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

Rabbit anti-(bovine prothrombin fragment 1) antibodies were fractionated by using fragment-1 affinity chromatography in the absence of metal ions, and showed an absolute requirement for the presence of metal ions in their interactions with bovine fragment 1 or prothrombin. These antibodies were employed to evaluate both the rate constants for a protein conformation change and the equilibrium metal-ion binding to isolated bovine fragment 1 and intact prothrombin. The close similarity of the rates obtained for the conformation change in fragment 1 and those observed in prothrombin indicated that the same process is involved in both proteins and that the non-fragment-1 region of the prothrombin has essentially no effect on this process in the fragment-1 region. Equilibrium metal-ion-binding studies indicate that the details of the metal-ion-binding process in fragment 1 and prothrombin are essentially the same. We conclude that the metal-ion-binding behaviour of the fragment-1 domain of intact prothrombin is identical with that of isolated fragment 1.

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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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New Fluorescence PET Systems Based on N2S2Pyridine-Anthracene-Containing Macrocyclic Ligands. Spectrophotometric, Spectrofluorimetric, and Metal Ion Binding Studies

Inorganic Chemistry ◽

10.1021/ic050926d ◽

2005 ◽

Vol 44 (22) ◽

pp. 8105-8115 ◽

Cited By ~ 51

Author(s):

Abel Tamayo ◽

Carlos Lodeiro ◽

Lluis Escriche ◽

Jaume Casabó ◽

Berta Covelo ◽

...

Keyword(s):

Metal Ion ◽

Macrocyclic Ligands ◽

Ion Binding ◽

Metal Ion Binding ◽

Binding Studies

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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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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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