DNA interaction with biologically active metal ions. Cooperativity of metal ion binding at compacting of DNA.

The interaction of Cu2+, Mn2+ and Ca2+ ions with DNA in aqueous and water-ethanol solutions at different metal ion concentrations was studied by IR-spectroscopy. At sufficiently high DNA concentrations, DNA interaction with Cu2+, Ca2+ and Mn2+ ions results in compacting of DNA in the aqueous solutions. This process shows a very high cooperativity. In the presence of alcohol, DNA condensation takes place at much lower concentrations of metal ions used than in pure aqueous solution. Binding constants and cooperativity of the metal ion binding rise, and the non-monotonous dependencies of the binding degree, r, on the concentration of free metal ions, Cf, become pronounced. Binding isotherms take the S-like form similar to van der Waals isotherms for phase transitions of the liquid-vapour type. Cu2+ and Ca2+ ion binding to DNA in water-ethanol solutions also results in compacting of DNA macromolecule. The process is characterised by a high positive cooperativity and has a phase transition character.

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New multidentate ligands. XXI. Synthesis, proton, and metal ion binding affinities of N,N′,N″-tris[2-(N-hydroxycarbamoyl)ethyl]-1,3,5-benzenetricarboxamide (BAMTPH)

Canadian Journal of Chemistry ◽

10.1139/v83-470 ◽

1983 ◽

Vol 61 (12) ◽

pp. 2740-2744 ◽

Cited By ~ 15

Author(s):

Isao Yoshida ◽

Ichiro Murase ◽

Ramunas J. Motekaitis ◽

Arthur E. Martell

Keyword(s):

Metal Ions ◽

Metal Ion ◽

Binding Constants ◽

Cation Binding ◽

Ion Binding ◽

Binding Affinities ◽

Metal Ion Binding ◽

Trivalent Metal ◽

Equilibrium Data ◽

Trivalent Metal Ions

Synthesis of a new tris-bidentate multidentate ligand, N,N′,N″-tris[2-(N-hydroxycarbamoyl)ethyl]-1,3,5-benzenetricarboxamide (BAMTPH), designed for the binding of trivalent metal ions such as Fe(III), Ga(III), and Al(III), is described. Its cation binding affinities for hydrogen ion and for Fe(III), Co(II), Ni(II), Cu(II), Zn(II), Ga(III), and Al(III) ions are described, and the equilibrium data are compared with those of analogous ligands. The binding constants of trivalent metal ions with the ligand do not show a chelate effect relative to the binding to individual bidentate hydroxamic acids.

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Selective metal ion binding at the calcium-binding sites of the sea urchin extraembryonic coat protein hyalin

Biochemistry and Cell Biology ◽

10.1139/o89-119 ◽

1989 ◽

Vol 67 (11-12) ◽

pp. 808-812 ◽

Cited By ~ 4

Author(s):

John J. Robinson

Keyword(s):

Coat Protein ◽

Metal Ions ◽

Sea Urchin ◽

Binding Sites ◽

Metal Ion ◽

Divalent Cations ◽

Biologically Active ◽

Ion Binding ◽

Metal Ion Binding ◽

Competition Assays

The interaction of metal ions with the sea urchin extraembryonic coat protein hyalin was investigated. Hyalin, immobilized on nitrocellulose membrane, bound Ca2+ and this interaction was disrupted by ruthenium red and selective metal ions. The divalent cations Cd2+ and Mn2+, when present at a concentration of 30 μM, displaced hyalin-bound Ca2+. In competition assays, 1 mM Cd2+ or 3 mM Mn2+ were effective competitors with Ca2+ for binding to hyalin. Cobalt, at a concentration of 30 μM, was unable to displace protein-bound Ca2+, but was effective in competition assays at a concentration of at least 10 mM. Magnesium and the monovalent cation Cs+ were unable to disrupt Ca2+–hyalin interaction. Interestingly, Cd2+, Mn2+, and Co2+ mimicked the biological effects of Ca2+ on the hyalin self-association reaction. These results clearly demonstrate that the Ca2+-binding sites on hyalin can selectively accommodate other divalent cations in a biologically active configuration.Key words: calcium, metal ion, binding, hyalin.

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The influence of metal-ion binding on the structure and surface composition of Sonic Hedgehog: a combined classical and hybrid QM/MM MD study

Physical Chemistry Chemical Physics ◽

10.1039/c6cp03960j ◽

2016 ◽

Vol 18 (32) ◽

pp. 22254-22265 ◽

Cited By ~ 7

Author(s):

Manuel Hitzenberger ◽

Thomas S. Hofer

Keyword(s):

Metal Ions ◽

Sonic Hedgehog ◽

Binding Sites ◽

Metal Ion ◽

Surface Composition ◽

Quantum Mechanical ◽

Ion Binding ◽

Metal Ion Binding ◽

Structural Impact

The interaction of metal ions with Shh binding-sites and their structural impact are assessed via classical and quantum mechanical simulations.

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Functional characterization of the dimerization domain of the ferric uptake regulator (Fur) of Pseudomonas aeruginosa

Biochemical Journal ◽

10.1042/bj20061168 ◽

2006 ◽

Vol 400 (3) ◽

pp. 385-392 ◽

Cited By ~ 4

Author(s):

Erdeni Bai ◽

Federico I. Rosell ◽

Bao Lige ◽

Marcia R. Mauk ◽

Barbara Lelj-Garolla ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Metal Ions ◽

Binding Site ◽

Metal Ion ◽

Association Constants ◽

Ion Binding ◽

Ferric Uptake Regulator ◽

Metal Ion Binding ◽

Dimerization Domain ◽

High Affinity

The functional properties of the recombinant C-terminal dimerization domain of the Pseudomonas aeruginosa Fur (ferric uptake regulator) protein expressed in and purified from Escherichia coli have been evaluated. Sedimentation velocity measurements demonstrate that this domain is dimeric, and the UV CD spectrum is consistent with a secondary structure similar to that observed for the corresponding region of the crystallographically characterized wild-type protein. The thermal stability of the domain as determined by CD spectroscopy decreases significantly as pH is increased and increases significantly as metal ions are added. Potentiometric titrations (pH 6.5) establish that the domain possesses a high-affinity and a low-affinity binding site for metal ions. The high-affinity (sensory) binding site demonstrates association constants (KA) of 10(±7)×106, 5.7(±3)×106, 2.0(±2)×106 and 2.0(±3)×104 M−1 for Ni2+, Zn2+, Co2+ and Mn2+ respectively, while the low-affinity (structural) site exhibits association constants of 1.3(±2)×106, 3.2(±2)×104, 1.76(±1)×105 and 1.5(±2)×103 M−1 respectively for the same metal ions (pH 6.5, 300 mM NaCl, 25 °C). The stability of metal ion binding to the sensory site follows the Irving–Williams order, while metal ion binding to the partial sensory site present in the domain does not. Fluorescence experiments indicate that the quenching resulting from binding of Co2+ is reversed by subsequent titration with Zn2+. We conclude that the domain is a reasonable model for many properties of the full-length protein and is amenable to some analyses that the limited solubility of the full-length protein prevents.

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Bromine substituted aminonaphthoquinones: synthesis, characterization, DFT and metal ion binding studies

RSC Advances ◽

10.1039/c6ra20970j ◽

2016 ◽

Vol 6 (91) ◽

pp. 88010-88029 ◽

Cited By ~ 6

Author(s):

Gunjan Agarwal ◽

Dipali N. Lande ◽

Debamitra Chakrovarty ◽

Shridhar P. Gejji ◽

Prajakta Gosavi-Mirkute ◽

...

Keyword(s):

Metal Ions ◽

Metal Ion ◽

Ion Binding ◽

Metal Ion Binding ◽

Binding Studies

Bromine substituted aminonaphthoquinones – chemosensors for metal ions.

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Tb3+ luminescence studies of Escherichia coli glutamine synthetase provides metal ion binding constants.

Journal of Inorganic Biochemistry ◽

10.1016/0162-0134(93)85206-n ◽

1993 ◽

Vol 51 (1-2) ◽

pp. 170

Author(s):

Luis P. Reynaldo ◽

Toru Maruyama ◽

William DeW. Horrocks ◽

Joseph.J. Villafranca

Keyword(s):

Escherichia Coli ◽

Glutamine Synthetase ◽

Metal Ion ◽

Binding Constants ◽

Ion Binding ◽

Metal Ion Binding

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Synthesis, photophysics, electrochemistry and metal ion-binding studies of rhenium(i) complexes with crown ether pendants: selective and specific binding properties for various metal ions

New Journal of Chemistry ◽

10.1039/b415951a ◽

2005 ◽

Vol 29 (1) ◽

pp. 165 ◽

Cited By ~ 12

Author(s):

Keith Man-Chung Wong ◽

Wei-Ping Li ◽

Kung-Kai Cheung ◽

Vivian Wing-Wah Yam

Keyword(s):

Crown Ether ◽

Metal Ions ◽

Metal Ion ◽

Specific Binding ◽

Ion Binding ◽

Metal Ion Binding ◽

Binding Studies ◽

Binding Properties

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Computational approaches for de novo design and redesign of metal-binding sites on proteins

Bioscience Reports ◽

10.1042/bsr20160179 ◽

2017 ◽

Vol 37 (2) ◽

Cited By ~ 12

Author(s):

Gunseli Bayram Akcapinar ◽

Osman Ugur Sezerman

Keyword(s):

Metal Ions ◽

Metal Binding ◽

Binding Sites ◽

Metal Ion ◽

De Novo ◽

De Novo Design ◽

Ion Binding ◽

Chemical Transformations ◽

Metal Ion Binding ◽

Metal Binding Sites

Metal ions play pivotal roles in protein structure, function and stability. The functional and structural diversity of proteins in nature expanded with the incorporation of metal ions or clusters in proteins. Approximately one-third of these proteins in the databases contain metal ions. Many biological and chemical processes in nature involve metal ion-binding proteins, aka metalloproteins. Many cellular reactions that underpin life require metalloproteins. Most of the remarkable, complex chemical transformations are catalysed by metalloenzymes. Realization of the importance of metal-binding sites in a variety of cellular events led to the advancement of various computational methods for their prediction and characterization. Furthermore, as structural and functional knowledgebase about metalloproteins is expanding with advances in computational and experimental fields, the focus of the research is now shifting towards de novo design and redesign of metalloproteins to extend nature’s own diversity beyond its limits. In this review, we will focus on the computational toolbox for prediction of metal ion-binding sites, de novo metalloprotein design and redesign. We will also give examples of tailor-made artificial metalloproteins designed with the computational toolbox.

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