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Prejanò M, Toscano M, Marino T. Periodicity of the Affinity of Lanmodulin for Trivalent Lanthanides and Actinides: Structural and Electronic Insights from Quantum Chemical Calculations. Inorg Chem 2023; 62:7461-7470. [PMID: 37128767 DOI: 10.1021/acs.inorgchem.3c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lanmodulin (LanM) is the first identified macrochelator that has naturally evolved to sequester ions of rare earth elements (REEs) such as Y and all lanthanides, reversibly. This natural protein showed a 106 times better affinity for lanthanide cations than for Ca, which is a naturally abundant and biologically relevant element. Recent experiments have shown that its metal ion binding activity can be further extended to some actinides, like Np, Pu, and Am. For this reason, it was thought that LanM could be adopted for the separation of REE ions and actinides, thus increasing the interest in its potential use for industry-oriented applications. In this work, a systematic study of the affinity of LanM for lanthanides and actinides has been carried out, taking into account all trivalent ions belonging to the 4f (from La to Lu) and 5f (from Ac to Lr) series, starting from their chemistry in solution. On the basis of a recently published nuclear magnetic resonance structure, a model of the LanM-binding site was built and a detailed structural and electronic description of initial aquo- and LanM-metal ion complexes was provided. The obtained binding energies are in agreement with the available experimental data. A possible reason that could explain the origin of the affinity of LanM for these metal ions is also discussed.
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Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Marirosa Toscano
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci, 87036 Rende, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci, 87036 Rende, Italy
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Hoyer E, Knöppel J, Liebmann M, Steppert M, Raiwa M, Herczynski O, Hanspach E, Zehner S, Göttfert M, Tsushima S, Fahmy K, Oertel J. Calcium binding to a disordered domain of a type III-secreted protein from a coral pathogen promotes secondary structure formation and catalytic activity. Sci Rep 2019; 9:7115. [PMID: 31068617 PMCID: PMC6506597 DOI: 10.1038/s41598-019-42898-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/10/2019] [Indexed: 01/05/2023] Open
Abstract
Strains of the Gram-negative bacterium Vibrio coralliilyticus cause the bleaching of corals due to decomposition of symbiotic microalgae. The V. coralliilyticus strain ATCC BAA-450 (Vc450) encodes a type III secretion system (T3SS). The gene cluster also encodes a protein (locus tag VIC_001052) with sequence homology to the T3SS-secreted nodulation proteins NopE1 and NopE2 of Bradyrhizobium japonicum (USDA110). VIC_001052 has been shown to undergo auto-cleavage in the presence of Ca2+ similar to the NopE proteins. We have studied the hitherto unknown secondary structure, Ca2+-binding affinity and stoichiometry of the “metal ion-inducible autocleavage” (MIIA) domain of VIC_001052 which does not possess a classical Ca2+-binding motif. CD and fluorescence spectroscopy revealed that the MIIA domain is largely intrinsically disordered. Binding of Ca2+ and other di- and trivalent cations induced secondary structure and hydrophobic packing after partial neutralization of the highly negatively charged MIIA domain. Mass spectrometry and isothermal titration calorimetry showed two Ca2+-binding sites which promote structure formation with a total binding enthalpy of −110 kJ mol−1 at a low micromolar Kd. Putative binding motifs were identified by sequence similarity to EF-hand domains and their structure analyzed by molecular dynamics simulations. The stoichiometric Ca2+-dependent induction of structure correlated with catalytic activity and may provide a “host-sensing” mechanism that is shared among pathogens that use a T3SS for efficient secretion of disordered proteins.
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Affiliation(s)
- Elisabeth Hoyer
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany.,Ludwig-Maximilians-Universität München, Department of Biology I, Microbiology, Großhaderner Str. 2, D-82152, Planegg-Martinsried, Germany
| | - Julius Knöppel
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Martina Liebmann
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Michael Steppert
- Leibniz University Hannover, Institute of Radioecology and Radiation Protection, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Manuel Raiwa
- Leibniz University Hannover, Institute of Radioecology and Radiation Protection, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Olivia Herczynski
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Erik Hanspach
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Susanne Zehner
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Michael Göttfert
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Satoru Tsushima
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Jana Oertel
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany.
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Götzke L, Schaper G, März J, Kaden P, Huittinen N, Stumpf T, Kammerlander KK, Brunner E, Hahn P, Mehnert A, Kersting B, Henle T, Lindoy LF, Zanoni G, Weigand JJ. Coordination chemistry of f-block metal ions with ligands bearing bio-relevant functional groups. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Zhou B, Wang Z, Tian Y, Wang Z, Yang B. Electrochemical study of the interaction between Eu3+ and ciliate Euplotes octocarinatus centrin. Electrochim Acta 2010; 55:4124-9. [DOI: 10.1016/j.electacta.2010.02.084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Bowen LM, Muller G, Riehl JP, Dupureur CM. Lanthanide spectroscopic studies of the dinuclear and Mg(II)-dependent PvuII restriction endonuclease. Biochemistry 2005; 43:15286-95. [PMID: 15568821 DOI: 10.1021/bi0486278] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type II restriction enzymes are homodimeric systems that bind four to eight base pair palindromic recognition sequences of DNA and catalyze metal ion-dependent phosphodiester cleavage. While Mg(II) is required for cleavage in these enzymes, in some systems Ca(II) promotes avid substrate binding and sequence discrimination. These properties make them useful model systems for understanding the roles of alkaline earth metal ions in nucleic acid processing. We have previously shown that two Ca(II) ions stimulate DNA binding by PvuII endonuclease and that the trivalent lanthanide ions Tb(III) and Eu(III) support subnanomolar DNA binding in this system. Here we capitalize on this behavior, employing a unique combination of luminescence spectroscopy and DNA binding assays to characterize Ln(III) binding behavior by this enzyme. Upon excitation of tyrosine residues, the emissions of both Tb(III) and Eu(III) are enhanced severalfold. This enhancement is reduced by the addition of a large excess of Ca(II), indicating that these ions bind in the active site. Poor enhancements and affinities in the presence of the active site variant E68A indicate that Glu68 is an important Ln(III) ligand, similar to that observed with Ca(II), Mg(II), and Mn(II). At low micromolar Eu(III) concentrations in the presence of enzyme (10-20 microM), Eu(III) excitation (7)F(0) --> (5)D(0) spectra yield one dominant peak at 579.2 nm. A second, smaller peak at 579.4 nm is apparent at high Eu(III) concentrations (150 microM). Titration data for both Tb(III) and Eu(III) fit well to a two-site model featuring a strong site (K(d) = 1-3 microM) and a much weaker site (K(d) approximately 100-200 microM). Experiments with the E68A variant indicate that the Glu68 side chain is not required for the binding of this second Ln(III) equivalent; however, the dramatic increase in DNA binding affinity around 100 microM Ln(III) for the wild-type enzyme and metal-enhanced substrate affinity for E68A are consistent with functional relevance for this weaker site. This discrimination of sites should make it possible to use lanthanide substitution and lanthanide spectroscopy to probe individual metal ion binding sites, thus adding an important tool to the study of restriction enzyme structure and function.
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Affiliation(s)
- Lori M Bowen
- Department of Chemistry and Biochemistry, University of Missouri St. Louis, St. Louis, Missouri 63121, USA
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Abstract
Ion binding is a term that assumes that the ion is included in the solvation sphere characterising the biomolecule. The binding forces are not clearly stated except for electrostatic attraction; weak forces (hydrogen bonds and Van der Waals forces) are likely involved. Many publications have dealt with ion binding to proteins and the consequences over the past 10 years, but only a few studies were performed using high-performance liquid chromatography (HPLC: ion exchange, reversed phase without the well-identified immobilised metal affinity chromatography) and capillary zone electrophoresis (CZE). This review focuses on the binding of proteins and DNAs mainly to the oxyanions (phosphate, borate, citrate) and amines used as buffers for both the HPLC eluent and the background electrolyte of CZE. Such specific ion adsorption on biomolecules is evidenced by physico-chemical characteristics such as the mobility or retention volume, closely associated with the net charge, which differ from the expected or experimental data obtained under the conditions of an indifferent electrolyte. It is shown that ion binding to proteins is a key parameter in the electrostatic repulsion between the free protein and a fouled membrane in the ultrafiltration separation of a protein mixture.
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Affiliation(s)
- Murielle Rabiller-Baudry
- Laboratoire des Procédés de Séparation, Université Rennes 1, UC INRA, Campus de Beaulieu, Bat. 10A, 263 Avenue du Général Leclerc, CS 74205, 35042 Rennes Cedex, France.
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Abstract
Oscillation is found in many biological systems, and among them the enzymatic oscillatory reaction has been well studied using an enzyme solution. We show in this study for the first time that oscillation occurs when catalase is immobilized to controlled pore glass (CPG). The oscillatory wave mode changes with the distance among the CPG, electrode, or dialysis membrane. The lower substrate concentration results in oscillation with a longer period. This tendency agrees with a previous study using an enzyme solution. Furthermore, we show that the oscillation occurs when no dialysis membrane is used. These results show the wider applicability of the system to analysis or novel device fabrication.
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Affiliation(s)
- Satoshi Sasaki
- School of Bionics, Tokyo University of Technology, 1404-1, Katakura, Hachioji, Tokyo 192-0982, Japan
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Liu HG, Lee YI, Qin WP, Jang K, Kim S, Feng XS. Distinct composite structure and properties of Eu(phen)2Cl3(H2O)2 in poly(methyl methacrylate) and polyvinylpyrrolidone. J Appl Polym Sci 2004. [DOI: 10.1002/app.20375] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
The possibility of selectively substituting one or more lanthanides into the four canonical calcium binding sites of calcium-loaded vertebrate calmodulin (CaM) was investigated by monitoring changes in the (1)H-(15)N HSQC NMR spectra of the (15)N-enriched protein upon titration with Yb(3+). The affinity of lanthanides for both N-terminal sites I and II is only moderately higher than that of calcium, and comparable with that of calcium for the two C-terminal sites. This situation induces binding of lanthanides to other noncanonical sites located at the interdomain linker, the N- and C-terminal ends, and at the inter-EF-hand linkers. Therefore, mutants were designed to alter the metal binding properties of calcium sites I (D22N, D24E), II (D58N, N60D, D58N-N60D), III (N97D), II-III (N60D-N97D), and IV (D129N), as well as of the inter-EF-hand linker of the N-terminal domain (N42K, T44K). The most striking effects were obtained for the N60D mutant at site II, as selective lanthanide binding is achieved even in the presence of excess calcium, and little or no population of the noncanonical sites occurs. Similar although less pronounced effects were observed for the N97D mutant. These findings allow us to better define some of the determinants of the relative affinities of calcium and lanthanides in CaM and, by extension, in other calcium binding proteins. Finally, by using CaM samples containing only three of the four calcium ions, it was possible to prepare well-defined Ca(3)Ln-CaM derivatives (Ln = Tb, Dy, Tm, and Yb), with interesting properties as NMR probes.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
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Chroni S, Ghanotakis DF. Accessibility of tyrosine Y(.)(Z) to exogenous reductants and Mn(2+) in various Photosystem II preparations. Biochim Biophys Acta 2001; 1504:432-7. [PMID: 11245806 DOI: 10.1016/s0005-2728(01)00159-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reduction of tyrosine Y(.)(Z) by benzidine and exogenous Mn(2+) was studied by kinetic EPR experiments in various Photosystem II (PSII) preparations. Using lanthanide treated PSII membranes it was demonstrated that neither the extrinsic polypeptides (17, 23 and 33 kDa) nor the Mn complex block the accessibility of Y(.)(Z) to exogenous reductants, such as benzidine. In addition, it was shown that in the presence of the native Mn complex exogenous Mn(2+) does not reduce Y(.)(Z).
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Affiliation(s)
- S Chroni
- Department of Chemistry, University of Crete, PO Box 1470, 71409 Heraklion, Crete, Greece
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Rawashdeh-Omary MA, Larochelle CL, Patterson HH. Tunable Energy Transfer from Dicyanoaurate(I) and Dicyanoargentate(I) Donor Ions to Terbium(III) Acceptor Ions in Pure Crystals. Inorg Chem 2000. [DOI: 10.1021/ic990510y] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manal A. Rawashdeh-Omary
- Department of Chemistry and Department of Physics and Astronomy, University of Maine, Orono, Maine 04469
| | - C. L. Larochelle
- Department of Chemistry and Department of Physics and Astronomy, University of Maine, Orono, Maine 04469
| | - Howard H. Patterson
- Department of Chemistry and Department of Physics and Astronomy, University of Maine, Orono, Maine 04469
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Abstract
The self-assembly of dinuclear triple helical lanthanide ion complexes (helicates), in aqueous solution, is investigated utilizing laser-induced, lanthanide luminescence spectroscopy. A series of dinuclear lanthanide (III) helicates (Ln(III)) based on 2,6-pyridinedicarboxylic acid (dipicolinic acid, dpa) coordinating units was synthesized by linking two dpa moieties using the organic diamines (1R,2R)-diaminocyclohexane (chxn-R,R) and 4,4'-diaminodiphenylmethane (dpm). Luminescence excitation spectroscopy of the Eu3+ 7F0-->5D0 transition shows the apparent cooperative formation of neutral triple helical complexes in aqueous solution, with a [Eu2L3] stoichiometry. Eu3+ excitation peak wavelengths and excited-state lifetimes correspond to those of the [Eu(dpa)3]3- model complex. CD studies of the Nd(III) helicate Nd2(dpa-chxn-R,R)3 reveal optical activity of the f-f transitions, indicating that the chiral linking group induces a stable chirality at the metal ion center. Molecular mechanics calculations using CHARMm suggest that the delta delta configuration at the Nd3+ ion centers is induced by the chxn-R,R linker. Stability constants were determined for both ligands with Eu3+, yielding identical results: log K = 31.6 +/- 0.2 (K in units of M-4). Metal-metal distances calculated from Eu3+-->Nd3+ energy-transfer experiments show that the complexes have metal-metal distances close to those calculated by molecular modeling. The fine structure in the Tb3+ emission bands is consistent with the approximate D3 symmetry as anticipated for helicates.
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Affiliation(s)
- J J Lessmann
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, 16802
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Chaudhuri D, Horrocks WD, Amburgey JC, Weber DJ. Characterization of lanthanide ion binding to the EF-hand protein S100 beta by luminescence spectroscopy. Biochemistry 1997; 36:9674-80. [PMID: 9245399 DOI: 10.1021/bi9704358] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
S100 beta is a member of a group of low-molecular weight acidic calcium binding proteins widely distributed in the vertebrate nervous system containing two helix-loop-helix calcium binding motifs (sites I and II). In addition, S100 beta also has auxiliary Zn2+ binding sites that are distinct from the Ca2+ binding sites. Luminescence spectroscopy using Eu3+ and Tb3+ as spectroscopic probes for Ca2+ is used to characterize the Ca2+ binding sites of this protein. Eu3+-bound S100 beta shows two distinct Eu3+ binding environments from both the excitation spectrum and Eu3+ excited state lifetimes. Eu3+ bound to the classical EF hand site II has a Kd of 660 +/- 20 nM, whereas the dissociation constant for the pseudo-EF hand site I is significantly weaker. Lifetimes in H2O and D2O lead to the finding that there are four water molecules coordinated to the Eu3+ in the weakly binding site I and two water molecules to the tightly binding site II. Site II in S100 beta expectedly is very similar to high-affinity Ln3+ binding domains I and II in calmodulin. Eu3+ luminescence experiments with Zn2+-loaded S100 beta show that the lifetime for Eu3+ in site I in Zn2+-loaded S100 beta is significantly different than that in the absence of Zn2+. Tyrosine-17-sensitized Tb3+ luminescence experiments indicate that the Tb3+ occupying the proximal weaker binding site I is sensitized, whereas Tb3+ in site II is not. The distance between sites I and II (15.0 +/- 0.4 A) in S100 beta was determined from Forster-type energy transfer in D2O solutions containing bound Eu3+ donor and Nd3+ acceptor ions. For Zn2+-S100 beta, the intersite distance is reduced to 13 +/- 0.3 A. Location of histidine-15 close to pseudo-EF site I suggests that Zn2+ binding likely changes the conformation of this site, causing a reduction of the intersite distance by approximately 2 A.
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Affiliation(s)
- D Chaudhuri
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore 21201, USA
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