
The COVID-19 pandemic has generated a major interest in designing inhibitors to prevent SARS-CoV-2 binding on host cells to protect against infection. One promising approach to such research utilizes molecular dynamics simulation to identify potential inhibitors that can prevent the interaction between spike (S) protein on the virus and angiotensin converting enzyme 2 (ACE2) receptor on the host cells. In these studies, many groups have chosen to exclude the ACE2-bound zinc (Zn) ion, which is critical for its enzymatic activity. While the relatively distant location of Zn ion from the S protein binding site (S1 domain), combined with the difficulties in modeling this ion has motivated the decision of exclusion, Zn can potentially contribute to the structural stability of the entire protein, and thus, may have implications on S protein-ACE2 interaction. In this study, the authors model both the ACE2-S1 and ACE2-inhibitor (mAb) system to investigate if there are variations in structure and the readouts due to the presence of Zn ion. Although distant from the S1 or inhibitor binding region, inclusion/exclusion of Zn has statistically significant effects on the structural stability and binding free energy in these systems. In particular, the binding free energy of the ACE2-S1 and ACE2-inhibitor structures is - 3.26 and - 14.8 kcal/mol stronger, respectively, in the Zn-bound structure than in the Zn-free structures. This finding suggests that including Zn may be important in screening potentially inhibitors and may be particularly important in modeling monoclonal antibodies, which may be more sensitive to changes in antigen structure.
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Affiliation(s)
- Peter R. Fatouros
- Department of Chemical and Biomolecular Engineering, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699 USA
| | - Urmi Roy
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699 USA
| | - Shantanu Sur
- Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699 USA
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Kim HJ, Kang HK. Effects of In Ovo Injection of Zinc or Diet Supplementation of Zinc on Performance, Serum Biochemical Profiles, and Meat Quality in Broilers. Animals (Basel) 2022; 12:ani12050630. [PMID: 35268199 PMCID: PMC8909355 DOI: 10.3390/ani12050630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Zinc (Zn) is known as an essential trace mineral that plays a key role in metabolic processes such as synthesis, stability, and catalytic activity of many proteins in broilers. In ovo technology provides an alternative for delivering nutrient compounds to the embryo prior to hatching by injecting small amounts of material into a broiler egg during hatching. In this study, the in ovo injection of Zn and dietary supplementation of Zn were evaluated on their effects on growth performance, serum biochemical profiles, and meat quality in broilers. In ovo injection and Zn supplementation (i.e., 200 mg/kg) increased (p < 0.05) body weight and immunoglobulin G (IgG) compared to broilers fed with the control diet. In ovo injection group decreased (p < 0.05) feed conversion ratios compared to broilers fed with the no injection group. Our results indicated that broilers fed with a diet supplemented with 200 mg/kg of Zn could ameliorate growth performance, immune responses, and increase the unsaturated fatty acids of breast meat. The findings of this result highlighted that the diet supplemented with Zn has the effect to improve performance, blood immune response, and fatty acid profile of breast meat. Abstract This study investigated the main effects of the in ovo injection of inorganic zinc (Zn) or diet supplementation of Zn on performance, serum biochemical profiles, and breast meat quality in broilers. A total of 480 one-day-old broilers (Ross 308) were randomly divided into four groups: the control (Con, noninjected and basal diet), in ovo (injected 60 mg Zn/egg at 18 embryonic days of incubation and basal diet), Zn100 (noninjected and basal diet with Zn (100 mg/kg) for 35 days), and Zn200 (noninjected and basal diet with Zn (200 mg/kg) for 35 days) groups. The dietary supplementation of Zn increased feed intake (2860.42–2861.08 g), weight (1975.06–1985.25 g), and weight gain (1936.36–1946.53 g) compared to Con (2785.74, 1891.38, and 1852.62 g, respectively) after five weeks of age. No significant difference was found in biochemical parameters and leukocyte and erythrocyte levels in the blood among the four different groups. In ovo injected or supplemental Zn (100 and 200 mg/kg) increased IgG in the blood of broilers. Zn200 increased polyunsaturated fatty acids, and saturated fatty acid contents were reduced in breast meat compared with Con. In conclusion, Zn supplementation at 200 mg/kg could improve the weight, feed intake, blood immune response, and fatty acid profile of breast meat.
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7
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Pillai SB, Wilcox RJ, Hillis BG, Losey BP, Martin JD. Understanding the Water-in-Salt to Salt-in-Water Characteristics across the Zinc Chloride : Water Phase Diagram. J Phys Chem B 2022; 126:2265-2278. [PMID: 35139641 DOI: 10.1021/acs.jpcb.1c10530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using a series of time- and temperature-resolved synchrotron diffraction experiments, the relationship between multiple polymorphs of ZnCl2 and its respective hydrates is established. The δ-phase is found to be the pure anhydrous phase, while the α, β, and γ phases result from partial hydration. Diffraction, gravimetric, and calorimetric measurements across the entire ZnCl2·R H2O, 0 > R > ∞ composition range using ultrapure, doubly sublimed ZnCl2 establish the ZnCl2 : H2O phase diagram. The results are consistent with the existence of crystalline hydrates at R = 1.33, 3, and 4.5 and identify a mechanistic pathway for hydration. All water is not removed from hydrated ZnCl2 until the system is heated above its melting point. While hydration/dehydration is reversible in concentrated solutions, dehydration from dilute aqueous solutions can result in loss of HCl, the source of hydroxide impurities commonly found in commercial ZnCl2 preparations. The strong interaction between ZnCl2 and water exerts a significant impact on the solvent water such that the system exhibits a deep eutectic at a composition of about R = 7 (87.5 mol %) and a eutectic temperature below -60 °C.
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Affiliation(s)
- Shelby B Pillai
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Robert J Wilcox
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Berkley G Hillis
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Bradley P Losey
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - James D Martin
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
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8
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Liu S, Abboud MI, John T, Mikhailov V, Hvinden I, Walsby-Tickle J, Liu X, Pettinati I, Cadoux-Hudson T, McCullagh JSO, Schofield CJ. Roles of metal ions in the selective inhibition of oncogenic variants of isocitrate dehydrogenase 1. Commun Biol 2021; 4:1243. [PMID: 34725432 PMCID: PMC8560763 DOI: 10.1038/s42003-021-02743-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 10/04/2021] [Indexed: 12/29/2022] Open
Abstract
Cancer linked isocitrate dehydrogenase (IDH) 1 variants, notably R132H IDH1, manifest a 'gain-of-function' to reduce 2-oxoglutarate to 2-hydroxyglutarate. High-throughput screens have enabled clinically useful R132H IDH1 inhibitors, mostly allosteric binders at the dimer interface. We report investigations on roles of divalent metal ions in IDH substrate and inhibitor binding that rationalise this observation. Mg2+/Mn2+ ions enhance substrate binding to wt IDH1 and R132H IDH1, but with the former manifesting lower Mg2+/Mn2+ KMs. The isocitrate-Mg2+ complex is the preferred wt IDH1 substrate; with R132H IDH1, separate and weaker binding of 2-oxoglutarate and Mg2+ is preferred. Binding of R132H IDH1 inhibitors at the dimer interface weakens binding of active site Mg2+ complexes; their potency is affected by the Mg2+ concentration. Inhibitor selectivity for R132H IDH1 over wt IDH1 substantially arises from different stabilities of wt and R132H IDH1 substrate-Mg2+ complexes. The results reveal the importance of substrate-metal ion complexes in wt and R132H IDH1 catalysis and the basis for selective R132H IDH1 inhibition. Further studies on roles of metal ion complexes in TCA cycle and related metabolism, including from an evolutionary perspective, are of interest.
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Affiliation(s)
- Shuang Liu
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Department of Natural Sciences, Lebanese American University, Byblos/Beirut, Lebanon
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ingvild Hvinden
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Xiao Liu
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ilaria Pettinati
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom Cadoux-Hudson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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Madjroh N, Mellou E, Æbelø L, Davies PA, Söderhielm PC, Jensen AA. Probing the molecular basis for signal transduction through the Zinc-Activated Channel (ZAC). Biochem Pharmacol 2021; 193:114781. [PMID: 34560053 DOI: 10.1016/j.bcp.2021.114781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/18/2022]
Abstract
The molecular basis for the signal transduction through the classical Cys-loop receptors (CLRs) has been delineated in great detail. The Zinc-Activated Channel (ZAC) constitutes a so far poorly elucidated fifth branch of the CLR superfamily, and in this study we explore the molecular mechanisms underlying ZAC signaling in Xenopus oocytes by two-electrode voltage clamp electrophysiology. In studies of chimeric receptors fusing either the extracellular domain (ECD) or the transmembrane/intracellular domain (TMD-ICD) of ZAC with the complementary domains of 5-HT3A serotonin or α1 glycine receptors, serotonin and Zn2+/H+ evoked robust concentration-dependent currents in 5-HT3A/ZAC- and ZAC/α1-Gly-expressing oocytes, respectively, suggesting that Zn2+ and protons activate ZAC predominantly through its ECD. The molecular basis for Zn2+-mediated ZAC signaling was probed further by introduction of mutations of His, Cys, Glu and Asp residues in this domain, but as none of the mutants tested displayed substantially impaired Zn2+ functionality compared to wild-type ZAC, the location of the putative Zn2+ binding site(s) in the ECD was not identified. Finally, the functional importance of Leu246 (Leu9') in the transmembrane M2 α-helix of ZAC was investigated by Ala, Val, Ile and Thr substitutions. In concordance with findings for this highly conserved residue in classical CLRs, the ZACL9'X mutants exhibited left-shifted agonist concentration-response relationships, markedly higher degrees of spontaneous activity and slower desensitization kinetics compared to wild-type ZAC. In conclusion, while ZAC is an atypical CLR in terms of its (identified) agonists and channel characteristics, its signal transduction seems to undergo similar conformational transitions as those in the classical CLR.
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Affiliation(s)
- Nawid Madjroh
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Eleni Mellou
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Laura Æbelø
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Paul A Davies
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, United States
| | - Pella C Söderhielm
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø 2100, Denmark.
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10
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Frühauf A, Meyer-Almes FJ. Non-Hydroxamate Zinc-Binding Groups as Warheads for Histone Deacetylases. Molecules 2021; 26:5151. [PMID: 34500583 PMCID: PMC8434074 DOI: 10.3390/molecules26175151] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Histone deacetylases (HDACs) remove acetyl groups from acetylated lysine residues and have a large variety of substrates and interaction partners. Therefore, it is not surprising that HDACs are involved in many diseases. Most inhibitors of zinc-dependent HDACs (HDACis) including approved drugs contain a hydroxamate as a zinc-binding group (ZBG), which is by far the biggest contributor to affinity, while chemical variation of the residual molecule is exploited to create more or less selectivity against HDAC isozymes or other metalloproteins. Hydroxamates have a propensity for nonspecificity and have recently come under considerable suspicion because of potential mutagenicity. Therefore, there are significant concerns when applying hydroxamate-containing compounds as therapeutics in chronic diseases beyond oncology due to unwanted toxic side effects. In the last years, several alternative ZBGs have been developed, which can replace the critical hydroxamate group in HDACis, while preserving high potency. Moreover, these compounds can be developed into highly selective inhibitors. This review aims at providing an overview of the progress in the field of non-hydroxamic HDACis in the time period from 2015 to present. Formally, ZBGs are clustered according to their binding mode and structural similarity to provide qualitative assessments and predictions based on available structural information.
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Affiliation(s)
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany;
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11
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Biswal HS, Kumar Sahu A, Frontera A, Bauzá A. Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function. J Chem Inf Model 2021; 61:3945-3954. [PMID: 34375103 PMCID: PMC8525862 DOI: 10.1021/acs.jcim.1c00594] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Understanding the structural and functional implications of metal ions is of pivotal significance to chemical biology. Herein, we report first time the evidence of spodium bonds (SpB's, an attractive noncovalent force involving elements from group 12 and electron-rich species) in tetrahedral Zn-binding sites. Through a combined crystallographic (PDB analysis) and computational (ab initio calculations) study, we demonstrate that Zn SpB's are abundant and might be involved in protein structure and enzyme inhibition.
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Affiliation(s)
- Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, 752050 Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, 752050 Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
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Rajendiran M, Trivedi HM, Chen D, Gajendrareddy P, Chen L. Recent Development of Active Ingredients in Mouthwashes and Toothpastes for Periodontal Diseases. Molecules 2021; 26:molecules26072001. [PMID: 33916013 PMCID: PMC8037529 DOI: 10.3390/molecules26072001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 01/01/2023] Open
Abstract
Periodontal diseases like gingivitis and periodontitis are primarily caused by dental plaque. Several antiplaque and anti-microbial agents have been successfully incorporated into toothpastes and mouthwashes to control plaque biofilms and to prevent and treat gingivitis and periodontitis. The aim of this article was to review recent developments in the antiplaque, anti-gingivitis, and anti-periodontitis properties of some common compounds in toothpastes and mouthwashes by evaluating basic and clinical studies, especially the ones published in the past five years. The common active ingredients in toothpastes and mouthwashes included in this review are chlorhexidine, cetylpyridinium chloride, sodium fluoride, stannous fluoride, stannous chloride, zinc oxide, zinc chloride, and two herbs—licorice and curcumin. We believe this comprehensive review will provide useful up-to-date information for dental care professionals and the general public regarding the major oral care products on the market that are in daily use.
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Affiliation(s)
- Meenakshi Rajendiran
- The Center for Wound Healing and Tissue Regeneration, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - Harsh M Trivedi
- Colgate-Palmolive Company, Piscataway, NJ 08854, USA; (H.M.T.); (D.C.)
| | - Dandan Chen
- Colgate-Palmolive Company, Piscataway, NJ 08854, USA; (H.M.T.); (D.C.)
| | - Praveen Gajendrareddy
- The Center for Wound Healing and Tissue Regeneration, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Correspondence: (P.G.); (L.C.); Tel.: +1-312-413-8405 (P.G.); +1-312-413-5387 (L.C.)
| | - Lin Chen
- The Center for Wound Healing and Tissue Regeneration, Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Correspondence: (P.G.); (L.C.); Tel.: +1-312-413-8405 (P.G.); +1-312-413-5387 (L.C.)
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13
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Zhang C, Maslar D, Minckley TF, LeJeune KD, Qin Y. Spontaneous, synchronous zinc spikes oscillate with neural excitability and calcium spikes in primary hippocampal neuron culture. J Neurochem 2021; 157:1838-1849. [PMID: 33638177 DOI: 10.1111/jnc.15334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/23/2021] [Indexed: 12/19/2022]
Abstract
Zinc has been suggested to act as an intracellular signaling molecule due to its regulatory effects on numerous protein targets including enzymes, transcription factors, ion channels, neurotrophic factors, and postsynaptic scaffolding proteins. However, intracellular zinc concentration is tightly maintained at steady levels under natural physiological conditions. Dynamic changes in intracellular zinc concentration have only been detected in certain types of cells that are exposed to pathologic stimuli or upon receptor ligand binding. Unlike calcium, the ubiquitous signaling metal ion that can oscillate periodically and spontaneously in various cells, spontaneous zinc oscillations have never been reported. In this work, we made the novel observation that the developing neurons generated spontaneous and synchronous zinc spikes in primary hippocampal cultures using a fluorescent zinc sensor, FluoZin-3. Blocking of glutamate receptor-dependent calcium influx depleted the zinc spikes, suggesting that these zinc spikes were driven by the glutamate-mediated spontaneous neural excitability and calcium spikes that have been characterized in early developing neurons. Simultaneous imaging of calcium or pH together with zinc, we uncovered that a downward pH spike was evoked with each zinc spike and this transient cellular acidification occurred downstream of calcium spikes but upstream of zinc spikes. Our results suggest that spontaneous, synchronous zinc spikes were generated through calcium influx-induced cellular acidification, which liberates zinc from intracellular zinc binding ligands. Given that changes in zinc concentration can modulate activities of proteins essential for synapse maturation and neuronal differentiation, these zinc spikes might act as important signaling roles in neuronal development.
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Affiliation(s)
- Chen Zhang
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Drew Maslar
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Taylor F Minckley
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Kate D LeJeune
- Department of Biological Sciences, University of Denver, Denver, CO, USA
| | - Yan Qin
- Department of Biological Sciences, University of Denver, Denver, CO, USA
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Kircheva N, Dobrev S, Nikolova V, Angelova S, Dudev T. Zinc and Its Critical Role in Retinitis pigmentosa: Insights from DFT/SMD Calculations. Inorg Chem 2020; 59:17347-17355. [DOI: 10.1021/acs.inorgchem.0c02664] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nikoleta Kircheva
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kl. Ohridski”, 1164 Sofia, Bulgaria
| | - Silvia Angelova
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kl. Ohridski”, 1164 Sofia, Bulgaria
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Jardin C, Chaves G, Musset B. Assessing Structural Determinants of Zn 2+ Binding to Human H V1 via Multiple MD Simulations. Biophys J 2020; 118:1221-1233. [PMID: 31972155 DOI: 10.1016/j.bpj.2019.12.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/20/2019] [Accepted: 12/27/2019] [Indexed: 01/02/2023] Open
Abstract
Voltage-gated proton channels (HV1) are essential for various physiological tasks but are strongly inhibited by Zn2+ cations. Some determinants of Zn2+ binding have been elucidated experimentally and in computational studies. However, the results have always been interpreted under the assumption that Zn2+ binds to monomeric HV1 despite evidence that HV1 expresses as a dimer and that the dimer has a higher affinity for zinc than the monomer and experimental data that suggest coordination in the dimer interface. The results of former studies are also controversial, e.g., supporting either one single or two binding sites. Some structural determinants of the binding are still elusive. We performed a series of molecular dynamics simulations to address different structures of the human proton channel, the monomer and two plausible dimer conformations, to compare their respective potential to interact with and bind Zn2+ via the essential histidines. The series consisted of several copies of the system to generate independent trajectories and increase the significance compared to a single simulation. The amount of time simulated totals 29.9 μs for 126 simulations of systems comprising ∼59,000 to ∼187,000 atoms. Our approach confirms the existence of two binding sites in monomeric and dimeric human HV1. The dimer interface is more efficient for attracting and binding Zn2+ via the essential histidines than the monomer or a dimer with the histidines in the periphery. The higher affinity is due to the residues in the dimer interface that create an attractive electrostatic potential funneling the zinc cations toward the binding sites.
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Affiliation(s)
- Christophe Jardin
- Institute of Physiology and Pathophysiology, Klinikum Nuremberg Medical School, Paracelsus Medical University, Nuremberg, Germany
| | - Gustavo Chaves
- Institute of Physiology and Pathophysiology, Klinikum Nuremberg Medical School, Paracelsus Medical University, Nuremberg, Germany
| | - Boris Musset
- Institute of Physiology and Pathophysiology, Klinikum Nuremberg Medical School, Paracelsus Medical University, Nuremberg, Germany.
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16
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Kachuee R, Abdi-Benemar H, Mansoori Y, Sánchez-Aparicio P, Seifdavati J, Elghandour MMMY, Guillén RJ, Salem AZM. Effects of Sodium Selenite, L-Selenomethionine, and Selenium Nanoparticles During Late Pregnancy on Selenium, Zinc, Copper, and Iron Concentrations in Khalkhali Goats and Their Kids. Biol Trace Elem Res 2019; 191:389-402. [PMID: 30600505 DOI: 10.1007/s12011-018-1618-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/16/2018] [Indexed: 01/02/2023]
Abstract
The objective of this study was to evaluate the effect of organic, inorganic, and selenium nanoparticle supplements at the final stage of pregnancy on selenium, zinc, copper, and iron concentrations of goats and placental, colostrum, and milk transfer of these trace minerals from goats to their kids. Forty pregnant Khalkhali goats (30 ± 5 kg) were randomly allocated to four treatments including (1) no supplement (control), 0.6 mg Se head-1 day-1 of selenomethionine (SM), 0.6 mg Se head-1 day-1 of selenium nanoparticles (SN), and 0.6 mg Se head-1 day-1 of sodium selenite (SS), from 4 weeks before the expected day of delivery to delivery day. Blood samples were taken from the goats 4 weeks before the expected day of delivery and on the kidding day. Colostrum samples were collected from the goats immediately after kidding. Instantly after delivery, newborn kids were taken apart from their dams and their blood samples were collected from the jugular vein, before they drank their first colostrums and at 7, 14, 21, and 28 after birthday. The results demonstrated that the whole blood and serum Se concentration was greater in Se-supplemented goats compared with the control (P < 0.05). The total Se content of the whole blood and serum was higher in SN than in SM (P < 0.05) and SS goats (P < 0.05). At birth, the whole blood and serum concentration of Se was decreased (P < 0.05) in kids of SN-treated goats contrasted with the control ones (P < 0.05). The copper content of goats and their kids in treated goats was greater compared with control goats except for SN treated, which was decreased (P < 0.05). It was totally vice versa with Zn content trend in the whole blood, serum, and colostrum (P < 0.05), which was also concomitant with an increase in Fe content of kids of supplemented goats at birth and first week of life (P < 0.05). These results seem to indicate a higher efficacy of placental and colostral transfer of Se into kids of SM-treated goats when contrasted with either receiving comparable doses of SN or SS. It could be concluded that Se supplementation can affect and correlate with Cu, Zn, and Fe levels, and this effect depends a lot on the chemical or physical variety of Se supplementation.
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Affiliation(s)
- Rasool Kachuee
- Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Hossein Abdi-Benemar
- Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran.
| | - Yaghoub Mansoori
- Department of Applied Chemistry, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Pedro Sánchez-Aparicio
- Department of Pharmacology, Anesthesia and Analgesia, Faculty of Veterinary Medicine and Animal Science, Autonomous University of the State of Mexico, Toluca, State of Mexico, Mexico
| | - Jamal Seifdavati
- Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mona M M Y Elghandour
- Department of Animal Nutrition, Faculty of Veterinary Medicine and Animal Science, Autonomous University of the State of Mexico, Toluca, State of Mexico, Mexico
| | | | - Abdelfattah Z M Salem
- Department of Animal Nutrition, Faculty of Veterinary Medicine and Animal Science, Autonomous University of the State of Mexico, Toluca, State of Mexico, Mexico.
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17
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Lee YM, Grauffel C, Chen T, Sargsyan K, Lim C. Factors Governing the Different Functions of Zn2+-Sites with Identical Ligands in Proteins. J Chem Inf Model 2019; 59:3946-3954. [DOI: 10.1021/acs.jcim.9b00617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu-Ming Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Ting Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 300 Taiwan
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18
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Kisko M, Bouain N, Safi A, Medici A, Akkers RC, Secco D, Fouret G, Krouk G, Aarts MGM, Busch W, Rouached H. LPCAT1 controls phosphate homeostasis in a zinc-dependent manner. eLife 2018; 7:e32077. [PMID: 29453864 PMCID: PMC5826268 DOI: 10.7554/elife.32077] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 02/15/2018] [Indexed: 12/25/2022] Open
Abstract
All living organisms require a variety of essential elements for their basic biological functions. While the homeostasis of nutrients is highly intertwined, the molecular and genetic mechanisms of these dependencies remain poorly understood. Here, we report a discovery of a molecular pathway that controls phosphate (Pi) accumulation in plants under Zn deficiency. Using genome-wide association studies, we first identified allelic variation of the Lyso-PhosphatidylCholine (PC) AcylTransferase 1 (LPCAT1) gene as the key determinant of shoot Pi accumulation under Zn deficiency. We then show that regulatory variation at the LPCAT1 locus contributes significantly to this natural variation and we further demonstrate that the regulation of LPCAT1 expression involves bZIP23 TF, for which we identified a new binding site sequence. Finally, we show that in Zn deficient conditions loss of function of LPCAT1 increases the phospholipid Lyso-PhosphatidylCholine/PhosphatidylCholine ratio, the expression of the Pi transporter PHT1;1, and that this leads to shoot Pi accumulation.
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Affiliation(s)
- Mushtak Kisko
- BPMP, Univ Montpellier, CNRS, INRA, SupAgroMontpellierFrance
| | - Nadia Bouain
- BPMP, Univ Montpellier, CNRS, INRA, SupAgroMontpellierFrance
| | - Alaeddine Safi
- BPMP, Univ Montpellier, CNRS, INRA, SupAgroMontpellierFrance
| | - Anna Medici
- BPMP, Univ Montpellier, CNRS, INRA, SupAgroMontpellierFrance
| | - Robert C Akkers
- Laboratory of GeneticsWageningen UniversityWageningenNetherlands
| | - David Secco
- BPMP, Univ Montpellier, CNRS, INRA, SupAgroMontpellierFrance
| | | | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRA, SupAgroMontpellierFrance
| | - Mark GM Aarts
- Laboratory of GeneticsWageningen UniversityWageningenNetherlands
| | - Wolfgang Busch
- Gregor Mendel InstituteAustrian Academy of Sciences, Vienna BiocenterViennaAustria
- Plant Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaUnited States
| | - Hatem Rouached
- BPMP, Univ Montpellier, CNRS, INRA, SupAgroMontpellierFrance
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19
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Kisko M, Bouain N, Safi A, Medici A, Akkers RC, Secco D, Fouret G, Krouk G, Aarts MG, Busch W, Rouached H. LPCAT1 controls phosphate homeostasis in a zinc-dependent manner. eLife 2018; 7:32077. [PMID: 29453864 DOI: 10.7554/elife.32077.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 02/15/2018] [Indexed: 05/22/2023] Open
Abstract
All living organisms require a variety of essential elements for their basic biological functions. While the homeostasis of nutrients is highly intertwined, the molecular and genetic mechanisms of these dependencies remain poorly understood. Here, we report a discovery of a molecular pathway that controls phosphate (Pi) accumulation in plants under Zn deficiency. Using genome-wide association studies, we first identified allelic variation of the Lyso-PhosphatidylCholine (PC) AcylTransferase 1 (LPCAT1) gene as the key determinant of shoot Pi accumulation under Zn deficiency. We then show that regulatory variation at the LPCAT1 locus contributes significantly to this natural variation and we further demonstrate that the regulation of LPCAT1 expression involves bZIP23 TF, for which we identified a new binding site sequence. Finally, we show that in Zn deficient conditions loss of function of LPCAT1 increases the phospholipid Lyso-PhosphatidylCholine/PhosphatidylCholine ratio, the expression of the Pi transporter PHT1;1, and that this leads to shoot Pi accumulation.
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Affiliation(s)
- Mushtak Kisko
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Nadia Bouain
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Alaeddine Safi
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Anna Medici
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Robert C Akkers
- Laboratory of Genetics, Wageningen University, Wageningen, Netherlands
| | - David Secco
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | | | - Gabriel Krouk
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
| | - Mark Gm Aarts
- Laboratory of Genetics, Wageningen University, Wageningen, Netherlands
| | - Wolfgang Busch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Hatem Rouached
- BPMP, Univ Montpellier, CNRS, INRA, SupAgro, Montpellier, France
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20
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Valasatava Y, Rosato A, Furnham N, Thornton JM, Andreini C. To what extent do structural changes in catalytic metal sites affect enzyme function? J Inorg Biochem 2018; 179:40-53. [PMID: 29161638 PMCID: PMC5760197 DOI: 10.1016/j.jinorgbio.2017.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/09/2023]
Abstract
About half of known enzymatic reactions involve metals. Enzymes belonging to the same superfamily often evolve to catalyze different reactions on the same structural scaffold. The work presented here investigates how functional differentiation, within superfamilies that contain metalloenzymes, relates to structural changes at the catalytic metal site. In general, when the catalytic metal site is unchanged across the enzymes of a superfamily, the functional differentiation within the superfamily tends to be low and the mechanism conserved. Conversely, all types of structural changes in the metal binding site are observed for superfamilies with high functional differentiation. Overall, the catalytic role of the metal ions appears to be one of the most conserved features of the enzyme mechanism within metalloenzyme superfamilies. In particular, when the catalytic role of the metal ion does not involve a redox reaction (i.e. there is no exchange of electrons with the substrate), this role is almost always maintained even when the site undergoes significant structural changes. In these enzymes, functional diversification is most often associated with modifications in the surrounding protein matrix, which has changed so much that the enzyme chemistry is significantly altered. On the other hand, in more than 50% of the examples where the metal has a redox role in catalysis, changes at the metal site modify its catalytic role. Further, we find that there are no examples in our dataset where metal sites with a redox role are lost during evolution. SYNOPSIS In this paper we investigate how functional diversity within superfamilies of metalloenzymes relates to structural changes at the catalytic metal site. Evolution tends to strictly conserve the metal site. When changes occur, they do not modify the catalytic role of non-redox metals whereas they affect the role of redox-active metals.
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Affiliation(s)
- Yana Valasatava
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Janet M Thornton
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Claudia Andreini
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy.
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21
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Crystal Chemistry of Zinc Quinaldinate Complexes with Pyridine-Based Ligands. CRYSTALS 2018. [DOI: 10.3390/cryst8010052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Lalegani A, Khaledi Sardashti M, Gajda R, Woźniak K. Synthesis and characterization of two new zinc(II) coordination polymers with bidentate flexible ligands: Formation of a 2D structure with (44.62)-sql topology. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.08.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Agarwal A, Avarebeel S, Choudhary NS, Goudar M, Tejaswini CJ. Correlation of Trace Elements in Patients of Chronic Liver Disease with Respect to Child- Turcotte- Pugh Scoring System. J Clin Diagn Res 2017; 11:OC25-OC28. [PMID: 29207755 DOI: 10.7860/jcdr/2017/26519.10655] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/17/2017] [Indexed: 12/12/2022]
Abstract
Introduction Zinc, copper, manganese and magnesium are essential trace elements whose role in chronic liver disease and its complications is not clear. Aim To study the concentration of these elements in patients with Chronic Liver Disease (CLD) with respect to Child-Torcotte-Pugh (CTP) scoring. Materials and Methods This was an observational study carried out in the Department of Medicine, JSS Hospital, Mysore, India, between October 2013 and October 2015. A total of 75 patients with cirrhosis were prospectively enrolled. Severity of liver disease was assessed based on CTP score and patients were grouped into Class A, B and C. Routine investigations were done and following trace elements were assessed in all-zinc, copper, manganese and magnesium. Results The serum concentrations of zinc decreased with severity of liver disease, and the mean difference between different severity classes was statistically significant (p<0.001). There was a significant negative correlation between zinc and CTP Score (r= -0.439; p<0.001). Copper concentration was increased in patients with more severe cirrhosis and mean level difference of copper among the CTP groups were statistically significant (p<0.001). Moreover, copper showed significant positive correlation with CTP Score (r=0.385; p<0.001). The serum levels of manganese were significantly higher in patients with CTP C class in comparison to patients with CTP A and B class (p<0.05); Manganese showed significant positive correlation with CTP Score (r=0.271; p= 0.019). The concentrations of magnesium did not differ significantly between CTP class with the mean level difference not statistically significant. Conclusion Increasing liver dysfunction alters the metabolism of trace elements towards excess of copper and deficiency of zinc.
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Affiliation(s)
- Amit Agarwal
- Junior Resident, Department of Medicine, JSS Medical College, Mysuru, Karnataka, India
| | - Shilpa Avarebeel
- Senior Resident, Department of Medicine, JSS Medical College, Mysuru, Karnataka, India
| | - Narendra S Choudhary
- Consultant, Department of Hepatology, Medanta Institute of Digestive and Hepatobiliary Sciences, Gurgaon, Haryana, India
| | - Mohan Goudar
- Professor, Department of Medicine, JSS Medical College, Mysuru, Karnataka, India
| | - C J Tejaswini
- Assistant Professor, Department of Medicine, JSS Medical College, Mysuru, Karnataka, India
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Kučerka N, Dushanov E, Kholmurodov KT, Katsaras J, Uhríková D. Calcium and Zinc Differentially Affect the Structure of Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3134-3141. [PMID: 28277666 DOI: 10.1021/acs.langmuir.6b03228] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Interactions of calcium (Ca2+) and zinc (Zn2+) cations with biomimetic membranes made of dipalmitoylphosphatidylcholine (DPPC) were studied by small angle neutron diffraction (SAND). Experiments show that the structure of these lipid bilayers is differentially affected by the two divalent cations. Initially, both Ca2+ and Zn2+ cause DPPC bilayers to thicken, while further increases in Ca2+ concentration result in the bilayer thinning, eventually reverting to having the same thickness as pure DPPC. The binding of Zn2+, on the other hand, causes the bilayers to swell to a maximum thickness, and the addition of more Zn2+ does not result in a further thickening of the membrane. Agreement between our results obtained using oriented planar membranes and those from vesicular samples implies that the effect of cations on bilayer thickness is the result of electrostatic interactions, rather than geometrical constraints due to bilayer curvature. This notion is further reinforced by MD simulations. Finally, the radial distribution functions reveal a strong interaction between Ca2+ and the phosphate oxygens, while Zn2+ shows a much weaker binding specificity.
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Affiliation(s)
- Norbert Kučerka
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava , 83232 Bratislava, Slovakia
| | | | | | - John Katsaras
- Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Daniela Uhríková
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava , 83232 Bratislava, Slovakia
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Thompson RB, Fierke CA. Measuring and Imaging Metal Ions With Fluorescence-Based Biosensors: Speciation, Selectivity, Kinetics, and Other Issues. Methods Enzymol 2017; 589:281-299. [PMID: 28336067 DOI: 10.1016/bs.mie.2017.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Fluorescence-based biosensors have shown themselves to be a powerful tool for the study of a variety of chemical species in biological systems, notably including metal ions. This chapter provides an overview of several important issues in using such sensors to study metallobiochemistry. These issues include selectivity for the analyte over potential interferents, including those that do not themselves induce a signal, the different forms in which metal ions are found (speciation), the utility of metal ion buffers, and the importance of kinetics in studying metal ion binding reactions. Finally, the chapter briefly discusses some of the issues in understanding whole-organism distribution of metal ions and its control.
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Affiliation(s)
- Richard B Thompson
- University of Maryland School of Medicine, Baltimore, MD, United States.
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Kokan Z, Perić B, Vazdar M, Marinić Ž, Vikić-Topić D, Meštrović E, Kirin SI. Metal-induced supramolecular chirality inversion of small self-assembled molecules in solution. Chem Commun (Camb) 2017; 53:1945-1948. [DOI: 10.1039/c6cc09203a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first example of supramolecular chirality inversion of small self-assembled ligands in solution by complexation to metal ions is presented.
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27
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Soudek P, Ursu M, Petrová Š, Vaněk T. Improving crop tolerance to heavy metal stress by polyamine application. Food Chem 2016; 213:223-229. [DOI: 10.1016/j.foodchem.2016.06.087] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 05/30/2016] [Accepted: 06/24/2016] [Indexed: 01/09/2023]
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28
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Drici N, Krallafa MA. Effect of mutation on the stabilization energy of HIV-1 zinc fingers: a hybrid local self-consistent field/molecular mechanics investigation. J Biol Inorg Chem 2016; 22:109-119. [DOI: 10.1007/s00775-016-1411-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/03/2016] [Indexed: 11/27/2022]
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29
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Donadio G, Di Martino R, Oliva R, Petraccone L, Del Vecchio P, Di Luccia B, Ricca E, Isticato R, Di Donato A, Notomista E. A new peptide-based fluorescent probe selective for zinc(ii) and copper(ii). J Mater Chem B 2016; 4:6979-6988. [PMID: 32263564 DOI: 10.1039/c6tb00671j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel metal ion-sensitive fluorescent peptidyl-probe has been designed based on the most common five-residue repeat in mammalian histidine rich glycoproteins (HRGs). A dansyl-amide moiety at the N-terminus and a tryptophan residue at the C-terminus of the peptide were added as they can act as a FRET (fluorescence resonance energy transfer) pair. The dansyl fluorophore was chosen also because it frequently shows strong CHEF (chelation enhanced fluorescence) and solvatochromic effects. The designed peptide, dansyl-HPHGHW-NH2 (dH3w), showed a selective fluorescence turn-on response to Zn2+ in aqueous solutions at pH 7.0 when excited at both 295 nm and 340 nm, thus indicating that both FRET and CHEF or solvatochromic effects are active in the metal/peptide complex. Steady-state fluorescence and isothermal titration calorimetry (ITC) measurements demonstrated that two peptide molecules bind to one zinc ion with an association constant Ka = 5.7 × 105 M-1 at 25 °C and pH 7.0. The fluorescence response to Zn2+ was not influenced by Pb2+, Cd2+, Mn2+, Fe2+, Fe3+, Mg2+, Ca2+, K+ and Na+ ions and only slightly influenced by Co2+ and Ni2+. Copper(ii), at concentrations as low as 5 μM, caused a strong quenching of both free and Zn2+ complexed dH3w. The determination of the binding parameters for Cu2+ has shown that one copper ion binds to one dH3w molecule with an association constant of 1.2 × 106 M-1 thus confirming the higher affinity of peptide for Cu2+ than for Zn2+. Finally, we demonstrated that dH3w can penetrate into HeLa cells and could thus be used for the determination of intracellular Zn2+ and Cu2+ concentrations.
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Affiliation(s)
- Giuliana Donadio
- Department of Biology University of Naples Federico II, Via Cintia, 80126, Naples, Italy.
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Taraphder S, Maupin CM, Swanson JJ, Voth GA. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J Phys Chem B 2016; 120:8389-404. [PMID: 27063577 PMCID: PMC5003118 DOI: 10.1021/acs.jpcb.6b02166] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/06/2016] [Indexed: 11/28/2022]
Abstract
The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II.
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Affiliation(s)
- Srabani Taraphder
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - C. Mark Maupin
- Department
of Chemical and Biological Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United
States
| | - Jessica
M. J. Swanson
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
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31
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Ray S, Gunzburg MJ, Wilce M, Panjikar S, Anand R. Structural Basis of Selective Aromatic Pollutant Sensing by the Effector Binding Domain of MopR, an NtrC Family Transcriptional Regulator. ACS Chem Biol 2016; 11:2357-65. [PMID: 27362503 DOI: 10.1021/acschembio.6b00020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phenol and its derivatives are common pollutants that are present in industrial discharge and are major xenobiotics that lead to water pollution. To monitor as well as improve water quality, attempts have been made in the past to engineer bacterial in vivo biosensors. However, due to the paucity of structural information, there is insufficiency in gauging the factors that lead to high sensitivity and selectivity, thereby impeding development. Here, we present the crystal structure of the sensor domain of MopR (MopR(AB)) from Acinetobacter calcoaceticus in complex with phenol and its derivatives to a maximum resolution of 2.5 Å. The structure reveals that the N-terminal residues 21-47 possess a unique fold, which are involved in stabilization of the biological dimer, and the central ligand binding domain belongs to the "nitric oxide signaling and golgi transport" fold, commonly present in eukaryotic proteins that bind long-chain fatty acids. In addition, MopR(AB) nests a zinc atom within a novel zinc binding motif, crucial for maintaining structural integrity. We propose that this motif is crucial for orchestrated motions associated with the formation of the effector binding pocket. Our studies reveal that residues W134 and H106 play an important role in ligand binding and are the key selectivity determinants. Furthermore, comparative analysis of MopR with XylR and DmpR sensor domains enabled the design of a MopR binding pocket that is competent in binding DmpR-specific ligands. Collectively, these findings pave way towards development of specific/broad based biosensors, which can act as useful tools for detection of this class of pollutants.
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Affiliation(s)
- Shamayeeta Ray
- IITB-Monash Research Academy, Mumbai 400076, Maharashtra, India
| | - Menachem J. Gunzburg
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Matthew Wilce
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Santosh Panjikar
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Australian Synchrotron, Clayton, Victoria 3168, Australia
| | - Ruchi Anand
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
- Wadhwani
Research Center for Bioengineering, IIT Bombay, Mumbai 400076, India
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32
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Wang G, Linsley R, Norimatsu Y. External Zn2+binding to cysteine-substituted cystic fibrosis transmembrane conductance regulator constructs regulates channel gating and curcumin potentiation. FEBS J 2016; 283:2458-75. [DOI: 10.1111/febs.13752] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 05/02/2016] [Accepted: 05/11/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Guangyu Wang
- Department of Physiology and Pharmacology; Oregon Health & Sciences University; Portland OR USA
- Department of Drug Research and Development; Institute of Biophysical Medico-chemistry; Reno NV USA
- Department of Physiology and Membrane Biology; University of California School of Medicine; Davis CA USA
| | | | - Yohei Norimatsu
- Department of Physiology; Kirksville College of Osteopathic Medicine; A.T. Still University; Kirksville MO USA
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33
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Salah SM, Yajing G, Dongdong C, Jie L, Aamir N, Qijuan H, Weimin H, Mingyu N, Jin H. Seed priming with polyethylene glycol regulating the physiological and molecular mechanism in rice (Oryza sativa L.) under nano-ZnO stress. Sci Rep 2015; 5:14278. [PMID: 26419216 PMCID: PMC4588511 DOI: 10.1038/srep14278] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/21/2015] [Indexed: 01/04/2023] Open
Abstract
The present study was designed to highlight the impact of seed priming with polyethylene glycol on physiological and molecular mechanism of two cultivars of Oryza sativa L. under different levels of zinc oxide nanorods (0, 250, 500 and 750 mg L(-1)). Plant growth parameters were significantly increased in seed priming with 30% PEG under nano-ZnO stress in both cultivars. Whereas, this increase was more prominent in cultivar Qian You No. 1 as compared to cultivar Zhu Liang You 06. Significant increase in photosynthetic pigment with PEG priming under stress. Antioxidant enzymes activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) as well as malondialdehyde (MDA) contents were significantly reduced with PEG priming under nano-ZnO stress. Gene expression analysis also suggested that expression of APXa, APXb, CATa, CATb, CATc, SOD1, SOD2 and SOD3 genes were down regulated with PEG priming as compared to non-primed seeds under stress. The ultrastructural analysis showed that leaf mesophyll and root cells were significantly damaged under nano-ZnO stress in both cultivars but the damage was prominent in Zhu Liang You 06. However, seed priming with PEG significantly alleviate the toxic effects of nano-ZnO stress and improved the cell structures of leaf and roots in both cultivars.
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Affiliation(s)
- Sheteiwy Mohamed Salah
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Department of Agronomy, Faculty of Agriculture, Mansoura University, Mansoura 35516, Egypt
| | - Guan Yajing
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Cao Dongdong
- Zhejiang Nongke Seed Industry Limited Company, Hangzhou, 310021, China
| | - Li Jie
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nawaz Aamir
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University Multan, 60000 Pakistan
| | - Hu Qijuan
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hu Weimin
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ning Mingyu
- National Agricultural Technology Extension Service Center, China
| | - Hu Jin
- Seed Science Center, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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34
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Isaia F, Aragoni MC, Arca M, Bettoschi A, Caltagirone C, Castellano C, Demartin F, Lippolis V, Pivetta T, Valletta E. Zinc(II)-methimazole complexes: synthesis and reactivity. Dalton Trans 2015; 44:9805-14. [PMID: 25928254 DOI: 10.1039/c5dt00917k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The tetrahedral S-coordinated complex [Zn(MeImHS)4](ClO4)2, synthesised from the reaction of [Zn(ClO4)2] with methimazole (1-methyl-3H-imidazole-2-thione, MeImHS), reacts with triethylamine to yield the homoleptic complex [Zn(MeImS)2] (MeImS = anion methimazole). ESI-MS and MAS (13)C-NMR experiments supported MeImS acting as a (N,S)-chelating ligand. The DFT-optimised structure of [Zn(MeImS)2] is also reported and the main bond lengths compared to those of related Zn-methimazole complexes. The complex [Zn(MeImS)2] reacts under mild conditions with methyl iodide and separates the novel complex [Zn(MeImSMe)2I2] (MeImSMe = S-methylmethimazole). X-ray diffraction analysis of the complex shows a ZnI2N2 core, with the methyl thioethers uncoordinated to zinc. Conversely, the reaction of [Zn(MeImS)2] with hydroiodic acid led to the formation of the complex [Zn(MeImHS)2I2] having a ZnI2S2 core with the neutral methimazole units S-coordinating the metal centre. The Zn-coordinated methimazole can markedly modify the coordination environment when changing from its thione to thionate form and vice versa. The study of the interaction of the drug methimazole with the complex [Zn(MeIm)4](2+) (MeIm = 1-methylimidazole) - as a model for Zn-enzymes containing a N4 donor set from histidine residues - shows that methimazole displaces only one of the coordinated MeIm molecules; the formation constant of the mixed complex [Zn(MeIm)3(MeImHS)](2+) was determined.
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Affiliation(s)
- Francesco Isaia
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, 09042 Monserrato (CA), Italy.
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35
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Marschner A, Klein CD. Metal promiscuity and metal-dependent substrate preferences of Trypanosoma brucei methionine aminopeptidase 1. Biochimie 2015; 115:35-43. [PMID: 25921435 DOI: 10.1016/j.biochi.2015.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 04/15/2015] [Indexed: 12/21/2022]
Abstract
Methionine aminopeptidases play a major role in posttranslational protein processing and are therefore promising targets for the discovery of novel therapeutical agents. We here describe the heterologous expression, purification, and characterization of recombinant Trypanosoma brucei methionine aminopeptidase, type 1 (TbMetAP1). We investigated the dependency of TbMetAP1 activity on pH and metal cofactor (type and concentration) using in particular the substrates Met-Gly-Met-Met and Met-AMC along with related compounds, and determined kinetic values (Km, vmax, kcat). The optimal pH for TbMetAP1 activity is between 7.0 and 8.0. Surprisingly, the two substrates have different cofactor requirements: Both substrates are processed by the cobalt-activated TbMetAP1, but only the Met-Gly-Met-Met substrate is processed with nearly identical catalytical properties by the zinc-activated enzyme. Depending on the substrate, various other metal ions (iron(II), manganese, nickel) were also accepted as cofactors. Two aspects of this work are relevant for the biochemistry of MetAPs and further drug discovery efforts: 1. Zinc, and not cobalt ions are probably the physiological cofactor of TbMetAP1 and possibly other MetAPs. 2. In MetAP assays for compound screening, the combination of the Met-AMC substrate with cobalt, manganese or iron ions may not represent the physiological reality, thereby leading to results that can not be extrapolated towards a phenotypic effect.
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Affiliation(s)
- Aline Marschner
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
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36
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Gao YZ, Zhang YA, Zhang J. Synthesis, structures, and magnetic properties of tetranuclear nickel and cobalt complexes with 2-mercaptobenzoxazole. INORG CHEM COMMUN 2015. [DOI: 10.1016/j.inoche.2015.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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37
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Wilcox RJ, Losey BP, Folmer JCW, Martin JD, Zeller M, Sommer R. Crystalline and Liquid Structure of Zinc Chloride Trihydrate: A Unique Ionic Liquid. Inorg Chem 2015; 54:1109-19. [DOI: 10.1021/ic5024532] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert J. Wilcox
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Bradley P. Losey
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Jacob C. W. Folmer
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - James D. Martin
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Matthias Zeller
- Department
of Chemistry, Youngstown State University, Youngstown, Ohio, 44555, United States
| | - Roger Sommer
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
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38
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Bharati P, Bharti A, Chaudhari U, Bharty M, Kashyap S, Singh UP, Singh N. Trinuclear supramolecular Zn(II) complexes derived from N′-(pyridine carbonyl) hydrazine carboperthioates: Synthesis, structural characterization, luminescent properties and metalloaromaticity. Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2014.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Jahanian R, Rasouli E. Effects of dietary substitution of zinc-methionine for inorganic zinc sources on growth performance, tissue zinc accumulation and some blood parameters in broiler chicks. J Anim Physiol Anim Nutr (Berl) 2014; 99:50-58. [DOI: 10.1111/jpn.12213] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 05/13/2014] [Indexed: 11/29/2022]
Affiliation(s)
- R. Jahanian
- Department of Animal Sciences; College of Agriculture; Isfahan University of Technology; Isfahan Iran
| | - E. Rasouli
- Department of Animal Sciences; College of Agriculture; Isfahan University of Technology; Isfahan Iran
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40
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41
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Polozov RV, Sivozhelezov VS, Chirgadze YN, Ivanov VV. Recognition rules for binding of Zn-Cys2His2 transcription factors to operator DNA. J Biomol Struct Dyn 2014; 33:253-66. [PMID: 24460547 DOI: 10.1080/07391102.2013.879074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The molecules of Zn-finger transcription factors consist of several similar small protein units. We analyzed the crystal structures 46 basic units of 22 complexes of Zn-Cys2His2 family with the fragments of operator DNA. We showed that the recognition of DNA occurs via five protein contacts. The canonical binding positions of the recognizing α-helix were -1, 3, 6, and 7, which make contacts with the tetra-nucleotide sequence ZXYZ of the coding DNA strand; here the canonical binding triplet is underlined. The non-coding DNA strand forms only one contact at α-helix position 2. We have discovered that there is a single highly conservative contact His7α with the phosphate group of nucleotide Z, which precedes each triplet XYZ of the coding DNA chain. This particular contact is invariant for the all Zn-Cys2His2 family with high frequency of occurrence 83%, which we considered as an invariant recognition rule. We have also selected a previously unreported Zn-Cys2His2-Arg subfamily of 21 Zn-finger units bound with DNA triplets, which make two invariant contacts with residues Arg6α and His7α with the coding DNA chain. These contacts show frequency of occurrence 100 and 90%, and are invariant recognition rule. Three other variable protein-DNA contacts are formed mainly with the bases and specify the recognition patterns of individual factor units. The revealed recognition rules are inherent for the Zn-Cys2His2 family and Zn-Cys2His2-Arg subfamily of different taxonomic groups and can distinguish members of these families from any other family of transcription factors.
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Affiliation(s)
- R V Polozov
- a Institute of Theoretical Experimental Biophysics, Russian Academy of Sciences , Pushchino 142290 , Moscow Region , Russia
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42
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Divalent Metal Cations in DNA–Phospholipid Binding. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-12-418698-9.00004-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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43
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44
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Lee YM, Lin YF, Lim C. Factors Controlling the Role of Zn and Reactivity of Zn-bound Cysteines in Proteins: Application to Drug Target Discovery. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201300392] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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45
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Zhou L, Li S, Su Y, Yi X, Zheng A, Deng F. Interaction between Histidine and Zn(II) Metal Ions over a Wide pH as Revealed by Solid-State NMR Spectroscopy and DFT Calculations. J Phys Chem B 2013; 117:8954-65. [DOI: 10.1021/jp4041937] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Lei Zhou
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
- Graduate School, the Chinese Academy of Sciences, Beijing 100029, China
| | - Shenhui Li
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Yongchao Su
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Xianfeng Yi
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
- Graduate School, the Chinese Academy of Sciences, Beijing 100029, China
| | - Anmin Zheng
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Feng Deng
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
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46
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Khandar AA, White J, Taghvaee-Yazdeli T, Hosseini-Yazdi SA, McArdle P. Structural effects of potentially hexadentate Schiff base ligands involving pyrrolic, etheric or thioetheric donors towards zinc(II) cation: Synthesis, characterization and crystal structures. Inorganica Chim Acta 2013. [DOI: 10.1016/j.ica.2013.02.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Phukan N, Baruah JB. A supramolecular assembly and complexes of zinc 2-hydoxy-3-naphthoate. RSC Adv 2013. [DOI: 10.1039/c2ra22811d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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48
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Tam HH, Asthagiri D, Paulaitis ME. Coordination state probabilities and the solvation free energy of Zn2+ in aqueous methanol solutions. J Chem Phys 2012; 137:164504. [DOI: 10.1063/1.4759452] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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49
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D'Antonio EL, Hai Y, Christianson DW. Structure and function of non-native metal clusters in human arginase I. Biochemistry 2012; 51:8399-409. [PMID: 23061982 DOI: 10.1021/bi301145n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Various binuclear metal ion clusters and complexes have been reconstituted in crystalline human arginase I by removing the Mn(2+)(2) cluster of the wild-type enzyme with metal chelators and subsequently soaking the crystalline apoenzyme in buffer solutions containing NiCl(2) or ZnCl(2). X-ray crystal structures of these metal ion variants are correlated with catalytic activity measurements that reveal differences resulting from metal ion substitution. Additionally, treatment of crystalline Mn(2+)(2)-human arginase I with Zn(2+) reveals for the first time the structural basis for inhibition by Zn(2+), which forms a carboxylate-histidine-Zn(2+) triad with H141 and E277. The imidazole side chain of H141 is known to be hyper-reactive, and its chemical modification or mutagenesis is known to similarly compromise catalysis. The reactive substrate analogue 2(S)-amino-6-boronohexanoic acid (ABH) binds as a tetrahedral boronate anion to Mn(2+)(2), Co(2+)(2), Ni(2+)(2), and Zn(2+)(2) clusters in human arginase I, and it can be stabilized by a third inhibitory Zn(2+) ion coordinated by H141. Because ABH binds as an analogue of the tetrahedral intermediate and its flanking transition states in catalysis, this implies that the various metallo-substituted enzymes are capable of some level of catalysis with an actual substrate. Accordingly, we establish the following trend for turnover number (k(cat)) and catalytic efficiency (k(cat)/K(M)): Mn(2+) > Ni(2+) ≈ Co(2+) ≫ Zn(2+). Therefore, Mn(2+) is required for optimal catalysis by human arginase I.
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Affiliation(s)
- Edward L D'Antonio
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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Tiwari MK, Singh RK, Singh R, Jeya M, Zhao H, Lee JK. Role of conserved glycine in zinc-dependent medium chain dehydrogenase/reductase superfamily. J Biol Chem 2012; 287:19429-39. [PMID: 22500022 DOI: 10.1074/jbc.m111.335752] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The medium-chain dehydrogenase/reductase (MDR) superfamily consists of a large group of enzymes with a broad range of activities. Members of this superfamily are currently the subject of intensive investigation, but many aspects, including the zinc dependence of MDR superfamily proteins, have not yet have been adequately investigated. Using a density functional theory-based screening strategy, we have identified a strictly conserved glycine residue (Gly) in the zinc-dependent MDR superfamily. To elucidate the role of this conserved Gly in MDR, we carried out a comprehensive structural, functional, and computational analysis of four MDR enzymes through a series of studies including site-directed mutagenesis, isothermal titration calorimetry, electron paramagnetic resonance (EPR), quantum mechanics, and molecular mechanics analysis. Gly substitution by other amino acids posed a significant threat to the metal binding affinity and activity of MDR superfamily enzymes. Mutagenesis at the conserved Gly resulted in alterations in the coordination of the catalytic zinc ion, with concomitant changes in metal-ligand bond length, bond angle, and the affinity (K(d)) toward the zinc ion. The Gly mutants also showed different spectroscopic properties in EPR compared with those of the wild type, indicating that the binding geometries of the zinc to the zinc binding ligands were changed by the mutation. The present results demonstrate that the conserved Gly in the GHE motif plays a role in maintaining the metal binding affinity and the electronic state of the catalytic zinc ion during catalysis of the MDR superfamily enzymes.
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