scholarly journals Applications of Coordination Chemistry in Biological Systems

2014 ◽  
Vol 70 (a1) ◽  
pp. C1376-C1376
Author(s):  
Gurpreet Kaur ◽  
Richard Hartshorn
Keyword(s):  
Metal Ions ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Hydrolytic Enzymes ◽  
Dinuclear Complexes ◽  
X Ray Diffraction ◽  
X Ray ◽  
Nitrophenyl Phosphate ◽  
Hydrolysis Of

A novel 2,2′:6′,2″-terpyridine–picolylamine-based bridging ligand has been synthesized and fully characterized using a variety of analysis techniques including single crystal X-ray diffraction. As shown in figure (a), the ligand has both tridentate and bidentate metal binding sites available to coordinate with various metal ions. By varying the size of anions both dinuclear complexes and supramolecular assemblies have been produced. Addition of metal salts containing small anions like halides result in formation of Cu2L and Zn2L dinuclear complexes, figure (b), where one metal ion binds at each of the binding sites of the ligand. The metal ions in these complexes mimic active site of the hydrolytic enzymes and promote phosphatediester hydrolysis of model DNA/RNA compounds. Nearly ten times increase in the rate of hydrolysis of bis(p-nitrophenyl)phosphate (BNPP) is observed in comparison to the parent terpyridine and picolylamine complexes under physiological conditions. Larger anions like PF6-, ClO4-, SO42- , NO3- result in formation of Zn4L4 type squares via. head-to-head and tail-to-tail, HH-TT, (H=tridentate site, T=bidentate site) coordination of the ligand. The octahedrally bound Zn(II) ion between two tridentate sites can be replaced with Fe(II) to prepare Fe2Zn2L4 squares. A flat molecule of terephthalic acid was also deliberately encapsulated in the middle of the Fe2Zn2L4 square as shown in figure (c). The head-to-tail, HT, coordination of the ligand in case of Ni(II) results in formation of decanickel wheels, like [Ni10L10Cl4(H2O)6](Cl)15Br·~140H2O shown in figure (d). Due to the large structure of the molecule X-ray crystallographic studies rather have been quite challenging.

scholarly journals Location-specific quantification of protein-bound metal ions by X-ray anomalous dispersion: Q-XAD

2019 ◽  
Vol 75 (8) ◽  
pp. 764-771 ◽  
Author(s):  
Julia J. Griese ◽  
Martin Högbom
Keyword(s):  
Metal Ions ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Anomalous Dispersion ◽  
Data Sets ◽  
Data Set ◽  
X Ray ◽  
Anomalous Data ◽  
Specific Metal

Here, a method is described which exploits X-ray anomalous dispersion (XAD) to quantify mixtures of metal ions in the binding sites of proteins and can be applied to metalloprotein crystals of average quality. This method has successfully been used to study site-specific metal binding in a protein from the R2-like ligand-binding oxidase family which assembles a heterodinuclear Mn/Fe cofactor. While previously only the relative contents of Fe and Mn in each metal-binding site have been assessed, here it is shown that the method can be extended to quantify the relative occupancies of at least three different transition metals, enabling complex competition experiments. The number of different metal ions that can be quantified is only limited by the number of high-quality anomalous data sets that can be obtained from one crystal, as one data set has to be collected for each transition-metal ion that is present (or is suspected to be present) in the protein, ideally at the absorption edge of each metal. A detailed description of the method, Q-XAD, is provided.

scholarly journals Crystallographic and X-ray absorption spectroscopic characterization of Helicobacter pylori UreE bound to Ni2+ and Zn2+ reveals a role for the disordered C-terminal arm in metal trafficking

2012 ◽  
Vol 441 (3) ◽  
pp. 1017-1035 ◽  
Author(s):  
Katarzyna Banaszak ◽  
Vlad Martin-Diaconescu ◽  
Matteo Bellucci ◽  
Barbara Zambelli ◽  
Wojciech Rypniewski ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Metal Ions ◽  
Metal Binding ◽  
Metal Ion ◽  
Mutual Influence ◽  
Accurate Information ◽  
Metal Ion Binding ◽  
X Ray ◽  
X Ray Absorption

The survival and growth of the pathogen Helicobacter pylori in the gastric acidic environment is ensured by the activity of urease, an enzyme containing two essential Ni2+ ions in the active site. The metallo-chaperone UreE facilitates in vivo Ni2+ insertion into the apoenzyme. Crystals of apo-HpUreE (H. pylori UreE) and its Ni2+- and Zn2+-bound forms were obtained from protein solutions in the absence and presence of the metal ions. The crystal structures of the homodimeric protein, determined at 2.00 Å (apo), 1.59 Å (Ni2+) and 2.52 Å (Zn2+) resolution, show the conserved proximal and solvent-exposed His102 residues from two adjacent monomers invariably involved in metal binding. The C-terminal regions of the apoprotein are disordered in the crystal, but acquire significant ordering in the presence of the metal ions due to the binding of His152. The analysis of X-ray absorption spectral data obtained using solutions of Ni2+- and Zn2+-bound HpUreE provided accurate information of the metal-ion environment in the absence of solid-state effects. These results reveal the role of the histidine residues at the protein C-terminus in metal-ion binding, and the mutual influence of protein framework and metal-ion stereo-electronic properties in establishing co-ordination number and geometry leading to metal selectivity.

scholarly journals Investigation of the nature of the two metal-binding sites in 5-aminolaevulinic acid dehydratase from Escherichia coli

1994 ◽  
Vol 300 (2) ◽  
pp. 373-381 ◽  
Author(s):  
P Spencer ◽  
P M Jordan
Keyword(s):  
Escherichia Coli ◽  
Metal Ions ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Protein Fluorescence ◽  
Metal Binding Sites ◽  
Aminolaevulinic Acid ◽  
Acid Dehydratase ◽  
Aminolaevulinic Acid Dehydratase

Two distinct metal-binding sites, termed alpha and beta, have been characterized in 5-aminolaevulinic acid dehydratase from Escherichia coli. The alpha-site binds a Zn2+ ion that is essential for catalytic activity. This site can also utilize other metal ions able to function as a Lewis acid in the reaction mechanism, such as Mg2+ or Co2+. The beta-site is exclusively a transition-metal-ion-binding site thought to be involved in protein conformation, although a metal bound at this site only appears to be essential for activity if Mg2+ is to be bound at the alpha-site. The alpha- and beta-sites may be distinguished from one another by their different abilities to bind divalent-metal ions at different pH values. The occupancy of the beta-site with Zn2+ results in a decrease of protein fluorescence at pH 6. Occupancy of the alpha- and beta-sites with Co2+ results in u.v.-visible spectral changes. Spectroscopic studies with Co2+ have tentatively identified three cysteine residues at the beta-site and one at the alpha-site. Reaction with N-ethyl[14C]maleimide preferentially labels cysteine-130 at the alpha-site when Co2+ occupies the beta-site.

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

2017 ◽  
Vol 37 (2) ◽  
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.

scholarly journals Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5221
Author(s):  
Salvatore La Gatta ◽  
Linda Leone ◽  
Ornella Maglio ◽  
Maria De Fenza ◽  
Flavia Nastri ◽  
...  
Keyword(s):  
Metal Ions ◽  
Binding Site ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Structural Determinants ◽  
Binding Properties ◽  
Tetrahedral Geometry ◽  
Design Synthesis ◽  
Metal Binding Sites

Understanding the structural determinants for metal ion coordination in metalloproteins is a fundamental issue for designing metal binding sites with predetermined geometry and activity. In order to achieve this, we report in this paper the design, synthesis and metal binding properties of METP3, a homodimer made up of a small peptide, which self assembles in the presence of tetrahedrally coordinating metal ions. METP3 was obtained through a redesign approach, starting from the previously developed METP molecule. The undecapeptide sequence of METP, which dimerizes to house a Cys4 tetrahedral binding site, was redesigned in order to accommodate a Cys2His2 site. The binding properties of METP3 were determined toward different metal ions. Successful assembly of METP3 with Co(II), Zn(II) and Cd(II), in the expected 2:1 stoichiometry and tetrahedral geometry was proven by UV-visible spectroscopy. CD measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. Finally, NMR data of the Zn(II)-METP3 complex, together with a retrostructural analysis of the Cys-X-X-His motif in metalloproteins, allowed us to define the model structure. All the results establish the suitability of the short METP sequence for accommodating tetrahedral metal binding sites, regardless of the first coordination ligands.

Structure of oxalate-substituted diferric mare lactoferrin at 2.7 Å resolution

1999 ◽  
Vol 55 (11) ◽  
pp. 1792-1798 ◽  
Author(s):  
Ashwani K. Sharma ◽  
Tej P. Singh
Keyword(s):  
Crystal Structure ◽  
Metal Ions ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Anion Binding ◽  
Human Lactoferrin ◽  
Final Model ◽  
High Affinity ◽  
Oxalate Anion

Lactoferrin binds two Fe3+ and two CO^{2-}_{3} ions with high affinity. It can also bind other metal ions and anions. In order to determine the perturbations in the environments of the binding sites in the N and C lobes and elsewhere in the protein, the crystal structure of oxalate-substituted diferric mare lactoferrin has been determined at 2.7 Å resolution. The final model has a crystallographic R factor of 21.3% for all data in the resolution range 17.0–2.7 Å. The substitution of an oxalate anion does not perturb the overall structure of the protein, but produces several significant changes at the metal-binding and anion-binding sites. The binding of the oxalate anion is symmetrical in both the N and C lobes, unlike in diferric dioxalate human lactoferrin, where the oxalate anion binds the metal ion symmetrically in the C lobe and asymmetrically in the N lobe.

Identification of acid-insoluble filter-plugging compounds and optimal acid-washing procedures for tubular backpulse pressure filters

TAPPI Journal ◽  
2011 ◽  
Vol 10 (1) ◽  
pp. 17-23
Author(s):  
KEVIN TAYLOR ◽  
RICH ADDERLY ◽  
GAVIN BAXTER
Keyword(s):  
Calcium Sulfate ◽  
Membrane Filter ◽  
Sulfamic Acid ◽  
Xrd Analysis ◽  
Metal Sulfides ◽  
X Ray Diffraction ◽  
X Ray ◽  
Gypsum Formation ◽  
Acid Washing ◽  
Hydrolysis Of

Over time, performance of tubular backpulse pressure filters in kraft mills deteriorates, even with regular acid washing. Unscheduled filter replacement due to filter plugging results in significant costs and may result in mill downtime. We identified acid-insoluble filter-plugging materials by scanning electron microscope/energy-dispersion X-ray spectroscopy (SEM/EDS) and X-ray diffraction (XRD) analysis in both polypropylene and Gore-Tex™ membrane filter socks. The major filter-plugging components were calcium sulfate (gypsum), calcium phosphate (hydroxylapatite), aluminosilicate clays, metal sulfides, and carbon. We carried out detailed sample analysis of both the standard acid-washing procedure and a modified procedure. Filter plugging by gypsum and metal sulfides appeared to occur because of the acid-washing procedure. Gypsum formation on the filter resulted from significant hydrolysis of sulfamic acid solution at temperatures greater than 130°F. Modification of the acid-washing procedure greatly reduced the amount of gypsum and addition of a surfactant to the acid reduced wash time and mobilized some of the carbon from the filter. With surfactant, acid washing was 95% complete after 40 min.

Investigation of the products of carbothermal reduction of yttrium oxide by the hydrolysis method

1984 ◽  
Vol 49 (4) ◽  
pp. 936-943 ◽  
Author(s):  
Bohumil Hájek ◽  
Pavel Karen ◽  
Vlastimil Brožek
Keyword(s):  
Yttrium Oxide ◽  
Carbothermal Reduction ◽  
Stoichiometric Ratio ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrolysis Method ◽  
Sample Decomposition ◽  
Products Of Reaction ◽  
Hydrolysis Of ◽  
Lower Carbon

For the investigation of the products of reaction of yttrium oxide with carbon mixed in various proportions, the chemical and X-ray diffraction methods of analysis were combined with the gas chromatographic analysis of the mixture of hydrocarbons and hydrogen formed on the sample decomposition with water. The carboreduction of Y2O3 was examined at relatively low temperatures, convenient for obtaining the reaction intermediates in higher yields. At 1 600 °C and pressures of 10-3 Pa the reduction of a mixture of Y2O3 with carbon in a stoichiometric ratio of 1 : 7 yields YC2 in equilibrium with 20% of Y2OC phase. At lower carbon contents (down to the Y2O3 : C ratio of 1 : 2) tha fraction of the Y2OC phase increases up to approximately 30%. In addition to Y2O3, the reaction mixture contains also Y2C, Y2OC and a phase giving propyne on hydrolysis. The presence of traces of C3 hydrocarbons and small amounts of methane in the product of hydrolysis of the carbide sample prepared by the carbothermal reduction of the oxide can be explained in terms of the occurrence of the Y15C19 phase, probably substituted in part by oxygen, and of the Y2OC phase. The results are compared with those obtained previously for the Sc2O3 + C system.

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