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Journal articles on the topic 'Metal ion binding'

Author: Grafiati

Published: 4 June 2021

Last updated: 15 February 2022

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1

MOHAN, ABHILASH, SHARMILA ANISHETTY, and PENNATHUR GAUTAM. "GLOBAL METAL-ION BINDING PROTEIN FINGERPRINT: A METHOD TO IDENTIFY MOTIF-LESS METAL-ION BINDING PROTEINS." Journal of Bioinformatics and Computational Biology 08, no. 04 (August 2010): 717–26. http://dx.doi.org/10.1142/s0219720010004884.

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Metal-ion binding proteins play a vital role in biological processes. Identifying putative metal-ion binding proteins is through knowledge-based methods. These involve the identification of specific motifs that characterize a specific class of metal-ion binding protein. Metal-ion binding motifs have been identified for the common metal ions. A robust global fingerprint that is useful in identifying a metal-ion binding protein from a non-metal-ion binding protein has not been devised. Such a method will help in identifying novel metal-ion binding proteins and proteins that do not possess a canonical metal-ion binding motif. We have used a set of physico-chemical parameters of metal-ion binding proteins encoded by the genes CzcA, CzcB and CzcD as a training set to supervised classifiers and have been able to identify several other metal ion binding proteins leading us to believe that metal-ion binding proteins have a global fingerprint, which cannot be pinned down to a single feature of the protein sequence.

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2

DiTusa, Charles A., Keith A. McCall, Trine Christensen, Mrinal Mahapatro, Carol A. Fierke, and Eric J. Toone. "Thermodynamics of Metal Ion Binding. 2. Metal Ion Binding by Carbonic Anhydrase Variants†." Biochemistry 40, no. 18 (May 2001): 5345–51. http://dx.doi.org/10.1021/bi0017327.

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3

Elinder, Fredrik, and Peter Århem. "Metal ion effects on ion channel gating." Quarterly Reviews of Biophysics 36, no. 4 (November 2003): 373–427. http://dx.doi.org/10.1017/s0033583504003932.

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1. Introduction 3742. Metals in biology 3783. The targets: structure and function of ion channels 3804. General effects of metal ions on channels 3824.1 Three types of general effect 3824.2 The main regulators 3835. Effects on gating: mechanisms and models 3845.1 Screening surface charges (Mechanism A) 3875.1.1 The classical approach 3875.1.1.1 Applying the Grahame equation 3885.1.2 A one-site approach 3915.2 Binding and electrostatically modifying the voltage sensor (Mechanism B) 3915.2.1 The classical model 3915.2.1.1 The classical model as state diagram – introducing basic channel kinetics 3925.2.2 A one-site approach 3955.2.2.1 Explaining state-dependent binding – a simple electrostatic mechanism 3955.2.2.2 The relation between models assuming binding to smeared and to discrete charges 3965.2.2.3 The special case of Zn2+ – no binding in the open state 3965.2.2.4 Opposing effects of Cd2+ on hyperpolarization-activated channels 3985.3 Binding and interacting non-electrostatically with the voltage sensor (Mechanism C) 3985.3.1 Combining mechanical slowing of opening and closing with electrostatic modification of voltage sensor 4005.4 Binding to the pore – a special case of one-site binding models (Mechanism D) 4005.4.1 Voltage-dependent pore-block – adding extra gating 4015.4.2 Coupling pore block to gating 4025.4.2.1 The basic model again 4025.4.2.2 A special case – Ca2+ as necessary cofactor for closing 4035.4.2.3 Expanding the basic model – Ca2+ affecting a voltage-independent step 4045.5 Summing up 4056. Quantifying the action: comparing the metal ions 4076.1 Steady-state parameters are equally shifted 4076.2 Different metal ions cause different shifts 4086.3 Different metal ions slow gating differently 4106.4 Block of ion channels 4127. Locating the sites of action 4127.1 Fixed surface charges involved in screening 4137.2 Binding sites 4137.2.1 Group 2 ions 4147.2.2 Group 12 ions 4148. Conclusions and perspectives 4159. Appendix 41610. Acknowledgements 41811. References 418Metal ions affect ion channels either by blocking the current or by modifying the gating. In the present review we analyse the effects on the gating of voltage-gated channels. We show that the effects can be understood in terms of three main mechanisms. Mechanism A assumes screening of fixed surface charges. Mechanism B assumes binding to fixed charges and an associated electrostatic modification of the voltage sensor. Mechanism C assumes binding and an associated non-electrostatic modification of the gating. To quantify the non-electrostatic effect we introduced a slowing factor, A. A fourth mechanism (D) is binding to the pore with a consequent pore block, and could be a special case of Mechanisms B or C. A further classification considers whether the metal ion affects a single site or multiple sites. Analysing the properties of these mechanisms and the vast number of studies of metal ion effects on different voltage-gated ion channels we conclude that group 2 ions mainly affect channels by classical screening (a version of Mechanism A). The transition metals and the Zn group ions mainly bind to the channel and electrostatically modify the gating (Mechanism B), causing larger shifts of the steady-state parameters than the group 2 ions, but also different shifts of activation and deactivation curves. The lanthanides mainly bind to the channel and both electrostatically and non-electrostatically modify the gating (Mechanisms B and C). With the exception of the ether-à-go-go-like channels, most channel types show remarkably similar ion-specific sensitivities.

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4

Findlay, Wendy A., Gary S. Shaw, and Brian D. Sykes. "Metal ion binding by proteins." Current Opinion in Structural Biology 2, no. 1 (February 1992): 57–60. http://dx.doi.org/10.1016/0959-440x(92)90177-9.

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5

Findlay, Wendy A., Gary S. Shaw, and Brian D. Sykes. "Metal-ion binding by proteins." Current Biology 2, no. 3 (March 1992): 126. http://dx.doi.org/10.1016/0960-9822(92)90246-7.

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6

DiTusa, Charles A., Trine Christensen, Keith A. McCall, Carol A. Fierke, and Eric J. Toone. "Thermodynamics of Metal Ion Binding. 1. Metal Ion Binding by Wild-Type Carbonic Anhydrase†." Biochemistry 40, no. 18 (May 2001): 5338–44. http://dx.doi.org/10.1021/bi001731e.

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7

Ramyakrishna, K., and M. Sudhamani. "The metal binding potential of a dairy isolate." Journal of Water Reuse and Desalination 7, no. 4 (October 28, 2016): 429–41. http://dx.doi.org/10.2166/wrd.2016.127.

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Excess iron in water resources can lead to health hazards and problems. The ability of lactic acid bacteria to bind iron has not yet been widely studied. In the present study, sorption of iron ions from aqueous solutions onto lactic acid bacterium was determined. Elemental analyses were carried out by inductively coupled plasma optical emission spectrometry. The kinetics of Fe(III) biosorption was investigated at different initial concentrations of metal ion. The highest uptake capacity was found to be 16 mg of Fe(III) per gram of adsorbent with a contact time of 24 hr and at initial metal ion concentration of 34 mg/L. The uptake capacity of Fe(III) ion varied from 83.2 to 46.7% across the range of initial metal ion concentrations. The equilibrium data were evaluated by Langmuir and Freundlich isotherms, and were found to fit better with the latter (R2 = 0.9999). The surface morphology of the biomass and percentage of metal was characterized by using a scanning electron microscope equipped with energy dispersive X-ray spectroscopy. The functional groups on the cell wall surface of biomass involved in biosorption of heavy metals were studied by Fourier transform infrared spectroscopy spectrum.

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8

Baldwin, Graham S., Michael F. Bailey, B. Philip Shehan, Ioulia Sims, and Raymond S. Norton. "Tyrosine modification enhances metal-ion binding." Biochemical Journal 416, no. 1 (October 28, 2008): 77–84. http://dx.doi.org/10.1042/bj20081059.

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Tyrosine sulfation is a common modification of many proteins, and the ability to phosphorylate tyrosine residues is an intrinsic property of many growth-factor receptors. In the present study, we have utilized the peptide hormone CCK8 (cholecystokinin), which occurs naturally in both sulfated and unsulfated forms, as a model to investigate the effect of tyrosine modification on metal-ion binding. The changes in absorbance and fluorescence emission on Fe3+ binding indicated that tyrosine sulfation or phosphorylation increased the stoichiometry from 1 to 2, without greatly affecting the affinity (0.6–2.8 μM at pH 6.5). Measurement of Ca2+ binding with a Ca2+-selective electrode revealed that phosphorylated CCK8 bound two Ca2+ ions. CCK8 and sulfated CCK8 each bound only one Ca2+ ion with lower affinity. Binding of Ca2+, Zn2+ or Bi3+ to phosphorylated CCK8 did not cause any change in absorbance, but substantially increased the change in absorbance on subsequent addition of Fe3+. The results of the present study demonstrate that tyrosine modification may increase the affinity of metal-ion binding to peptides, and imply that metal ions may directly regulate many signalling pathways.

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9

Mauk, A. Grant, Marcia R. Mauk, Bao Lige, and Geoffrey R. Moore. "Metal ion binding to human hemopexin." Journal of Inorganic Biochemistry 96, no. 1 (July 2003): 49. http://dx.doi.org/10.1016/s0162-0134(03)80488-9.

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10

Mauk, Marcia R., Federico I. Rosell, Barbara Lelj-Garolla, Geoffrey R. Moore, and A. Grant Mauk. "Metal Ion Binding to Human Hemopexin†." Biochemistry 44, no. 6 (February 2005): 1864–71. http://dx.doi.org/10.1021/bi0481747.

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11

Fattorusso, R., G. Morelli, A. Lombardi, F. Nastri, O. Maglio, G. D'Auria, C. Pedone, and V. Pavone. "Design of metal ion binding peptides." Biopolymers 37, no. 6 (1995): 401–10. http://dx.doi.org/10.1002/bip.360370607.

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12

Lindoy, L. F. "Tailoring macrocycles for metal ion binding." Pure and Applied Chemistry 69, no. 10 (January 1, 1997): 2179–86. http://dx.doi.org/10.1351/pac199769102179.

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13

Stutzenberger, F. J. "Metal ion binding byPithomyces chartarum conidia." Journal of Industrial Microbiology 14, no. 3-4 (March 1995): 233–39. http://dx.doi.org/10.1007/bf01569933.

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14

Ponthieu, M., F. Juillot, T. Hiemstra, W. H. van Riemsdijk, and M. F. Benedetti. "Metal ion binding to iron oxides." Geochimica et Cosmochimica Acta 70, no. 11 (June 2006): 2679–98. http://dx.doi.org/10.1016/j.gca.2006.02.021.

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15

JOHANSSON, C., and T. DRAKENBERG. "ChemInform Abstract: Metal-Ion NMR Studies of Ion Binding." ChemInform 22, no. 7 (August 23, 2010): no. http://dx.doi.org/10.1002/chin.199107373.

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16

Sun, Li-Zhen, and Shi-Jie Chen. "Predicting RNA-Metal Ion Binding with Ion Dehydration Effects." Biophysical Journal 116, no. 2 (January 2019): 184–95. http://dx.doi.org/10.1016/j.bpj.2018.12.006.

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17

Urresti, Saioa, Alan Cartmell, Feng Liu, Paul H. Walton, and Gideon J. Davies. "Structural studies of the unusual metal-ion site of the GH124 endoglucanase from Ruminiclostridium thermocellum." Acta Crystallographica Section F Structural Biology Communications 74, no. 8 (August 1, 2018): 496–505. http://dx.doi.org/10.1107/s2053230x18006842.

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The recent discovery of `lytic' polysaccharide monooxygenases, copper-dependent enzymes for biomass degradation, has provided new impetus for the analysis of unusual metal-ion sites in carbohydrate-active enzymes. In this context, the CAZY family GH124 endoglucanase from Ruminiclostridium thermocellum contains an unusual metal-ion site, which was originally modelled as a Ca2+ site but features aspartic acid, asparagine and two histidine imidazoles as coordinating residues, which are more consistent with a transition-metal binding environment. It was sought to analyse whether the GH124 metal-ion site might accommodate other metals. It is demonstrated through thermal unfolding experiments that this metal-ion site can accommodate a range of transition metals (Fe2+, Cu2+, Mn2+ and Ni2+), whilst the three-dimensional structure and mass spectrometry show that one of the histidines is partially covalently modified and is present as a 2-oxohistidine residue; a feature that is rarely observed but that is believed to be involved in an `off-switch' to transition-metal binding. Atomic resolution (<1.1 Å) complexes define the metal-ion site and also reveal the binding of an unusual fructosylated oligosaccharide, which was presumably present as a contaminant in the cellohexaose used for crystallization. Although it has not been possible to detect a biological role for the unusual metal-ion site, this work highlights the need to study some of the many metal-ion sites in carbohydrate-active enzymes that have long been overlooked or previously mis-assigned.

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18

Bischof, Helmut, Sandra Burgstaller, Markus Waldeck-Weiermair, Thomas Rauter, Maximilian Schinagl, Jeta Ramadani-Muja, Wolfgang F. Graier, and Roland Malli. "Live-Cell Imaging of Physiologically Relevant Metal Ions Using Genetically Encoded FRET-Based Probes." Cells 8, no. 5 (May 22, 2019): 492. http://dx.doi.org/10.3390/cells8050492.

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Essential biochemical reactions and processes within living organisms are coupled to subcellular fluctuations of metal ions. Disturbances in cellular metal ion homeostasis are frequently associated with pathological alterations, including neurotoxicity causing neurodegeneration, as well as metabolic disorders or cancer. Considering these important aspects of the cellular metal ion homeostasis in health and disease, measurements of subcellular ion signals are of broad scientific interest. The investigation of the cellular ion homeostasis using classical biochemical methods is quite difficult, often even not feasible or requires large cell numbers. Here, we report of genetically encoded fluorescent probes that enable the visualization of metal ion dynamics within individual living cells and their organelles with high temporal and spatial resolution. Generally, these probes consist of specific ion binding domains fused to fluorescent protein(s), altering their fluorescent properties upon ion binding. This review focuses on the functionality and potential of these genetically encoded fluorescent tools which enable monitoring (sub)cellular concentrations of alkali metals such as K+, alkaline earth metals including Mg2+ and Ca2+, and transition metals including Cu+/Cu2+ and Zn2+. Moreover, we discuss possible approaches for the development and application of novel metal ion biosensors for Fe2+/Fe3+, Mn2+ and Na+.

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19

Kobuke, Yoshiaki, Katsuaki Kokubo, and Megumu Munakata. "Cooperative Metal Ion Binding by Metal-Organized Crown Ether." Journal of the American Chemical Society 117, no. 51 (December 1995): 12751–58. http://dx.doi.org/10.1021/ja00156a012.

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20

Zheng, Heping, David R. Cooper, Przemyslaw J. Porebski, Ivan G. Shabalin, Katarzyna B. Handing, and Wladek Minor. "CheckMyMetal: a macromolecular metal-binding validation tool." Acta Crystallographica Section D Structural Biology 73, no. 3 (February 22, 2017): 223–33. http://dx.doi.org/10.1107/s2059798317001061.

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Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites.CheckMyMetal(CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. TheCMMserver can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites. Guidelines for metal-site modeling and validation in macromolecules are illustrated by several practical examples grouped by the type of metal. These examples showCMMusers (and crystallographers in general) problems they may encounter during the modeling of a specific metal ion.

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21

Antsuki, T., D. Sano, and T. Omura. "Functional metal-binding proteins by metal-stimulated bacteria for the development of an innovative metal removal technology." Water Science and Technology 47, no. 10 (May 1, 2003): 109–15. http://dx.doi.org/10.2166/wst.2003.0551.

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Heavy metal pollution has become an environmental problem throughout the world because heavy metals can be accumulated into the food chain and bring about serious problems, not only for ecosystems but also for human health. In this study, functional metal-binding proteins (FMBPs) were isolated from a metal-stimulated activated sludge culture with the aim of applying them to an innovative metal removal technology. Activated sludge bacteria was cultured in growth media including copper ion, and the stimulation of protein production by copper ion led to the 14% increase in a quantity of extracted crude proteins per 1 g of bacterial cell pellet (wet). In order to isolate FMBPs, extracted crude proteins were applied to the immobilized metal affinity column in which each of copper, nickel and zinc was used as a ligand. Several FMBPs were succesfully isolated from copper-stimulated bacteria. One of FMBPs (molecular weight of about 40 kDa) exhibited an ability to adsorb all three metals. The multi metal-binding property of this FMBP could be applied to an innovative metal removal technology. Furthermore, isolated FMBPs that could capture only one kind of heavy metal would also be attractive as a metal adsorbent in recovering a specific metal as a resource from wastewater, including several heavy metals.

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22

Perera, Rukshan, Syed Ashraf, and Anja Mueller. "The binding of metal ions to molecularly-imprinted polymers." Water Science and Technology 75, no. 7 (January 23, 2017): 1643–50. http://dx.doi.org/10.2166/wst.2017.036.

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Imprinting polymerization is a flexible method to make resins specific for different compounds. Imprinting polymerization involves the polymerization of the resin in the presence of a template, here cadmium ions or arsenate. The template is then removed by washing, leaving specific binding sites in the resin. In water treatment, the removal of toxic metal ions is difficult due to the limited affinity of these ions to ion exchange resins. Imprinting polymerization of ion-exchange resins is used to develop resins with high capacity and some selectivity for cadmium ions or arsenate for water treatment that still function as general ion-exchange resins. A minimum binding capacity of 325 meq/g was achieved for cadmium ions. Competition experiments elucidate the type of bonds present in the imprinting complex. The capacity and bond types for the cadmium ions and arsenate were contrasted. In the case of cadmium, metal-ligand bonds provide significant specificity of binding, although significant binding also occurs to non-specific surface sites. Arsenate ions are larger than cadmium ions and can only bind via ionic and hydrogen bonds, which are weaker than metal-ligand bonds. This results in lower specificity for arsenate. Additionally, diffusion into the resin is a limiting factor due to the larger size of the arsenate ion. These data elucidate the bonds formed between metal ions and the imprinting sites as well as other parameters that increase the capacity for heavy metals and arsenate.

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23

DeRose, Victoria J. "Metal ion binding to catalytic RNA molecules." Current Opinion in Structural Biology 13, no. 3 (June 2003): 317–24. http://dx.doi.org/10.1016/s0959-440x(03)00077-0.

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24

Martin, R. Bruce. "Nucleoside sites for transition metal ion binding." Accounts of Chemical Research 18, no. 2 (February 1985): 32–38. http://dx.doi.org/10.1021/ar00110a001.

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25

Casey, Kasha, Jessica Thomas, Zamyra Lambert, and Douglas L. Strout. "Metal-Ion Binding to High-Energy N12C4." Journal of Physical Chemistry A 113, no. 27 (July 9, 2009): 7888–91. http://dx.doi.org/10.1021/jp900561z.

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26

Mihan, Francesco Yafteh, Silvia Bartocci, Michele Bruschini, Paolo De Bernardin, Gianpiero Forte, Ilaria Giannicchi, and Antonella Dalla Cort. "Ion-Pair Recognition by Metal - Salophen and Metal - Salen Complexes." Australian Journal of Chemistry 65, no. 12 (2012): 1638. http://dx.doi.org/10.1071/ch12353.

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The development of heteroditopic receptor systems that can simultaneously bind cationic and anionic species is one of the most challenging research topics in supramolecular chemistry, attracting the attention of a large number of research groups worldwide. Such an interest is due especially to the fact that the overall receptor–ion-pair complex is neutral and this can be advantageous in many situations, such as salt solubilization and extraction, and membrane-transport applications. Receptors designed for ion-pair complexation are molecules comprising well-known anion-binding motifs and familiar cation-binding sites. An important family of compounds that can use metal Lewis-acidic centres for anion recognition and that can be easily derivatized to introduce an additional binding site for the cation is metal–salophen and metal–salen complexes. This short review shows that the high versatility of salen and salophen ligands and of the corresponding metal complexes allows, through simple modifications of the basic skeleton, the obtention of highly efficient receptors for ion pairs.

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27

Emanuelli, Tatiana. "A enzima delta-aminolevullnato desidratase." Ciência e Natura 19, no. 19 (December 10, 1997): 201. http://dx.doi.org/10.5902/2179460x34316.

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Delta-aminolevulinic acid dehydratase (ALA-D, EC 4.2.1.24) is a sulfhydryl-containing enzyme that asymetrically condenses two molecules of delta-aminolevulinic acid (ALA), catalyzing the formation of porphobilinogen, the monopyrrole precursor of ali biological tetrapyrroles (corrins, porphyrins, chlorins). The two ALA molecules have been termed Aside ALA and P-side ALA in reference to their fates as the acetyl and propionyl halves of the product. P-side ALA binds first and forms a Schiffbase with an active-site Iysine. ALA-D is a cytosolic enzyme present in mammals, plants, fungi and bacteria. Bovine enzyme has a molecular mass of 280 000 Da and is composed of eight similar subunits of 35 000 Da, but only four of the subunits form a Schiff-base with the substrate (half-site reactivity). ALA-D from all organisms requires a bivalent metal ion for activity. Although the considerable sequence conservation among ALA-D enzyme from various organisms, there are species-dependent differences in metal ion requirements for enzyme activity. ALA-D is a zinc-dependent enzyme in animals, yeast and some bacteria. Mammalian enzyme bounds 8 zinc ions/octamer. Bovine ALA-D contains two types of Zn2+ binding sites (A and B), each at a stoichiometry of four per octamer. A-metal-ion-binding sites, with a single cysteine residue among its ligands, bind the four zinc ions essential for ALA-D activity (catalytic zinc), which plays a role in A-side ALA binding, in inter-ALA bond formation and in product binding. B-metal-ion-binding sites, with four cysteine residues among its ligands, bind zinc ions refered to as structural, which seems to be involved in the protection of sulfhydryl groups from oxidation. An A-zinc-ion-binding site has been proposed to be present at a number of four per octamer on the enzyme from plants, but has not been demonstrated yet. ALA-D from plants contains two types of magnesium binding sites: four B-metal-ion-binding sites (bind magnesium essential for ALA-D activity) and eight C-metal-ion-binding sites (bind magnesium that activates the enzyme but is not essential for activity). The cysteine-rich sequence of mammalian ALA-D that presumably corresponds to the B-metalion-binding site is replaced by an aspartate-rich sequence in plant ALA-D, probably accounting for the difference on metal-ion requirement (Mg2+ instead of Zn2+ on B-metal-ion-binding site from plant ALA-D). E. coli ALA-D binds eight Zn2+ (presumably four at A-metal-ion-binding site and four at B-metalion-binding site) and eight Mg2+ (presumably at C-metal-ion-binding site) per octamer. Due to its sulfhydrilic nature ALA-D is inhibited by heavy metals such as lead and mercury, serving as a measure of metal intoxication. In addition the inhibition of this enzyme has been implicated with pathological changes observed in some types of porphyrias, hepatorenal tyrosinemia and after lead or mercury exposure. ALA-D inhibition may impair haeme biosynthesis and leads to ALA accumulation, which besides being a potent agonist of y-aminobutiric acid autoreceptors may act as a prooxidant.

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Merlot, Angelica M., Danuta S. Kalinowski, Zaklina Kovacevic, Patric J. Jansson, Sumit Sahni, Michael L. H. Huang, Darius J. R. Lane, Hiu Lok, and Des R. Richardson. "Exploiting Cancer Metal Metabolism using Anti-Cancer Metal- Binding Agents." Current Medicinal Chemistry 26, no. 2 (March 14, 2019): 302–22. http://dx.doi.org/10.2174/0929867324666170705120809.

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Metals are vital cellular elements necessary for multiple indispensable biological processes of living organisms, including energy transduction and cell proliferation. Interestingly, alterations in metal levels and also changes in the expression of proteins involved in metal metabolism have been demonstrated in a variety of cancers. Considering this and the important role of metals for cell growth, the development of drugs that sequester metals has become an attractive target for the development of novel anti-cancer agents. Interest in this field has surged with the design and development of new generations of chelators of the thiosemicarbazone class. These ligands have shown potent anticancer and anti-metastatic activity in vitro and in vivo. Due to their efficacy and safe toxicological assessment, some of these agents have recently entered multi-center clinical trials as therapeutics for advanced and resistant tumors. This review highlights the role and changes in homeostasis of metals in cancer and emphasizes the pre-clinical development and clinical assessment of metal ion-binding agents, namely, thiosemicarbazones, as antitumor agents.

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29

Sano, D., K. Myojo, and T. Omura. "Heavy metal-binding proteins from metal-stimulated bacteria as a novel adsorbent for metal removal technology." Water Science and Technology 53, no. 6 (March 1, 2006): 221–26. http://dx.doi.org/10.2166/wst.2006.200.

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Water pollution with toxic heavy metals is of growing concern because heavy metals could bring about serious problems for not only ecosystems in the water environment but also human health. Some metal removal technologies have been in practical use, but much energy and troublesome treatments for chemical wastes are required to operate these conventional technologies. In this study, heavy metal-binding proteins (HMBPs) were obtained from metal-stimulated activated sludge culture with affinity chromatography using copper ion as a ligand. Two-dimensional electrophoresis revealed that a number of proteins in activated sludge culture were recovered as HMBPs for copper ion. N-termini of five HMBPs were determined, and two of them were found to be newly discovered proteins for which no amino acid sequences in protein databases were retrieved at more than 80% identities. Metal-coordinating amino acids occupied 38% of residues in one of the N-terminal sequences of the newly discovered HMBPs. Since these HMBPs were expected to be stable under conditions of water and wastewater treatments, it would be possible to utilize HMBPs as novel adsorbents for heavy metal removal if mass volume of HMBPs can be obtained with protein cloning techniques.

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30

Tipping, E., S. Lofts, and J. E. Sonke. "Humic Ion-Binding Model VII: a revised parameterisation of cation-binding by humic substances." Environmental Chemistry 8, no. 3 (2011): 225. http://dx.doi.org/10.1071/en11016.

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Environmental contextNatural organic matter exerts a powerful control on chemical conditions in waters and soils, affecting pH and influencing the biological availability, transport and retention of metals. To quantify the reactions, we collated a wealth of laboratory data covering 40 metals and acid–base reactions, and used them to parameterise the latest in a series of Humic Ion-Binding Models. Model VII is now available to interpret field data, and contribute to the prediction of environmental chemistry. AbstractHumic Ion-Binding Model VII aims to predict the competitive reactions of protons and metals with natural organic matter in soils and waters, based on laboratory results with isolated humic and fulvic acids (HA and FA). Model VII is simpler in its postulated multidentate metal binding sites than the previous Model VI. Three model parameters were eliminated by using a formal relationship between monodentate binding to strong- and weak-acid oxygen-containing ligands, and removing factors that provide ranges of ligand binding strengths. Thus Model VII uses a single adjustable parameter, the equilibrium constant for monodentate binding to strong-acid (carboxylate) groups (KMA), for each metallic cation. Proton-binding parameters, and mean values of log KMA were derived by fitting 248 published datasets (28 for protons, 220 for cationic metals). Default values of log KMA for FA were obtained by combining the fitted values for FA, results for HA, and the relationship for different metals between log KMA and equilibrium constants for simple oxygen-containing ligands. The equivalent approach was used for HA. The parameterised model improves on Model VI by incorporating more metals (40), providing better descriptions of metal binding at higher pH, and through more internally consistent parameter values.

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31

Aramini, James M., and Hans J. Vogel. "Quadrupolar metal ion NMR studies of metalloproteins." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 210–22. http://dx.doi.org/10.1139/o98-037.

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We present a summary of the quadrupolar metal ion NMR studies of metalloproteins conducted in our laboratory in recent years. The approaches we employ can be subdivided into two categories: (i) the use of low-frequency metal nuclei to probe metal ion binding sites in small proteins, exemplified by 43Ca NMR studies of alpha-lactalbumins and calcium-binding lysozymes, and (ii) the novel detection of the central transition of half-integer quadrupolar nuclei of moderate frequency bound to large metalloproteins, typified by 27Al, 45Sc, 69,71Ga, and 51V NMR studies of the transferrins. We highlight the chemical information regarding the nature of metal ion binding sites that can be obtained from this technique and emphasize the salient parameters that an investigator must consider to successfully apply quadrupolar NMR to the study of biological macromolecules.Key words: quadrupolar NMR, metalloproteins, transferrins.

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32

Drake, Lawrence R., Carl E. Hensman, Shan Lin, Gary D. Rayson, and Paul J. Jackson. "Characterization of Metal Ion Binding Sites on Datura Innoxia by Using Lanthanide Ion Probe Spectroscopy." Applied Spectroscopy 51, no. 10 (October 1997): 1476–83. http://dx.doi.org/10.1366/0003702971939253.

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The excitation spectra associated with the 7F0↦5D0 transition of Eu+3 has been used to examine the binding sites on cell wall fragments of Datura innoxia. Both native and esterified cell wall fragments were each examined at pH 5 and pH 2 to determine the contributions to metal ion sorption from both the carboxylate and sulfonate functional groups. The excitation spectra have been de-convoluted into the individual groups responsible for metal ion uptake. At least four unique binding sites can be described as being responsible for metal ion uptake. The higher affinity sites involve carboxylates in the binding of Eu+3 in a tridentate (3:1 ligand-to-metal ratio) configuration.

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33

Alcantara, Rochelle T., Dahlia C. Apodaca, and Manuel R. De Guzman. "The Effect of the Presence of Cu2+ and Fe3+ Metal Ions on the Sorption of Mercuric Ion (Hg2+) by Sargassum cristaefolium." ASEAN Journal of Chemical Engineering 7, no. 1 & 2 (June 1, 2007): 147. http://dx.doi.org/10.22146/ajche.50138.

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Previous studies have indicated that the seaweed Sargassum cristaefolium is capable of binding with metal ions. The metal sorbing property of S. cristaefolium suggests its possible participation in the removal of Hg2+ ions in water and wastewater. However, the potential application of S. cristaefolium for environmental remediation and precious metals recovery depends on the understanding of the other factors that could play a role in the sorption process. This study illustrates the effects of some variables, such as pH and temperature, and that of the presence of other metal ions on the sorption process involving the binding of Hg2+ ions to S. cristaefolium. The uptake of Hg2+ ion was found to be affected by the initial concentration and the charge densities of the competing ions. Cu2+ ion shows a stronger affinity to Sargassum in the three metal systems of Hg2+, Cu2+, and Fe3+ ions. On the other hand, results show that Fe3+ ion is not a potential competitor for binding sites considering that no Fe3+ ion uptake by Sargassum has been observed.

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34

Kim, Young Joo, Kenji Kono, and Toru Takagishi. "Effects of Added Metal Ions on the Interaction of Wool Keratin Derivatives and an Azo Dye Carrying Hydroxyl Groups." Textile Research Journal 62, no. 5 (May 1992): 275–78. http://dx.doi.org/10.1177/004051759206200504.

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The extent of binding of chrome violet, which is a monoazo dye involving two hydroxyl groups in the o and o' positions to an azo group, by wool keratin derivatives such as S-carboxymethylated, S-cyanoethylated, and regenerated keratin derivatives is markedly enhanced in the presence of Co2+ ion. The amount of binding in the presence of 1 times 10-4 mol/I of Co2+ ion increases by a factor of 12∼20 compared to that in the absence of the metal ion. Cu2+, Ni2+, and Zn2+ ions do not perceptibly influence the binding affinity of the dye. Al3+ ion, in contrast, suppresses the binding. To further investigate the action of added metal ions, we prepared a cobalt-complex dye and compared its binding property for the polymers with that of chrome violet in the presence of metal ions. We also measured the binding of the metal ions by the polymers. Co2+ ion did not exhibit remarkable binding affinity toward the polymers. Some possible mechanisms for enhancing chrome violet binding by the addition of Co2+ ion are described.

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35

Van Bastelaere, P. B. M., M. Callens, W. A. E. Vangrysperre, and H. L. M. Kersters-Hilderson. "Binding characteristics of Mn2+, Co2+ and Mg2+ ions with several d-xylose isomerases." Biochemical Journal 286, no. 3 (September 15, 1992): 729–35. http://dx.doi.org/10.1042/bj2860729.

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D-Xylose isomerases are metal-ion (Mn2+, Co2+, Mg2+)-requiring tetrameric enzymes. Both the stoichiometry and the binding constants have been determined by titrating the metal-ion-free enzymes from five organisms (Actinomycetaceae and more divergent bacteria) with the respective metal ions using the enzyme activity as indicator of active complex-formation. The following characteristics have been observed for each specific isomerase: (i) two essential metal ion sites (one structural and one catalytic) exist per subunit; (ii) the metal ion binding at one site does not affect the binding at the other site; (iii) of the four possible configurations E, aE, Eb and aEb, only the double-occupied enzyme is active; (iv) the metal ion activation is a time-dependent process; (v) the dissociation constants for both the structural and catalytic sites may be identical or may differ by one or higher orders of magnitude; (vi) metal ion binding is stronger in the order Mn2+ greater than Co2+ much greater than Mg2+; (vii) pronounced increases in Km values concomitant with decreasing equivalents of metal ion added are only observed in the presence of Mg2+ ions.

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36

McMILLEN, Lyle, Ifor R. BEACHAM, and Dennis M. BURNS. "Cobalt activation of Escherichia coli 5'-nucleotidase is due to zinc ion displacement at only one of two metal-ion-binding sites." Biochemical Journal 372, no. 2 (June 1, 2003): 625–30. http://dx.doi.org/10.1042/bj20021800.

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Escherichia coli 5′-nucleotidase activity is stimulated 30- to 50-fold in vitro by the addition of Co2+. Seven residues from conserved sequence motifs implicated in the catalytic and metal-ion-binding sites of E. coli 5′-nucleotidase (Asp41, His43, Asp84, His117, Glu118, His217 and His252) were selected for modification using site-directed mutagenesis of the cloned ushA gene. On the basis of comparative studies between the resultant mutant proteins and the wild-type enzyme, a model is proposed for E. coli 5′-nucleotidase in which a Co2+ ion may displace the Zn2+ ion at only one of two metal-ion-binding sites; the other metal-ion-binding site retains the Zn2+ ion already present. The studies reported herein suggest that displacement occurs at the metal-ion-binding site consisting of residues Asp84, Asn116, His217 and His252, leading to the observed increase in 5′-nucleotidase activity.

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37

CLUGSTON, Susan L., Rieko YAJIMA, and John F. HONEK. "Investigation of metal binding and activation of Escherichia coli glyoxalase I: kinetic, thermodynamic and mutagenesis studies." Biochemical Journal 377, no. 2 (January 15, 2004): 309–16. http://dx.doi.org/10.1042/bj20030271.

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GlxI (glyoxalase I) isomerizes the hemithioacetal formed between glutathione and methylglyoxal. Unlike other GlxI enzymes, Escherichia coli GlxI exhibits no activity with Zn2+ but maximal activation with Ni2+. To elucidate further the metal site in E. coli GlxI, several approaches were undertaken. Kinetic studies indicate that the catalytic metal ion affects the kcat without significantly affecting the Km for the substrate. Inductively coupled plasma analysis and isothermal titration calorimetry confirmed one metal ion bound to the enzyme, including Zn2+, which produces an inactive enzyme. Isothermal titration calorimetry was utilized to determine the relative binding affinity of GlxI for various bivalent metals. Each metal ion examined bound very tightly to GlxI with an association constant (Ka)>107 M−1, with the exception of Mn2+ (Ka of the order of 106 M−1). One of the ligands to the catalytic metal, His5, was altered to glutamine, a side chain found in the Zn2+-active Homo sapiens GlxI. The affinity of the mutant protein for all bivalent metals was drastically decreased. However, low levels of activity were now observed for Zn2+-bound GlxI. Although this residue has a marked effect on metal binding and activation, it is not the sole factor determining the differential metal activation between the human and E. coli GlxI enzymes.

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38

Frøystein, Nils Åge, Jeffery T. Davis, Brian R. Reid, Einar Sletten, Björn O. Roos, Pekka Pietikäinen, Harri Setälä, Marit Trætteberg, Ahmad Nasiri, and Tadashi Tsuda. "Sequence-Selective Metal Ion Binding to DNA Oligonucleotides." Acta Chemica Scandinavica 47 (1993): 649–57. http://dx.doi.org/10.3891/acta.chem.scand.47-0649.

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39

Steinkopf, Signe, Einar Sletten, Annette Lauridsen, Carl E. Olsen, Søren Brøgger Christensen, A. J. Kondow, Kirpal S. Bisht, Virinder S. Parmar, and George W. Francis. "Sequence-Selective Metal Ion Binding to DNA Hexamers." Acta Chemica Scandinavica 48 (1994): 388–92. http://dx.doi.org/10.3891/acta.chem.scand.48-0388.

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40

Steinkopf, Signe, Achilleas Garoufis, Willy Nerdal, Einar Sletten, Dorota Pawlak, Barbara Pniewska, Danuta Rasała, and Ryszard Gawinecki. "Sequence-Selective Metal Ion Binding to DNA Oligomers." Acta Chemica Scandinavica 49 (1995): 495–502. http://dx.doi.org/10.3891/acta.chem.scand.49-0495.

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41

Lippert, Bernhard. "Multiplicity of metal ion binding patterns to nucleobases." Coordination Chemistry Reviews 200-202 (May 2000): 487–516. http://dx.doi.org/10.1016/s0010-8545(00)00260-5.

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42

Ariki, M., and J. K. Lanyi. "Characterization of metal ion-binding sites in bacteriorhodopsin." Journal of Biological Chemistry 261, no. 18 (June 1986): 8167–74. http://dx.doi.org/10.1016/s0021-9258(19)83892-9.

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43

Fernández-Botello, Alfonso, Raquel B. Gómez-Coca, Antonı́n Holý, Virtudes Moreno, and Helmut Sigel. "Metal-ion binding properties of O-phosphonatomethylcholine (PMCh−)." Inorganica Chimica Acta 331, no. 1 (March 2002): 109–16. http://dx.doi.org/10.1016/s0020-1693(01)00763-0.

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44

Serda, R. E., and M. T. Henzl. "Metal ion-binding properties of avian thymic hormone." Journal of Biological Chemistry 266, no. 11 (April 1991): 7291–99. http://dx.doi.org/10.1016/s0021-9258(20)89643-4.

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45

Rotureau, Elise, and Herman P. van Leeuwen. "Kinetics of Metal Ion Binding by Polysaccharide Colloids." Journal of Physical Chemistry A 112, no. 31 (August 2008): 7177–84. http://dx.doi.org/10.1021/jp800472g.

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46

Bastian, Matthias, and Helmut Sigel. "On the metal ion binding properties of orotidine." Inorganica Chimica Acta 178, no. 2 (December 1990): 249–59. http://dx.doi.org/10.1016/s0020-1693(00)86789-4.

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47

BLANDL, Tamas, Jaroslav ZAJICEK, Mary PROROK, and J. Francis CASTELLINO. "Metal-ion-binding properties of synthetic conantokin-G." Biochemical Journal 328, no. 3 (December 15, 1997): 777–83. http://dx.doi.org/10.1042/bj3280777.

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The secondary structure of the synthetic 17-residue peptide, conantokin-G (con-G), a γ-carboxyglutamate-containing marine cone snail neuroactive protein, is altered from a random conformation to one containing a very high level (> 70%) of α-helix on binding of multivalent cations. The proportion of α-helix formed correlated well with the size of the cation and ranged from a low of approx. 7% with large cations, such as Ba2+, to more than 70% with smaller cations, such as Mn2+, Mg2+ and Zn2+. The valency of the multivalent cation was not as important, since tervalent lanthanides (Eu3+, Gd3+ and Tb3+) of ionic radius 106-109 pm induced similar levels (50-60%) of helix to those induced by Ca2+ and Cd2+ (ionic radii 109 and 114 pm respectively). Although the correlation was not as tight, smaller cations of the same valency allowed the helical transition to occur at lower concentrations than the larger cations. The spectroscopic and spectrometric properties of some of these cations permitted a more detailed analysis of the molecular nature of the cation-con-G binding. EPR-based titrations with Mn2+ provided a binding isotherm that was deconvoluted to a single class of 2-3 Mn2+ sites of average Kd 3.9 μM. This number of sites was similar to that for Ca2+ [Prorok, Warder, Blandl and Castellino (1996) Biochemistry 35, 16528-16534], but a much lower Kd was displayed with Mn2+. Determinations by 1H NMR of the longitudinal relaxation rates of the water protons in Mn2+/con-G solutions at different magnetic field strengths corresponding to the proton Langmuir frequencies of 24, 300 and 500 MHz permitted calculation of the hydration number of Mn2+ in the complex, which was found to be 1.0. This indicates that five of the six co-ordination sites of Mn2+ are occupied by peptide atoms, probably oxygens. Titrations of the changes in Tb3+ fluorescence as a result of its binding to con-G gave an EC50 of 58 μM, a value nearly identical with that obtained by titration of the change in helicity of the peptide as a function of Tb3+ concentration. This shows that the macroscopic binding of Tb3+ to con-G is directly responsible for the alteration in secondary structure of the peptide. Finally, Cd2+ was found to be an extremely suitable cation for an NMR-based investigation of the amino acid residues of apo-con-G that are perturbed by cation binding. In a limited example of the results of this study, it was discovered that originally equivalent CH2Δ protons of Arg13 became distinctly magnetically non-equivalent in the Cd2+-bound helical form of con-G. This indicates that Arg13 is situated in the helix in such a way that the mobility of its side chain is highly restricted. In conclusion, the data show that a variety of multivalent cations with measurable spectroscopic and spectrometric properties interact similarly with con-G and generate extensive α-helical conformation in this peptide.

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48

Naik, Radhika, Guiqing Wen, Dharmaprakash MS, Sabrina Hureau, Akira Uedono, Xungai Wang, Xin Liu, Peter G. Cookson, and Suzanne V. Smith. "Metal ion binding properties of novel wool powders." Journal of Applied Polymer Science 115, no. 3 (February 5, 2010): 1642–50. http://dx.doi.org/10.1002/app.31206.

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49

LINDOY, L. F. "ChemInform Abstract: Tailoring Macrocycles for Metal-Ion Binding." ChemInform 29, no. 8 (June 23, 2010): no. http://dx.doi.org/10.1002/chin.199808295.

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50

BASTIAN, M., and H. SIGEL. "ChemInform Abstract: Metal Ion Binding Properties of Orotidine." ChemInform 22, no. 21 (August 23, 2010): no. http://dx.doi.org/10.1002/chin.199121058.

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