The relative influence of metal ion binding sites in the I-like domain and the interface with the hybrid domain on rolling and firm adhesion by integrin alpha4beta7.

Science.gov (United States)

Chen, JianFeng; Takagi, Junichi; Xie, Can; Xiao, Tsan; Luo, Bing-Hao; Springer, Timothy A

2004-12-31

We examined the effect of conformational change at the beta(7) I-like/hybrid domain interface on regulating the transition between rolling and firm adhesion by integrin alpha(4)beta(7). An N-glycosylation site was introduced into the I-like/hybrid domain interface to act as a wedge and to stabilize the open conformation of this interface and hence the open conformation of the alpha(4) beta(7) headpiece. Wild-type alpha(4)beta(7) mediates rolling adhesion in Ca(2+) and Ca(2+)/Mg(2+) but firm adhesion in Mg(2+) and Mn(2+). Stabilizing the open headpiece resulted in firm adhesion in all divalent cations. The interaction between metal binding sites in the I-like domain and the interface with the hybrid domain was examined in double mutants. Changes at these two sites can either counterbalance one another or be additive, emphasizing mutuality and the importance of multiple interfaces in integrin regulation. A double mutant with counterbalancing deactivating ligand-induced metal ion binding site (LIMBS) and activating wedge mutations could still be activated by Mn(2+), confirming the importance of the adjacent to metal ion-dependent adhesion site (ADMIDAS) in integrin activation by Mn(2+). Overall, the results demonstrate the importance of headpiece allostery in the conversion of rolling to firm adhesion.

Mutational analysis of divalent metal ion binding in the active site of class II α-mannosidase from sulfolobus solfataricus

DEFF Research Database (Denmark)

Hansen, Dennis K.; Webb, Helen; Nielsen, Jonas Willum

2015-01-01

Mutational analysis of Sulfolobus solfataricus class II α-mannosidase was focused on side chains that interact with the hydroxyls of the-1 mannosyl of the substrate (Asp-534) or form ligands to the active site divalent metal ion (His-228 and His-533) judged from crystal structures of homologous e......, although less dramatically with some activating metal ions. No major differences in the pH dependence between wild-type and mutant enzymes were found in the presence of different metal ions. The pH optimum was 5, but enzyme instability was observed at pH...

Novel bis-(−)-nor-meptazinol derivatives act as dual binding site AChE inhibitors with metal-complexing property

Energy Technology Data Exchange (ETDEWEB)

Zheng, Wei [Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 200032 (China); NPFPC Key Laboratory of Contraceptives and Devices, Shanghai Institute of Planned Parenthood Research, 2140 Xietu Road, Shanghai 200032 (China); Li, Juan [Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiaotong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Qiu, Zhuibai [Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 200032 (China); Xia, Zheng [Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiaotong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Li, Wei [Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 200032 (China); Yu, Lining; Chen, Hailin; Chen, Jianxing [NPFPC Key Laboratory of Contraceptives and Devices, Shanghai Institute of Planned Parenthood Research, 2140 Xietu Road, Shanghai 200032 (China); Chen, Yan; Hu, Zhuqin; Zhou, Wei; Shao, Biyun; Cui, Yongyao [Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiaotong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China); Xie, Qiong, E-mail: xiejoanxq@gmail.com [Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 200032 (China); Chen, Hongzhuan, E-mail: yaoli@shsmu.edu.cn [Department of Pharmacology, Institute of Medical Sciences, Shanghai Jiaotong University School of Medicine, 280 South Chongqing Road, Shanghai 200025 (China)

2012-10-01

The strategy of dual binding site acetylcholinesterase (AChE) inhibition along with metal chelation may represent a promising direction for multi-targeted interventions in the pathophysiological processes of Alzheimer's disease (AD). In the present study, two derivatives (ZLA and ZLB) of a potent dual binding site AChE inhibitor bis-(−)-nor-meptazinol (bis-MEP) were designed and synthesized by introducing metal chelating pharmacophores into the middle chain of bis-MEP. They could inhibit human AChE activity with IC{sub 50} values of 9.63 μM (for ZLA) and 8.64 μM (for ZLB), and prevent AChE-induced amyloid-β (Aβ) aggregation with IC{sub 50} values of 49.1 μM (for ZLA) and 55.3 μM (for ZLB). In parallel, molecular docking analysis showed that they are capable of interacting with both the catalytic and peripheral anionic sites of AChE. Furthermore, they exhibited abilities to complex metal ions such as Cu(II) and Zn(II), and inhibit Aβ aggregation triggered by these metals. Collectively, these results suggest that ZLA and ZLB may act as dual binding site AChEIs with metal-chelating potency, and may be potential leads of value for further study on disease-modifying treatment of AD. -- Highlights: ► Two novel bis-(−)-nor-meptazinol derivatives are designed and synthesized. ► ZLA and ZLB may act as dual binding site AChEIs with metal-chelating potency. ► They are potential leads for disease-modifying treatment of Alzheimer's disease.

Novel bis-(−)-nor-meptazinol derivatives act as dual binding site AChE inhibitors with metal-complexing property

International Nuclear Information System (INIS)

Zheng, Wei; Li, Juan; Qiu, Zhuibai; Xia, Zheng; Li, Wei; Yu, Lining; Chen, Hailin; Chen, Jianxing; Chen, Yan; Hu, Zhuqin; Zhou, Wei; Shao, Biyun; Cui, Yongyao; Xie, Qiong; Chen, Hongzhuan

2012-01-01

The strategy of dual binding site acetylcholinesterase (AChE) inhibition along with metal chelation may represent a promising direction for multi-targeted interventions in the pathophysiological processes of Alzheimer's disease (AD). In the present study, two derivatives (ZLA and ZLB) of a potent dual binding site AChE inhibitor bis-(−)-nor-meptazinol (bis-MEP) were designed and synthesized by introducing metal chelating pharmacophores into the middle chain of bis-MEP. They could inhibit human AChE activity with IC 50 values of 9.63 μM (for ZLA) and 8.64 μM (for ZLB), and prevent AChE-induced amyloid-β (Aβ) aggregation with IC 50 values of 49.1 μM (for ZLA) and 55.3 μM (for ZLB). In parallel, molecular docking analysis showed that they are capable of interacting with both the catalytic and peripheral anionic sites of AChE. Furthermore, they exhibited abilities to complex metal ions such as Cu(II) and Zn(II), and inhibit Aβ aggregation triggered by these metals. Collectively, these results suggest that ZLA and ZLB may act as dual binding site AChEIs with metal-chelating potency, and may be potential leads of value for further study on disease-modifying treatment of AD. -- Highlights: ► Two novel bis-(−)-nor-meptazinol derivatives are designed and synthesized. ► ZLA and ZLB may act as dual binding site AChEIs with metal-chelating potency. ► They are potential leads for disease-modifying treatment of Alzheimer's disease.

Soil-modified carbon paste electrode: a useful tool in environmental assessment of heavy metal ion binding interactions.

Science.gov (United States)

Svegl, I G; Ogorevc, B

2000-08-01

Carbon paste electrodes (CPEs) modified with different soils in their native form were prepared to create a soil-like solid phase suitable for application in studies of heavy metal ion uptake and binding interactions. The preparation of CPEs modified with five different soils was examined and their heavy metal ion uptake behavior investigated using a model Cu(II) aqueous solution. Metal ions were accumulated under open circuit conditions and were determined after a medium exchange using differential pulse anodic stripping voltammetry, applying preelectrolysis at -0.7 V. The soil-modified CPE accumulation behavior, including the linearity of the current response versus Cu(II) concentration, the influence of the pH on the solution, and the uptake kinetics, was thoroughly investigated. The correlation between the soil-modified CPE uptake capability and the standard soil parameters, such as ion exchange capacity, soil pH, organic matter and clay content, were evaluated for all five examined soils. The influence of selected endogenous cations (K(I), Ca(II), Fe(III)) on the transfer of Cu(II) ions from a solution to the simulated soil solid phase was examined and is discussed. Preliminary examinations of the soil-modified CPE uptake behavior with some exogenous heavy metal ions of strong environmental interest (Pb(II), Hg(II), Cd(II) and Ag(I)) are also presented. This work demonstrates some attractive possibilities for the application of a soil-modified CPE in studying soil-heavy metal ion binding interactions, with a further potential use as a new environmental sensor appropriate for fist on-site testing of polluted soils.

Yeast enolase: mechanism of activation by metal ions.

Science.gov (United States)

Brewer, J M

1981-01-01

Yeast enolase as prepared by current procedures is inherently chemically homogeneous, though deamidation and partial denaturation can produce electrophoretically distinct forms. A true isozyme of the enzyme exists but does not survive the purification procedure. The chemical sequence for both has been established. The enzyme behaves in solution like a compact, nearly spherical molecule of moderate hydration. Strong intramolecular forces maintain the structure of the individual subunits. The enzyme as isolated is dimeric. If dissociated in the presence of magnesium ions and substrate, then the subunits are active, but if the dissociation occurs in the absence of metal ions, they are inactive until they have reassociated and undergone a first order "annealing" process. Magnesium (II) enhances association. The interaction between the subunits is hydrophobic in character. The enzyme can bind up to 2 mol of most metal ions in "conformational" sites which then allows up to 2 mol of substrate or some substrate analogue to bind. This is not sufficient for catalysis, but conformational metal ions do more than just allow substrate binding. A change in the environment of the metal ions occurs on substrate or substrate analogue binding. There is an absolute correlation between the occurrence of a structural change undergone by the 3-amino analogue of phosphoenolpyruvate and whether the metal ions produce any level of enzymatic activity. For catalysis, two more moles of metal ions, called "catalytic", must bind. There is evidence that the enzymatic reaction involves a carbanion mechanism. It is likely that two more moles of metal ion can bind which inhibit the reaction. The requirement for 2 mol of metal ion per subunit which contribute in different ways to catalysis is exhibited by a number of other enzymes.

Ion binding by humic and fulvic acids: A computational procedure based on functional site heterogeneity and the physical chemistry of polyelectrolyte solutions

International Nuclear Information System (INIS)

Marinsky, J.A.; Reddy, M.M.; Ephraim, J.; Mathuthu, A.

1988-04-01

Ion binding equilibria for humic and fulvic acids are examined from the point of view of functional site heterogeneity and the physical chemistry of polyelectrolyte solutions. A detailed explanation of the potentiometric properties of synthetic polyelectrolytes and ion-exchange gels is presented first to provide the basis for a parallel consideration of the potentiometric properties exhibited by humic and fulvic acids. The treatment is then extended to account for functional site heterogeneity. Sample results are presented for analysis of the ion-binding reactions of a standard soil fulvic acid (Armadale Horizons Bh) with this approach to test its capability for anticipation of metal ion removal from solution. The ultimate refined model is shown to be adaptable, after appropriate consideration of the heterogeneity and polyelectrolyte factors, to programming already available for the consideration of ion binding by inorganics in natural waters. (orig.)

Metal ion site engineering indicates a global toggle switch model for seven-transmembrane receptor activation

DEFF Research Database (Denmark)

Elling, Christian E; Frimurer, Thomas M; Gerlach, Lars-Ole

2006-01-01

for monoamine binding in TM-III, was used as the starting point to engineer activating metal ion sites between the extracellular segments of the beta2-adrenergic receptor. Cu(II) and Zn(II) alone and in complex with aromatic chelators acted as potent (EC50 decreased to 0.5 microm) and efficacious agonists...

Human chorionic ganodotropin binding sites in the human endometrium

International Nuclear Information System (INIS)

Bhattacharya, S.; Banerjee, J.; Sen, S.; Manna, P.R.

1993-01-01

The existence of high-affinity and low-capacity specific binding sites for luteinizing hormone/human chorionic gonadotropin (hCG) has been reported in porcine, rabbit and rat uteri. The authors have identified the hCG binding sites in the human endometrium collected from 35-42-year-old ovulatory and anovulatory women. The binding characteristics of hCG to endometrial tissue preparations from ovulatory and anovulatory women showed saturability with high affinity and low capacity. Scatchard plot analysis showed the dissociation constant of specific binding sites in the ovulatory women to be 3.5x10 -10 mol/l and in anovulatory women to be 3.1x10 -10 mol/l. The maximum binding capacity varied considerably between ovulatory and anovulatory endometrium. Among the divalent metal ions tested Zn 2+ effected a remarkable increase in [ 125 I]hCG binding to the endometrium, whereas Mn 2+ showed a marginal increase and other metal ions did not have any effect. Data obtained with human endometrium indicate an influence of the functional state of the ovary on [ 125 I]hCG binding to endometrium. 14 refs., 3 figs

A Mononuclear Non-Heme Manganese(IV)-Oxo Complex Binding Redox-Inactive Metal Ions

Energy Technology Data Exchange (ETDEWEB)

Chen, Junying; Lee, Yong-Min; Davis, Katherine M.; Wu, Xiujuan; Seo, Mi Sook; Cho, Kyung-Bin; Yoon, Heejung; Park, Young Jun; Fukuzumi, Shunichi; Pushkar, Yulia N.; Nam, Wonwoo [Ewha; (Purdue); (Osaka)

2013-05-29

Redox-inactive metal ions play pivotal roles in regulating the reactivities of high-valent metal–oxo species in a variety of enzymatic and chemical reactions. A mononuclear non-heme Mn(IV)–oxo complex bearing a pentadentate N₅ ligand has been synthesized and used in the synthesis of a Mn(IV)–oxo complex binding scandium ions. The Mn(IV)–oxo complexes were characterized with various spectroscopic methods. The reactivities of the Mn(IV)–oxo complex are markedly influenced by binding of Sc³⁺ ions in oxidation reactions, such as a ~2200-fold increase in the rate of oxidation of thioanisole (i.e., oxygen atom transfer) but a ~180-fold decrease in the rate of C–H bond activation of 1,4-cyclohexadiene (i.e., hydrogen atom transfer). The present results provide the first example of a non-heme Mn(IV)–oxo complex binding redox-inactive metal ions that shows a contrasting effect of the redox-inactive metal ions on the reactivities of metal–oxo species in the oxygen atom transfer and hydrogen atom transfer reactions.

The Relative Influence of Metal Ion Binding Sites in the I-like Domain and the Interface with the Hybrid Domain on Rolling and Firm Adhesion by Integrin α4β7*

Science.gov (United States)

Chen, JianFeng; Takagi, Junichi; Xie, Can; Xiao, Tsan; Luo, Bing-Hao; Springer, Timothy A.

2015-01-01

We examined the effect of conformational change at the β7 I-like/hybrid domain interface on regulating the transition between rolling and firm adhesion by integrin α4β7. An N-glycosylation site was introduced into the I-like/hybrid domain interface to act as a wedge and to stabilize the open conformation of this interface and hence the open conformation of the α4β7 headpiece. Wild-type α4β7 mediates rolling adhesion in Ca2+ and Ca2+/Mg2+ but firm adhesion in Mg2+ and Mn2+. Stabilizing the open headpiece resulted in firm adhesion in all divalent cations. The interaction between metal binding sites in the I-like domain and the interface with the hybrid domain was examined in double mutants. Changes at these two sites can either counterbalance one another or be additive, emphasizing mutuality and the importance of multiple interfaces in integrin regulation. A double mutant with counterbalancing deactivating ligand-induced metal ion binding site (LIMBS) and activating wedge mutations could still be activated by Mn2+, confirming the importance of the adjacent to metal ion-dependent adhesion site (ADMIDAS) in integrin activation by Mn2+. Overall, the results demonstrate the importance of headpiece allostery in the conversion of rolling to firm adhesion. PMID:15448154

Thermodynamics of binding interactions between extracellular polymeric substances and heavy metals by isothermal titration microcalorimetry.

Science.gov (United States)

Yan, Peng; Xia, Jia-Shuai; Chen, You-Peng; Liu, Zhi-Ping; Guo, Jin-Song; Shen, Yu; Zhang, Cheng-Cheng; Wang, Jing

2017-05-01

Extracellular polymeric substances (EPS) play a crucial role in heavy metal bio-adsorption using activated sludge, but the interaction mechanism between heavy metals and EPS remains unclear. Isothermal titration calorimetry was employed to illuminate the mechanism in this study. The results indicate that binding between heavy metals and EPS is spontaneous and driven mainly by enthalpy change. Extracellular proteins in EPS are major participants in the binding process. Environmental conditions have significant impact on the adsorption performance. Divalent and trivalent cations severely impeded the binding of heavy metal ions to EPS. Electrostatic interaction mainly attributed to competition between divalent cations and heavy metal ions; trivalent cations directly competed with heavy metal ions for EPS binding sites. Trivalent cations were more competitive than divalent cations for heavy metal ion binding because they formed complexing bonds. This study facilitates a better understanding about the interaction between heavy metals and EPS in wastewater treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of metal-ion replacement on pyrazinamidase activity: A quantum mechanical study.

Science.gov (United States)

Khadem-Maaref, Mahmoud; Mehrnejad, Faramarz; Phirouznia, Arash

2017-05-01

Pyrazinamidase (PZase), a metalloenzyme, is responsible for acidic modification of pyrazinamide (PZA), a drug used in tuberculosis treatment. The metal coordination site of the enzyme is able to coordinate various divalent metal cofactors. Previous experimental studies have demonstrated that metal ions, such as Co 2+ , Mn 2+ , and Zn 2+ , are able to reactivate metal-depleted PZase, while others including Cu 2+ , Fe 2+ , and Mg 2+ , cannot restore activity. In this study, we investigated binding of various metal ions to the metal coordination site (MCS) of the enzyme using quantum mechanical calculations. We calculated the metal-ligand (residue) binding energy and the atomic partial charges in the presence of various ions. The results indicated that the tendency of alkaline earth metals to bind to PZase MCS is very low and not suitable for enzyme structural and catalytic function. In contrast, Co 2+ and Ni 2+ ions have very high binding affinity and are favorable to the structural and functional properties of the enzyme. Furthermore, we observed that the rate at which Ni 2+ , Co 2+ and Fe 2+ ions in PZase MCS polarize the OH bond of coordinated water molecules is much higher than the polarization rate created by other ions. This finding suggests that the coordination of Ni 2+ , Co 2+ , or Fe 2+ to PZase facilitates the deprotonation of coordinated water molecules to generate a nucleophile that catalyzes the enzymatic reaction. Copyright © 2017 Elsevier Inc. All rights reserved.

Engineering of specific uranyl-coordination sites in the calcium-binding motif of Calmodulin

International Nuclear Information System (INIS)

Beccia, M.; Pardoux, R.; Sauge-Merle, S.; Bremond, N.; Lemaire, D.; Berthomieu, C.; Delangle, P.; Guilbaud, P.

2014-01-01

Complete text of publication follows: Characterization of heavy metals interactions with proteins is fundamental for understanding the molecular factors and mechanisms governing ions toxicity and speciation in cells. This line of research will also help in developing new molecules able to selectively and efficiently bind toxic metal ions, which could find application for bio-detection or bioremediation purposes. We have used the regulatory calcium-binding protein Calmodulin (CaM) from A. thaliana as a structural model and, starting from it, we have designed various mutants by site-directed mutagenesis. We have analysed thermodynamics of uranyl ion binding to both sites I and II of CaM N-terminal domain and we have identified structural factors governing this interaction. Selectivity for uranyl ion has been tested by studying reactions of the investigated peptides with Ca 2+ , in the same conditions used for UO 2 2+ . Spectro-fluorimetric titrations and FTIR analysis have shown that the affinity for uranyl increases by phosphorylation of a threonine in site I, especially approaching the physiological pH, where the phospho-threonine side chain is deprotonated. Based on structural models obtained by Molecular Dynamics, we tested the effect of a two residues deletion on site I properties. We obtained an almost two orders of magnitude increase in affinity for uranyl, with a sub-nanomolar dissociation constant for the uranyl complex with the non phosphorylated peptide, and an improved uranyl/calcium selectivity. Allosteric effects depending on Ca 2+ and UO 2 2+ binding have been investigated by comparing thermodynamic parameters obtained for mutants having both sites I and II able to chelate metal ions with those of mutants consisting of just one active site

Conserved epitope on several human vitamin K-dependent proteins: location of the antigenic site and influence of metal ions on antibody binding

International Nuclear Information System (INIS)

Church, W.R.; Messier, T.; Howard, P.R.; Amiral, J.; Meyer, D.; Mann, K.G.

1988-01-01

A murine monoclonal antibody (designated H-11) produced by injecting mice with purified human protein C was found to bind several human vitamin K-dependent proteins. Using a solid-phase competitive radioimmunoassay with antibody immobilized onto microtiter plates, binding of 125 I-labeled protein C to the antibody was inhibited by increasing amounts of protein C, prothrombin, and Factors X and VII over a concentration range of 1 x 10 -8 to 1 x 10 -6 M. Chemical treatment of prothrombin with a variety of agents did not destroy the antigenic site recognized by the antibody as measured by immunoblotting of prothrombin or prothrombin derivative immobilized onto nitrocellulose. Immunoblotting of purified vitamin K-dependent polypeptides with the monoclonal antibody following sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electrophoretic transfer to nitrocellulose indicated that the antigenic site was found on the light chains of protein C and Factor X. The exact location of the antigenic determinant for antibody H-11 was established using synthetic peptides. Comparison of protein sequences of bovine and human vitamin K-dependent proteins suggests that the sequence Phe-Leu-Glu-Glu-Xaa-Arg/Lys is required for antibody binding. Increasing concentrations of Ca 2+ , Mg 2+ , or Mn 2+ partially inhibited binding of 125 I-protein C to the antibody in a solid-phase assay system with half-maximal binding observed at divalent metal ion concentrations of 2, 4, and 0.6 mM, respectively. The antigenic site thus recognized by monoclonal antibody H-11 is located at the amino-terminal region in the highly conserved γ-carboxyglutamic acid-containing domains of several, but not all, vitamin K-dependent proteins

Metal ion-dependent DNAzymes and their applications as biosensors.

Science.gov (United States)

Lan, Tian; Lu, Yi

2012-01-01

Long considered to serve solely as the genetic information carrier, DNA has been shown in 1994 to be able to act as DNA catalysts capable of catalyzing a trans-esterification reaction similar to the action of ribozymes and protein enzymes. Although not yet found in nature, numerous DNAzymes have been isolated through in vitro selection for catalyzing many different types of reactions in the presence of different metal ions and thus become a new class of metalloenzymes. What remains unclear is how DNA can carry out catalysis with simpler building blocks and fewer functional groups than ribozymes and protein enzymes and how DNA can bind metal ions specifically to perform these functions. In the past two decades, many biochemical and biophysical studies have been carried out on DNAzymes, especially RNA-cleaving DNAzymes. Important insights have been gained regarding their metal-dependent activity, global folding, metal binding sites, and catalytic mechanisms for these DNAzymes. Because of their high metal ion selectivity, one of the most important practical applications for DNAzymes is metal ion detection, resulting in highly sensitive and selective fluorescent, colorimetric, and electrochemical sensors for a wide range of metal ions such as Pb(2+), UO2 2 +,[Formula: see text] including paramagnetic metal ions such as Cu(2+). This chapter summarizes recent progresses in in vitro selection of metal ion-selective DNAzymes, their biochemical and biophysical studies and sensing applications.

THE EFFECTS OF COPPER AND ZINC IONS DURING THEIR BINDING WITH HUMAN SERUM γ-GLOBULIN

Directory of Open Access Journals (Sweden)

S. B. Cheknev

2006-01-01

Full Text Available Abstract. Conformational changes of human serum γ-globulin were studied during and after its binding with copper and zinc ions, using molecular ultrafiltration and differential spectrophotometry. The contents of nonbound metals in the filtrate were evaluated, resp., with sodium diethyl thyocarbamate and o-phenanthroline. It has been shown that copper and zinc exhibited common biological properties during their interactions with protein, but the binding differed sufficiently under similar experimental conditions. E.g., it was confirmed that copper was more active at the external sites of γ-globulin molecule, whereas zinc demonstrated tropicity for the areas of protein intraglobular compartments. The metal-binding sites have been described that differ in their parameters of interactions with cations and their spatial location within globular domains. Approaches are suggested for dynamic analysis of saturation for these differently located sites by the metal ions. We discuss the issues of altered conformational state of the γ-globulin molecule during the binding of cations, as well as potential usage of these data in clinical immunology.

Binding selectivity of vitamin K3 based chemosensors towards nickel(II) and copper(II) metal ions

Science.gov (United States)

Patil, Amit; Lande, Dipali N.; Nalkar, Archana; Gejji, Shridhar P.; Chakrovorty, Debamitra; Gonnade, Rajesh; Moniz, Tânia; Rangel, Maria; Pereira, Eulália; Salunke-Gawali, Sunita

2017-09-01

The vitamin K3 derivatives 2-methyl-3-[(pyridin-2-ylmethyl)-amino]-1,4-naphthoquinone (M-1), 2-methyl-3-[(pyridin-2-ylethyl)-amino]-1,4-naphthoquinone (M-2), 2-methyl-3-((2-(thiophen-2-yl)methyl)amino)naphthalene-1,4-dione (M-3) and 2-methyl-3-((2-(thiophen-2-yl)ethyl)amino)naphthalene-1,4-dione (M-4) have been synthesized, characterized and studied for their chemosensor abilities towards transition metal ions. Crystal structures of M-1 to M-4 revealed a variety of Nsbnd H⋯O, Csbnd H⋯O, Csbnd H⋯π and π⋯π interactions. Minor variations in such interactions by chemical stimuli such as metal ions, results in change in color that can be visualized by naked eyes. It has been shown that electronic structure and 1H NMR, vibrational as well as electronic spectra from the density functional theory agree well with the experiments. The metal ion binding in ethanol, ethanol-water and in mild base triethylamine brings forth recognizing ability of M-1 toward Ni2+ whereas M-2 exhibits large sensing ability for Cu2+ ion. Interestingly M-1 display varying metal ion binding specificity in different solvents with the association constant in ethanol being 11,786 M-1 for Ni2+ compared to 9462 M-1 for the Cu2+. A reversal in preferential binding of M-2 with the respective association constants being 4190 M-1 and 6370 M-1 is discernible.

Metal binding proteins, recombinant host cells and methods

Science.gov (United States)

Summers, Anne O.; Caguiat, Jonathan J.

2004-06-15

The present disclosure provides artificial heavy metal binding proteins termed chelons by the inventors. These chelons bind cadmium and/or mercuric ions with relatively high affinity. Also disclosed are coding sequences, recombinant DNA molecules and recombinant host cells comprising those recombinant DNA molecules for expression of the chelon proteins. In the recombinant host cells or transgenic plants, the chelons can be used to bind heavy metals taken up from contaminated soil, groundwater or irrigation water and to concentrate and sequester those ions. Recombinant enteric bacteria can be used within the gastrointestinal tracts of animals or humans exposed to toxic metal ions such as mercury and/or cadmium, where the chelon recombinantly expressed in chosen in accordance with the ion to be rededicated. Alternatively, the chelons can be immobilized to solid supports to bind and concentrate heavy metals from a contaminated aqueous medium including biological fluids.

Proton and metal ion binding to natural organic polyelectrolytes-I. Studies with synthetic model compounds

Science.gov (United States)

Marinsky, J.A.; Reddy, M.M.

1984-01-01

A unified physico-chemical model, based on a modified Henderson-Hasselbalch equation, for the analysis of ion complexation reactions involving charged polymeric systems is presented and verified. In this model pH = pKa+p(??Ka) + log(??/1 - ??) where Ka is the intrinsic acid dissociation constant of the ionizable functional groups on the polymer, ??Ka is the deviation of the intrinsic constant due to electrostatic interaction between the hydrogen ion and the polyanion, and alpha (??) is the polyacid degree of ionization. Using this approach pKa values for repeating acidic units of polyacrylic (PAA) and polymethacrylic (PMA) acids were found to be 4.25 ?? 0.03 and 4.8 ?? 0.1, respectively. The polyion electrostatic deviation term derived from the potentiometric titration data (i.e. p(??Ka)) is used to calculate metal ion concentration at the complexation site on the surface of the polyanion. Intrinsic cobalt-polycarboxylate binding constants (7.5 for PAA and 5.6 for PMA), obtained using this procedure, are consistent with the range of published binding constants for cobalt-monomer carboxylate complexes. In two phase systems incorporation of a Donnan membrane potential term allows determination of the intrinsic pKa of a cross-linked PMA gel, pKa = 4.83, in excellent agreement with the value obtained for the linear polyelectrolyte and the monomer. Similarly, the intrinsic stability constant for cobalt ion binding to a PMA-gel (??CoPMA+ = 11) was found to be in agreement with the linear polyelectrolyte analogue and the published data for cobalt-carboxylate monodentate complexes. ?? 1984.

Removal and recovery of toxic metal ions from aqueous waste sites using polymer pendant ligands

International Nuclear Information System (INIS)

Fish, D.

1996-01-01

The purpose of this project is to investigate the use of polymer pendant ligand technology to remove and recover toxic metal ions from DOE aqueous waste sites. Polymer pendant lgiands are organic ligands, anchored to crosslinked, modified divinylbenzene-polystyrene beads, that can selectively complex metal ions. The metal ion removal step usually occurs through a complexation or ion exchange phenomena, thus recovery of the metal ions and reuse of the beads is readily accomplished

Effects of site substitution and metal ion addition on doped manganites

CERN Document Server

Pradhan, A K; Roul, B K; Sahu, D R; Muralidhar, M

2002-01-01

We report transport, magnetization and transmission electron microscopy studies of the effects of A-and B-site substitution, and the addition of metal ions such as Pt, Ag and Sr, on doped ABO sub 3 perovskites, where A = La, Pr etc and B = Mn. Disorder induced by such substitution changes the behaviour of the charge-ordered (CO) state significantly. A-and B-site substitution suppresses the CO phase due to size mismatch and disorder produced by inhomogeneity. On the other hand, addition of metal ions such as Pt and Ag improves several colossal-magnetoresistance properties significantly due to microstructural effects and enhanced current percolation through grain boundaries.

A catalytic metal ion interacts with the cleavage site G•U wobble in the HDV ribozyme†

Science.gov (United States)

Chen, Jui-Hui; Gong, Bo; Bevilacqua, Philip C.; Carey, Paul R.; Golden, Barbara L.

2009-01-01

The HDV ribozyme self-cleaves by a chemical mechanism involving general acid-base catalysis to generate a 2′,3′-cyclic phosphate and a 5′-hydroxyl termini. Biochemical studies from several laboratories have implicated C75 as the general acid and hydrated magnesium as the general base. We have previously shown that C75 has a pKa shifted > 2 pH units toward neutrality [Gong, B., Chen, J. H., Chase, E., Chadalavada, D. M., Yajima, R., Golden, B. L., Bevilacqua, P. C., and Carey, P. R. (2007) J. Am. Chem. Soc. 129, 13335–13342.], while in crystal structures, it is well-positioned for proton transfer. However no crystallographic evidence for a hydrated magnesium poised to serve as a general base in the reaction has been observed in high-resolution crystal structures of various reaction states and mutants. Herein, we use solution kinetic experiments and parallel Raman crystallographic studies to examine the effects of pH on rate and Mg2+-binding properties of wild-type and 7-deazaguanosine mutants of the HDV ribozyme. These data suggest that a previously-unobserved hydrated magnesium ion interacts with the N7 of the cleavage site G•U wobble base pair. Integrating this metal ion binding site with the available crystal structures provides a new three-dimensional model for the active site of the ribozyme that accommodates all available biochemical data and appears competent for catalysis. The position of this metal is consistent with a role of a magnesium-bound hydroxide as a general base as dictated by biochemical data. PMID:19178151

Fabrication of supramolecular frameworks by tuning the binding site ...

Indian Academy of Sciences (India)

Administrator

Fabrication of supramolecular frameworks by tuning the binding site of a tripodal ligand with d. 10 metal ions 803. Table 1. Crystal data and structure refinement parameters for 1 and 2. 1 .... e-mail: deposit@ccdc.cam.ac.uk web: http://www. ccdc. cam.ac.uk/deposit]. Supplementary figures and tables can be found in website ...

Binding of heavy metal ions in aggregates of microbial cells, EPS and biogenic iron minerals measured in-situ using metal- and glycoconjugates-specific fluorophores

Science.gov (United States)

Hao, Likai; Guo, Yuan; Byrne, James M.; Zeitvogel, Fabian; Schmid, Gregor; Ingino, Pablo; Li, Jianli; Neu, Thomas R.; Swanner, Elizabeth D.; Kappler, Andreas; Obst, Martin

2016-05-01

Aggregates consisting of bacterial cells, extracellular polymeric substances (EPS) and Fe(III) minerals formed by Fe(II)-oxidizing bacteria are common at bulk or microscale chemical interfaces where Fe cycling occurs. The high sorption capacity and binding capacity of cells, EPS, and minerals controls the mobility and fate of heavy metals. However, it remains unclear to which of these component(s) the metals will bind in complex aggregates. To clarify this question, the present study focuses on 3D mapping of heavy metals sorbed to cells, glycoconjugates that comprise the majority of EPS constituents, and Fe(III) mineral aggregates formed by the phototrophic Fe(II)-oxidizing bacteria Rhodobacter ferrooxidans SW2 using confocal laser scanning microscopy (CLSM) in combination with metal- and glycoconjugates-specific fluorophores. The present study evaluated the influence of glycoconjugates, microbial cell surfaces, and (biogenic) Fe(III) minerals, and the availability of ferrous and ferric iron on heavy metal sorption. Analyses in this study provide detailed knowledge on the spatial distribution of metal ions in the aggregates at the sub-μm scale, which is essential to understand the underlying mechanisms of microbe-mineral-metal interactions. The heavy metals (Au3+, Cd2+, Cr3+, CrO42-, Cu2+, Hg2+, Ni2+, Pd2+, tributyltin (TBT) and Zn2+) were found mainly sorbed to cell surfaces, present within the glycoconjugates matrix, and bound to the mineral surfaces, but not incorporated into the biogenic Fe(III) minerals. Statistical analysis revealed that all ten heavy metals tested showed relatively similar sorption behavior that was affected by the presence of sorbed ferrous and ferric iron. Results in this study showed that in addition to the mineral surfaces, both bacterial cell surfaces and the glycoconjugates provided most of sorption sites for heavy metals. Simultaneously, ferrous and ferric iron ions competed with the heavy metals for sorption sites on the organic

Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination.

Science.gov (United States)

Dokmanić, Ivan; Sikić, Mile; Tomić, Sanja

2008-03-01

Metal ions are constituents of many metalloproteins, in which they have either catalytic (metalloenzymes) or structural functions. In this work, the characteristics of various metals were studied (Cu, Zn, Mg, Mn, Fe, Co, Ni, Cd and Ca in proteins with known crystal structure) as well as the specificity of their environments. The analysis was performed on two data sets: the set of protein structures in the Protein Data Bank (PDB) determined with resolution metal ion and its electron donors and the latter was used to assess the preferred coordination numbers and common combinations of amino-acid residues in the neighbourhood of each metal. Although the metal ions considered predominantly had a valence of two, their preferred coordination number and the type of amino-acid residues that participate in the coordination differed significantly from one metal ion to the next. This study concentrates on finding the specificities of a metal-ion environment, namely the distribution of coordination numbers and the amino-acid residue types that frequently take part in coordination. Furthermore, the correlation between the coordination number and the occurrence of certain amino-acid residues (quartets and triplets) in a metal-ion coordination sphere was analysed. The results obtained are of particular value for the identification and modelling of metal-binding sites in protein structures derived by homology modelling. Knowledge of the geometry and characteristics of the metal-binding sites in metalloproteins of known function can help to more closely determine the biological activity of proteins of unknown function and to aid in design of proteins with specific affinity for certain metals.

Characterisation of the effect of ion channel modulators on I1-imidazoline binding sites in bovine adrenal medulla

International Nuclear Information System (INIS)

Musgrave, I.F.; Kotsopoulos, D.; Hughes, R.A.

1998-01-01

Full text: The structure of I 1 -imidazoline binding sites is still unknown and we have proposed that they represent ion channels (i). In these experiments we characterised the effects of the known ion channel modulators methyltriphenylphosphonium (MTPP), 4-aminopyridine (4-AP) and tetraethyl ammonium (TEA) on [ 3 H] clonidine binding in bovine adrenal medullary membranes as these membranes have a relatively well defined I 1 -imidazoline binding site (Molderings et al, 1993). Membranes from bovine adrenal medulla's were prepared by a minor modification of the method of Rapier et al. [ 3 H] Clonidine binding was performed by the method of Ernsberger et al (3), with [ 3 H] clonidine (62 Ci/mmol) used at a final concentration of 5 nM. [ 3 H] Clonidine binding was displaced from bovine adrenal medullary membranes by adrenergic drugs with the order of potency being oxymetazoline > clonidine > moxonidine = idazoxan >> yonimbine. This order of potency is consistent with previous studies of I 1 -imidazoline binding sites (4). Non-linear curve fitting to this data was consistent with a single site model. Both TEA and 4-AP displaced [ H] clonidine with similar potency to its effect on ion channels, TEA having a EC>> of 54 ± 0.3 μM (n=3). The displacement of [ 3 H] clonidine produced by both TEA and 4-AP also fitted to a single site model. Displacement of [ 3 H] clonidine by MTPP fitted a two site model (p 1 -imidazoline binding sites defined with [ 3 H] clonidine may represent ion channels. We have used this data to perform molecular modelling and have determined a common conformation of I 1 -prefering ligands which will aid in the development of I 1 -selective ligands in the future. Copyright (1998) Australian Neuroscience Society

Crystal Structures of Apo and Metal-Bound Forms of the UreE Protein from Helicobacter pylori: Role of Multiple Metal Binding Sites

Energy Technology Data Exchange (ETDEWEB)

Shi, Rong; Munger, Christine; Asinas, Abdalin; Benoit, Stephane L.; Miller, Erica; Matte, Allan; Maier, Robert J.; Cygler, Miroslaw (McGill); (Georgia); (Biotech Res.)

2010-10-22

The crystal structure of the urease maturation protein UreE from Helicobacter pylori has been determined in its apo form at 2.1 {angstrom} resolution, bound to Cu{sup 2+} at 2.7 {angstrom} resolution, and bound to Ni{sup 2+} at 3.1 {angstrom} resolution. Apo UreE forms dimers, while the metal-bound enzymes are arranged as tetramers that consist of a dimer of dimers associated around the metal ion through coordination by His102 residues from each subunit of the tetramer. Comparison of independent subunits from different crystal forms indicates changes in the relative arrangement of the N- and C-terminal domains in response to metal binding. The improved ability of engineered versions of UreE containing hexahistidine sequences at either the N-terminal or C-terminal end to provide Ni{sup 2+} for the final metal sink (urease) is eliminated in the H102A version. Therefore, the ability of the improved Ni{sup 2+}-binding versions to deliver more nickel is likely an effect of an increased local concentration of metal ions that can rapidly replenish transferred ions bound to His102.

Engineering of microorganisms towards recovery of rare metal ions

Energy Technology Data Exchange (ETDEWEB)

Kuroda, Kouichi; Ueda, Mitsuyoshi [Kyoto Univ. (Japan). Div. of Applied Life Sciences

2010-06-15

The bioadsorption of metal ions using microorganisms is an attractive technology for the recovery of rare metal ions as well as removal of toxic heavy metal ions from aqueous solution. In initial attempts, microorganisms with the ability to accumulate metal ions were isolated from nature and intracellular accumulation was enhanced by the overproduction of metal-binding proteins in the cytoplasm. As an alternative, the cell surface design of microorganisms by cell surface engineering is an emerging strategy for bioadsorption and recovery of metal ions. Cell surface engineering was firstly applied to the construction of a bioadsorbent to adsorb heavy metal ions for bioremediation. Cell surface adsorption of metal ions is rapid and reversible. Therefore, adsorbed metal ions can be easily recovered without cell breakage, and the bioadsorbent can be reused or regenerated. These advantages are suitable for the recovery of rare metal ions. Actually, the cell surface display of a molybdate-binding protein on yeast led to the enhanced adsorption of molybdate, one of the rare metal ions. An additional advantage is that the cell surface display system allows high-throughput screening of protein/peptide libraries owing to the direct evaluation of the displayed protein/peptide without purification and concentration. Therefore, the creation of novel metal-binding protein/ peptide and engineering of microorganisms towards the recovery of rare metal ions could be simultaneously achieved. (orig.)

Modulation of individual steps in group I intron catalysis by a peripheral metal ion.

Science.gov (United States)

Forconi, Marcello; Piccirilli, Joseph A; Herschlag, Daniel

2007-10-01

Enzymes are complex macromolecules that catalyze chemical reactions at their active sites. Important information about catalytic interactions is commonly gathered by perturbation or mutation of active site residues that directly contact substrates. However, active sites are engaged in intricate networks of interactions within the overall structure of the macromolecule, and there is a growing body of evidence about the importance of peripheral interactions in the precise structural organization of the active site. Here, we use functional studies, in conjunction with published structural information, to determine the effect of perturbation of a peripheral metal ion binding site on catalysis in a well-characterized catalytic RNA, the Tetrahymena thermophila group I ribozyme. We perturbed the metal ion binding site by site-specifically introducing a phosphorothioate substitution in the ribozyme's backbone, replacing the native ligands (the pro-R (P) oxygen atoms at positions 307 and 308) with sulfur atoms. Our data reveal that these perturbations affect several reaction steps, including the chemical step, despite the absence of direct contacts of this metal ion with the atoms involved in the chemical transformation. As structural probing with hydroxyl radicals did not reveal significant change in the three-dimensional structure upon phosphorothioate substitution, the effects are likely transmitted through local, rather subtle conformational rearrangements. Addition of Cd(2+), a thiophilic metal ion, rescues some reaction steps but has deleterious effects on other steps. These results suggest that native interactions in the active site may have been aligned by the naturally occurring peripheral residues and interactions to optimize the overall catalytic cycle.

Water-soluble metal-binding polymers with ultrafiltration: A technology for the removal, concentration, and recovery of metal ions from aqueous streams

International Nuclear Information System (INIS)

Smith, B.F.; Robison, T.W.; Jarvinen, G.D.

1997-01-01

The use of water-soluble metal-binding polymers coupled with ultrafiltration (UF) is a technology under development to selectively concentrate and recover valuable or regulated metal-ions from dilute process or waste waters. The polymers have a sufficiently large molecular size that they can be separated and concentrated using commercially available UF technology. The polymers can then be reused by changing the solution conditions to release the metal-ions, which are recovered in a concentrated form for recycle or disposal. Pilot-scale demonstrations have been completed for a variety of waste streams containing low concentrations of metal ions including electroplating wastes (zinc and nickel) and nuclear waste streams (plutonium and americium). Many other potential commercial applications exist including remediation of contaminated solids. An overview of both the pilot-scale demonstrated applications and small scale testing of this technology are presented

Water-soluble metal-binding polymers with ultrafiltration: A technology for the removal, concentration, and recovery of metal ions from aqueous streams

Energy Technology Data Exchange (ETDEWEB)

Smith, B.F.; Robison, T.W.; Jarvinen, G.D.

1997-12-31

The use of water-soluble metal-binding polymers coupled with ultrafiltration (UF) is a technology under development to selectively concentrate and recover valuable or regulated metal-ions from dilute process or waste waters. The polymers have a sufficiently large molecular size that they can be separated and concentrated using commercially available UF technology. The polymers can then be reused by changing the solution conditions to release the metal-ions, which are recovered in a concentrated form for recycle or disposal. Pilot-scale demonstrations have been completed for a variety of waste streams containing low concentrations of metal ions including electroplating wastes (zinc and nickel) and nuclear waste streams (plutonium and americium). Many other potential commercial applications exist including remediation of contaminated solids. An overview of both the pilot-scale demonstrated applications and small scale testing of this technology are presented.

pH-dependence of the specific binding of Cu(II) and Zn(II) ions to the amyloid-β peptide

International Nuclear Information System (INIS)

Ghalebani, Leila; Wahlström, Anna; Danielsson, Jens; Wärmländer, Sebastian K.T.S.; Gräslund, Astrid

2012-01-01

Highlights: ► Cu(II) and Zn(II) display pH-dependent binding to the Aβ(1–40) peptide. ► At pH 7.4 both metal ions display residue-specific binding to the Aβ peptide. ► At pH 5.5 the binding specificity is lost for Zn(II). ► Differential Cu(II) and Zn(II) binding may help explain metal-induced AD toxicity. -- Abstract: Metal ions like Cu(II) and Zn(II) are accumulated in Alzheimer’s disease amyloid plaques. The amyloid-β (Aβ) peptide involved in the disease interacts with these metal ions at neutral pH via ligands provided by the N-terminal histidines and the N-terminus. The present study uses high-resolution NMR spectroscopy to monitor the residue-specific interactions of Cu(II) and Zn(II) with 15 N- and 13 C, 15 N-labeled Aβ(1–40) peptides at varying pH levels. At pH 7.4 both ions bind to the specific ligands, competing with one another. At pH 5.5 Cu(II) retains its specific histidine ligands, while Zn(II) seems to lack residue-specific interactions. The low pH mimics acidosis which is linked to inflammatory processes in vivo. The results suggest that the cell toxic effects of redox active Cu(II) binding to Aβ may be reversed by the protective activity of non-redox active Zn(II) binding to the same major binding site under non-acidic conditions. Under acidic conditions, the protective effect of Zn(II) may be decreased or changed, since Zn(II) is less able to compete with Cu(II) for the specific binding site on the Aβ peptide under these conditions.

Carrageenans as a new source of drugs with metal binding properties.

Science.gov (United States)

Khotimchenko, Yuri S; Khozhaenko, Elena V; Khotimchenko, Maxim Y; Kolenchenko, Elena A; Kovalev, Valeri V

2010-04-01

Carrageenans are abundant and safe non-starch polysaccharides exerting their biological effects in living organisms. Apart from their known pro-inflammation properties and some pharmacological activity, carrageenans can also strongly bind and hold metal ions. This property can be used for creation of the new drugs for elimination of metals from the body or targeted delivery of these metal ions for healing purposes. Metal binding activity of different carrageenans in aqueous solutions containing Y(3+) or Pb(2+) ions was studied in a batch sorption system. The metal uptake by carrageenans is not affected by the change of the pH within the range from 2.0 to 6.0. The rates and binding capacities of carrageenans regarding metal ions were evaluated. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants, and the sorption isothermal data could be explained well by the Langmuir equation. The results obtained through the study suggest that kappa-, iota-, and lambda-carrageenans are favorable sorbents. The largest amount of Y(3+) and Pb(2+) ions are bound by iota-carrageenan. Therefore, it can be concluded that this type of polysaccharide is the more appropriate substance for elaboration of the drugs with high selective metal binding properties.

Carrageenans as a New Source of Drugs with Metal Binding Properties

Directory of Open Access Journals (Sweden)

Yuri S. Khotimchenko

2010-04-01

Full Text Available Carrageenans are abundant and safe non-starch polysaccharides exerting their biological effects in living organisms. Apart from their known pro-inflammation properties and some pharmacological activity, carrageenans can also strongly bind and hold metal ions. This property can be used for creation of the new drugs for elimination of metals from the body or targeted delivery of these metal ions for healing purposes. Metal binding activity of different carrageenans in aqueous solutions containing Y3+ or Pb2+ ions was studied in a batch sorption system. The metal uptake by carrageenans is not affected by the change of the pH within the range from 2.0 to 6.0. The rates and binding capacities of carrageenans regarding metal ions were evaluated. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants, and the sorption isothermal data could be explained well by the Langmuir equation. The results obtained through the study suggest that κ-, ι-, and λ-carrageenans are favorable sorbents. The largest amount of Y3+ and Pb2+ ions are bound by i-carrageenan. Therefore, it can be concluded that this type of polysaccharide is the more appropriate substance for elaboration of the drugs with high selective metal binding properties.

Crystal structure of glucose isomerase in complex with xylitol inhibitor in one metal binding mode.

Science.gov (United States)

Bae, Ji-Eun; Kim, In Jung; Nam, Ki Hyun

2017-11-04

Glucose isomerase (GI) is an intramolecular oxidoreductase that interconverts aldoses and ketoses. These characteristics are widely used in the food, detergent, and pharmaceutical industries. In order to obtain an efficient GI, identification of novel GI genes and substrate binding/inhibition have been studied. Xylitol is a well-known inhibitor of GI. In Streptomyces rubiginosus, two crystal structures have been reported for GI in complex with xylitol inhibitor. However, a structural comparison showed that xylitol can have variable conformation at the substrate binding site, e.g., a nonspecific binding mode. In this study, we report the crystal structure of S. rubiginosus GI in a complex with xylitol and glycerol. Our crystal structure showed one metal binding mode in GI, which we presumed to represent the inactive form of the GI. The metal ion was found only at the M1 site, which was involved in substrate binding, and was not present at the M2 site, which was involved in catalytic function. The O 2 and O 4 atoms of xylitol molecules contributed to the stable octahedral coordination of the metal in M1. Although there was no metal at the M2 site, no large conformational change was observed for the conserved residues coordinating M2. Our structural analysis showed that the metal at the M2 site was not important when a xylitol inhibitor was bound to the M1 site in GI. Thus, these findings provided important information for elucidation or engineering of GI functions. Copyright © 2017 Elsevier Inc. All rights reserved.

A biosystem for removal of metal ions from water

Energy Technology Data Exchange (ETDEWEB)

Kilbane, J.J. II.

1990-01-01

The presence of heavy metal ions in ground and surface waters constitutes a potential health risk and is an environmental concern. Moreover, processes for the recovery of valuable metal ions are of interest. Bioaccumulation or biosorption is not only a factor in assessing the environmental risk posed by metal ions; it can also be used as a means of decontamination. A biological system for the removal and recovery of metal ions from contaminated water is reported here. Exopolysaccharide-producing microorganisms, including a methanotrophic culture, are demonstrated to have superior metal binding ability, compared with other microbial cultures. This paper describes a biosorption process in which dried biomass obtained from exopolysaccharide-producing microorganisms is encapsulated in porous plastic beads and is used for metal ion binding and recovery. 22 refs., 13 figs.

Binding of Mn-deoxyribonucleoside Triphosphates to the Active Site of the DNA Polymerase of Bacteriophage T7

Energy Technology Data Exchange (ETDEWEB)

B Akabayov; C Richardson

2011-12-31

Divalent metal ions are crucial as cofactors for a variety of intracellular enzymatic activities. Mg{sup 2+}, as an example, mediates binding of deoxyribonucleoside 5'-triphosphates followed by their hydrolysis in the active site of DNA polymerase. It is difficult to study the binding of Mg{sup 2+} to an active site because Mg{sup 2+} is spectroscopically silent and Mg{sup 2+} binds with low affinity to the active site of an enzyme. Therefore, we substituted Mg{sup 2+} with Mn{sup 2+}:Mn{sup 2+} that is not only visible spectroscopically but also provides full activity of the DNA polymerase of bacteriophage T7. In order to demonstrate that the majority of Mn{sup 2+} is bound to the enzyme, we have applied site-directed titration analysis of T7 DNA polymerase using X-ray near edge spectroscopy. Here we show how X-ray near edge spectroscopy can be used to distinguish between signal originating from Mn{sup 2+} that is free in solution and Mn{sup 2+} bound to the active site of T7 DNA polymerase. This method can be applied to other enzymes that use divalent metal ions as a cofactor.

A Transition Metal-Binding, Trimeric βγ-Crystallin from Methane-Producing Thermophilic Archaea, Methanosaeta thermophila.

Science.gov (United States)

Srivastava, Shanti Swaroop; Jamkhindikar, Aditya Anand; Raman, Rajeev; Jobby, Maroor K; Chadalawada, Swathi; Sankaranarayanan, Rajan; Sharma, Yogendra

2017-03-07

βγ-Crystallins are important constituents of the vertebrate eye lens, whereas in microbes, they are prevalent as Ca 2+ -binding proteins. In archaea, βγ-crystallins are conspicuously confined to two methanogens, viz., Methanosaeta and Methanosarcina. One of these, i.e., M-crystallin from Methanosarcina acetivorans, has been shown to be a typical Ca 2+ -binding βγ-crystallin. Here, with the aid of a high-resolution crystal structure and isothermal titration calorimetry, we report that "Methallin", a βγ-crystallin from Methanosaeta thermophila, is a trimeric, transition metal-binding protein. It binds Fe, Ni, Co, or Zn ion with nanomolar affinity, which is consistent even at 55 °C, the optimal temperature for the methanogen's growth. At the center of the protein trimer, the metal ion is coordinated by six histidines, two from each protomer, leading to an octahedral geometry. Small-angle X-ray scattering analysis confirms that the trimer seen in the crystal lattice is a biological assembly; this assembly dissociates to monomers upon removal of the metal ion. The introduction of two histidines (S17H/S19H) into a homologous βγ-crystallin, Clostrillin, allows it to bind nickel at the introduced site, though with micromolar affinity. However, because of the lack of a compatible interface, nickel binding could not induce trimerization, affirming that Methallin is a naturally occurring trimer for high-affinity transition metal binding. While βγ-crystallins are known to bind Ca 2+ and form homodimers and oligomers, the transition metal-binding, trimeric Methallin is a new paradigm for βγ-crystallins. The distinct features of Methallin, such as nickel or iron binding, are also possible imprints of biogeochemical changes during the period of its origin.

A New Metal Binding Domain Involved in Cadmium, Cobalt and Zinc Transport

Energy Technology Data Exchange (ETDEWEB)

Smith, Aaron T. [Northwestern Univ., Evanston, IL (United States); Barupala, Dulmini [Wayne State Univ., Detroit, MI (United States); Stemmler, Timothy L. [Wayne State Univ., Detroit, MI (United States); Rosenzweig, Amy C. [Northwestern Univ., Evanston, IL (United States)

2015-07-20

In the P1B-ATPases, which couple cation transport across membranes to ATP hydrolysis, are central to metal homeostasis in all organisms. An important feature of P1B-ATPases is the presence of soluble metal binding domains (MBDs) that regulate transport activity. Only one type of MBD has been characterized extensively, but bioinformatics analyses indicate that a diversity of MBDs may exist in nature. Here we report the biochemical, structural and functional characterization of a new MBD from the Cupriavidus metallidurans P_1B-4-ATPase CzcP (CzcP MBD). The CzcP MBD binds two Cd²⁺, Co²⁺ or Zn²⁺ ions in distinct and unique sites and adopts an unexpected fold consisting of two fused ferredoxin-like domains. Both in vitro and in vivo activity assays using full-length CzcP, truncated CzcP and several variants indicate a regulatory role for the MBD and distinct functions for the two metal binding sites. Moreover, these findings elucidate a previously unknown MBD and suggest new regulatory mechanisms for metal transport by P_1B-ATPases.

Metal Ion Controlled Polymorphism of a Peptide

DEFF Research Database (Denmark)

Hemmingsen, Lars Bo Stegeager; Jancso, Attila; Szunyogh, Daniel

2011-01-01

ions on fully or partially unstructured proteins, or the effect of metal ions on protein aggregation. Metal ions may be employed to fold (or misfold) individual peptides in a controlled manner depending on the potential metal ion coordinating amino acid side chains (Cys, His, Asp, Glu......In this work a metal ion binding model dodecapeptide was investigated in terms of its capacity to adopt different structures depending on the metal ion to peptide stoichiometry. The dodecapeptide is much simpler than real proteins, yet displays sufficient complexity to model the effect of metal......, …) in the peptide, and the ligand and structural preferences of the metal ion (in our studies Zn2+, Cd2+, Hg2+, Cu+/2+). Simultaneously, new species such as metal ion bridged ternary complexes or even oligomers may be formed. In recent previous studies we have observed similar polymorphism of zinc finger model...

MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids.

Science.gov (United States)

Andreini, Claudia; Cavallaro, Gabriele; Rosato, Antonio; Valasatava, Yana

2013-11-25

We developed a new software tool, MetalS(2), for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. On our example data sets, MetalS(2) unveiled structural similarities that other programs for protein structure comparison do not consistently point out and overall identified a larger number of structurally similar MFSs. MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool ( http://metalweb.cerm.unifi.it/tools/metals2/).

Effects of urea, metal ions and surfactants on the binding of baicalein with bovine serum albumin

Directory of Open Access Journals (Sweden)

Atanu Singha Roy

2016-08-01

Full Text Available The interaction of baicalein with bovine serum albumin (BSA was investigated with the help of spectroscopic and molecular docking studies. The binding affinity of baicalein towards BSA was estimated to be in order of 105 M−1 from fluorescence quenching studies. Negative ΔH° (−5.66±0.14 kJ/mol and positive (ΔS° (+79.96±0.65 J/mol K indicate the presence of electrostatic interactions along with the hydrophobic forces that result in a positive ΔS°. The hydrophobic association of baicalein with BSA diminishes in the presence of sodium dodecyl sulfate (SDS due to probable hydrophobic association of baicalein with SDS, resulting in a negative ΔS° (−40.65±0.87 J/mol K. Matrix-assisted laser desorption ionization/time of flight (MALDI--TOF experiments indicate a 1:1 complexation between baicalein and BSA. The unfolding and refolding phenomena of BSA were investigated in the absence and presence of baicalein using steady-state and fluorescence lifetime measurements. It was observed that the presence of urea ruptured the non-covalent interaction between baicalein and BSA. The presence of metal ions (Ag+, Mg2+, Ni2+, Mn2+, Co2+and Zn2+ increased the binding affinity of ligand towards BSA. The changes in conformational aspects of BSA after ligand binding were also investigated using circular dichroism (CD and Fourier transform infrared (FT-IR spectroscopic techniques. Site selectivity studies following molecular docking analyses indicated the binding of baicalein to site 1 (subdomain IIA of BSA.

Thermodynamic and structural properties of the specific binding between Ag⁺ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair.

Science.gov (United States)

Torigoe, Hidetaka; Okamoto, Itaru; Dairaku, Takenori; Tanaka, Yoshiyuki; Ono, Akira; Kozasa, Tetsuo

2012-11-01

Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag(+) ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag(+) ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag(+) ion. Isothermal titration calorimetry demonstrated that the Ag(+) ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10(6) M(-1), which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag(+) ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag(+) ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences. Copyright © 2012 Elsevier

Expressing a bacterial mercuric ion binding protein in plant for phytoremediation of heavy metals.

Science.gov (United States)

Hsieh, Ju-Liang; Chen, Ching-Yi; Chiu, Meng-Hsuen; Chein, Mei-Fang; Chang, Jo-Shu; Endo, Ginro; Huang, Chieh-Chen

2009-01-30

A specific mercuric ion binding protein (MerP) originating from transposon TnMERI1 of Bacillus megaterium strain MB1 isolated from Minamata Bay displayed good adsorption capability for a variety of heavy metals. In this study, the Gram-positive MerP protein was expressed in transgenic Arabidopsis to create a model system for phytoremediation of heavy metals. Under control of an actin promoter, the transgenic Arabidpsis showed higher tolerance and accumulation capacity for mercury, cadium and lead when compared with the control plant. Results from confocal microscopy analysis also indicate that MerP was localized at the cell membrane and vesicles of plant cells. The developed transgenic plants possessing excellent metal-accumulative ability could have potential applications in decontamination of heavy metals.

Ion Binding Energies Determining Functional Transport of ClC Proteins

Science.gov (United States)

Yu, Tao; Guo, Xu; Zou, Xian-Wu; Sang, Jian-Ping

2014-06-01

The ClC-type proteins, a large family of chloride transport proteins ubiquitously expressed in biological organisms, have been extensively studied for decades. Biological function of ClC proteins can be reflected by analyzing the binding situation of Cl- ions. We investigate ion binding properties of ClC-ec1 protein with the atomic molecular dynamics simulation approach. The calculated electrostatic binding energy results indicate that Cl- at the central binding site Scen has more binding stability than the internal binding site Sint. Quantitative comparison between the latest experimental heat release data isothermal titration calorimetry (ITC) and our calculated results demonstrates that chloride ions prefer to bind at Scen than Sint in the wild-type ClC-ec1 structure and prefer to bind at Sext and Scen than Sint in mutant E148A/E148Q structures. Even though the chloride ions make less contribution to heat release when binding to Sint and are relatively unstable in the Cl- pathway, they are still part contributors for the Cl- functional transport. This work provides a guide rule to estimate the importance of Cl- at the binding sites and how chloride ions have influences on the function of ClC proteins.

Site-specific tagging proteins with a rigid, small and stable transition metal chelator, 8-hydroxyquinoline, for paramagnetic NMR analysis

Energy Technology Data Exchange (ETDEWEB)

Yang, Yin; Huang, Feng [Nankai University, State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) (China); Huber, Thomas [Australian National University, Research School of Chemistry (Australia); Su, Xun-Cheng, E-mail: xunchengsu@nankai.edu.cn [Nankai University, State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) (China)

2016-02-15

Design of a paramagnetic metal binding motif in a protein is a valuable way for understanding the function, dynamics and interactions of a protein by paramagnetic NMR spectroscopy. Several strategies have been proposed to site-specifically tag proteins with paramagnetic lanthanide ions. Here we report a simple approach of engineering a transition metal binding motif via site-specific labelling of a protein with 2-vinyl-8-hydroxyquinoline (2V-8HQ). The protein-2V-8HQ adduct forms a stable complex with transition metal ions, Mn(II), Co(II), Ni(II), Cu(II) and Zn(II). The paramagnetic effects generated by these transition metal ions were evaluated by NMR spectroscopy. We show that 2V-8HQ is a rigid and stable transition metal binding tag. The coordination of the metal ion can be assisted by protein sidechains. More importantly, tunable paramagnetic tensors are simply obtained in an α-helix that possesses solvent exposed residues in positions i and i + 3, where i is the residue to be mutated to cysteine, i + 3 is Gln or Glu or i − 4 is His. The coordination of a sidechain carboxylate/amide or imidazole to cobalt(II) results in different structural geometries, leading to different paramagnetic tensors as shown by experimental data.

Role of four conserved aspartic acid residues of EF-loops in the metal ion binding and in the self-assembly of ciliate Euplotes octocarinatus centrin.

Science.gov (United States)

Liu, Wen; Duan, Lian; Sun, Tijian; Yang, Binsheng

2016-12-01

Ciliate Euplotes octocarinatus centrin (EoCen) is an EF-hand calcium-binding protein closely related to the prototypical calcium sensor protein calmodulin. Four mutants (D37K, D73K, D110K and D146K) were created firstly to elucidate the importance of the first aspartic acid residues (Asp37, Asp73, Asp110 and Asp146) in the beginning of the four EF-loops of EoCen. Aromatic-sensitized Tb 3+ fluorescence indicates that the aspartic acid residues are very important for the metal-binding of EoCen, except for Asp73 (in EF-loop II). Resonance light scattering (RLS) measurements for different metal ions (Ca 2+ and Tb 3+ ) binding proteins suggest that the order of four conserved aspartic acid residues for contributing to the self-assembly of EoCen is Asp37 > Asp146 > Asp110 > Asp73. Cross-linking experiment also exhibits that Asp37 and Asp146 play critical role in the self-assembly of EoCen. Asp37, in site I, which is located in the N-terminal domain, plays the most important role in the metal ion-dependent self-assembly of EoCen, and there is cooperativity between N-terminal and C-terminal domain (especially the site IV). In addition, the dependence of Tb 3+ induced self-assembly of EoCen and the mutants on various factors, including ionic strength and pH, were characterized using RLS. Finally, 2-p-toluidinylnaphthalene-6-sulfonate (TNS) binding, ionic strength and pH control experiments indicate that in the process of EoCen self-assembly, molecular interactions are mediated by both electrostatic and hydrophobic forces, and the hydrophobic interaction has the important status.

Europium ion as a probe for binding sites to carrageenans

International Nuclear Information System (INIS)

Ramos, Ana P.; Goncalves, Rogeria R.; Serra, Osvaldo A.; Zaniquelli, Maria Elisabete D.; Wong, Kenneth

2007-01-01

Carrageenans, sulfated polysaccharides extracted from red algae, present a coil-helix transition and helix aggregation dependence on the type and concentration of counterions. In this study, we focus attention on a mixed valence counterion system: Eu 3+ /Na + or K + with different gel-forming carrageenans: kappa, iota, and kappa-2. Results of stationary and time-dependent luminescence showed to be a suitable tool to probe ion binding to both the negatively charged sulfate group and the hydroxyl groups present in the biopolymer. For lower europium ion concentrations, a single longer decay emission lifetime was detected, which was attributed to the binding of europium ion to the carrageenan sulfate groups. An additional decay ascribed to europium binding to hydroxyl groups was observed above a threshold concentration, and this decay was dependent on the carrageenan charge density. Symmetry of the europium ion microenvironment was estimated by the ratio between the intensities of its emission bands, which has been shown to depend on the concentration of europium ions and on the specificity of the monovalent counterion bound to the carrageenan

Europium ion as a probe for binding sites to carrageenans

Energy Technology Data Exchange (ETDEWEB)

Ramos, Ana P.; Goncalves, Rogeria R.; Serra, Osvaldo A. [Departamento de Quimica, Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo 14040-901 (Brazil); Zaniquelli, Maria Elisabete D. [Departamento de Quimica, Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo 14040-901 (Brazil)], E-mail: medzaniquelli@ffclrp.usp.br; Wong, Kenneth [Laboratorio de Fisico-Quimica, Centro de Pesquisas de Paulinia, Rhodia Brasil, Paulinia, Sao Paulo (Brazil)

2007-12-15

Carrageenans, sulfated polysaccharides extracted from red algae, present a coil-helix transition and helix aggregation dependence on the type and concentration of counterions. In this study, we focus attention on a mixed valence counterion system: Eu{sup 3+}/Na{sup +} or K{sup +} with different gel-forming carrageenans: kappa, iota, and kappa-2. Results of stationary and time-dependent luminescence showed to be a suitable tool to probe ion binding to both the negatively charged sulfate group and the hydroxyl groups present in the biopolymer. For lower europium ion concentrations, a single longer decay emission lifetime was detected, which was attributed to the binding of europium ion to the carrageenan sulfate groups. An additional decay ascribed to europium binding to hydroxyl groups was observed above a threshold concentration, and this decay was dependent on the carrageenan charge density. Symmetry of the europium ion microenvironment was estimated by the ratio between the intensities of its emission bands, which has been shown to depend on the concentration of europium ions and on the specificity of the monovalent counterion bound to the carrageenan.

Competition of dipositive metal ions for Fe (III) binding sites in chelation therapy of Iron Load

International Nuclear Information System (INIS)

Rehmani, Fouzia S.

2005-01-01

Iron overload is a condition in which excessive iron deposited in the liver, kidney and spleen of human beings in the patients of beta thalassemia and sickle cell anemia. Instead of its importance iron could be toxic when in excess, it damages the tissues. For the treatment of iron overload, a drug desferrioxamine mesylate has been used. It is linear trihydroxamic acid, a natural siderophore produced by streptomyces which removes the extra iron from body. Salicylhydroxamate type siderphore. In present research salicylhydroxamate was used for the complexation with dipositive metal ions which are available in biological environments such as Mn (II), Co (II), Ni (II) and Cu (II). The aim of our work was to study the competition reactions between Fe (III) and other dipositive ions; to calculate the thermodynamic data of chelation of these metal ions complexes with hydroxamate by computer program and comparison with hydroxamate complexes. (author)

Development of METAL-ACTIVE SITE and ZINCCLUSTER tool to predict active site pockets.

Science.gov (United States)

Ajitha, M; Sundar, K; Arul Mugilan, S; Arumugam, S

2018-03-01

The advent of whole genome sequencing leads to increasing number of proteins with known amino acid sequences. Despite many efforts, the number of proteins with resolved three dimensional structures is still low. One of the challenging tasks the structural biologists face is the prediction of the interaction of metal ion with any protein for which the structure is unknown. Based on the information available in Protein Data Bank, a site (METALACTIVE INTERACTION) has been generated which displays information for significant high preferential and low-preferential combination of endogenous ligands for 49 metal ions. User can also gain information about the residues present in the first and second coordination sphere as it plays a major role in maintaining the structure and function of metalloproteins in biological system. In this paper, a novel computational tool (ZINCCLUSTER) is developed, which can predict the zinc metal binding sites of proteins even if only the primary sequence is known. The purpose of this tool is to predict the active site cluster of an uncharacterized protein based on its primary sequence or a 3D structure. The tool can predict amino acids interacting with a metal or vice versa. This tool is based on the occurrence of significant triplets and it is tested to have higher prediction accuracy when compared to that of other available techniques. © 2017 Wiley Periodicals, Inc.

Oxidative damage to collagen and related substrates by metal ion/hydrogen peroxide systems

DEFF Research Database (Denmark)

Hawkins, C L; Davies, Michael Jonathan

1997-01-01

. In this study electron paramagnetic resonance spectroscopy with spin trapping has been used to identify radicals formed on collagen and related materials by metal ion-H2O2 mixtures. Attack of the hydroxyl radical, from a Fe(II)-H2O2 redox couple, on collagen peptides gave signals from both side chain (.CHR...... are similar to those from the alpha-carbon site of peptides and the side-chain of lysine. Enzymatic digestion of the large, protein-derived, species releases similar low-molecular-weight adducts. The metal ion employed has a dramatic effect on the species observed. With Cu(I)-H2O2 or Cu(II)-H2O2 instead of Fe(II)-H......2O2, evidence has been obtained for: i) altered sites of attack and fragmentation, ii) C-terminal decarboxylation, and iii) hydrogen abstraction at N-terminal alpha-carbon sites. This altered behaviour is believed to be due to the binding of copper ions to some substrates and hence site...

Importance of diffuse metal ion binding to RNA.

Science.gov (United States)

Tan, Zhi-Jie; Chen, Shi-Jie

2011-01-01

RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding.

Heavy metals binding properties of esterified lemon

Energy Technology Data Exchange (ETDEWEB)

Arslanoglu, Hasan; Altundogan, Hamdi Soner [Department of Chemical Engineering, Firat University, 23279 Elazig (Turkey); Tumen, Fikret, E-mail: ftumen@firat.edu.tr [Department of Chemical Engineering, Firat University, 23279 Elazig (Turkey)

2009-05-30

Sorption of Cd{sup 2+}, Cr{sup 3+}, Cu{sup 2+}, Ni{sup 2+}, Pb{sup 2+} and Zn{sup 2+} onto a carboxyl groups-rich material prepared from lemon was investigated in batch systems. The results revealed that the sorption is highly pH dependent. Sorption kinetic data indicated that the equilibrium was achieved in the range of 30-240 min for different metal ions and sorption kinetics followed the pseudo-second-order model for all metals studied. Relative sorption rate of various metal cations was found to be in the general order of Ni{sup 2+} > Cd{sup 2+} > Cu{sup 2+} > Pb{sup 2+} > Zn{sup 2+} > Cr{sup 3+}. The binding characteristics of the sorbent for heavy metal ions were analyzed under various conditions and isotherm data was accurately fitted to the Langmuir equation. The metal binding capacity order calculated from Langmuir isotherm was Pb{sup 2+} > Cu{sup 2+} > Ni{sup 2+} > Cd{sup 2+} > Zn{sup 2+} > Cr{sup 3+}. The mean free energy of metal sorption process calculated from Dubinin-Radushkevich parameter and the Polanyi potential was found to be in the range of 8-11 kJ mol{sup -1} for the metals studied showing that the main mechanism governing the sorption process seems to be ion exchange. The basic thermodynamic parameters of metals ion sorption process were calculated by using the Langmuir constants obtained from equilibration study. The {Delta}G{sup o} and {Delta}H{sup o} values for metals ion sorption on the lemon sorbent showed the process to be spontaneous and exothermic in nature. Relatively low {Delta}H{sup o} values revealed that physical adsorption significantly contributed to the mechanism.

The role of metallic ions in nano-bio hybrid catalysts from ab initio first principles

Science.gov (United States)

Behera, Sushant; Deb, Pritam

We employ high-accuracy linear-scaling density functional theory calculations with a near-complete basis set and a minimal parameter implicit solvent model, within the self-consistent calculation, on silver ion assimilated on bacteriorhodopsin (bR) at specific binding sites. The geometry optimization indicates the formation of stable active sites at the interface of nano-bio hybrid and density of states reflects the metallic behavior of the active sites. Detailed kinetics of the catalytic reaction is revealed using ab initio electronic structure calculations. We observed that the metal ion incorporated active sites are more efficient in electrolytic splitting of water than pristine sites due to their less value of Gibbs free energy for hydrogen evolution reaction and strong synergistic effect. The volcano plot analysis and free energy diagram are considered to understan hydrogen evolution efficiency. Moreover, the essential role of metallic ion on catalytic efficiency is elucidated. DBT, Government of India, vide Grant No BT/357/NE/TBP/ 2012. DST, GoI for financial support under INSPIRE Fellowship(IF150325).

A differential scanning calorimetric study of the effects of metal ions, substrate/product, substrate analogues and chaotropic anions on the thermal denaturation of yeast enolase 1.

Science.gov (United States)

Brewer, J M; Wampler, J E

2001-03-14

The thermal denaturation of yeast enolase 1 was studied by differential scanning calorimetry (DSC) under conditions of subunit association/dissociation, enzymatic activity or substrate binding without turnover and substrate analogue binding. Subunit association stabilizes the enzyme, that is, the enzyme dissociates before denaturing. The conformational change produced by conformational metal ion binding increases thermal stability by reducing subunit dissociation. 'Substrate' or analogue binding additionally stabilizes the enzyme, irrespective of whether turnover is occurring, perhaps in part by the same mechanism. More strongly bound metal ions also stabilize the enzyme more, which we interpret as consistent with metal ion loss before denaturation, though possibly the denaturation pathway is different in the absence of metal ion. We suggest that some of the stabilization by 'substrate' and analogue binding is owing to the closure of moveable polypeptide loops about the active site, producing a more 'closed' and hence thermostable conformation.

Cellulose Nanocrystals Obtained from Rice By-Products and Their Binding Potential to Metallic Ions

Directory of Open Access Journals (Sweden)

Vanessa L. Albernaz

2015-01-01

Full Text Available The present study aimed to develop and optimize a method to obtain cellulose nanocrystals from the agricultural by-products rice husk and straw and to evaluate their electrostructural modifications in the presence of metallic ions. First, different particle formation conditions and routes were tested and analyzed by spectrophotometry, dynamic light scattering (DLS, and Zeta potential measurements. Then, electrostructural effects of ions Na(I, Cd(II, and Al(III on the optimized nanoparticles were analyzed by atomic force microscopy (AFM, scanning electron microscopy (SEM, and electrical conductivity (EC assessments. The produced cellulose nanocrystals adopted a rod-like shape. AFM height distribution and EC data indicated that the nanocrystals have more affinity in binding with Na(I > Al(III > Cd(II. These data suggest that the use of these cellulose nanocrystals in the bioremediation field is promising, both in metal sorption from wastewater and as an alternative for water desalination.

Synthesis, characterization, anti-microbial, DNA binding and cleavage studies of Schiff base metal complexes

Directory of Open Access Journals (Sweden)

Poomalai Jayaseelan

2016-09-01

Full Text Available A novel Schiff base ligand has been prepared by the condensation between butanedione monoxime with 3,3′-diaminobenzidine. The ligand and metal complexes have been characterized by elemental analysis, UV, IR, 1H NMR, conductivity measurements, EPR and magnetic studies. The molar conductance studies of Cu(II, Ni(II, Co(II and Mn(II complexes showed non-electrolyte in nature. The ligand acts as dibasic with two N4-tetradentate sites and can coordinate with two metal ions to form binuclear complexes. The spectroscopic data of metal complexes indicated that the metal ions are complexed with azomethine nitrogen and oxyimino nitrogen atoms. The binuclear metal complexes exhibit octahedral arrangements. DNA binding properties of copper(II metal complex have been investigated by electronic absorption spectroscopy. Results suggest that the copper(II complex bind to DNA via an intercalation binding mode. The nucleolytic cleavage activities of the ligand and their complexes were assayed on CT-DNA using gel electrophoresis in the presence and absence of H2O2. The ligand showed increased nuclease activity when administered as copper complex and copper(II complex behave as efficient chemical nucleases with hydrogen peroxide activation. The anti-microbial activities and thermal studies have also been studied. In anti-microbial activity all complexes showed good anti-microbial activity higher than ligand against gram positive, gram negative bacteria and fungi.

Formation of Mixed-Ligand Complexes of Pd2+ with Nucleoside 5'-Monophosphates and Some Metal-Ion-Binding Nucleoside Surrogates

Directory of Open Access Journals (Sweden)

Oleg Golubev

2014-10-01

Full Text Available Formation of mixed-ligand Pd2+ complexes between canonical nucleoside 5'-monophosphates and five metal-ion-binding nucleoside analogs has been studied by 1H-NMR spectroscopy to test the ability of these nucleoside surrogates to discriminate between unmodified nucleobases by Pd2+-mediated base pairing. The nucleoside analogs studied included 2,6-bis(3,5-dimethylpyrazol-1-yl-, 2,6-bis(1-methylhydrazinyl- and 6-(3,5-dimethylpyrazol-1-yl-substituted 9-(β-d-ribofuranosylpurines 1–3, and 2,4-bis(3,5-dimethylpyrazol-1-yl- and 2,4-bis(1-methylhydrazinyl-substituted 5-(β-d-ribofuranosyl-pyrimidines 4–5. Among these, the purine derivatives 1-3 bound Pd2+ much more tightly than the pyrimidine derivatives 4, 5 despite apparently similar structures of the potential coordination sites. Compounds 1 and 2 formed markedly stable mixed-ligand Pd2+ complexes with UMP and GMP, UMP binding favored by 1 and GMP by 2. With 3, formation of mixed-ligand complexes was retarded by binding of two molecules of 3 to Pd2+.

Metal ion sequestration: An exciting dimension for molecularly ...

African Journals Online (AJOL)

The use of a tight binding macrocyclic ligand to complex a metal ion so that this serves as receptee on the Molecularly Imprinted Polymer (MIP) receptor as described here affords a sequestration route for a targeted metal ion, with potential for environmental remediation and restoration applications. Ethylene glycol ...

Covalent modifications of the amyloid beta peptide by hydroxynonenal: Effects on metal ion binding by monomers and insights into the fibril topology.

Science.gov (United States)

Grasso, G; Komatsu, H; Axelsen, P H

2017-09-01

Amyloid β peptides (Aβ) and metal ions are associated with oxidative stress in Alzheimer's disease (AD). Oxidative stress, acting on ω-6 polyunsaturated fatty acyl chains, produces diverse products, including 4-hydroxy-2-nonenal (HNE), which can covalently modify the Aβ that helped to produce it. To examine possible feedback mechanisms involving Aβ, metal ions and HNE production, the effects of HNE modification and fibril formation on metal ion binding was investigated. Results indicate that copper(II) generally inhibits the modification of His side chains in Aβ by HNE, but that once modified, copper(II) still binds to Aβ with high affinity. Fibril formation protects only one of the three His residues in Aβ from HNE modification, and this protection is consistent with proposed models of fibril structure. These results provide insight into a network of biochemical reactions that may be operating as a consequence of oxidative stress in AD, or as part of the pathogenic process. Copyright © 2016. Published by Elsevier Inc.

Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites

Energy Technology Data Exchange (ETDEWEB)

Radka, Christopher D.; DeLucas, Lawrence J.; Wilson, Landon S.; Lawrenz, Matthew B.; Perry, Robert D.; Aller, Stephen G.

2017-06-30

Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. InYersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA is polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.

Extracellular Membrane-proximal Domain of HAb18G/CD147 Binds to Metal Ion-dependent Adhesion Site (MIDAS) Motif of Integrin β1 to Modulate Malignant Properties of Hepatoma Cells*

Science.gov (United States)

Li, Yong; Wu, Jiao; Song, Fei; Tang, Juan; Wang, Shi-Jie; Yu, Xiao-Ling; Chen, Zhi-Nan; Jiang, Jian-Li

2012-01-01

Several lines of evidence suggest that HAb18G/CD147 interacts with the integrin variants α3β1 and α6β1. However, the mechanism of the interaction remains largely unknown. In this study, mammalian protein-protein interaction trap (MAPPIT), a mammalian two-hybrid method, was used to study the CD147-integrin β1 subunit interaction. CD147 in human hepatocellular carcinoma (HCC) cells was interfered with by small hairpin RNA. Nude mouse xenograft model and metastatic model of HCC were used to detect the role of CD147 in carcinogenesis and metastasis. We found that the extracellular membrane-proximal domain of HAb18G/CD147 (I-type domain) binds at the metal ion-dependent adhesion site in the βA domain of the integrin β1 subunit, and Asp179 in the I-type domain of HAb18G/CD147 plays an important role in the interaction. The levels of the proteins that act downstream of integrin, including focal adhesion kinase (FAK) and phospho-FAK, were decreased, and the cytoskeletal structures of HCC cells were rearranged bearing the HAb18G/CD147 deletion. Simultaneously, the migration and invasion capacities, secretion of matrix metalloproteinases, colony formation rate in vitro, and tumor growth and metastatic potential in vivo were decreased. These results indicate that the interaction of HAb18G/CD147 extracellular I-type domain with the integrin β1 metal ion-dependent adhesion site motif activates the downstream FAK signaling pathway, subsequently enhancing the malignant properties of HCC cells. PMID:22130661

Selective metal binding to Cys-78 within endonuclease V causes an inhibition of catalytic activities without altering nontarget and target DNA binding

International Nuclear Information System (INIS)

Prince, M.A.; Friedman, B.; Gruskin, E.A.; Schrock, R.D. III; Lloyd, R.S.

1991-01-01

T4 endonuclease V is a pyrimidine dimer-specific DNA repair enzyme which has been previously shown not to require metal ions for either of its two catalytic activities or its DNA binding function. However, we have investigated whether the single cysteine within the enzyme was able to bind metal salts and influence the various activities of this repair enzyme. A series of metals (Hg2+, Ag+, Cu+) were shown to inactivate both endonuclease Vs pyrimidine dimer-specific DNA glycosylase activity and the subsequent apurinic nicking activity. The binding of metal to endonuclease V did not interfere with nontarget DNA scanning or pyrimidine dimer-specific binding. The Cys-78 codon within the endonuclease V gene was changed by oligonucleotide site-directed mutagenesis to Thr-78 and Ser-78 in order to determine whether the native cysteine was directly involved in the enzyme's DNA catalytic activities and whether the cysteine was primarily responsible for the metal binding. The mutant enzymes were able to confer enhanced ultraviolet light (UV) resistance to DNA repair-deficient Escherichia coli at levels equal to that conferred by the wild type enzyme. The C78T mutant enzyme was purified to homogeneity and shown to be catalytically active on pyrimidine dimer-containing DNA. The catalytic activities of the C78T mutant enzyme were demonstrated to be unaffected by the addition of Hg2+ or Ag+ at concentrations 1000-fold greater than that required to inhibit the wild type enzyme. These data suggest that the cysteine is not required for enzyme activity but that the binding of certain metals to that amino acid block DNA incision by either preventing a conformational change in the enzyme after it has bound to a pyrimidine dimer or sterically interfering with the active site residue's accessibility to the pyrimidine dimer

Strontium and barium in aqueous solution and a potassium channel binding site

Science.gov (United States)

Chaudhari, Mangesh I.; Rempe, Susan B.

2018-06-01

Ion hydration structure and free energy establish criteria for understanding selective ion binding in potassium (K+) ion channels and may be significant to understanding blocking mechanisms as well. Recently, we investigated the hydration properties of Ba2+, the most potent blocker of K+ channels among the simple metal ions. Here, we use a similar method of combining ab initio molecular dynamics simulations, statistical mechanical theory, and electronic structure calculations to probe the fundamental hydration properties of Sr2+, which does not block bacterial K+ channels. The radial distribution of water around Sr2+ suggests a stable 8-fold geometry in the local hydration environment, similar to Ba2+. While the predicted hydration free energy of -331.8 kcal/mol is comparable with the experimental result of -334 kcal/mol, the value is significantly more favorable than the -305 kcal/mol hydration free energy of Ba2+. When placed in the innermost K+ channel blocking site, the solvation free energies and lowest energy structures of both Sr2+ and Ba2+ are nearly unchanged compared with their respective hydration properties. This result suggests that the block is not attributable to ion trapping due to +2 charge, and differences in blocking behavior arise due to free energies associated with the exchange of water ligands for channel ligands instead of free energies of transfer from water to the binding site.

Ion activity and distribution of heavy metals in acid mine drainage polluted subtropical soils

International Nuclear Information System (INIS)

Li Yongtao; Becquer, Thierry; Dai Jun; Quantin, Cecile; Benedetti, Marc F.

2009-01-01

The oxidative dissolution of mine wastes gives rise to acidic, metal-enriched mine drainage (AMD) and has typically posed an additional risk to the environment. The poly-metallic mine Dabaoshan in South China is an excellent test site to understand the processes affecting the surrounding polluted agricultural fields. Our objectives were firstly to investigate metal ion activity in soil solution, distribution in solid constituents, and spatial distribution in samples, secondly to determine dominant environment factors controlling metal activity in the long-term AMD-polluted subtropical soils. Soil Column Donnan Membrane Technology (SC-DMT) combined with sequential extraction shows that unusually large proportion of the metal ions are present as free ion in the soil solutions. The narrow range of low pH values prevents any pH effects during the binding onto oxides or organic matter. The differences in speciation of the soil solutions may explain the different soil degradation observed between paddy and non-paddy soils. - First evidence of the real free metal ion concentrations in acid mine drainage context in tropical systems

Simulations of hydrogen sorption in rht-MOF-1: identifying the binding sites through explicit polarization and quantum rotation calculations

KAUST Repository

Pham, Tony

2014-01-01

Grand canonical Monte Carlo (GCMC) simulations of hydrogen sorption were performed in rht-MOF-1, a metal-organic framework (MOF) that consists of isophthalate groups joined by copper paddlewheel clusters and Cu3O trimers through tetrazolate moeities. This is a charged rht-MOF that contains extra-framework nitrate counterions within the material. For the simulations performed herein, excellent agreement with experiment was achieved for the simulated hydrogen sorption isotherms and calculated isosteric heat of adsorption, Qst, values only when using a polarizable potential. Thermodynamic agreement is demonstrated via comparing to experimental isotherms and binding sites are revealed by combining simulation and inelastic neutron scattering (INS) data. Simulations involving explicit many-body polarization interactions assisted in the determination of the binding sites in rht-MOF-1 through the distribution of the induced dipoles that led to strong adsorbate interactions. Four distinct hydrogen sorption sites were determined from the polarization distribution: the nitrate ions located in the corners of the truncated tetrahedral cages, the Cu2+ ions of the paddlewheels that project into the truncated tetrahedral and truncated octahedral cages (Cu1 ions), the Cu2+ ions of the Cu3O trimers (Cu3 ions), and the sides of the paddlewheels in the cuboctahedral cage. The simulations revealed that the initial sorption sites for hydrogen in rht-MOF-1 are the nitrate ions; this site corresponds to the high initial Qst value for hydrogen (9.5 kJ mol-1) in the MOF. The radial distribution functions, g(r), about the Cu2+ ions at various loadings revealed that the Cu1 ions are the preferred open-metal sorption sites for hydrogen at low loading, while the Cu3 ions become occupied at higher loadings. The validation of the aforementioned sorption sites in rht-MOF-1 was confirmed by calculating the two-dimensional quantum rotational levels about each site and comparing the levels to the

Nanostructured Block Polymer Membranes as High Capacity Adsorbers for the Capture of Metal Ions from Water

Science.gov (United States)

Boudouris, Bryan; Weidman, Jacob; Mulvenna, Ryan; Phillip, William

The efficient removal of metal ions from aqueous streams is of significant import in applications ranging from industrial waste treatment to the purification of drinking water. An emerging paradigm associated with this separation is one that utilizes membrane adsorbers as a means by which to bind metal salt contaminants. Here, we demonstrate that the casting of an A-B-C triblock polymer using the self-assembly and non-solvent induced phase separation (SNIPS) methodology results in a nanoporous membrane geometry. The nature of the triblock polymer affords an extremely high density of binding sites within the membrane. As such, we demonstrate that the membranes with binding capacities equal to that of state-of-the-art packed bed columns. Moreover, because the affinity of the C moiety can be tuned, highly selective binding events can occur based solely on the chemistry of the block polymer and the metal ions in solution (i.e., in a manner that is independent of the size of the metal ions). Due to these combined facts, these membranes efficiently remove heavy metal (e.g., lead- and cadmium-based) salts from contaminated water streams with greater than 95% efficiency. Finally, we show that the membranes can be regenerated through a simple treatment in order to provide long-lasting adsorber systems as well. Thus, it is anticipated that these nanostructured triblock polymer membranes are a platform by which to obtain next-generation water purification processes.

Human Hsp70 molecular chaperone binds two calcium ions within the ATPase domain.

Science.gov (United States)

Sriram, M; Osipiuk, J; Freeman, B; Morimoto, R; Joachimiak, A

1997-03-15

in protein structure as a result of calcium binding may facilitate phosphorylation. A small, but significant, movement of metal ions and sidechains could position catalytically important threonine residues for phosphorylation. The second calcium site represents a new calcium-binding motif that can play a role in the stabilization of protein structure. We discuss how the information about catalytic events in the active site could be transmitted to the peptide-binding domain.

Effects of complexing compounds on sorption of metal ions to cement

Energy Technology Data Exchange (ETDEWEB)

Loevgren, Lars [Umeaa Univ. (Sweden). Inorganic chemistry

2005-12-15

This present report is a literature review addressing the effects of complexing ligands on the sorption of radionuclides to solid materials of importance for repositories of radioactive waste. Focus is put on laboratory studies of metal ion adsorption to cement in presence of chelating agents under strongly alkaline conditions. As background information, metal sorption to different mineral and cement phases in ligand free systems is described. Furthermore, surface complexation model (SCM) theories are introduced. According to surface complexation theories these interactions occur at specific binding sites at the particle/water interface. Adsorption of cationic metals is stronger at high pH, and the adsorption of anions occurs preferentially at low pH. The adsorption of ions to mineral surfaces is a result of both chemical bonding and electrostatic attraction between the ions and charged mineral surfaces. By combining uptake data with spectroscopic information the sorption can be explained on a molecular level by structurally sound surface complexation models. Most of the metal sorption studies reviewed are dealing with minerals exhibiting oxygen atoms at their surfaces, mainly oxides of Fe(II,III) and Al(III), and aluminosilicates. Investigations of radionuclides are focused on clay minerals, above all montmorillonite and illite. Which mechanism that is governing the metal ion adsorption to a given mineral is to a large extent depending on the metal adsorbed. For instance, sorption of Ni to montmorillonite can occur by formation of inner-sphere mononuclear surface complexes located at the edges of montmorillonite platelets and by formation of a Ni phyllosilicate phase parallel to montmorillonite layers. Also metal uptake to cement materials can occur by different mechanisms. Cationic metals can both be attached to cement (calcium silicate hydrate, CSH) and hardened cement paste (HCP) by formation of inner-sphere complexes at specific surface sites and by

Decreased Sensitivity to Changes in the Concentration of Metal Ions as the Basis for the Hyperactivity of DtxR(E175K)

Energy Technology Data Exchange (ETDEWEB)

D’Aquino, J. Alejandro; Denninger, Andrew R.; Moulin, Aaron G.; D’Aquino, Katharine E.; Ringe, Dagmar; (Harvard-Med); (Brandeis)

2010-01-12

The metal-ion-activated diphtheria toxin repressor (DtxR) is responsible for the regulation of virulence and other genes in Corynebacterium diphtheriae. A single point mutation in DtxR, DtxR(E175K), causes this mutant repressor to have a hyperactive phenotype. Mice infected with Mycobacterium tuberculosis transformed with plasmids carrying this mutant gene show reduced signs of the tuberculosis infection. Corynebacterial DtxR is able to complement mycobacterial IdeR and vice versa. To date, an explanation for the hyperactivity of DtxR(E175K) has remained elusive. In an attempt to address this issue, we have solved the first crystal structure of DtxR(E175K) and characterized this mutant using circular dichroism, isothermal titration calorimetry, and other biochemical techniques. The results show that although DtxR(E175K) and the wild type have similar secondary structures, DtxR(E175K) gains additional thermostability upon activation with metal ions, which may lead to this mutant requiring a lower concentration of metal ions to reach the same levels of thermostability as the wild-type protein. The E175K mutation causes binding site 1 to retain metal ion bound at all times, which can only be removed by incubation with an ion chelator. The crystal structure of DtxR(E175K) shows an empty binding site 2 without evidence of oxidation of Cys102. The association constant for this low-affinity binding site of DtxR(E175K) obtained from calorimetric titration with Ni(II) is K{sub a} = 7.6 {+-} 0.5 x 10{sup 4}, which is very similar to the reported value for the wild-type repressor, K{sub a} = 6.3 x 10{sup 4}. Both the wild type and DtxR(E175K) require the same amount of metal ion to produce a shift in the electrophoretic mobility shift assay, but unlike the wild type, DtxR(E175K) binding to its cognate DNA [tox promoter-operator (toxPO)] does not require metal-ion supplementation in the running buffer. In the timescale of these experiments, the Mn(II)-DtxR(E175K)-toxPO complex

A computational study of adsorption of divalent metal ions on graphene oxide

Directory of Open Access Journals (Sweden)

Somphob Thompho

2017-12-01

Full Text Available Adsorption of divalent metal ions (Pb2+,Cd2+, Zn2+,Cu2+ on graphene oxide (GO was studied using density functional theory (DFT. Adsorption geometries and energies, as well as the nature of the binding energy, were calculated for the interaction of divalent metal ions with oxygen-containing groups on the surface of GO. The configurations of the complexes were modeled by placing the divalent metal ions above the center and perpendicular to the surface. Binding of Cu2+ to the GO sheet was predicted to be much stronger than that for other divalent metal ions. Calculated results show good agreement with experimental observations and provide useful information for environmental pollution cleanup.

Electrospray Ionization Mass Spectrometry: From Cluster Ions to Toxic metal Ions in Biology

Energy Technology Data Exchange (ETDEWEB)

Lentz, Nicholas B. [Iowa State Univ., Ames, IA (United States)

2007-01-01

This dissertation focused on using electrospray ionization mass spectrometry to study cluster ions and toxic metal ions in biology. In Chapter 2, it was shown that primary, secondary and quarternary amines exhibit different clustering characteristics under identical instrument conditions. Carbon chain length also played a role in cluster ion formation. In Chapters 3 and 4, the effects of solvent types/ratios and various instrumental parameters on cluster ion formation were examined. It was found that instrument interface design also plays a critical role in the cluster ion distribution seen in the mass spectrum. In Chapter 5, ESI-MS was used to investigate toxic metal binding to the [Gln¹¹]-amyloid β-protein fragment (1-16). Pb and Cd bound stronger than Zn, even in the presence of excess Zn. Hg bound weaker than Zn. There are endless options for future work on cluster ions. Any molecule that is poorly ionized in positive ion mode can potentially show an increase in ionization efficiency if an appropriate anion is used to produce a net negative charge. It is possible that drug protein or drug/DNA complexes can also be stabilized by adding counter-ions. This would preserve the solution characteristics of the complex in the gas phase. Once in the gas phase, CID could determine the drug binding location on the biomolecule. There are many research projects regarding toxic metals in biology that have yet to be investigated or even discovered. This is an area of research with an almost endless future because of the changing dynamics of biological systems. What is deemed safe today may show toxic effects in the future. Evolutionary changes in protein structures may render them more susceptible to toxic metal binding. As the understanding of toxicity evolves, so does the demand for new toxic metal research. New instrumentation designs and software make it possible to perform research that could not be done in the past. What was undetectable yesterday will

Selective recovery of gold and other metal ions from an algal biomass

Energy Technology Data Exchange (ETDEWEB)

Darnall, D.W.; Greene, B.; Henzl, M.T.; Hosea, J.M.; McPherson, R.A.; Sneddon, J.; Alexander, M.D.

1986-02-01

The authors observed that the pH dependence of the binding of Au/sup 3 +/, Ag/sup +/, and Hg/sup 2 +/ to the algae Chlorella vulgaris is different than the binding of other metal ions. Between pH 5 and 7, a variety of metal ions bind strongly to the cell surface. Most of these algal-bound metal ions can be selectively desorbed by lowering the pH to 2; however, Au/sup 3 +/, Hg/sup 2 +/, and Ag/sup +/ are all bound strongly at pH 2. Addition of a strong ligand at different pHs is required to elute these ions from the algal surface. Algal-bound gold and mercury can be selectively eluted by using mercaptoethanol. An elution scheme is demonstrated for the binding and selective recovery of Cu/sup 2 +/, Zn/sup 2 +/, Au/sup 3 +/, and Hg/sup 2 +/ from an equimolar mixture. 20 references, 2 figures.

Theoretical examination of the trapping of ion-implanted hydrogen in metals

International Nuclear Information System (INIS)

Myers, S.M.; Nordlander, P.; Besenbacher, F.; Norskov, J.K.

1986-01-01

Theoretical analysis of the defect trapping of ion-implanted hydrogen in metals has been extended in two respects. A new transport formalism has been developed which takes account not only of the diffusion, trapping, and surface release of the hydrogen, which were included in earlier treatments, but also the diffusion, recombination, agglomeration, and surface annihilation of the vacancy and interstitial traps. In addition, effective-medium theory has been used to examine multiple hydrogen occupancy of the vacancy, and, for the fcc structure, appreciable binding enthalpies relative to the solution site have been found for occupancies of up to six. These extensions have been employed to model the depth distribution of ion-implanted hydrogen in Ni and Al during linear ramping of temperature, and the results have been used to interpret previously published data from these metals. The agreement between theory and experiment is good for both systems. In the case of Ni, the two experimentally observed hydrogen-release stages are both accounted for in terms of trapping at vacancies with a binding enthalpy that depends upon occupancy in accord with effective-medium theory

GenProBiS: web server for mapping of sequence variants to protein binding sites.

Science.gov (United States)

Konc, Janez; Skrlj, Blaz; Erzen, Nika; Kunej, Tanja; Janezic, Dusanka

2017-07-03

Discovery of potentially deleterious sequence variants is important and has wide implications for research and generation of new hypotheses in human and veterinary medicine, and drug discovery. The GenProBiS web server maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein-protein, protein-nucleic acid, protein-compound, and protein-metal ion binding sites. The concept of a protein-compound binding site is understood in the broadest sense, which includes glycosylation and other post-translational modification sites. Binding sites were defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach with new improvements introduced in GenProBiS. Binding site surfaces were generated as three-dimensional grids encompassing the space occupied by predicted ligands. The server allows intuitive visual exploration of comprehensively mapped variants, such as human somatic mis-sense mutations related to cancer and non-synonymous single nucleotide polymorphisms from 21 species, within the predicted binding sites regions for about 80 000 PDB protein structures using fast WebGL graphics. The GenProBiS web server is open and free to all users at http://genprobis.insilab.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Application of Sargassum biomass to remove heavy metal ions from synthetic multi-metal solutions and urban storm water runoff.

Science.gov (United States)

Vijayaraghavan, K; Teo, Ting Ting; Balasubramanian, R; Joshi, Umid Man

2009-05-30

The ability of Sargassum sp. to biosorb four metal ions, namely lead, copper, zinc, and manganese from a synthetic multi-solute system and real storm water runoff has been investigated for the first time. Experiments on synthetic multi-solute systems revealed that Sargassum performed well in the biosorption of all four metal ions, with preference towards Pb, followed by Cu, Zn, and Mn. The solution pH strongly affected the metal biosorption, with pH 6 being identified as the optimal condition for achieving maximum biosorption. Experiments at different biosorbent dosages revealed that good biosorption capacity as well as high metal removal efficiency was observed at 3g/L. The biosorption kinetics was found to be fast with equilibrium being attained within 50 min. According to the Langmuir isotherm model, Sargassum exhibited maximum uptakes of 214, 67.5, 24.2 and 20.2mg/g for lead, copper, zinc, and manganese, respectively in single-solute systems. In multi-metal systems, strong competition between four metal ions in terms of occupancy binding sites was observed, and Sargassum showed preference in the order of Pb>Cu>Zn>Mn. The application of Sargassum to remove four heavy metal ions in real storm water runoff revealed that the biomass was capable of removing the heavy metal ions. However, the biosorption performance was slightly lower compared to that of synthetic metal solutions. Several factors were responsible for this difference, and the most important factor is the presence of other contaminants such as anions, organics, and other trace metals in the runoff.

Glutamate Water Gates in the Ion Binding Pocket of Na(+) Bound Na(+), K(+)-ATPase

DEFF Research Database (Denmark)

Han, Minwoo; Kopec, Wojciech; Solov'yov, Ilia A

2017-01-01

III is always protonated. Glutamic acid residues in the three binding sites act as water gates, and their deprotonation triggers water entry to the binding sites. From DFT calculations of Na(+) binding energies, we conclude that three protons in the binding site are needed to effectively bind Na......The dynamically changing protonation states of the six acidic amino acid residues in the ion binding pocket of the Na(+), K(+) -ATPase (NKA) during the ion transport cycle are proposed to drive ion binding, release and possibly determine Na(+) or K(+) selectivity. We use molecular dynamics (MD......(+) from water and four are needed to release them in the next step. Protonation of Asp926 in site III will induce Na(+) release, and Glu327, Glu954 and Glu779 are all likely to be protonated in the Na(+) bound occluded conformation. Our data provides key insights into the role of protons in the Na...

Assessment of the Binding of Protons, Al and Fe to Biochar at Different pH Values and Soluble Metal Concentrations

Directory of Open Access Journals (Sweden)

Tan Dang

2018-01-01

Full Text Available Biochar can retain large amounts of protons and metals in the drainage water from acid sulfate soils and mine sites. Metal sorption can, however, be influenced by many factors, such as pH and metal composition. This study investigated proton, Al, and Fe retention capacity of eucalyptus biochar (1% w/v at different pH and metal concentrations. In the absence of metals, the biochar had a high proton binding capacity, (up to 0.035 mmol of H+, whereas its capacity to retain hydroxide ions was limited. A batch experiment was carried out at pH 4 and pH 7 with 10−6, 10−5, 10−4, 10−3, and 10−2 M of added Fe or Al. Added metals precipitated considerably prior to addition of the biochar except that Al remained highly soluble at pH 4. The biochar had a high retention capacity for Al and Fe; at high (>1 mM concentrations, over 80% of soluble metals were retained. Metal competition for binding sites of both Al and Fe at different ratios was investigated, but increasing concentrations of one metal did not reduce retention of the other. The results confirmed that biochar has high metal binding capacity under both acidic and neutral conditions.

Effect of metal ions on de novo aggregation of full-length prion protein

International Nuclear Information System (INIS)

Giese, Armin; Levin, Johannes; Bertsch, Uwe; Kretzschmar, Hans

2004-01-01

It is well established that the prion protein (PrP) contains metal ion binding sites with specificity for copper. Changes in copper levels have been suggested to influence incubation time in experimental prion disease. Therefore, we studied the effect of heavy metal ions (Cu 2+ , Mn 2+ , Ni 2+ , Co 2+ , and Zn 2+ ) in vitro in a model system that utilizes changes in the concentration of SDS to induce structural conversion and aggregation of recombinant PrP. To quantify and characterize PrP aggregates, we used fluorescently labelled PrP and cross-correlation analysis as well as scanning for intensely fluorescent targets in a confocal single molecule detection system. We found a specific strong pro-aggregatory effect of Mn 2+ at low micromolar concentrations that could be blocked by nanomolar concentration of Cu 2+ . These findings suggest that metal ions such as copper and manganese may also affect PrP conversion in vivo

[Adsorption of heavy metals on the surface of birnessite relationship with its Mn average oxidation state and adsorption sites].

Science.gov (United States)

Wang, Yan; Tan, Wen-Feng; Feng, Xiong-Han; Qiu, Guo-Hong; Liu, Fan

2011-10-01

Adsorption characteristics of mineral surface for heavy metal ions are largely determined by the type and amount of surface adsorption sites. However, the effects of substructure variance in manganese oxide on the adsorption sites and adsorption characteristics remain unclear. Adsorption experiments and powder X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) were combined to examine the adsorption characteristics of Pb2+, Cu2+, Zn2+ and Cd2+ sequestration by birnessites with different Mn average oxidation state (AOS), and the Mn AOS dependent adsorption sites and adsorption characteristics. The results show that the maximum adsorption capacity of Pb2+, Cu2+, Zn2+ and Cd2+ increased with increasing birnessite Mn AOS. The adsorption capacity followed the order of Pb2+ > Cu2+ > Zn2+ > Cd2+. The observations suggest that there exist two sites on the surface of birnessite, i. e., high-binding-energy site (HBE site) and low-binding-energy site (LBE site). With the increase of Mn AOS for birnessites, the amount of HBE sites for heavy metal ions adsorption remarkably increased. On the other hand, variation in the amount of LBE sites was insignificant. The amount of LBE sites is much more than those of HBE sites on the surface of birnessite with low Mn AOS. Nevertheless, both amounts on the surface of birnessite with high Mn AOS are very close to each other. Therefore, the heavy metal ions adsorption capacity on birnessite is largely determined by the amount of HBE sites. On birnessite surface, adsorption of Cu2+, Zn2+, and Cd2+ mostly occurred at HBE sites. In comparison with Zn2+ and Cd2+, more Cu2+ adsorbed on the LBW sites. Pb2+ adsorption maybe occupy at both LBE sites and HBE sites simultaneously.

Construction of Insulin 18-mer Nanoassemblies Driven by Coordination to Iron(II) and Zinc(II) Ions at Distinct Sites

DEFF Research Database (Denmark)

Munch, Henrik K.; Nygaard, Jesper; Christensen, Niels Johan

2016-01-01

Controlled self-assembly (SA) of proteins offers the possibility to tune their properties or to create new materials. Herein, we present the synthesis of a modified human insulin (HI) with two distinct metal-ion binding sites, one native, the other abiotic, enabling hierarchical SA through...

Interaction of antihypertensive drug amiloride with metal ions in micellar medium using fluorescence spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Gujar, Varsha; Pundge, Vijaykumar; Ottoor, Divya, E-mail: divya@chem.unipune.ac.in

2015-05-15

Steady state and life time fluorescence spectroscopy have been employed to study the interaction of antihypertensive drug amiloride with biologically important metal ions i.e. Cu{sup 2+}, Fe{sup 2+}, Ni{sup 2+} and Zn{sup 2+} in various micellar media (anionic SDS (sodium dodecyl sulfate), nonionic TX-100 (triton X-100) and cationic CTAB (cetyl trimethyl ammonium bromide)). It was observed that fluorescence properties of drug remain unaltered in the absence of micellar media with increasing concentration of metal ions. However, addition of Cu{sup 2+}, Fe{sup 2+} and Ni{sup 2+} caused fluorescence quenching of amiloride in the presence of anionic micelle, SDS. Binding of drug with metal ions at the charged micellar interface could be the possible reason for this pH-dependent metal-mediated fluorescence quenching. There were no remarkable changes observed due to metal ions addition when drug was present in cationic and nonionic micellar medium. The binding constant and bimolecular quenching constant were evaluated and compared for the drug–metal complexes using Stern–Volmer equation and fluorescence lifetime values. - Highlights: • Interaction of amiloride with biologically important metal ions, Fe{sup 2+}, Cu{sup 2+}, Ni{sup 2+} and Zn{sup 2+}. • Monitoring the interaction in various micelle at different pH by fluorescence spectroscopy. • Micelles acts as receptor, amiloride as transducer and metal ions as analyte in the present system. • Interaction study provides pH dependent quenching and binding mechanism of drug with metal ions.

Interaction of antihypertensive drug amiloride with metal ions in micellar medium using fluorescence spectroscopy

International Nuclear Information System (INIS)

Gujar, Varsha; Pundge, Vijaykumar; Ottoor, Divya

2015-01-01

Steady state and life time fluorescence spectroscopy have been employed to study the interaction of antihypertensive drug amiloride with biologically important metal ions i.e. Cu 2+ , Fe 2+ , Ni 2+ and Zn 2+ in various micellar media (anionic SDS (sodium dodecyl sulfate), nonionic TX-100 (triton X-100) and cationic CTAB (cetyl trimethyl ammonium bromide)). It was observed that fluorescence properties of drug remain unaltered in the absence of micellar media with increasing concentration of metal ions. However, addition of Cu 2+ , Fe 2+ and Ni 2+ caused fluorescence quenching of amiloride in the presence of anionic micelle, SDS. Binding of drug with metal ions at the charged micellar interface could be the possible reason for this pH-dependent metal-mediated fluorescence quenching. There were no remarkable changes observed due to metal ions addition when drug was present in cationic and nonionic micellar medium. The binding constant and bimolecular quenching constant were evaluated and compared for the drug–metal complexes using Stern–Volmer equation and fluorescence lifetime values. - Highlights: • Interaction of amiloride with biologically important metal ions, Fe 2+ , Cu 2+ , Ni 2+ and Zn 2+ . • Monitoring the interaction in various micelle at different pH by fluorescence spectroscopy. • Micelles acts as receptor, amiloride as transducer and metal ions as analyte in the present system. • Interaction study provides pH dependent quenching and binding mechanism of drug with metal ions

The metal binding potential of a dairy isolate

Directory of Open Access Journals (Sweden)

K. Ramyakrishna

2017-12-01

Full Text Available 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.

Cupryphans, metal-binding, redox-active, redesigned conopeptides.

Science.gov (United States)

Barba, Marco; Sobolev, Anatoli P; Romeo, Cristina; Schininà, M Eugenia; Pietraforte, Donatella; Mannina, Luisa; Musci, Giovanni; Polticelli, Fabio

2009-03-01

Contryphans are bioactive peptides, isolated from the venom of marine snails of the genus Conus, which are characterized by the short length of the polypeptide chain and the high degree of unusual post-translational modifications. The cyclization of the polypeptide chain through a single disulphide bond, the presence of two conserved Pro residues, and the epimerization of a Trp/Leu residue confer to Contryphans a stable and well-defined structure in solution, conserved in all members of the family, and tolerant to multiple substitutions. The potential of Contryphans as scaffolds for the design of redox-active (macro)molecules was tested by engineering a copper-binding site on two different variants of the natural peptide Contryphan-Vn. The binding site was designed by computational modeling, and the redesigned peptides were synthesized and characterized by optical, fluorescence, electron spin resonance, and nuclear magnetic resonance spectroscopy. The novel peptides, named Cupryphan and Arg-Cupryphan, bind Cu(2+) ions with a 1:1 stoichiometry and a K(d) in the 100 nM range. Other divalent metals (e.g., Zn(2+) and Mg(2+)) are bound with much lower affinity. In addition, Cupryphans catalyze the dismutation of superoxide anions with an activity comparable to other nonpeptidic superoxide dismutase mimics. We conclude that the Contryphan motif represents a natural robust scaffold which can be engineered to perform different functions, providing additional means for the design of catalytically active mini metalloproteins.

Fungitoxicity of metal ions

Energy Technology Data Exchange (ETDEWEB)

Somers, E

1961-01-01

The in vitro fungistatic activity of some twenty-four metal cations has been determine against Alternaria tenuis and Botrytis fabae. The metal salts, mainly nitrates, were tested in aqueous solution without added spore germination stimulant. The logarithm of the metal ion concentration at the ED 50 value has been found to conform to the exponenttial relationship with electronegativity proposed by Danielli and Davies (1951). These results are discussed in relation to the site of action of metal cations on the fungal cell.

UTSA-74: A MOF-74 Isomer with Two Accessible Binding Sites per Metal Center for Highly Selective Gas Separation

KAUST Repository

Luo, Feng

2016-04-26

A new metal-organic framework Zn2(H2O)-(dobdc)·0.5(H2O) (UTSA-74, H4dobdc = 2,5-dioxido-1,4-benzenedicarboxylic acid), Zn-MOF-74/CPO-27-Zn isomer, has been synthesized and structurally characterized. It has a novel four coordinated fgl topology with one-dimensional channels of about 8.0 Å. Unlike metal sites in the wellestablished MOF-74 with a rod-packing structure in which each of them is in a five coordinate square pyramidal coordination geometry, there are two different Zn2+ sites within the binuclear secondary building units in UTSA-74 in which one of them (Zn1) is in a tetrahedral while another (Zn2) in an octahedral coordination geometry. After activation, the two axial water molecules on Zn2 sites can be removed, generating UTSA-74a with two accessible gas binding sites per Zn2 ion. Accordingly, UTSA-74a takes up a moderately high and comparable amount of acetylene (145 cm3/cm3) to Zn-MOF-74. Interestingly, the accessible Zn2+ sites in UTSA-74a are bridged by carbon dioxide molecules instead of being terminally bound in Zn-MOF-74, so UTSA-74a adsorbs a much smaller amount of carbon dioxide (90 cm3/cm3) than Zn-MOF-74 (146 cm3/cm3) at room temperature and 1 bar, leading to a superior MOF material for highly selective C2H2/CO2 separation. X-ray crystal structures, gas sorption isotherms, molecular modeling, and simulated and experimental breakthroughs comprehensively support this result. © 2016 American Chemical Society.

Functional analysis of the citrate activator CitO from Enterococcus faecalis implicates a divalent metal in ligand binding

Directory of Open Access Journals (Sweden)

Victor S. Blancato

2016-02-01

Full Text Available The regulator of citrate metabolism, CitO, from Enterococcus faecalis belongs to the FCD family within the GntR superfamily. In the presence of citrate, CitO binds to cis-acting sequences located upstream of the cit promoters inducing the expression of genes involved in citrate utilization. The quantification of the molecular binding affinities, performed by isothermal titration calorimetry (ITC, indicated that CitO has a high affinity for citrate (KD= 1.2±0.2 µM, while it did not recognize other metabolic intermediates. Based on a structural model of CitO where a putative small molecule and a metal binding site were identified, it was hypothesized that the metal ion is required for citrate binding. In agreement with this model, citrate binding to CitO sharply decreased when the protein was incubated with EDTA. This effect was reverted by the addition of Ni2+, and Zn2+ to a lesser extent. Structure-based site-directed mutagenesis was conducted and it was found that changes to alanine in residues Arg97 and His191 resulted in decreased binding affinities for citrate, as determined by EMSA and ITC. Further assays using lacZ fusions confirmed that these residues in CitO are involved in sensing citrate in vivo. These results indicate that the molecular modifications induced by a ligand and a metal binding in the C-terminal domain of CitO are required for optimal DNA binding activity, and consequently, transcriptional activation.

Global Structural Flexibility of Metalloproteins Regulates Reactivity of Transition Metal Ion in the Protein Core: An Experimental Study Using Thiol-subtilisin as a Model Protein.

Science.gov (United States)

Matsuo, Takashi; Kono, Takamasa; Shobu, Isamu; Ishida, Masaya; Gonda, Katsuya; Hirota, Shun

2018-02-21

The functions of metal-containing proteins (metalloproteins) are determined by the reactivities of transition metal ions at their active sites. Because protein macromolecular structures have several molecular degrees of freedom, global structural flexibility may also regulate the properties of metalloproteins. However, the influence of this factor has not been fully delineated in mechanistic studies of metalloproteins. Accordingly, we have investigated the relationship between global protein flexibility and the characteristics of a transition metal ion in the protein core using thiol-subtilisin (tSTL) with a Cys-coordinated Cu 2+ ion as a model system. Although tSTL has two Ca 2+ -binding sites, the Ca 2+ -binding status hardly affects its secondary structure. Nevertheless, guanidinium-induced denaturation and amide H/D exchange indicated the increase in the structural flexibility of tSTL by the removal of bound Ca 2+ ions. Electron paramagnetic resonance and absorption spectral changes have revealed that the protein flexibility determines the characteristics of a Cu 2+ ion in tSTL. Therefore, global protein flexibility should be recognized as an important factor that regulates the properties of metalloproteins. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adsorption of heavy metals ions on portulaca oleracea plants

International Nuclear Information System (INIS)

Naqvi, R.R.

2005-01-01

The aim of this study is to report the ability of portulaca oleracea (Fershi in Urdu) biomass grown in uncontaminated soils to adsorb or uptake lead, cadmium, arsenic, cobalt and copper from aqueous solutions. In order to help understand the metal binding mechanism, laboratory experiments performance to determine optimal binding, and binding capacity for each of the above mentioned metals. These experiments were carried out for the mass of crushed portulaca stems. Portulaca is a plant that grows abundantly in temperature climate in the area of Quetta Balochistan. It has reddish stem and thick succulent leaves. This plant has been found to be good adsorbent for heavy metals ions. (author)

DISTINCT ROLES OF β1 MIDAS, ADMIDAS AND LIMBS CATION-BINDING SITES IN LIGAND RECOGNITION BY INTEGRIN α2β1*

Science.gov (United States)

Valdramidou, Dimitra; Humphries, Martin J.; Mould, A. Paul

2012-01-01

Integrin-ligand interactions are regulated in a complex manner by divalent cations, and previous studies have identified ligand-competent, stimulatory, and inhibitory cation-binding sites. In collagen-binding integrins, such as α2β1, ligand recognition takes place exclusively at the α subunit I domain. However, activation of the αI domain depends on its interaction with a structurally similar domain in the β subunit known as the I-like or βI domain. The top face of the βI domain contains three cation-binding sites: the metal-ion dependent adhesion site (MIDAS), the ADMIDAS (adjacent to MIDAS) and LIMBS (ligand-associated metal binding site). The role of these sites in controlling ligand binding to the αI domain has yet to be elucidated. Mutation of the MIDAS or LIMBS completely blocked collagen binding to α2β1; in contrast mutation of the ADMIDAS reduced ligand recognition but this effect could be overcome by the activating mAb TS2/16. Hence, the MIDAS and LIMBS appear to be essential for the interaction between αI and βI whereas occupancy of the ADMIDAS has an allosteric effect on the conformation of βI. An activating mutation in the α2 I domain partially restored ligand binding to the MIDAS and LIMBS mutants. Analysis of the effects of Ca2+, Mg2+ and Mn2+ on ligand binding to these mutants showed that the MIDAS is a ligand-competent site through which Mn2+ stimulates ligand binding, whereas the LIMBS is a stimulatory Ca2+-binding site, occupancy of which increases the affinity of Mg2+ for the MIDAS. PMID:18820259

Parkinson Disease Protein DJ-1 Binds Metals and Protects against Metal-induced Cytotoxicity*

Science.gov (United States)

Björkblom, Benny; Adilbayeva, Altynai; Maple-Grødem, Jodi; Piston, Dominik; Ökvist, Mats; Xu, Xiang Ming; Brede, Cato; Larsen, Jan Petter; Møller, Simon Geir

2013-01-01

The progressive loss of motor control due to reduction of dopamine-producing neurons in the substantia nigra pars compacta and decreased striatal dopamine levels are the classically described features of Parkinson disease (PD). Neuronal damage also progresses to other regions of the brain, and additional non-motor dysfunctions are common. Accumulation of environmental toxins, such as pesticides and metals, are suggested risk factors for the development of typical late onset PD, although genetic factors seem to be substantial in early onset cases. Mutations of DJ-1 are known to cause a form of recessive early onset Parkinson disease, highlighting an important functional role for DJ-1 in early disease prevention. This study identifies human DJ-1 as a metal-binding protein able to evidently bind copper as well as toxic mercury ions in vitro. The study further characterizes the cytoprotective function of DJ-1 and PD-mutated variants of DJ-1 with respect to induced metal cytotoxicity. The results show that expression of DJ-1 enhances the cells' protective mechanisms against induced metal toxicity and that this protection is lost for DJ-1 PD mutations A104T and D149A. The study also shows that oxidation site-mutated DJ-1 C106A retains its ability to protect cells. We also show that concomitant addition of dopamine exposure sensitizes cells to metal-induced cytotoxicity. We also confirm that redox-active dopamine adducts enhance metal-catalyzed oxidation of intracellular proteins in vivo by use of live cell imaging of redox-sensitive S3roGFP. The study indicates that even a small genetic alteration can sensitize cells to metal-induced cell death, a finding that may revive the interest in exogenous factors in the etiology of PD. PMID:23792957

Pb(II) and Hg(II) binding to $\\textit{de novo}$ designed proteins studied by $^{204m}$Pb- and $^{199m}$Hg-Perturbed Angular Correlation of $\\gamma$-rays (PAC) spectroscopy : Clues to heavy metal toxicity

CERN Multimedia

2002-01-01

$\\textit{De novo}$ design of proteins combined with PAC spectroscopy offers a unique and powerful approach to the study of fundamental chemistry of heavy metal-protein interactions, and thus of the mechanisms underlying heavy metal toxicity. In this project we focus on Pb(II) and Hg(II) binding to designed three stranded coiled coil proteins with one or two binding sites, mimicking a variety of naturally occurring thiolate-rich metal ion binding sites in proteins. The $^{204m}$Pb- and $^{199m}$Hg-PAC experiments will complement data already recorded with EXAFS, NMR, UV-Vis and CD spectroscopies.

Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs+-selective binding site

International Nuclear Information System (INIS)

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Matsumoto, Fumiko; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu; Adachi, Motoyasu; Tamada, Taro; Kawamoto, Masahide; Tokunaga, Hiroko; Ishibashi, Matsujiro; Blaber, Michael; Tokunaga, Masao; Kuroki, Ryota

2015-01-01

The tertiary structure of a β-lactamase derived from the halobacterium Chromohalobacter sp. 560 (HaBLA) was determined by X-ray crystallography. Three unique Sr 2+ -binding sites and one Cs + -binding site were discovered in the HaBLA molecule. Environmentally friendly absorbents are needed for Sr 2+ and Cs + , as the removal of the radioactive Sr 2+ and Cs + that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs + or Sr 2+ . The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P3 1 using X-ray crystallography. Moreover, the locations of bound Sr 2+ and Cs + ions were identified by anomalous X-ray diffraction. The location of one Cs + -specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na + (90 mM Na + /10 mM Cs + ). From an activity assay using isothermal titration calorimetry, the bound Sr 2+ and Cs + ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs + -binding site provides important information that is useful for the design of artificial Cs + -binding sites that may be useful in the bioremediation of radioactive isotopes

Molecular mechanism of AMD3100 antagonism in the CXCR4 receptor: transfer of binding site to the CXCR3 receptor

DEFF Research Database (Denmark)

Rosenkilde, Mette M; Gerlach, Lars-Ole; Jakobsen, Janus S

2004-01-01

, respectively. Metal ion binding in the cyclam rings of AMD3100 increased its dependence on Asp(262) and provided a tighter molecular map of the binding site, where borderline mutational hits became clear hits for the Zn(II)-loaded analog. The proposed binding site for AMD3100 was confirmed by a gradual build......-up in the rather distinct CXCR3 receptor, for which the compound normally had no effect. Introduction of only a Glu at position VII:06 and the removal of a neutralizing Lys residue at position VII:02 resulted in a 1000-fold increase in affinity of AMD3100 to within 10-fold of its affinity in CXCR4. We conclude...

Highly sensitive colour change system within slight differences in metal ion concentrations based on homo-binuclear complex formation equilibrium for visual threshold detection of trace metal ions

International Nuclear Information System (INIS)

Mizuguchi, Hitoshi; Atsumi, Hiroshi; Hashimoto, Keigo; Shimada, Yasuhiro; Kudo, Yuki; Endo, Masatoshi; Yokota, Fumihiko; Shida, Junichi; Yotsuyanagi, Takao

2004-01-01

A new technique of expressing slight differences in metal ion concentrations by clear difference in colour was established for visual threshold detection of trace metal ions. The proposed method is based on rapid change of the mole fraction of the homo-binuclear complex (M 2 L) about a ligand in a narrow range of the total metal ion concentration (M T ) in a small excess, in case the second metal ion is bound to the reagent molecule which can bind two metal ions. Theoretical simulations showed that the highly sensitive colour change within slight differences in metal ion concentrations would be realized under the following conditions: (i) both of the stepwise formation constants of complex species are sufficiently large; (ii) the stepwise formation constant of the 1:1 complex (ML) is larger than that of M 2 L; and (iii) the absorption spectrum of M 2 L is far apart from the other species in the visible region. Furthermore, the boundary of the colour region in M T would be readily controlled by the total ligand concentration (L T ). Based on this theory, the proposed model was verified with the 3,3'-bis[bis(carboxymethyl)amino]methyl derivatives of sulphonephthalein dyes such as xylenol orange (XO), methylthymol blue (MTB), and methylxylenol blue (MXB), which can bind two metal ions at both ends of a π-electron conjugated system. The above-mentioned model was proved with the iron(III)-XO system at pH 2. In addition, MTB and MXB were suitable reagents for the visual threshold detection of trivalent metal ions such as iron(III), aluminium(III), gallium(III) and indium(III) ion in slightly acidic media. The proposed method has been applied successfully as a screening test for aluminium(III) ion in river water sampled at the downstream area of an old mine

Selective recognition by novel calix system: ICT based chemosensor for metal ions

Energy Technology Data Exchange (ETDEWEB)

Bhatt, Keyur D.; Makwana, Bharat A.; Vyas, Disha J.; Mishra, Divya R.; Jain, Vinod K., E-mail: drvkjain@hotmail.com

2014-02-15

A new calix[4]pyrrole derivative bearing four dansyl groups through hydroxyl groups has been synthesized and duly characterized by FT-IR, NMR and ESI-MS. Tetra dansylated calix[4]pyrrole (TDCP) shows selective behavior for U(VI), Th(IV) and Fe(III) ions among all other metal ions, e.g. Li(I), Na(I), K(I), Ca(II), Ni(II), Cd(II), Cu(II), Zn(II), Pb(II), Hg(II) and Ag(I), in the absorption spectra as well as in the emission spectra. The absorption spectra show a bathochromic shift while the emission spectra along with red-shift exhibit quenching for U(VI), Th(IV) and Fe(III) ions. The binding constants, stoichiometry and quantum yields have been determined. The mechanism of quenching by Stern–Vohmer equation has also been discussed. -- highlights: • A new selective turn-off fluorescent sensor i.e. tetra dansylated calix[4]pyrrole (TDCP) was synthesized and characterized. • The sensor shows selective behavior for U(VI), Th(IV) and Fe(III) ions among various other metal ions. • The absorption spectra show a bathochromic shift while the emission spectra along with red-shift exhibit quenching for U(VI), Th(IV) and Fe(III) ions. • The sensor binds metal ions in 1:1 stoichiometry with good binding constant.

Selective recognition by novel calix system: ICT based chemosensor for metal ions

International Nuclear Information System (INIS)

Bhatt, Keyur D.; Makwana, Bharat A.; Vyas, Disha J.; Mishra, Divya R.; Jain, Vinod K.

2014-01-01

A new calix[4]pyrrole derivative bearing four dansyl groups through hydroxyl groups has been synthesized and duly characterized by FT-IR, NMR and ESI-MS. Tetra dansylated calix[4]pyrrole (TDCP) shows selective behavior for U(VI), Th(IV) and Fe(III) ions among all other metal ions, e.g. Li(I), Na(I), K(I), Ca(II), Ni(II), Cd(II), Cu(II), Zn(II), Pb(II), Hg(II) and Ag(I), in the absorption spectra as well as in the emission spectra. The absorption spectra show a bathochromic shift while the emission spectra along with red-shift exhibit quenching for U(VI), Th(IV) and Fe(III) ions. The binding constants, stoichiometry and quantum yields have been determined. The mechanism of quenching by Stern–Vohmer equation has also been discussed. -- highlights: • A new selective turn-off fluorescent sensor i.e. tetra dansylated calix[4]pyrrole (TDCP) was synthesized and characterized. • The sensor shows selective behavior for U(VI), Th(IV) and Fe(III) ions among various other metal ions. • The absorption spectra show a bathochromic shift while the emission spectra along with red-shift exhibit quenching for U(VI), Th(IV) and Fe(III) ions. • The sensor binds metal ions in 1:1 stoichiometry with good binding constant

Sequence of ligand binding and structure change in the diphtheria toxin repressor upon activation by divalent transition metals.

Science.gov (United States)

Rangachari, Vijayaraghavan; Marin, Vedrana; Bienkiewicz, Ewa A; Semavina, Maria; Guerrero, Luis; Love, John F; Murphy, John R; Logan, Timothy M

2005-04-19

The diphtheria toxin repressor (DtxR) is an Fe(II)-activated transcriptional regulator of iron homeostatic and virulence genes in Corynebacterium diphtheriae. DtxR is a two-domain protein that contains two structurally and functionally distinct metal binding sites. Here, we investigate the molecular steps associated with activation by Ni(II)Cl(2) and Cd(II)Cl(2). Equilibrium binding energetics for Ni(II) were obtained from isothermal titration calorimetry, indicating apparent metal dissociation constants of 0.2 and 1.7 microM for two independent sites. The binding isotherms for Ni(II) and Cd(II) exhibited a characteristic exothermic-endothermic pattern that was used to infer the metal binding sequence by comparing the wild-type isotherm with those of several binding site mutants. These data were complemented by measuring the distance between specific backbone amide nitrogens and the first equivalent of metal through heteronuclear NMR relaxation measurements. Previous studies indicated that metal binding affects a disordered to ordered transition in the metal binding domain. The coupling between metal binding and structure change was investigated using near-UV circular dichroism spectroscopy. Together, the data show that the first equivalent of metal is bound by the primary metal binding site. This binding orients the DNA binding helices and begins to fold the N-terminal domain. Subsequent binding at the ancillary site completes the folding of this domain and formation of the dimer interface. This model is used to explain the behavior of several mutants.

Lanthanide and actinide ion phytoextraction: investigations of biosorption chemistry

International Nuclear Information System (INIS)

Rayson, Gary D.; Serna, Debbie D.; Moore, Jessica L.

2009-01-01

Investigations of the chemical interactions responsible for passive biosorption of a lanthanide (Eu (III)) and an actinide (U (VI)) metal ion is described. Spectroscopic methods for the elucidation of chemical functionalities on cultured anther cell walls from the plant Datura innoxia include metal ion luminescence measurements. These have revealed the presence of distinctly different binding environments involving one, two, and three carboxylate moieties for Eu (III) and UO 2 2+ binding and sulfonates (or sulfates) and phosphates for sequestration of Eu (III) on the uranyl ion, respectively. Additional investigations of the apparent affinities of these metals to this material have revealed the presence of both low and high affinity sites for the binding of Eu (III) with weak electrostatic attractions proposed for binding at high metal concentrations (i.e., low affinities) and surface coordination interactions responsible for higher affinities. Conversely, total uranyl ion binding revealed only a single distribution of interactions based on apparent affinities. (author)

Engineering of a calcium-ion binding site into the RC-LH1-PufX complex of Rhodobacter sphaeroides to enable ion-dependent spectral red-shifting.

Science.gov (United States)

Swainsbury, David J K; Martin, Elizabeth C; Vasilev, Cvetelin; Parkes-Loach, Pamela S; Loach, Paul A; Neil Hunter, C

2017-11-01

The reaction centre-light harvesting 1 (RC-LH1) complex of Thermochromatium (Tch.) tepidum has a unique calcium-ion binding site that enhances thermal stability and red-shifts the absorption of LH1 from 880nm to 915nm in the presence of calcium-ions. The LH1 antenna of mesophilic species of phototrophic bacteria such as Rhodobacter (Rba.) sphaeroides does not possess such properties. We have engineered calcium-ion binding into the LH1 antenna of Rba. sphaeroides by progressively modifying the native LH1 polypeptides with sequences from Tch. tepidum. We show that acquisition of the C-terminal domains from LH1 α and β of Tch. tepidum is sufficient to activate calcium-ion binding and the extent of red-shifting increases with the proportion of Tch. tepidum sequence incorporated. However, full exchange of the LH1 polypeptides with those of Tch. tepidum results in misassembled core complexes. Isolated α and β polypeptides from our most successful mutant were reconstituted in vitro with BChl a to form an LH1-type complex, which was stabilised 3-fold by calcium-ions. Additionally, carotenoid specificity was changed from spheroidene found in Rba. sphaeroides to spirilloxanthin found in Tch. tepidum, with the latter enhancing in vitro formation of LH1. These data show that the C-terminal LH1 α/β domains of Tch. tepidum behave autonomously, and are able to transmit calcium-ion induced conformational changes to BChls bound to the rest of a foreign antenna complex. Thus, elements of foreign antenna complexes, such as calcium-ion binding and blue/red switching of absorption, can be ported into Rhodobacter sphaeroides using careful design processes. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Multiheteromacrocycles that Complex Metal Ions. Second Progress Report, 1 May 1975 -- 30 April 1976

Science.gov (United States)

Cram, D. J.

1976-01-15

Objective is to develop cyclic and polycyclic host organic compounds to complex and lipophilize metal ions. Macrorings were synthesized: (OCH{sub 2} CH{sub 2} O CH{sub 2}COCH{sub 2} COCH{sub 2}){sub 2} and (OCH{sub 2} CH{sub 2} O CH{sub 2} COCH{sub 2} COCH{sub 2}){sub 3}. The smaller ring complexes divalent metals 10{sup 1+9} times better than the open-chain model CH{sub 3} O CH{sub 2} CO CH{sub 2} COCH{sub 2} O CH{sub 3}, and the order in which metal ions are complexed is Cu{sup 2+}, UO{sub 2}{sup 2+} greater than Ni{sup 2+} greater than Fe{sup 2+}, Co{sup 2+}, Zn{sup 2+}, Cd{sup 2+} greater than Mn{sup 2+}. The UO{sub 2}{sup 2+} and Cu{sup 2+} complexes were isolated and characterized. The larger ring complexes trivalent metals 10{sup 0.9-1.7} times better than the open- chain model compound, and the order is La{sup 3+}, Ce{sup 3+} greater than Cr{sup 3+}. Five other macrocycles were also synthesized, and their binding constants with Na, K, NH{sub 4}, and Cs picrates were measured. Six compounds containing one macroring and two inward-pointing ArOH or ArOCH{sub 3} groups were also prepared and tested for binding of Li, Na, K, Rb, and NH{sub 4} picrates. Racemic compounds containing two binaphthyls and its sulfur analog were prepared. Cage-shaped multiheteromacrocycles containing ten O ligand sites or four S and six O ligand sites were prepared and the binding capability of the first compound for picrates studied. Two ring systems with phosphonate ester groups were also prepared. (DLC)

Cleavage reactions of the complex ions derived from self-complementary deoxydinucleotides and alkali-metal ions using positive ion electrospray ionization with tandem mass spectrometry.

Science.gov (United States)

Xiang, Yun; Abliz, Zeper; Takayama, Mitsuo

2004-05-01

The dissociation reactions of the adduct ions derived from the four self-complementary deoxydinucleotides, d(ApT), d(TpA), d(CpG), d(GpC), and alkali-metal ions were studied in detail by positive ion electrospray ionization multiple-stage mass spectrometry (ESI-MS(n)). For the [M + H](+) ions of the four deoxydinucleotides, elimination of 5'-terminus base or loss of both of 5'-terminus base and a deoxyribose were the major dissociation pathway. The ESI-MS(n) spectra showed that Li(+), Na(+), and Cs(+) bind to deoxydinucleotides mainly by substituting the H(+) of phosphate group, and these alkali-metal ions preferred to bind to pyrimidine bases rather than purine bases. For a given deoxydinucleotide, the dissociation pathway of [M + K](+) ions differed clearly from that of [M + Li](+), [M + Na](+), and [M + Cs](+) ions. Some interesting and characteristic cleavage reactions were observed in the product-ion spectra of [M + K](+) ions, including direct elimination of deoxyribose and HPO(3) from molecular ions. The fragmentation behavior of the [M + K](+) and [M + W](+) (W = Li, Na, Cs) adduct ions depend upon the sequence of bases, the interaction between alkali-metal ions and nucleobases, and the steric hindrance caused by bases.

Rational Synthesis of Imprinted Organofunctional Sol-Gel Materials for Toxic Metal Separation - Final Report - 09/15/1997 - 09/14/2001

International Nuclear Information System (INIS)

Xue, Ziling; Barnes, Craig E.; Dai, Shang

2001-01-01

Current cost estimates for the environmental remediation of contaminated installations under the auspices of the Department of Energy (DOE) are staggering. On this basis alone, there is a critical need to develop the scientific basis for new approaches to the treatment and disposal of toxic metal ions from wastes or contaminated areas at many DOE sites. The overall goal of this project is to rationally design and synthesize imprinted, hybrid inorganic-organic sol-gel materials containing metal binding sites through template approaches, and to develop a scientific basis for metal ion binding and recognition by such tailored hybrid inorganic-organic materials. After removal of the template M, functionalized cavities are created which contain both grafted binding sites and functionality inherent to the silica network (Si-OH, Si-O-Si). These cavities are expected to 'recognize' and bind the target metal ions through the high affinities between the binding sites and M, and their retained shapes. Our approaches utilize both the metal ion binding and the tailored impressions of the template metal ions in the imprinted cavities. Such imprinted organofunctional sol-gel networks are expected to exhibit both high selectivity and capacity for binding targeted ions in fluid waste streams. The principles of sol-gel chemistry and imprinting techniques will guide our approaches to optimize the chemical and physical properties of the imprinted organofunctional sol-gel materials. Cold isotopes or non-radioactive surrogate ions of similar size and charge will be used in imprinting investigations to minimize hazardous waste production. The design strategy we will follow is based on imprinted binding sites cross-linked by rigid, hydrophilic inorganic SiO2 or M'O2 networks. These hydrophilic metal oxide-based materials are expected to exhibit fast ion mass transfer and binding kinetics in comparison to functionalized hydrophobic organic polymers. Success in this research will lead to a

Rational Synthesis of Imprinted Organofunctional Sol-Gel Materials for Toxic Metal Separation - Final Report - 09/15/1997 - 09/14/2001

Energy Technology Data Exchange (ETDEWEB)

Xue, Ziling (Ben); Barnes, Craig E.; Dai, Shang

2001-09-14

Current cost estimates for the environmental remediation of contaminated installations under the auspices of the Department of Energy (DOE) are staggering. On this basis alone, there is a critical need to develop the scientific basis for new approaches to the treatment and disposal of toxic metal ions from wastes or contaminated areas at many DOE sites. The overall goal of this project is to rationally design and synthesize imprinted, hybrid inorganic-organic sol-gel materials containing metal binding sites through template approaches, and to develop a scientific basis for metal ion binding and recognition by such tailored hybrid inorganic-organic materials. After removal of the template M, functionalized cavities are created which contain both grafted binding sites and functionality inherent to the silica network (Si-OH, Si-O-Si). These cavities are expected to ''recognize'' and bind the target metal ions through the high affinities between the binding sites and M, and their retained shapes. Our approaches utilize both the metal ion binding and the tailored impressions of the template metal ions in the imprinted cavities. Such imprinted organofunctional sol-gel networks are expected to exhibit both high selectivity and capacity for binding targeted ions in fluid waste streams. The principles of sol-gel chemistry and imprinting techniques will guide our approaches to optimize the chemical and physical properties of the imprinted organofunctional sol-gel materials. Cold isotopes or non-radioactive surrogate ions of similar size and charge will be used in imprinting investigations to minimize hazardous waste production. The design strategy we will follow is based on imprinted binding sites cross-linked by rigid, hydrophilic inorganic SiO{sub 2} or MiO{sub 2} networks. These hydrophilic metal oxide-based materials are expected to exhibit fast ion mass transfer and binding kinetics in comparison to functionalized hydrophobic organic polymers

Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris

International Nuclear Information System (INIS)

Axelrod, Herbert L.; Kozbial, Piotr; McMullan, Daniel; Krishna, S. Sri; Miller, Mitchell D.; Abdubek, Polat; Acosta, Claire; Astakhova, Tamara; Carlton, Dennis; Caruthers, Jonathan; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Elias, Ylva; Feuerhelm, Julie; Grzechnik, Slawomir K.; Grant, Joanna C.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; Marciano, David; Morse, Andrew T.; Murphy, Kevin D.; Nigoghossian, Edward; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Reyes, Ron; Rife, Christopher L.; Tien, Henry J.; Trout, Christina V.; Bedem, Henry van den; Weekes, Dana; White, Aprilfawn; Xu, Qingping; Zubieta, Chloe; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

2009-01-01

The crystal structure of an RmlC-type cupin with zinc acetate bound at the putative active site reveals significant differences from a previous structure without any bound ligand. The functional implications of the ligand-induced conformational changes are discussed. In the plant pathogen Xanthomonas campestris pv. campestris, the product of the tcmJ gene, XcTcmJ, encodes a protein belonging to the RmlC family of cupins. XcTcmJ was crystallized in a monoclinic space group (C2) in the presence of zinc acetate and the structure was determined to 1.6 Å resolution. Previously, the apo structure has been reported in the absence of any bound metal ion [Chin et al. (2006 ▶), Proteins, 65, 1046–1050]. The most significant difference between the apo structure and the structure of XcTcmJ described here is a reorganization of the binding site for zinc acetate, which was most likely acquired from the crystallization solution. This site is located in the conserved metal ion-binding domain at the putative active site of XcTcmJ. In addition, an acetate was also bound within coordination distance of the zinc. In order to accommodate this binding, rearrangement of a conserved histidine ligand is required as well as several nearby residues within and around the putative active site. These observations indicate that binding of zinc serves a functional role in this cupin protein

Non-Native Metal Ion Reveals the Role of Electrostatics in Synaptotagmin 1-Membrane Interactions.

Science.gov (United States)

Katti, Sachin; Nyenhuis, Sarah B; Her, Bin; Srivastava, Atul K; Taylor, Alexander B; Hart, P John; Cafiso, David S; Igumenova, Tatyana I

2017-06-27

C2 domains are independently folded modules that often target their host proteins to anionic membranes in a Ca 2+ -dependent manner. In these cases, membrane association is triggered by Ca 2+ binding to the negatively charged loop region of the C2 domain. Here, we used a non-native metal ion, Cd 2+ , in lieu of Ca 2+ to gain insight into the contributions made by long-range Coulombic interactions and direct metal ion-lipid bridging to membrane binding. Using X-ray crystallography, NMR, Förster resonance energy transfer, and vesicle cosedimentation assays, we demonstrate that, although Cd 2+ binds to the loop region of C2A/B domains of synaptotagmin 1 with high affinity, long-range Coulombic interactions are too weak to support membrane binding of individual domains. We attribute this behavior to two factors: the stoichiometry of Cd 2+ binding to the loop regions of the C2A and C2B domains and the impaired ability of Cd 2+ to directly coordinate the lipids. In contrast, electron paramagnetic resonance experiments revealed that Cd 2+ does support membrane binding of the C2 domains in full-length synaptotagmin 1, where the high local lipid concentrations that result from membrane tethering can partially compensate for lack of a full complement of divalent metal ions and specific lipid coordination in Cd 2+ -complexed C2A/B domains. Our data suggest that long-range Coulombic interactions alone can drive the initial association of C2A/B with anionic membranes and that Ca 2+ further augments membrane binding by the formation of metal ion-lipid coordination bonds and additional Ca 2+ ion binding to the C2 domain loop regions.

The study of zinc ions binding to casein.

Science.gov (United States)

Pomastowski, P; Sprynskyy, M; Buszewski, B

2014-08-01

The presented research was focused on physicochemical study of casein properties and the kinetics of zinc ions binding to the protein. Moreover, a fast and simple method of casein extraction from cow's milk has been proposed. Casein isoforms, zeta potential (ζ) and particle size of the separated caseins were characterized with the use of capillary electrophoresis, zeta potential analysis and field flow fractionation (FFF) technique, respectively. The kinetics of the metal-binding process was investigated in batch adsorption experiments. Intraparticle diffusion model, first-order and zero-order kinetic models were applied to test the kinetic experimental data. Analysis of changes in infrared bands registered for casein before and after zinc binding was also performed. The obtained results showed that the kinetic process of zinc binding to casein is not homogeneous but is expressed with an initial rapid stage with about 70% of zinc ions immobilized by casein and with a much slower second step. Maximum amount of bound zinc in the experimental conditions was 30.04mgZn/g casein. Copyright © 2014 Elsevier B.V. All rights reserved.

Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs{sup +}-selective binding site

Energy Technology Data Exchange (ETDEWEB)

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Matsumoto, Fumiko; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu; Adachi, Motoyasu; Tamada, Taro [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan); Kawamoto, Masahide [Kyushu Synchrotron Light Research Center, 8-7 Yayoigaoka, Tosu, Saga 841-0005 (Japan); Tokunaga, Hiroko; Ishibashi, Matsujiro [Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065 (Japan); Blaber, Michael [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan); Florida State University, 1115 West Call Street, Tallahassee, FL 32306-4300 (United States); Tokunaga, Masao [Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065 (Japan); Kuroki, Ryota, E-mail: kuroki.ryota@jaea.go.jp [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan)

2015-03-01

The tertiary structure of a β-lactamase derived from the halobacterium Chromohalobacter sp. 560 (HaBLA) was determined by X-ray crystallography. Three unique Sr{sup 2+}-binding sites and one Cs{sup +}-binding site were discovered in the HaBLA molecule. Environmentally friendly absorbents are needed for Sr{sup 2+} and Cs{sup +}, as the removal of the radioactive Sr{sup 2+} and Cs{sup +} that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs{sup +} or Sr{sup 2+}. The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P3{sub 1} using X-ray crystallography. Moreover, the locations of bound Sr{sup 2+} and Cs{sup +} ions were identified by anomalous X-ray diffraction. The location of one Cs{sup +}-specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na{sup +} (90 mM Na{sup +}/10 mM Cs{sup +}). From an activity assay using isothermal titration calorimetry, the bound Sr{sup 2+} and Cs{sup +} ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs{sup +}-binding site provides important information that is useful for the design of artificial Cs{sup +}-binding sites that may be useful in the bioremediation of radioactive isotopes.

Metal ion effects on enolase activity

International Nuclear Information System (INIS)

Lee, M.E.; Nowak, T.

1986-01-01

Most metal binding studies with yeast enolase suggest that two metals per monomer are required for catalytic activity. The functions of metal I and metal II have not been unequivocally defined. In a series of kinetic experiments where the concentration of MgII is kept constant at subsaturating levels (1mM), the addition of MnII or of ZnII gives a hyperbolic decrease in activity. The final velocity of these mixed metal systems is the same velocity obtained with either only MnII or ZnII respectively. The concentration of MnII (40 μM) or of Zn (2μM) which gives half maximal effect in the presence of (1mM) MgII is approximately the same as the Km' value for MnII (9μM) or ZnII (3μM) respectively. Direct binding of MnII to enolase in the absence and presence of MgII shows that MnII and MgII compete for the same metal site on enolase. In the presence of 2-phosphoglycerate (2-PGA) and MgII, only a single site is occupied by MnII. Results suggest MnII at site I and MgII at site II. PRR and high resolution 1 H and 31 P NMR studies of enzyme-ligand complexes containing MnII and MgII and MnII are consistent with this model. 31 P measurements allow a measure of the equilibrium constant (0.36) for enolase. Saturation transfer measurements yield net rate constants (k/sub f/ = 0.49s -1 ; k/sub r/ = 1.3s -1 ) for the overall reaction. These values are smaller than k/sub cat/ (38s -1 ) measured under analogous conditions. The cation at site I appears to determine catalytic activity

MANAGING TIGHT BINDING RECEPTORS FOR NEW SPEARATIONS TECHNOLOGIES

Energy Technology Data Exchange (ETDEWEB)

DARYLE H BUSCH RICHARD S GIVENS

2004-12-10

Much of the earth's pollution involves compounds of the metallic elements, including actinides, strontium, cesium, technetium, and RCRA metals. Metal ions bind to molecules called ligands, which are the molecular tools that can manipulate the metal ions under most conditions. This DOE-EMSP sponsored program strives (1) to provide the foundations for using the most powerful ligands in transformational separations technologies and (2) to produce seminal examples of their applications to separations appropriate to the DOE EM mission. These ultra tight-binding ligands can capture metal ions in the most competitive of circumstances (from mineralized sites, lesser ligands, and even extremely dilute solutions), but they react so slowly that they are useless in traditional separations methodologies. Two attacks on this problem are underway. The first accommodates to the challenging molecular lethargy by developing a seminal slow separations methodology termed the soil poultice. The second designs ligands that are only tight-binding while wrapped around the targeted metal ion, but can be put in place by switch-binding and removed by switch-release. We envision a kind of molecular switching process to accelerate the union between metal ion and tight-binding ligand. Molecular switching processes are suggested for overcoming the slow natural equilibration rate with which ultra tight-binding ligands combine with metal ions. Ligands that bind relatively weakly combine with metal ions rapidly, so the trick is to convert a ligand from a weak, rapidly binding species to a powerful, slow releasing ligand--during the binding of the ligand to the metal ion. Such switch-binding ligands must react with themselves, and the reaction must take place under the influence of the metal ion. For example, our generation 1 ligands showed that a well-designed linear ligand with ends that readily combine, forms a cyclic molecule when it wraps around a metal ion. Our generation 2 ligands are

Cellulose bearing Schiff base and carboxylic acid chelating groups: a low cost and green adsorbent for heavy metal ion removal from aqueous solution.

Science.gov (United States)

Saravanan, R; Ravikumar, L

2016-10-01

Chemically modified cellulose bearing metal binding sites like Schiff base and carboxylic acid groups was synthesized and characterized through Fourier transform infrared and solid state 13 C-nuclear magnetic resonance (NMR) analysis. The chemically modified cellulose (Cell-PA) adsorbent was examined for its metal ion uptake ability for Cu(II) and Pb(II) ions from aqueous solution. Kinetic and isotherm studies were carried out under optimum conditions. Pseudo-second-order kinetics and Langmuir isotherm fit well with the experimental data. Thermodynamic studies were also performed along with adsorption regeneration performance studies. The adsorbent (Cell-PA) shows high potential for the removal of Cu(II) and Pb(II) metal ions, and it shows antibacterial activity towards selected microorganisms.

Functional modulation of cerebral gamma-aminobutyric acidA receptor/benzodiazepine receptor/chloride ion channel complex with ethyl beta-carboline-3-carboxylate: Presence of independent binding site for ethyl beta-carboline-3-carboxylate

Energy Technology Data Exchange (ETDEWEB)

Taguchi, J.; Kuriyama, K. (Kyoto Prefectural Univ. of Medicine (Japan))

1990-05-01

Effect of ethyl beta-carboline-3-carboxylate (beta-CCE) on the function of gamma-aminobutyric acid (GABA)A receptor/benzodiazepine receptor/chloride ion channel complex was studied. Beta-CCE noncompetitively and competitively inhibited (3H)flunitrazepam binding to benzodiazepine receptor, but not (3H)muscimol binding to GABAA receptor as well as t-(3H)butylbicycloorthobenzoate (( 3H) TBOB) binding to chloride ion channel, in particulate fraction of the mouse brain. Ro15-1788 also inhibited competitively (3H) flunitrazepam binding. On the other hand, the binding of beta-(3H)CCE was inhibited noncompetitively and competitively by clonazepam and competitively by Ro15-1788. In agreement with these results, benzodiazepines-stimulated (3H)muscimol binding was antagonized by beta-CCE and Ro15-1788. Gel column chromatography for the solubilized fraction from cerebral particulate fraction by 0.2% sodium deoxycholate (DOC-Na) in the presence of 1 M KCl indicated that beta-(3H)CCE binding site was eluted in the same fraction (molecular weight, 250,000) as the binding sites for (3H)flunitrazepam, (3H)muscimol and (3H)TBOB. GABA-stimulated 36Cl- influx into membrane vesicles prepared from the bovine cerebral cortex was stimulated and attenuated by flunitrazepam and beta-CCE, respectively. These effects of flunitrazepam and beta-CCE on the GABA-stimulated 36Cl- influx were antagonized by Ro15-1788. The present results suggest that the binding site for beta-CCE, which resides on GABAA receptor/benzodiazepine receptor/chloride ion channel complex, may be different from that for benzodiazepine. Possible roles of beta-CCE binding site in the allosteric inhibitions on benzodiazepine binding site as well as on the functional coupling between chloride ion channel and GABAA receptor are also suggested.

Integrin activation dynamics between the RGD-binding site and the headpiece hinge.

Science.gov (United States)

Puklin-Faucher, Eileen; Vogel, Viola

2009-12-25

Integrins form mechanical links between the extracellular matrix and the cytoskeleton. Although integrin activation is known to be regulated by an allosteric conformational change, which can be induced from the extracellular or intracellular end of the molecule, little is known regarding the sequence of structural events by which signals propagate between distant sites. Here, we reveal with molecular dynamics simulations of the FnIII(10)-bound alpha(V)beta(3) integrin headpiece how the binding pocket and interdomain betaA/hybrid domain hinge on the distal end of the betaA domain are allosterically linked via a hydrophobic T-junction between the middle of the alpha1 helix and top of the alpha7 helix. The key results of this study are: 1) that this T-junction is induced by ligand binding and hinge opening, and thus displays bidirectionality; 2) that formation of this junction can be accelerated by ligand-mediated force; and 3) how formation of this junction is inhibited by Ca(2+) in place of Mg(2+) at the site adjacent to the metal ion-dependent adhesion site ("ADMIDAS"). Together with recent experimental evidence that integrin complexes can form catch bonds (i.e. become strengthened under force), as well as earlier evidence that Ca(2+) at the ADMIDAS results in lower binding affinity, these simulations provide a common structural model for the dynamic process by which integrins become activated.

Synthesis of new water-soluble metal-binding polymers: Combinatorial chemistry approach. 1997 mid-year progress report

International Nuclear Information System (INIS)

Smith, B.F.

1997-01-01

'The first objective of this research is to develop rapid discovery and optimization approaches to new water-soluble chelating polymers. A byproduct of the development approach will be the new, selective, and efficient metal-binding agents. The second objective is to evaluate the concept of using water and organic soluble polymers as new solid supports for combinatorial synthesis. The technology under development, Polymer Filtration (PF), is a technique to selectively remove or recover hazardous and valuable metal ions and radionuclides from various dilute aqueous streams. Not only can this technology be used to remediate contaminated soils and solid surfaces and treat aqueous wastes, it can also be incorporated into facilities as a pollution prevention and waste minimization technology. Polymer Filtration uses water-soluble metal-binding polymers to sequester metal ions in dilute solution. The water-soluble polymers have a sufficiently large molecular size that they can be separated and concentrated using commercial ultrafiltration technology. Water, small organic molecules, and unbound metals pass freely through the ultrafiltration membrane while concentrating the metal-binding polymer. The polymers can then be reused by changing the solution conditions to release the metal ions. The metal-ions are recovered in concentrated form for recycle or disposal using a diafiltration process. The water-soluble polymer can be recycled for further aqueous-stream processing. To advance Polymer Filtration technology to the selectivity levels required for DOE needs. fixture directions in Polymer Filtration must include rapid development, testing, and characterization of new metal-binding polymers. The development of new chelating molecules can be equated to the process of new drugs or new materials discovery. Thus, the authors want to build upon and adapt the combinatorial chemistry approaches developed for rapid molecule generation for the drug industry to the rapid

Mechanistic Inferences from the Binding of Ligands to LpxC, A Metal-Dependent Deacetylase

International Nuclear Information System (INIS)

Gennadios, H.; Whittington, D.; Li, X.; Fierke, C.; Christianson, D.

2006-01-01

The metal-dependent deacetylase LpxC catalyzes the first committed step of lipid A biosynthesis in Gram-negative bacteria. Accordingly, LpxC is an attractive target for the development of inhibitors that may serve as potential new antibiotics for the treatment of Gram-negative bacterial infections. Here, we report the 2.7 Angstroms resolution X-ray crystal structure of LpxC complexed with the substrate analogue inhibitor TU-514 and the 2.0 Angstroms resolution structure of LpxC complexed with imidazole. The X-ray crystal structure of LpxC complexed with TU-514 allows for a detailed examination of the coordination geometry of the catalytic zinc ion and other enzyme-inhibitor interactions in the active site. The hydroxamate group of TU-514 forms a bidentate chelate complex with the zinc ion and makes hydrogen bond interactions with conserved active site residues E78, H265, and T191. The inhibitor C-4 hydroxyl group makes direct hydrogen bond interactions with E197 and H58. Finally, the C-3 myristate moiety of the inhibitor binds in the hydrophobic tunnel of the active site. These intermolecular interactions provide a foundation for understanding structural aspects of enzyme-substrate and enzyme-inhibitor affinity. Comparison of the TU-514 complex with cacodylate and imidazole complexes suggests a possible substrate diphosphate binding site and highlights residues that may stabilize the tetrahedral intermediate and its flanking transition states in catalysis. Evidence of a catalytic zinc ion in the native zinc enzyme coordinated by H79, H238, D242, and two water molecules with square pyramidal geometry is also presented. These results suggest that the native state of this metallohydrolase may contain a pentacoordinate zinc ion, which contrasts with the native states of archetypical zinc hydrolases such as thermolysin and carboxypeptidase A

Metal ion separations with proton-ionizable Lariat Ethers and their polymers

International Nuclear Information System (INIS)

Bartsch, R.A.

1993-01-01

The preparation of novel and specific organic complexing agents may lead to the development of new separation systems for aqueous metal ions. Thus the introduction of highly lipophilic oximes led to the current utilization of these compounds as commercial extractants for the hydrometallurgy of nonferrous metals. Crown ethers (macrocyclic polyethers) have been employed in the laboratory-scale solvent extraction of alkali-metal, alkaline-earth, and other metal cations into organic phases. Attachment of side arms to crown ethers gives lariat ethers. The presence of one or more potential coordination sites in the side arm of the lariat ether may produce substantial changes in the selectivity and efficiency of metal ion complexation. It has been demonstrated that concomitant transfer of an aqueous phase anion into the organic medium is not required for metal ion extraction. This factor is of immense importance to potential practical applications of these proton-ionizable crown ethers in which the common, hard, aqueous phase anions would be involved. Another advantage of proton-ionizable lariat ethers is the ease with which extracted metal ions may be stripped from the organic phase by shaking with aqueous mineral acid. Thus both metal ion extraction and stripping are facilitated by pendent proton-ionizable groups. Most of the hazardous metal ion species in the Hanford Site tank wastes are members of the alkali-metal, alkaline-earth, lanthanide, and actinide families. These hard metal ion species prefer association with hard donor atoms, such as oxygens. Therefore, crown and lariat ethers are well-suited for complexation with such metal ion species

Uptake of metal ions by a silica-based tetraphenylporphyrin sorbent

Energy Technology Data Exchange (ETDEWEB)

Pyrzynska, K.; Sadowska, M.; Trojanowicz, M.

1999-09-01

The [5-p-carboxyphenyl-10,15,20-triphenyl]porphyrin (TPP) covalently attached to aminopropyl silica gel was examined with respect to the sorption of transition metal ions. The distribution coefficients (K{sub d}) are reported for some metal ions with this new sorbent as a function of pH. It was found that in optimum pH conditions the sorption of Cu(II) and Fe(III) is much faster than that of Co(II) and Cr(III). The binding of metal ions is strongly affected by the presence of various species accelerating the complex formation. The application of porphyrin ligands for preconcentration and metal-matrix separation was also examined using complex formation in solution coupled with an anion exchange resin and column chelation procedure, e.g. sorption of metal on an anion exchanger previously loaded with tetra(4-carboxyphenyl)porphyrin.

EPR study of manganese(II) binding to 55'-ATP, hemoglobin, and hemocyanin

Energy Technology Data Exchange (ETDEWEB)

Chang, S.S. (Duquesne Univ., Pittsburgh); Li, N.C.; Pratt, D.W.

1975-01-01

Several divalent metal ions affect the oxygen affinity of hemoglobin and hemocyanin. It is important, therefore, to understand the nature of metal-ion binding to these proteins. By comparing the EPR spectra of Mn(II), 0.001 M, in the absence and presence of carboxyhemoglobin or Limulus oxyhemocyanin (pH 7.3, Trizma buffer), the number of Mn binding sites, n, and the binding constant, K, can be determined. For carboxyhemoglobin, HbCO, we find 0.5 Mn binding sites per heme, K = 450 M/sup -1/. Each hemoglobin tetramer therefore binds two manganous ions suggesting that Mn(II), like Cu(II), may bind preferentially to one of the two types of subunits in hemoglobin. For hemocyanin, HcO/sub 2/, we find n = 5.8, K = 1.55 x 10/sup 3/ M/sup -1/. Each oxyhemocyanine therefore binds approximately six manganous ions, and the binding constant is three times larger than that for HbCO. We have also carried out similar experiments on 5'-ATP, and on solutions of HbCO and ATP containing McCl/sub 2/ or ZnCl/sub 2/. Zn(II) effectively competes with Mn(II) in binding hemoglobin and ATP, whereas Mg(II) does not, in accord with expectations from data on oxygen affinity of hemoglobin. (auth)

Synthesis and characterisation of 8-hydroxyquinoline-bovine serum albumin conjugates as metal ion chelating proteins

International Nuclear Information System (INIS)

Giraudi, G.; Baggiani, C.; Giovannoli, C.; Marletto, C.; Vanni, A.

1999-01-01

A derivative of 8-hydroxyquinoline (8-quinolinol, oxine) with a linking bridge containing a carboxylic group was covalently coupled to bovine serum albumin by the N-hydroxysuccinimide method to obtain stable monomeric conjugates with oxine to protein mole ratios up to 37. These conjugates were characterised spectrophotometrically and their complexation properties were confirmed by spectral analysis with and without the addition of Al(III), Cd(II), Co(II), Cu(II), Hg(II), Mn(II), Ni(II), Pb(II), V(IV), U(VI) and Zn(II) ions added. The maximum number of ions bound by these chelating proteins was determined spectrophotometrically by titration with metal ions at pH 6.0. The conjugates with a substitution ratio (moles of 8-hydroxyquinoline bound/mole of albumin) less than about 8 showed 1:1 binding with metal ions, while conjugates with higher substitution ratios were able to complex with 2:1 ratio of 8-hydroxyquinoline to metal ion. Association and dissociation kinetics of complexation with copper(II) ions showed a complex mechanism. The spectral and binding properties of these metal ion-binding proteins confirm that the coupling of the 8-hydroxyquinoline derivative to bovine serum albumin gives stable, water soluble, macromolecular chelating agents that retain the complexing ability of the original ligand. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

Oxidation of cyclohexane catalyzed by metal-ion-exchanged zeolites.

Science.gov (United States)

Sökmen, Ilkay; Sevin, Fatma

2003-08-01

The ion-exchange rates and capacities of the zeolite NaY for the Cu(II), Co(II), and Pb(II) metal ions were investigated. Ion-exchange equilibria were achieved in approximately 72 h for all the metal ions. The maximum ion exchange of metal ions into the zeolite was found to be 120 mg Pb(II), 110 mg Cu(II), and 100 mg Co(II) per gram of zeolite NaY. It is observed that the exchange capacity of a zeolite varies with the exchanged metal ion and the amount of metal ions exchanged into zeolite decreases in the sequence Pb(II) > Cu(II) > Co(II). Application of the metal-ion-exchanged zeolites in oxidation of cyclohexane in liquid phase with visible light was examined and it is observed that the order of reactivity of the zeolites for the conversion of cyclohexane to cyclohexanone and cyclohexanol is CuY > CoY > PbY. It is found that conversion increases by increase of the empty active sites of a zeolite and the formation of cyclohexanol is favored initially, but the cyclohexanol is subsequently converted to cyclohexanone.

Removal and recovery of metal ions from process and waste streams using polymer filtration

International Nuclear Information System (INIS)

Jarvinen, G.D.; Smith, B.F.; Robison, T.W.; Kraus, K.M.; Thompson, J.A.

1999-01-01

Polymer Filtration (PF) is an innovative, selective metal removal technology. Chelating, water-soluble polymers are used to selectively bind the desired metal ions and ultrafiltration is used to concentrate the polymer-metal complex producing a permeate with low levels of the targeted metal ion. When applied to the treatment of industrial metal-bearing aqueous process streams, the permeate water can often be reused within the process and the metal ions reclaimed. This technology is applicable to many types of industrial aqueous streams with widely varying chemistries. Application of PF to aqueous streams from nuclear materials processing and electroplating operations will be described

Single site porphyrine-like structures advantages over metals for selective electrochemical CO2 reduction

DEFF Research Database (Denmark)

Bagger, Alexander; Ju, Wen; Varela, Ana Sofia

2017-01-01

Currently, no catalysts are completely selective for the electrochemical CO2 Reduction Reaction (CO2RR). Based on trends in density functional theory calculations of reaction intermediates we find that the single metal site in a porphyrine-like structure has a simple advantage of limiting...... the competing Hydrogen Evolution Reaction (HER). The single metal site in a porphyrine-like structure requires an ontop site binding of hydrogen, compared to the hollow site binding of hydrogen on a metal catalyst surface. The difference in binding site structure gives a fundamental energy-shift in the scaling...... relation of ∼0.3eV between the COOH* vs. H* intermediate (CO2RR vs. HER). As a result, porphyrine-like catalysts have the advantage over metal catalyst of suppressing HER and enhancing CO2RR selectivity....

Domain-based small molecule binding site annotation

Directory of Open Access Journals (Sweden)

Dumontier Michel

2006-03-01

Full Text Available Abstract Background Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and function prediction, but small molecule binding site protein sequence annotation is sparse. The Small Molecule Interaction Database (SMID, a database of protein domain-small molecule interactions, was created using structural data from the Protein Data Bank (PDB. More importantly it provides a means to predict small molecule binding sites on proteins with a known or unknown structure and unlike prior approaches, removes large numbers of false positive hits arising from transitive alignment errors, non-biologically significant small molecules and crystallographic conditions that overpredict ion binding sites. Description Using a set of co-crystallized protein-small molecule structures as a starting point, SMID interactions were generated by identifying protein domains that bind to small molecules, using NCBI's Reverse Position Specific BLAST (RPS-BLAST algorithm. SMID records are available for viewing at http://smid.blueprint.org. The SMID-BLAST tool provides accurate transitive annotation of small-molecule binding sites for proteins not found in the PDB. Given a protein sequence, SMID-BLAST identifies domains using RPS-BLAST and then lists potential small molecule ligands based on SMID records, as well as their aligned binding sites. A heuristic ligand score is calculated based on E-value, ligand residue identity and domain entropy to assign a level of confidence to hits found. SMID-BLAST predictions were validated against a set of 793 experimental small molecule interactions from the PDB, of which 472 (60% of predicted interactions identically matched the experimental small molecule and of these, 344 had greater than 80% of the binding site residues correctly identified. Further, we estimate that 45% of predictions which were not observed in the PDB validation set may be true positives. Conclusion By

MetalS(3), a database-mining tool for the identification of structurally similar metal sites.

Science.gov (United States)

Valasatava, Yana; Rosato, Antonio; Cavallaro, Gabriele; Andreini, Claudia

2014-08-01

We have developed a database search tool to identify metal sites having structural similarity to a query metal site structure within the MetalPDB database of minimal functional sites (MFSs) contained in metal-binding biological macromolecules. MFSs describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such a local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. The database search tool, which we called MetalS(3) (Metal Sites Similarity Search), can be accessed through a Web interface at http://metalweb.cerm.unifi.it/tools/metals3/ . MetalS(3) uses a suitably adapted version of an algorithm that we previously developed to systematically compare the structure of the query metal site with each MFS in MetalPDB. For each MFS, the best superposition is kept. All these superpositions are then ranked according to the MetalS(3) scoring function and are presented to the user in tabular form. The user can interact with the output Web page to visualize the structural alignment or the sequence alignment derived from it. Options to filter the results are available. Test calculations show that the MetalS(3) output correlates well with expectations from protein homology considerations. Furthermore, we describe some usage scenarios that highlight the usefulness of MetalS(3) to obtain mechanistic and functional hints regardless of homology.

Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair.

Science.gov (United States)

Hofmann, H P; Limmer, S; Hornung, V; Sprinzl, M

1997-01-01

RNA molecules with high affinity for immobilized Ni2+ were isolated from an RNA pool with 50 randomized positions by in vitro selection-amplification. The selected RNAs preferentially bind Ni2+ and Co2+ over other cations from first series transition metals. Conserved structure motifs, comprising about 15 nt, were identified that are likely to represent the Ni2+ binding sites. Two conserved motifs contain an asymmetric purine-rich internal loop and probably a mismatch G-A base pair. The structure of one of these motifs was studied with proton NMR spectroscopy and formation of the G-A pair at the junction of helix and internal loop was demonstrated. Using Ni2+ as a paramagnetic probe, a divalent metal ion binding site near this G-A base pair was identified. Ni2+ ions bound to this motif exert a specific stabilization effect. We propose that small asymmetric purine-rich loops that contain a G-A interaction may represent a divalent metal ion binding site in RNA. PMID:9409620

The Role of Metal Binding in the Amyotrophic Lateral Sclerosis-Related Aggregation of Copper-Zinc Superoxide Dismutase

Directory of Open Access Journals (Sweden)

Ivana Sirangelo

2017-08-01

Full Text Available Protein misfolding and conformational changes are common hallmarks in many neurodegenerative diseases involving formation and deposition of toxic protein aggregates. Although many players are involved in the in vivo protein aggregation, physiological factors such as labile metal ions within the cellular environment are likely to play a key role. In this review, we elucidate the role of metal binding in the aggregation process of copper-zinc superoxide dismutase (SOD1 associated to amyotrophic lateral sclerosis (ALS. SOD1 is an extremely stable Cu-Zn metalloprotein in which metal binding is crucial for folding, enzymatic activity and maintenance of the native conformation. Indeed, demetalation in SOD1 is known to induce misfolding and aggregation in physiological conditions in vitro suggesting that metal binding could play a key role in the pathological aggregation of SOD1. In addition, this study includes recent advances on the role of aberrant metal coordination in promoting SOD1 aggregation, highlighting the influence of metal ion homeostasis in pathologic aggregation processes.

Factors Affecting the Binding of a Recombinant Heavy Metal-Binding Domain (CXXC motif Protein to Heavy Metals

Directory of Open Access Journals (Sweden)

Kamala Boonyodying

2012-06-01

Full Text Available A number of heavy metal-binding proteins have been used to study bioremediation. CXXC motif, a metal binding domain containing Cys-X-X-Cys motif, has been identified in various organisms. These proteins are capable of binding various types of heavy metals. In this study, heavy metal binding domain (CXXC motif recombinant protein encoded from mcsA gene of S. aureus were cloned and overexpressed in Escherichia coli. The factors involved in the metal-binding activity were determined in order to analyze the potential of recombinant protein for bioremediation. A recombinant protein can be bound to Cd2+, Co2+, Cu2+ and Zn2+. The thermal stability of a recombinant protein was tested, and the results showed that the metal binding activity to Cu2+ and Zn2+ still exist after treating the protein at 85ºC for 30 min. The temperature and pH that affected the metal binding activity was tested and the results showed that recombinant protein was still bound to Cu2+ at 65ºC, whereas a pH of 3-7 did not affect the metal binding E. coli harboring a pRset with a heavy metal-binding domain CXXC motif increased the resistance of heavy metals against CuCl2 and CdCl2. This study shows that metal binding domain (CXXC motif recombinant protein can be effectively bound to various types of heavy metals and may be used as a potential tool for studying bioremediation.

Specificity of the metalloregulator CueR for monovalent metal ions

DEFF Research Database (Denmark)

Szunyogh, Dániel; Szokolai, Hajnalka; Thulstrup, Peter Waaben

2015-01-01

(II) , and Hg(II) binding to model systems encompassing the metal-ion-binding loop of CueR from E. coli and V. cholerae. In the presence of Ag(I) , a conserved cysteine residue displays a pKa value for deprotonation of the thiol that is close to the physiological pH value. This property is only observed...

Investigation of metal ions sorption of brown peat moss powder

Science.gov (United States)

Kelus, Nadezhda; Blokhina, Elena; Novikov, Dmitry; Novikova, Yaroslavna; Chuchalin, Vladimir

2017-11-01

For regularities research of sorptive extraction of heavy metal ions by cellulose and its derivates from aquatic solution of electrolytes it is necessary to find possible mechanism of sorption process and to choice a model describing this process. The present article investigates the regularities of aliovalent metals sorption on brown peat moss powder. The results show that sorption isotherm of Al3+ ions is described by Freundlich isotherm and sorption isotherms of Na+ i Ni2+ are described by Langmuir isotherm. To identify the mechanisms of brown peat moss powder sorption the IR-spectra of the initial brown peat moss powder samples and brown peat moss powder samples after Ni (II) sorption were studied. Metal ion binding mechanisms by brown peat moss powder points to ion exchange, physical adsorption, and complex formation with hydroxyl and carboxyl groups.

Nature differences of humic acids fractions induced by extracted sequence as explanatory factors for binding characteristics of heavy metals.

Science.gov (United States)

Shi, Wenjing; Lü, Changwei; He, Jiang; En, He; Gao, Manshu; Zhao, Boyi; Zhou, Bin; Zhou, Haijun; Liu, Hualin; Zhang, Yu

2018-06-15

The composition and structure of Humic acid (HA) is so heterogeneous that it brings significant barriers to investigate the interaction between HA and heavy metal ions. The isolation of HA with relatively homogeneity is a key to reveal the binding mechanisms between HA and heavy metals. In this work, ten HA fractions (HAs) were obtained by sequential alkali extraction procedure and nature differences of the extracted HAs were considered as explanatory factors for binding characteristics of Cu 2+ , Pb 2+ and Cd 2+ . The results indicate that more large molecular weight (MW) HA subunits, less carboxyl and phenolic group contents, weaker aromaticity and polarity were measured with increasing extractions, inducing weaker binding capacity of HAs. Ligand binding and bi-Langmuir models indicated that the sorption capacity and binding affinity of earlier extracted HAs were higher than the latter ones. The peak area changes at 3427, 1599, and 619 cm -1 pre- and post-adsorption in FTIR spectra suggested carboxyl, phenolic and nitrogen-containing groups were involved in the adsorption process. At the same time, the peak area difference between HAs and HAs-metal (ΔS) of phenolic groups were 8.22-20.50, 6.81-21.11 and 10.66-19.80% for Cu 2+ , Pb 2+ and Cd 2+ , respectively, ΔS of carboxyl groups 6.64-17.03, 8.96-16.82 and 9.45-17.85% for Cu 2+ , Pb 2+ and Cd 2+ , respectively, ΔS of nitrogen-containing groups 0.33-0.48, 0.20-1.38 and 0.31-0.59% for Cu 2+ , Pb 2+ and Cd 2+ , respectively. ΔS of phenolic and carboxyl groups were larger than those of nitrogen-containing groups, implying that these two groups were the predominant binding sites suppliers for metal ions, which were also supported by the results of correlation analysis. This work is helpful to insight the environmental impacts of natural organic matter and the fate of heavy metals in natural environment. Copyright © 2018 Elsevier Inc. All rights reserved.

Integrin Activation Dynamics between the RGD-binding Site and the Headpiece Hinge*

Science.gov (United States)

Puklin-Faucher, Eileen; Vogel, Viola

2009-01-01

Integrins form mechanical links between the extracellular matrix and the cytoskeleton. Although integrin activation is known to be regulated by an allosteric conformational change, which can be induced from the extracellular or intracellular end of the molecule, little is known regarding the sequence of structural events by which signals propagate between distant sites. Here, we reveal with molecular dynamics simulations of the FnIII10-bound αVβ3 integrin headpiece how the binding pocket and interdomain βA/hybrid domain hinge on the distal end of the βA domain are allosterically linked via a hydrophobic T-junction between the middle of the α1 helix and top of the α7 helix. The key results of this study are: 1) that this T-junction is induced by ligand binding and hinge opening, and thus displays bidirectionality; 2) that formation of this junction can be accelerated by ligand-mediated force; and 3) how formation of this junction is inhibited by Ca2+ in place of Mg2+ at the site adjacent to the metal ion-dependent adhesion site (“ADMIDAS”). Together with recent experimental evidence that integrin complexes can form catch bonds (i.e. become strengthened under force), as well as earlier evidence that Ca2+ at the ADMIDAS results in lower binding affinity, these simulations provide a common structural model for the dynamic process by which integrins become activated. PMID:19762919

Metal ion release from metallothioneins: proteolysis as an alternative to oxidation.

Science.gov (United States)

Peroza, Estevão A; dos Santos Cabral, Augusto; Wan, Xiaoqiong; Freisinger, Eva

2013-09-01

Metallothioneins (MTs) are among others involved in the cellular regulation of essential Zn(II) and Cu(I) ions. However, the high binding affinity of these proteins requires additional factors to promote metal ion release under physiological conditions. The mechanisms and efficiencies of these processes leave many open questions. We report here a comprehensive analysis of the Zn(II)-release properties of various MTs with special focus on members of the four main subfamilies of plant MTs. Zn(II) competition experiments with the metal ion chelator 4-(2-pyridylazo)resorcinol (PAR) in the presence of the cellular redox pair glutathione (GSH)/glutathione disulfide (GSSG) show that plant MTs from the subfamilies MT1, MT2, and MT3 are remarkably more affected by oxidative stress than those from the Ec subfamily and the well-characterized human MT2 form. In addition, we evaluated proteolytic digestion with trypsin and proteinase K as an alternative mechanism for selective promotion of metal ion release from MTs. Also here the observed percentage of liberated metal ions depends strongly on the MT form evaluated. Closer evaluation of the data additionally allowed deducing the thermodynamic and kinetic properties of the Zn(II) release processes. The Cu(I)-form of chickpea MT2 was used to exemplify that both oxidation and proteolysis are also effective ways to increase the transfer of copper ions to other molecules. Zn(II) release experiments with the individual metal-binding domains of Ec-1 from wheat grain reveal distinct differences from the full-length protein. This triggers the question about the roles of the long cysteine-free peptide stretches typical for plant MTs.

Substrate specificity, metal binding properties, and spectroscopic characterization of the DapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae.

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Bienvenue, David L; Gilner, Danuta M; Davis, Ryan S; Bennett, Brian; Holz, Richard C

2003-09-16

The catalytic and structural properties of divalent metal ion cofactor binding sites in the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) from Haemophilus influenzae were investigated. Co(II)-substituted DapE enzyme was 25% more active than the Zn(II)-loaded form of the enzyme. Interestingly, Mn(II) can activate DapE, but only to approximately 20% of the Zn(II)-loaded enzyme. The order of the observed k(cat) values are Co(II) > Zn(II) > Cd(II) > Mn(II) >Ni(II) approximately equal Cu(II) approximately equal Mg(II). DapE was shown to only hydrolyze L,L-N-succinyl-diaminopimelic acid (L,L-SDAP) and was inactive toward D,L-, L,D-, and D,D-SDAP. DapE was also inactive toward several acetylated amino acids as well as D,L-succinyl aminopimelate, which differs from the natural substrate, L,L-SDAP, by the absence of the amine group on the amino acid side chain. These data imply that the carboxylate of the succinyl moiety and the amine form important interactions with the active site of DapE. The affinity of DapE for one versus two Zn(II) ions differs by nearly 2.2 x 10(3) times (K(d1) = 0.14 microM vs K(d2) = 300 microM). In addition, an Arrhenius plot was constructed from k(cat) values measured between 16 and 35 degrees C and was linear over this temperature range. The activation energy for [ZnZn(DapE)] was found to be 31 kJ/mol with the remaining thermodynamic parameters calculated at 25 degrees C being DeltaG(++) = 64 kJ/mol, DeltaH(++) = 28.5 kJ/mol, and DeltaS(++) = -119 J mol(-1) K(-1). Electronic absorption and EPR spectra of [Co_(DapE)] and [CoCo(DapE)] indicate that the first Co(II) binding site is five-coordinate, while the second site is octahedral. In addition, any spin-spin interaction between the two Co(II) ions in [CoCo(DapE)] is very weak. The kinetic and spectroscopic data presented herein suggest that the DapE from H. influenzae has similar divalent metal binding properties to the aminopeptidase from Aeromonas proteolytica (AAP), and

Identification of a divalent metal cation binding site in herpes simplex virus 1 (HSV-1) ICP8 required for HSV replication.

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Bryant, Kevin F; Yan, Zhipeng; Dreyfus, David H; Knipe, David M

2012-06-01

Herpes simplex virus 1 (HSV-1) ICP8 is a single-stranded DNA-binding protein that is necessary for viral DNA replication and exhibits recombinase activity in vitro. Alignment of the HSV-1 ICP8 amino acid sequence with ICP8 homologs from other herpesviruses revealed conserved aspartic acid (D) and glutamic acid (E) residues. Amino acid residue D1087 was conserved in every ICP8 homolog analyzed, indicating that it is likely critical for ICP8 function. We took a genetic approach to investigate the functions of the conserved ICP8 D and E residues in HSV-1 replication. The E1086A D1087A mutant form of ICP8 failed to support the replication of an ICP8 mutant virus in a complementation assay. E1086A D1087A mutant ICP8 bound DNA, albeit with reduced affinity, demonstrating that the protein is not globally misfolded. This mutant form of ICP8 was also recognized by a conformation-specific antibody, further indicating that its overall structure was intact. A recombinant virus expressing E1086A D1087A mutant ICP8 was defective in viral replication, viral DNA synthesis, and late gene expression in Vero cells. A class of enzymes called DDE recombinases utilize conserved D and E residues to coordinate divalent metal cations in their active sites. We investigated whether the conserved D and E residues in ICP8 were also required for binding metal cations and found that the E1086A D1087A mutant form of ICP8 exhibited altered divalent metal binding in an in vitro iron-induced cleavage assay. These results identify a novel divalent metal cation-binding site in ICP8 that is required for ICP8 functions during viral replication.

Structural analysis of substrate recognition by glucose isomerase in Mn2+ binding mode at M2 site in S. rubiginosus.

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Bae, Ji-Eun; Hwang, Kwang Yeon; Nam, Ki Hyun

2018-06-16

Glucose isomerase (GI) catalyzes the reversible enzymatic isomerization of d-glucose and d-xylose to d-fructose and d-xylulose, respectively. This is one of the most important enzymes in the production of high-fructose corn syrup (HFCS) and biofuel. We recently determined the crystal structure of GI from S. rubiginosus (SruGI) complexed with a xylitol inhibitor in one metal binding mode. Although we assessed inhibitor binding at the M1 site, the metal binding at the M2 site and the substrate recognition mechanism for SruGI remains the unclear. Here, we report the crystal structure of the two metal binding modes of SruGI and its complex with glucose. This study provides a snapshot of metal binding at the SruGI M2 site in the presence of Mn 2+ , but not in the presence of Mg 2+ . Metal binding at the M2 site elicits a configuration change at the M1 site. Glucose molecule can only bind to the M1 site in presence of Mn 2+ at the M2 site. Glucose and Mn 2+ at the M2 site were bridged by water molecules using a hydrogen bonding network. The metal binding geometry of the M2 site indicates a distorted octahedral coordination with an angle of 55-110°, whereas the M1 site has a relatively stable octahedral coordination with an angle of 85-95°. We suggest a two-step sequential process for SruGI substrate recognition, in Mn 2+ binding mode, at the M2 site. Our results provide a better understanding of the molecular role of the M2 site in GI substrate recognition. Copyright © 2018. Published by Elsevier Inc.

Dissociation and metal-binding characteristics of yellow lichen substances suggest a relationship with site preferences of lichens.

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Hauck, Markus; Jürgens, Sascha-René; Willenbruch, Karen; Huneck, Siegfried; Leuschner, Christoph

2009-01-01

Many species of lichen-forming fungi contain yellow or orange extracellular pigments belonging to the dibenzofurans (usnic acid), anthraquinones (e.g. parietin) or pulvinic acid group. These pigments are all equally efficient light screens, leading us to question the potential ecological and evolutionary significance of diversity in yellow and orange lichen substances. Here the hypothesis is tested that the different pigments differ in metal-binding characteristics, which suggest that they may contribute to adaptation to sites differing in pH and metal availability. UV spectroscopy was used to study the dissociation and the pH dependence of the metal-binding behaviour of seven isolated lichen substances in methanol. Metals applied were selected macro- and micro-nutrients (Cu(2+), Fe(2+), Fe(3+), Mg(2+), Mn(2+) and Zn(2+)). All the pigments studied are strong to moderate acids with pK(a1) values between 2.8 and 4.5. Metal complexation is common in the lichen substances studied. Complexation takes place under acidic conditions with usnic acid, but under alkaline conditions with parietin and most compounds of the pulvinic acid group. The pulvinic acid derivative rhizocarpic acid forms metal complexes both in the acidic and the alkaline range. Metal complexation by lichen substances could be a prerequisite for lichen substance-mediated control of metal uptake. Assuming such an effect at pH values where the affinity of the metal for the lichen substance is intermediate would explain the strong preference of lichens with usnic or rhizocarpic acids to acidic substrata. Moreover, it would explain the preference of lichens with parietin and some lichens with compounds of the pulvinic acid group either for nutrient-rich substrata at low pH or for calcareous substrata.

Chemical rescue of the post-translationally carboxylated lysine mutant of allantoinase and dihydroorotase by metal ions and short-chain carboxylic acids.

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Ho, Ya-Yeh; Huang, Yen-Hua; Huang, Cheng-Yang

2013-04-01

Bacterial allantoinase (ALLase) and dihydroorotase (DHOase) are members of the cyclic amidohydrolase family. ALLase and DHOase possess similar binuclear metal centers in the active site in which two metals are bridged by a post-translationally carboxylated lysine. In this study, we determined the effects of carboxylated lysine and metal binding on the activities of ALLase and DHOase. Although DHOase is a metalloenzyme, purified DHOase showed high activity without additional metal supplementation in a reaction mixture or bacterial culture. However, unlike DHOase, ALLase had no activity unless some specific metal ions were added to the reaction mixture or culture. Substituting the metal binding sites H59, H61, K146, H186, H242, or D315 with alanine completely abolished the activity of ALLase. However, the K146C, K146D and K146E mutants of ALLase were still active with about 1-6% activity of the wild-type enzyme. These ALLase K146 mutants were found to have 1.4-1.7 mol metal per mole enzyme subunit, which may indicate that they still contained the binuclear metal center in the active site. The activity of the K146A mutant of the ALLase and the K103A mutant of DHOase can be chemically rescued by short-chain carboxylic acids, such as acetic, propionic, and butyric acids, but not by ethanol, propan-1-ol, and imidazole, in the presence of Co2+ or Mn2+ ions. However, the activity was still ~10-fold less than that of wild-type ALLase. Overall, these results indicated that the 20 natural basic amino acid residues were not sufficiently able to play the role of lysine. Accordingly, we proposed that during evolution, the post-translational modification of carboxylated lysine in the cyclic amidohydrolase family was selected for promoting binuclear metal center self-assembly and increasing the nucleophilicity of the hydroxide at the active site for enzyme catalysis. This kind of chemical rescue combined with site-directed mutagenesis may also be used to identify a binuclear metal

The involvement of coordinative interactions in the binding of dihydrolipoamide dehydrogenase to titanium dioxide-Localization of a putative binding site.

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Dayan, Avraham; Babin, Gilad; Ganoth, Assaf; Kayouf, Nivin Samir; Nitoker Eliaz, Neta; Mukkala, Srijana; Tsfadia, Yossi; Fleminger, Gideon

2017-08-01

Titanium (Ti) and its alloys are widely used in orthodontic and orthopedic implants by virtue to their high biocompatibility, mechanical strength, and high resistance to corrosion. Biointegration of the implants with the tissue requires strong interactions, which involve biological molecules, proteins in particular, with metal oxide surfaces. An exocellular high-affinity titanium dioxide (TiO 2 )-binding protein (TiBP), purified from Rhodococcus ruber, has been previously studied in our lab. This protein was shown to be homologous with the orthologous cytoplasmic rhodococcal dihydrolipoamide dehydrogenase (rhDLDH). We have found that rhDLDH and its human homolog (hDLDH) share the TiO 2 -binding capabilities with TiBP. Intrigued by the unique TiO 2 -binding properties of hDLDH, we anticipated that it may serve as a molecular bridge between Ti-based medical structures and human tissues. The objective of the current study was to locate the region and the amino acids of the protein that mediate the protein-TiO 2 surface interaction. We demonstrated the role of acidic amino acids in the nonelectrostatic enzyme/dioxide interactions at neutral pH. The observation that the interaction of DLDH with various metal oxides is independent of their isoelectric values strengthens this notion. DLDH does not lose its enzymatic activity upon binding to TiO 2 , indicating that neither the enzyme undergoes major conformational changes nor the TiO 2 binding site is blocked. Docking predictions suggest that both rhDLDH and hDLDH bind TiO 2 through similar regions located far from the active site and the dimerization sites. The putative TiO 2 -binding regions of both the bacterial and human enzymes were found to contain a CHED (Cys, His, Glu, Asp) motif, which has been shown to participate in metal-binding sites in proteins. Copyright © 2017 John Wiley & Sons, Ltd.

Interpretation of Ocular Melanin Drug Binding Assays. Alternatives to the Model of Multiple Classes of Independent Sites.

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Manzanares, José A; Rimpelä, Anna-Kaisa; Urtti, Arto

2016-04-04

Melanin has a high binding affinity for a wide range of drugs. The determination of the melanin binding capacity and its binding affinity are important, e.g., in the determination of the ocular drug distribution, the prediction of drug effects in the eye, and the trans-scleral drug delivery. The binding parameters estimated from a given data set vary significantly when using different isotherms or different nonlinear fitting methods. In this work, the commonly used bi-Langmuir isotherm, which assumes two classes of independent sites, is confronted with the Sips isotherm. Direct, log-log, and Scatchard plots are used, and the interpretation of the binding curves in the latter is critically analyzed. In addition to the goodness of fit, the emphasis is placed on the physical meaning of the binding parameters. The bi-Langmuir model imposes a bimodal distribution of binding energies for the sites on the melanin granules, but the actual distribution is most likely continuous and unimodal, as assumed by the Sips isotherm. Hence, the latter describes more accurately the distribution of binding energies and also the experimental results of melanin binding to drugs and metal ions. Simulations are used to show that the existence of two classes of sites cannot be confirmed on the sole basis of the shape of the binding curve in the Scatchard plot, and that serious doubts may appear on the meaning of the binding parameters of the bi-Langmuir model. Experimental results of melanin binding to chloroquine and metoprolol are used to illustrate the importance of the choice of the binding isotherm and of the method used to evaluate the binding parameters.

Engineering [Ln(DPA){sub 3}]{sup 3-} binding sites in proteins: a widely applicable method for tagging proteins with lanthanide ions

Energy Technology Data Exchange (ETDEWEB)

Jia Xinying; Yagi, Hiromasa; Su Xuncheng; Stanton-Cook, Mitchell; Huber, Thomas; Otting, Gottfried, E-mail: gottfried.otting@anu.edu.au [Australian National University, Research School of Chemistry (Australia)

2011-08-15

Paramagnetic relaxation enhancements from unpaired electrons observed in nuclear magnetic resonance (NMR) spectra present powerful long-range distance restraints. The most frequently used paramagnetic tags, however, are tethered to the protein via disulfide bonds, requiring proteins with single cysteine residues for covalent attachment. Here we present a straightforward strategy to tag proteins site-specifically with paramagnetic lanthanides without a tether and independent of cysteine residues. It relies on preferential binding of the complex between three dipicolinic acid molecules (DPA) and a lanthanide ion (Ln{sup 3+}), [Ln(DPA){sub 3}]{sup 3-}, to a pair of positively charged amino acids whose charges are not compensated by negatively charged residues nearby. This situation rarely occurs in wild-type proteins, allowing the creation of specific binding sites simply by introduction of positively charged residues that are positioned far from glutamate or aspartate residues. The concept is demonstrated with the hnRNPLL RRM1 domain. In addition, we show that histidine- and arginine-tags present binding sites for [Ln(DPA){sub 3}]{sup 3-}.

The metal-binding function of metallothioneins and the state of antioxidant defense of carp gills under water pollution by heavy metals

International Nuclear Information System (INIS)

Stolyar, O.B.; Fal'fushins'ka, G.Yi.; Arsan, V.O.

2005-01-01

To investigate the influence of waterborne heavy metal ions on the metal-binding function of metallothioneins and the antioxidant defence in gills, carp (Cyprinus carpio L.) was exposed to copper, zinc, manganese, and lead ions in environmentally realistic concentrations (0.01, 0.1, 0.12, and 0.01 mg/l, respectively) or their mix for 14 days. The results indicate that the metal poisoning provokes the changes in the copper, manganese, and zinc contents in gills and their distribution among the molecular forms of metallothioneins and another tissue targets

Ion Exchange Kinetics of some Heavy Metals from Aqueous Solutions onto Poly(Acrylic Acid-Acrylo nitrle) Potassium Titanate

International Nuclear Information System (INIS)

El-Shorbagy, M.M.; El-Sadek, A.A.

2012-01-01

Composite inorganic-organic absorbers represent a group of inorganic ion exchangers modified using binding organic materials for preparation of larger size particles heaving higher granular strength. Such modification of originally powdered or microcrystalline inorganic ion exchangers makes their application in peaked beds possible-modified polyacrylonitrile (PAN) has been used as a universal binding polymer for a number of inorganic ion exchangers. The kinetic of ion exchange and sorption capacity of such composite absorbers is not influenced by the binding polymer mentioned above. These composites have been tested for separation and concentration of various contaminants from aqueous solutions. Their high selectivity and sorption efficiency are advantageous for treatment of various industrial waste waters. Removal of natural or artificial and the heavy metals, Pb, Cd and Zn ions. the influence of initial metal ion concentration and ph on metal ion removal has been studied. The process was found to follow a first order rate kinetics. The intra-particle diffusion of ions through pores in the adsorbent was to be the main rate limiting step. The selectivity order towards the ions was Pb(II) > Cd(II) > Zn(II)

Identification of a 3rd Na+ Binding Site of the Glycine Transporter, GlyT2.

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Nandhitha Subramanian

Full Text Available The Na+/Cl- dependent glycine transporters GlyT1 and GlyT2 regulate synaptic glycine concentrations. Glycine transport by GlyT2 is coupled to the co-transport of three Na+ ions, whereas transport by GlyT1 is coupled to the co-transport of only two Na+ ions. These differences in ion-flux coupling determine their respective concentrating capacities and have a direct bearing on their functional roles in synaptic transmission. The crystal structures of the closely related bacterial Na+-dependent leucine transporter, LeuTAa, and the Drosophila dopamine transporter, dDAT, have allowed prediction of two Na+ binding sites in GlyT2, but the physical location of the third Na+ site in GlyT2 is unknown. A bacterial betaine transporter, BetP, has also been crystallized and shows structural similarity to LeuTAa. Although betaine transport by BetP is coupled to the co-transport of two Na+ ions, the first Na+ site is not conserved between BetP and LeuTAa, the so called Na1' site. We hypothesized that the third Na+ binding site (Na3 site of GlyT2 corresponds to the BetP Na1' binding site. To identify the Na3 binding site of GlyT2, we performed molecular dynamics (MD simulations. Surprisingly, a Na+ placed at the location consistent with the Na1' site of BetP spontaneously dissociated from its initial location and bound instead to a novel Na3 site. Using a combination of MD simulations of a comparative model of GlyT2 together with an analysis of the functional properties of wild type and mutant GlyTs we have identified an electrostatically favorable novel third Na+ binding site in GlyT2 formed by Trp263 and Met276 in TM3, Ala481 in TM6 and Glu648 in TM10.

Theory Meets Experiment: Metal Ion Effects in HCV Genomic RNA Kissing Complex Formation

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Li-Zhen Sun

2017-12-01

Full Text Available The long-range base pairing between the 5BSL3. 2 and 3′X domains in hepatitis C virus (HCV genomic RNA is essential for viral replication. Experimental evidence points to the critical role of metal ions, especially Mg2+ ions, in the formation of the 5BSL3.2:3′X kissing complex. Furthermore, NMR studies suggested an important ion-dependent conformational switch in the kissing process. However, for a long time, mechanistic understanding of the ion effects for the process has been unclear. Recently, computational modeling based on the Vfold RNA folding model and the partial charge-based tightly bound ion (PCTBI model, in combination with the NMR data, revealed novel physical insights into the role of metal ions in the 5BSL3.2-3′X system. The use of the PCTBI model, which accounts for the ion correlation and fluctuation, gives reliable predictions for the ion-dependent electrostatic free energy landscape and ion-induced population shift of the 5BSL3.2:3′X kissing complex. Furthermore, the predicted ion binding sites offer insights about how ion-RNA interactions shift the conformational equilibrium. The integrated theory-experiment study shows that Mg2+ ions may be essential for HCV viral replication. Moreover, the observed Mg2+-dependent conformational equilibrium may be an adaptive property of the HCV genomic RNA such that the equilibrium is optimized to the intracellular Mg2+ concentration in liver cells for efficient viral replication.

Binding energy and preferred adsorption sites of CO on gold and silver-gold cluster cations: adsorption kinetics and quantum chemical calculations.

Science.gov (United States)

Neumaier, Marco; Weigend, Florian; Hampe, Oliver; Kappes, Manfred M

2008-01-01

We revisit the reactivity of trapped pure gold (Au(n)+, n cations (Ag(m)Au(n)+, m + n carbon monoxide as studied in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The experimental results are discussed in terms of ab initio computations which provide a comprehensive picture of the chemical binding behaviour (like binding energy, adsorption sites, associated vibrational frequencies) of CO to the noble metal as a function of cluster size and composition. Starting from results for pure gold cluster cations for which an overall decrease of CO binding energy with increasing cluster size was experimentally observed--from about 1.09 +/- 0.1 eV (for n = 6) to below 0.65 +/- 0.1 eV (for n > 26) we demonstrate that metal--CO bond energies correlate with the total electron density and with the energy of the lowest unoccupied molecular orbital (LUMO) on the bare metal cluster cation as obtained by density functional theory (DFT) computations. This is a consequence of the predominantly sigma-donating character of the CO-M bond. Further support for this concept is found by contrasting the predictions of binding energies to the experimental results for small alloy cluster cations (Ag(m)Au(n)+, 4 < m + n < 7) as a function of composition. Here, binding energy drops with increasing silver content, while CO still binds always in a head-on fashion to a gold atom. Finally we show how the CO stretch frequency of Ag(m)Au(n)CO+ may be used to identify possible adsorption sites and pre-screen favorable isomers.

Sensing of heavy metal ions by intrinsic TMV coat protein fluorescence

Science.gov (United States)

Bayram, Serene S.; Green, Philippe; Blum, Amy Szuchmacher

2018-04-01

We propose the use of a cysteine mutant of TMV coat protein as a signal transducer for the selective sensing and quantification of the heavy metal ions, Cd2+, Pb2+, Zn2+ and Ni2+ based on intrinsic tryptophan quenching. TMV coat protein is inexpensive, can be mass-produced since it is expressed and extracted from E-coli. It also displays several different functional groups, enabling a wide repertoire of bioconjugation chemistries; thus it can be easily integrated into functional devices. In addition, TMV-ion interactions have been widely reported and utilized for metallization to generate organic-inorganic hybrid composite novel materials. Building on these previous observations, we herein determine, for the first time, the TMV-ion binding constants assuming the static fluorescence quenching model. We also show that by comparing TMV-ion interactions between native and denatured coat protein, we can distinguish between chemically similar heavy metal ions such as cadmium and zinc ions.

Template-directed covalent conjugation of DNA to native antibodies, transferrin and other metal-binding proteins

Science.gov (United States)

Rosen, Christian B.; Kodal, Anne L. B.; Nielsen, Jesper S.; Schaffert, David H.; Scavenius, Carsten; Okholm, Anders H.; Voigt, Niels V.; Enghild, Jan J.; Kjems, Jørgen; Tørring, Thomas; Gothelf, Kurt V.

2014-09-01

DNA-protein conjugates are important in bioanalytical chemistry, molecular diagnostics and bionanotechnology, as the DNA provides a unique handle to identify, functionalize or otherwise manipulate proteins. To maintain protein activity, conjugation of a single DNA handle to a specific location on the protein is often needed. However, preparing such high-quality site-specific conjugates often requires genetically engineered proteins, which is a laborious and technically challenging approach. Here we demonstrate a simpler method to create site-selective DNA-protein conjugates. Using a guiding DNA strand modified with a metal-binding functionality, we directed a second DNA strand to the vicinity of a metal-binding site of His6-tagged or wild-type metal-binding proteins, such as serotransferrin, where it subsequently reacted with lysine residues at that site. This method, DNA-templated protein conjugation, facilitates the production of site-selective protein conjugates, and also conjugation to IgG1 antibodies via a histidine cluster in the constant domain.

Role of the Water–Metal Ion Bridge in Mediating Interactions between Quinolones and Escherichia coli Topoisomerase IV

Science.gov (United States)

2015-01-01

Although quinolones have been in clinical use for decades, the mechanism underlying drug activity and resistance has remained elusive. However, recent studies indicate that clinically relevant quinolones interact with Bacillus anthracis (Gram-positive) topoisomerase IV through a critical water–metal ion bridge and that the most common quinolone resistance mutations decrease drug activity by disrupting this bridge. As a first step toward determining whether the water–metal ion bridge is a general mechanism of quinolone–topoisomerase interaction, we characterized drug interactions with wild-type Escherichia coli (Gram-negative) topoisomerase IV and a series of ParC enzymes with mutations (S80L, S80I, S80F, and E84K) in the predicted bridge-anchoring residues. Results strongly suggest that the water–metal ion bridge is essential for quinolone activity against E. coli topoisomerase IV. Although the bridge represents a common and critical mechanism that underlies broad-spectrum quinolone function, it appears to play different roles in B. anthracis and E. coli topoisomerase IV. The water–metal ion bridge is the most important binding contact of clinically relevant quinolones with the Gram-positive enzyme. However, it primarily acts to properly align clinically relevant quinolones with E. coli topoisomerase IV. Finally, even though ciprofloxacin is unable to increase levels of DNA cleavage mediated by several of the Ser80 and Glu84 mutant E. coli enzymes, the drug still retains the ability to inhibit the overall catalytic activity of these topoisomerase IV proteins. Inhibition parallels drug binding, suggesting that the presence of the drug in the active site is sufficient to diminish DNA relaxation rates. PMID:25115926

Binding energies of cluster ions

International Nuclear Information System (INIS)

Parajuli, R.; Matt, S.; Scheier, P.; Echt, O.; Stamatovic, A.; Maerk, T.D.

2002-01-01

The binding energy of charged clusters may be measured by analyzing the kinetic energy released in the metastable decay of mass selected parent ions. Using finite heat bath theory to determine the binding energies of argon, neon, krypton, oxygen and nitrogen from their respective average kinetic energy released were carried out. A high-resolution double focussing two-sector mass spectrometer of reversed Nier-Johnson type geometry was used. MIKE ( mass-analysed ion kinetic energy) were measured to investigate decay reactions of mass-selected ions. For the inert gases neon (Ne n + ), argon (Ar n + ) and krypton (Kr n + ), it is found that the binding energies initially decrease with increasing size n and then level off at a value above the enthalpy of vaporization of the condensed phase. Oxygen cluster ions shown a characteristic dependence on cluster size (U-shape) indicating a change in the metastable fragmentation mechanism when going from the dimer to the decamer ion. (nevyjel)

MCTBI: a web server for predicting metal ion effects in RNA structures.

Science.gov (United States)

Sun, Li-Zhen; Zhang, Jing-Xiang; Chen, Shi-Jie

2017-08-01

Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg 2+ effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures. © 2017 Sun et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

A protein engineered to bind uranyl selectively and with femtomolar affinity

Science.gov (United States)

Zhou, Lu; Bosscher, Mike; Zhang, Changsheng; Özçubukçu, Salih; Zhang, Liang; Zhang, Wen; Li, Charles J.; Liu, Jianzhao; Jensen, Mark P.; Lai, Luhua; He, Chuan

2014-03-01

Uranyl (UO22+), the predominant aerobic form of uranium, is present in the ocean at a concentration of ~3.2 parts per 109 (13.7 nM) however, the successful enrichment of uranyl from this vast resource has been limited by the high concentrations of metal ions of similar size and charge, which makes it difficult to design a binding motif that is selective for uranyl. Here we report the design and rational development of a uranyl-binding protein using a computational screening process in the initial search for potential uranyl-binding sites. The engineered protein is thermally stable and offers very high affinity and selectivity for uranyl with a Kd of 7.4 femtomolar (fM) and >10,000-fold selectivity over other metal ions. We also demonstrated that the uranyl-binding protein can repeatedly sequester 30-60% of the uranyl in synthetic sea water. The chemical strategy employed here may be applied to engineer other selective metal-binding proteins for biotechnology and remediation applications.

QM/MM Molecular Dynamics Studies of Metal Binding Proteins

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Pietro Vidossich

2014-07-01

Full Text Available Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu and main group (Mg metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.

Metal ion-assisted self-assembly of complexes for controlled and sustained release of minocycline for biomedical applications

International Nuclear Information System (INIS)

Zhang, Zhiling; Wang, Zhicheng; Nong, Jia; Nix, Camilla A; Zhong, Yinghui; Ji, Hai-Feng

2015-01-01

This study reports the development of novel drug delivery complexes self-assembled by divalent metal ion-assisted coacervation for controlled and sustained release of a hydrophilic small drug molecule minocycline hydrochloride (MH). MH is a multifaceted agent that has demonstrated therapeutic effects in infection, inflammation, tumor, as well as cardiovascular, renal, and neurological disorders due to its anti-microbial, anti-inflammatory, and cytoprotective properties. However, the inability to translate the high doses used in experimental animals to tolerable doses in human patients limits its clinical application. Localized delivery can potentially expose the diseased tissue to high concentrations of MH that systemic delivery cannot achieve, while minimizing the side effects from systemic exposure. The strong metal ion binding-assisted interaction enabled high drug entrapment and loading efficiency, and stable long term release for more than 71 d. Released MH demonstrated potent anti-biofilm, anti-inflammatory, and neuroprotective activities. Furthermore, MH release from the complexes is pH-sensitive as the chelation between minocycline and metal ions decreases with pH, allowing ‘smart’ drug release in response to the severity of pathology-induced tissue acidosis. This novel metal ion binding-mediated drug delivery mechanism can potentially be applied to other drugs that have high binding affinity for metal ions and may lead to the development of new delivery systems for a variety of drugs. (paper)

Heavy metal biosorption sites in Penicillium cyclopium | Tsekova ...

African Journals Online (AJOL)

The biomass of Penicillium cyclopium was subjected to chemical treatment to study the role of the functional groups in the biosorption of heavy metal ions. The modifications of the functional groups were examined with infrared spectroscopy. Hydroxyl groups were identified as providing the major sites of heavy metal ...

Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels.

Science.gov (United States)

Shaya, David; Findeisen, Felix; Abderemane-Ali, Fayal; Arrigoni, Cristina; Wong, Stephanie; Nurva, Shailika Reddy; Loussouarn, Gildas; Minor, Daniel L

2014-01-23

Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail "neck", are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the "outer ion" site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies, shows that this site forms a previously unknown determinant of CaV high-affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily. © 2013. Published by Elsevier Ltd. All rights reserved.

Functional analysis of a potential regulatory K+-binding site in the Na+, K+-ATPase

DEFF Research Database (Denmark)

Schack, Vivien Rodacker; Vilsen, Bente

The Na+, K+-ATPase functions by actively transporting 3 Na+ ions out of and 2 K+ ions into the cell, thereby creating ion gradients crucial for many physiological processes. Recently, a combined structural and functional study of the closely related Ca2+-ATPase indicated the presence...... of a regulatory K+-binding site in the P-domain of the enzyme, identifying E732 as being of particular importance (Sorensen, Clausen et al. 2004). In addition, P709 is thought to play a significant role in the structural organization of this site. Both E732 and P709 are highly conserved among P-type ATPases (E732...... is present as either glutamic acid or aspartic acid), which supports their importance and additionally raises the question whether this site may play a general role among P-type ATPases. In Na+, K+-ATPase, K+ functions directly as a substrate for membrane binding sites, however, an additional regulatory...

Synthesis of new water-soluble metal-binding polymers: Combinatorial chemistry approach. 1998 annual progress report

International Nuclear Information System (INIS)

Kurth, M.J.; Miller, R.B.; Sawan, S.; Smith, B.F.

1998-01-01

'(1) Develop rapid discovery and optimization approaches to new water-soluble chelating polymers for use in Polymer Filtration (PF) systems, and (2) evaluate the concept of using water and organic soluble polymers as new solid supports for combinatorial synthesis. Polymer Filtration (PF), which uses water-soluble metal-binding polymers to sequester metal ions in dilute solution with ultrafiltration (UF) to separate the polymers, is a new technology to selectively remove or recover hazardous and valuable metal ions. Future directions in PF must include rapid development, testing, and characterization of new metal-binding polymers. Thus, the authors are building upon and adapting the combinatorial chemistry approach developed for rapid molecule generation for the drug industry to the rapid development of new chelating polymers. The authors have focused on four areas including the development of: (1) synthetic procedures, (2) small ultrafiltration equipment compatible with organic- and aqueous-based combinatorial synthesis, (3) rapid assay techniques, and (4) polymer characterization techniques.'

Metal Stabilization of Collagen and de Novo Designed Mimetic Peptides.

Science.gov (United States)

Parmar, Avanish S; Xu, Fei; Pike, Douglas H; Belure, Sandeep V; Hasan, Nida F; Drzewiecki, Kathryn E; Shreiber, David I; Nanda, Vikas

2015-08-18

We explore the design of metal binding sites to modulate triple-helix stability of collagen and collagen-mimetic peptides. Globular proteins commonly utilize metals to connect tertiary structural elements that are well separated in sequence, constraining structure and enhancing stability. It is more challenging to engineer structural metals into fibrous protein scaffolds, which lack the extensive tertiary contacts seen in globular proteins. In the collagen triple helix, the structural adjacency of the carboxy-termini of the three chains makes this region an attractive target for introducing metal binding sites. We engineered His3 sites based on structural modeling constraints into a series of designed homotrimeric and heterotrimeric peptides, assessing the capacity of metal binding to improve stability and in the case of heterotrimers, affect specificity of assembly. Notable enhancements in stability for both homo- and heteromeric systems were observed upon addition of zinc(II) and several other metal ions only when all three histidine ligands were present. Metal binding affinities were consistent with the expected Irving-Williams series for imidazole. Unlike other metals tested, copper(II) also bound to peptides lacking histidine ligands. Acetylation of the peptide N-termini prevented copper binding, indicating proline backbone amide metal-coordination at this site. Copper similarly stabilized animal extracted Type I collagen in a metal-specific fashion, highlighting the potential importance of metal homeostasis within the extracellular matrix.

Architectural design criteria for f-block metal ion sequestering agents. 1998 annual progress report

International Nuclear Information System (INIS)

Dixon, D.A.; Hay, B.P.; Paine, R.T.; Raymond, K.N.; Rogers, R.D.; Roundhill, D.M.

1998-01-01

'The objective of this project is to provide a means to optimize ligand architecture for f-block metal recognition. The authors strategy builds on an innovative and successful molecular modeling approach in developing polyether ligand design criteria for the alkali and alkaline earth cations. The hypothesis underlying this proposal is that differences in metal ion binding with multidentate ligands bearing the same number and type of donor groups are primarily attributable to intramolecular steric factors. They propose quantifying these steric factors through the application of molecular mechanics models. The research involves close integration of theoretical and experimental chemistry. The experimental work entails synthesizing novel ligands and experimentally determining structures and binding constants for metal ion complexation by series of ligands in which architecture is systematically varied. The theoretical work entails using electronic structure calculations to parameterize a molecular mechanics force field for a range of metal ions and ligand types. The resulting molecular mechanics force field will be used to predict low energy structures for unidentate, bidentate, and multidentate ligands and their metal complexes through conformational searches. Results will be analyzed to assess the relative importance of several steric factors including optimal M-L length, optimal geometry at the metal center, optimal geometry at the donor atoms (complementarity), and conformation prior to binding (preorganization). An accurate set of criteria for the design of ligand architecture will be obtained from these results. These criteria will enable researchers to target ligand structures for synthesis and thereby dramatically reduce the time and cost associated with metal-specific ligand development.'

Toxic metals (Ni2+, Pb2+, Hg2+) binding affinity of dissolved organic matter (DOM) derived from different ages municipal landfill leachate

Science.gov (United States)

Rikta, S. Y.; Tareq, Shafi M.; Uddin, M. Khabir

2018-03-01

Solid waste production is rapidly increasing in Bangladesh and landfill leachate is the consequence of the decomposition of this waste. These leachates contain heavy metals and significant amount of dissolved organic matter (DOM). DOM is known to have considerable role in heavy metals speciation. Hence, it is important to characterize DOM/leachate and evaluate toxic metals binding affinity of DOM. The objectives of this study were to characterize the DOM in landfill leachate through physico-chemical and optical analyses and to investigate the toxic metals (Ni2+, Pb2+ and Hg2+) binding affinity of three different ages (fresh sample L-1, young sample L-2 and mature sample L-3) DOM samples. Results suggested that leachate is a potential pollutant which contained very high organic pollutant load. Conditional stability constant (Log K) and percentages of fluorophores that correspond to metal binding (% f) values indicated that young DOM sample (L-2) had the highest binding affinity to all the three metals ions. In general, DOM samples showed the following order affinity to the metal ions; Ni2+ binding affinity: L-2 > L-3 > L-1, Pb2+ binding affinity: L-2 > L-3 > L-1 and Hg2+ binding affinity: L-2 > L-1 > L-3.

Evaluation of synthetic water-soluble metal-binding polymers with ultrafiltration for selective concentration of americium and plutonium

International Nuclear Information System (INIS)

Smith, B.F.; Gibson, R.R.; Jarvinen, G.D.; Jones, M.M.; Lu, M.T.; Robison, T.W.; Schroeder, N.C.; Stalnaker, N.

1997-01-01

Routine counting methods and ICP-MS are unable to directly measure the new US Department of Energy (DOE) regulatory level for discharge waters containing alpha-emitting radionuclides of 30 pCi/L total alpha or the 0.05 pCi/L regulatory level for Pu or Am activity required for surface waters at the Rocky Flats site by the State of Colorado. This inability indicates the need to develop rapid, reliable, and robust analytical techniques for measuring actinide metal ions, particularly americium and plutonium. Selective separation or preconcentration techniques would aid in this effort. Water-soluble metal-binding polymers in combination with ultrafiltration are shown to be an effective method for selectively removing dilute actinide ions from acidic solutions of high ionic strength. The actinide-binding properties of commercially available water-soluble polymers and several polymers which have been reported in the literature were evaluated. The functional groups incorporated in the polymers were pyrrolidone, amine, oxime, and carboxylic, phosphonic, or sulfonic acid. The polymer containing phosphonic acid groups gave the best results with high distribution coefficients and concentration factors for 241 Am(III) and 238 Pu(III)/(IV) at pH 4 to 6 and ionic strengths of 0.1 to 4

Final Technical Report: Targeting DOE-Relevant Ions with Supramolecular Strategies, DE-SC0010555

Energy Technology Data Exchange (ETDEWEB)

Bowman-James, Kristin [Univ. of Kansas, Lawrence, KS (United States). Dept. of Chemistry

2017-04-13

The effectiveness of three popular supramolecular strategies to selectively target negatively charged ions (anions) was evaluated. Ions of interest included oxo anions, particularly sulfate, that hamper nuclear waste remediation. Three objectives were pursued using a simple building block strategies and by strategically placing anion-binding sites at appropriate positions on organic host molecules. The goal of the first objective was to assess the influence of secondary, tertiary and quaternized amines on binding tetrahedral anions using mixed amide/amine macrocyclic and urea/amine hosts containing aromatic or heteroaromatic spacers. Objective 2 focused on the design of ion pair hosts, using mixed macrocyclic anion hosts joined through polyether linkages. Objective 3 was to explore the synthesis of new metal-linked extended macrocyclic frameworks to leverage anion binding. Key findings were that smaller 24-membered macrocycles provided the most complementary binding for sulfate ion and mixed urea/amine chelates showed enhanced binding over amide corollaries in addition to being highly selective for SO₄^2- in the presence of small quantities of water. In addition to obtaining prototype metal-linked macrocyclic anion hosts, a new dipincer ligand was designed that can be used to link macrocyclic or other supramolecular hosts in extended frameworks. When the tetraamide-based pincers are bound to two metal ions, an interesting phenomenon occurs. Upon deprotonation of the amides, two new protons appear between adjacent carbonyl pairs on the ligand, which may modify the chemistry, and metal-metal interactions in the complexes. Gel formation occurred for some of these extended hosts, and the physical properties are currently under investigation. The new tetracarboxamide-based pincers can also provide basic frameworks for double macrocycles capable of binding ion pairs as well as for binding metal ions and exploring intermetallic interactions through

Accumulation of metal ions by pectinates

Science.gov (United States)

Deiana, S.; Deiana, L.; Palma, A.; Premoli, A.; Senette, C.

2009-04-01

The knowledge of the mechanisms which regulate the interactions of metal ions with partially methyl esterified linear polymers of α-1,4 linked D-galacturonic acid units (pectinates), well represented in the root inner and outer apoplasm, is of great relevance to understand the processes which control their accumulation at the soil-root interface as well as their mobilization by plant metabolites. Accumulation of a metal by pectinates can be affected by the presence of other metals so that competition or distribution could be expected depending on the similar or different affinity of the metal ions towards the binding sites, mainly represented by the carboxylate groups. In order to better understand the mechanism of accumulation in the apoplasm of several metal ions, the sorption of Cd(II), Zn(II), Cu(II), Pb(II) and Cr(III) by a Ca-polygalacturonate gel, used as model of the soil-root interface, with a degree of esterification of 18% (PGAE1) and 65% (PGAE2) was studied at pH 3.0, 4.0, 5.0 and 6.0 in the presence of CaCl2 2.5 mM.. The results show that sorption increases with increasing both the initial metal concentration and pH. A similar sorption trend was evidenced for Cu(II) and Pb(II) and for Zn(II) and Cd(II), indicating that the mechanism of sorption for these two ionic couples is quite different. As an example, at pH 6.0 and an initial metal concentration equal to 2.0 mM, the amount of Cu(II) and Pb(II) sorbed was about 1.98 mg-1 of PGAE1 while that of Cd(II) and Zn(II) was about 1.2 mg-1. Cr(III) showed a rather different sorption trend and a much higher amount (2.8 mg-1of PGAE1 at pH 6.0) was recorded. The higher affinity of Cr(III) for the polysaccharidic matrix is attributable to the formation of Cr(III) polynuclear species in solution, as shown by the distribution diagrams obtained through the MEDUSA software. On the basis of these findings, the following affinity towards the PGAE1 can be assessed: Cr(III) > Cu(II) ? Pb(II) > Zn (II) ? Cd

Metal ion transporters and homeostasis.

OpenAIRE

Nelson, N

1999-01-01

Transition metals are essential for many metabolic processes and their homeostasis is crucial for life. Aberrations in the cellular metal ion concentrations may lead to cell death and severe diseases. Metal ion transporters play a major role in maintaining the correct concentrations of the various metal ions in the different cellular compartments. Recent studies of yeast mutants revealed key elements in metal ion homeostasis, including novel transport systems. Several of the proteins discover...

Metal ion reactive thin films using spray electrostatic LbL assembly.

Science.gov (United States)

Krogman, Kevin C; Lyon, Katharine F; Hammond, Paula T

2008-11-20

By using the spray-layer-by-layer (Spray-LbL) technique, the number of metal counterions trapped within LbL coatings is significantly increased by kinetically freezing the film short of equilibrium, potentially limiting interchain penetration and forcing chains to remain extrinsically compensated to a much greater degree than observed in the traditional dipped LbL technique. The basis for the enhanced entrapment of metal ions such as Cu2+, Fe2+, and Ag+ is addressed, including the equilibrium driving force for extrinsic compensation by soft versus hard metal ions and the impact of Spray-LbL on the kinetics of polymer-ion complexation. These polymer-bound metal-ion coatings are also demonstrated to be effective treatments for air filtration, functionalizing existing filters with the ability to strongly bind toxic industrial compounds such as ammonia or cyanide gases, as well as chemical warfare agent simulants such as chloroethyl ethyl sulfide. On the basis of results reported here, future work could extend this method to include other toxic soft-base ligands such as carbon monoxide, benzene, or organophosphate nerve agents.

[3]tetrahydrotrazodone binding. Association with serotonin binding sites

International Nuclear Information System (INIS)

Kendall, D.A.; Taylor, D.P.; Enna, S.J.

1983-01-01

High (17 nM) and low (603 nM) affinity binding sites for [ 3 ]tetrahydrotrazodone ([ 3 ] THT), a biologically active analogue of trazodone, have been identified in rat brain membranes. The substrate specificity, concentration, and subcellular and regional distributions of these sites suggest that they may represent a component of the serotonin transmitter system. Pharmacological analysis of [ 3 ]THT binding, coupled with brain lesion and drug treatment experiments, revealed that, unlike other antidepressants, [ 3 ] THT does not attach to either a biogenic amine transporter or serotonin binding sites. Rather, it would appear that [ 3 ]THT may be an antagonist ligand for the serotonin binding site. This probe may prove of value in defining the mechanism of action of trazodone and in further characterizing serotonin receptors

Binding of corroded ions to human saliva.

Science.gov (United States)

Mueller, H J

1985-05-01

Employing equilibrium dialysis, the binding abilities of Cu, Al, Co and Cr ions from corroded Cu-Al and Co-Cr dental casting alloys towards human saliva and two of its gel chromatographic fractions were determined. Results indicate that both Cu and Co bind to human saliva i.e. 0.045 and 0.027 mg/mg protein, respectively. Besides possessing the largest binding ability, Cu also possessed the largest binding capacity. The saturation of Cu binding was not reached up to the limit of 0.35 mg protein/ml employed in the tests, while Co reached full saturation at about 0.2 mg protein/ml. Chromium showed absolutely no binding to human saliva while Al ions did not pass through the dialysis membranes. Compared to the binding with solutions that were synthetically made up to contain added salivary-type proteins, it is shown that the binding to human saliva is about 1 order of magnitude larger, at least for Cu ions.

Facile synthesis of Fe3O4@PDA core-shell microspheres functionalized with various metal ions: A systematic comparison of commonly-used metal ions for IMAC enrichment.

Science.gov (United States)

Jiang, Jiebing; Sun, Xueni; Li, Yan; Deng, Chunhui; Duan, Gengli

2018-02-01

Metal ions differed greatly in affinity towards phosphopeptides, and thus it is essential to systematically compare the phosphopeptides enrichment ability of different metal ions usually used in the IMAC techniques. In this work, for the first time, eight metal ions, including Nb 5+ , Ti 4+ , Zr 4+ , Ga 3+ , Y 3+ , In 3+ , Ce 4+ , Fe 3+ , were immobilized on the polydopamine (PDA)-coated Fe 3 O 4 (denoted as Fe 3 O 4 @PDA-M n+ ), and systematically compared by the real biosamples, in addition to standard phosphopeptides. Fe 3 O 4 microspheres were synthesized via the solvothermal reaction, followed by self-polymerization of dopamine on the surface. Then through taking advantage of the hydroxyl and amino group of PDA, the eight metal ions were easily adhered to the surface of Fe 3 O 4 @PDA. After characterization, the resultant Fe 3 O 4 @PDA-M n+ microspheres were applied to phosphopeptides enrichment based on the binding affinity between metal ions and phosphopeptides. According to the results, different metal ions presented diverse phosphopeptides enrichment efficiency in terms of selectivity, sensitivity and the enrichment ability from real complex samples, and Fe 3 O 4 @PDA-Nb 5+ and Fe 3 O 4 @PDA-Ti 4+ showed obvious advantages of the phosphopeptides enrichment effect after the comparison. This systematic comparison may provide certain reference for the use and development of IMAC materials in the future. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluation of complexing agents and column temperature in ion chromatographic separation of alkali metals, alkaline earth metals and transition metals ion

International Nuclear Information System (INIS)

Kelkar, Anoop; Pandey, Ashish; Name, Anil B.; Das, D.K.; Behere, P.G.; Mohd Afzal

2015-01-01

The aim of ion chromatography method development is the resolution of all metal ions of interests. Resolution can be improved by changing the selectivity. Selectivity in chromatography can be altered by changes in mobile phase (eg eluent type, eluent strength) or through changes in stationary phase. Temperature has been used in altering the selectivity of particularly in reversed phase liquid chromatography and ion exchange chromatography. Present paper describe the retention behaviour of alkali metals, alkaline earth metals and transition metal ions on a silica based carboxylate function group containing analyte column. Alkali metals, alkaline earth metals and transition metal ions were detected by ion conductivity and UV-VIS detectors respectively

Quaternary Benzyltriethylammonium Ion Binding to the Na,K-ATPase: a Tool to Investigate Extracellular K+ Binding Reactions†

Science.gov (United States)

Peluffo, R. Daniel; González-Lebrero, Rodolfo M.; Kaufman, Sergio B.; Kortagere, Sandhya; Orban, Branly; Rossi, Rolando C.; Berlin, Joshua R.

2009-01-01

This study examined how the quaternary organic ammonium ion, benzyltriethylamine (BTEA), binds to the Na,K-ATPase to produce membrane potential (VM)-dependent inhibition and tested the prediction that such a VM-dependent inhibitor would display electrogenic binding kinetics. BTEA competitively inhibited K+ activation of Na,K-ATPase activity and steady-state 86Rb+ occlusion. The initial rate of 86Rb+ occlusion was decreased by BTEA to a similar degree whether it was added to the enzyme prior to or simultaneously with Rb+, a demonstration that BTEA inhibits the Na,K-ATPase without being occluded. Several BTEA structural analogues reversibly inhibited Na,K-pump current, but none blocked current in a VM-dependent manner except BTEA and its para-nitro derivative, pNBTEA. Under conditions that promoted electroneutral K+-K+ exchange by the Na,K-ATPase, step changes in VM elicited pNBTEA-activated ouabain-sensitive transient currents that had similarities to those produced with the K+ congener, Tl+. pNBTEA- and Tl+-dependent transient currents both displayed saturation of charge moved at extreme negative and positive VM, equivalence of charge moved during and after step changes in VM, and similar apparent valence. The rate constant (ktot) for Tl+-dependent transient current asymptotically approached a minimum value at positive VM. In contrast, ktot for pNBTEA-dependent transient current was a “U”-shaped function of VM with a minimum value near 0 mV. Homology models of the Na,K-ATPase alpha subunit suggested that quaternary amines can bind to two extracellularly-accessible sites, one of them located at K+ binding sites positioned between transmembrane helices 4, 5, and 6. Altogether, these data revealed important information about electrogenic ion binding reactions of the Na,K-ATPase that are not directly measurable during ion transport by this enzyme. PMID:19621894

Ion implantation and amorphous metals

International Nuclear Information System (INIS)

Hohmuth, K.; Rauschenbach, B.

1981-01-01

This review deals with ion implantation of metals in the high concentration range for preparing amorphous layers (>= 10 at%, implantation doses > 10 16 ions/cm 2 ). Different models are described concerning formation of amorphous phases of metals by ion implantation and experimental results are given. The study of amorphous phases has been carried out by the aid of Rutherford backscattering combined with the channeling technique and using transmission electron microscopy. The structure of amorphous metals prepared by ion implantation has been discussed. It was concluded that amorphous metal-metalloid compounds can be described by a dense-random-packing structure with a great portion of metal atoms. Ion implantation has been compared with other techniques for preparing amorphous metals and the adventages have been outlined

Ion implantation in metals

International Nuclear Information System (INIS)

Vook, F.L.

1977-02-01

The application of ion beams to metals is rapidly emerging as a promising area of research and technology. This report briefly describes some of the recent advances in the modification and study of the basic properties of metals by ion implantation techniques. Most of the research discussed illustrates some of the new and exciting applications of ion beams to metals which are under active investigation at Sandia Laboratories, Albuquerque

Quantitative autoradiographic distribution of L-[3H]glutamate-binding sites in rat central nervous system

International Nuclear Information System (INIS)

Greenamyre, J.T.; Young, A.B.; Penney, J.B.

1984-01-01

Quantitative autoradiography was used to determine the distribution of L-[3H]glutamate-binding sites in the rat central nervous system. Autoradiography was carried out in the presence of Cl- and Ca2+ ions. Scatchard plots and Hill coefficients of glutamate binding suggested that glutamate was interacting with a single population of sites having a K-D of about 300 nM and a capacity of 14.5 pmol/mg of protein. In displacement studies, ibotenate also appeared to bind to a single class of non-interacting sites with a KI of 28 microM. However, quisqualate displacement of [3H]glutamate binding revealed two well-resolved sites with KIS of 12 nM and 114 microM in striatum. These sites were unevenly distributed, representing different proportions of specific glutamate binding in different brain regions. The distribution of glutamate-binding sites correlated very well with the projection areas of putative glutamatergic pathways. This technique provides an extremely sensitive assay which can be used to gather detailed pharmacological and anatomical information about L-[3H]glutamate binding in the central nervous system

Non-noble metal graphene oxide-copper (II) ions hybrid electrodes for electrocatalytic hydrogen evolution reaction

KAUST Repository

Muralikrishna, S.; Ravishankar, T.N.; Ramakrishnappa, T.; Nagaraju, Doddahalli H.; Krishna Pai, Ranjith

2015-01-01

Non-noble metal and inexpensive graphene oxide-copper (II) ions (GO-Cu2+) hybrid catalysts have been explored for the hydrogen evolution reaction (HER). We were able to tune the binding abilities of GO toward the Cu2+ ions and hence their catalytic

Defect-impurity interactions in ion-implanted metals

International Nuclear Information System (INIS)

Turos, A.

1986-01-01

An overview of defect-impurity interactions in metals is presented. When point defects become mobile they migrate towards the sinks and on the way can be captured by impurity atoms forming stable associations so-called complexes. In some metallic systems complexes can also be formed athermally during ion implantation by trapping point defects already in the collision cascade. An association of a point defect with an impurity atom leads to its displacement from the lattice site. The structure and stability of complexes are strongly temperature dependent. With increasing temperature they dissociate or grow by multiple defect trapping. The appearance of freely migrating point defects at elevated temperatures, due to ion bombardment or thermal annealing, causes via coupling with defect fluxes, important impurity redistribution. Because of the sensitivity of many metal-in-metal implanted systems to radiation damage the understanding of this processes is essential for a proper interpretation of the lattice occupancy measurements and the optimization of implantation conditions. (author)

Structural studies on metal-serum albumin. 4

International Nuclear Information System (INIS)

Zhou Yongquia; Hu Xuying; Dou Chao; Liu Hong; Wang Sheyi; Shen Panwen

1992-01-01

There have been no detailed and reliable studies on the environment and configuration of Zn(II), Cd(II) and Hg(II) in the metal centers of human serum albumin and bovine serum albumin to date. In this paper the authentic evidence for the involvement of the cystinyl sulfur atoms in the ligation to the zinc group ions has been obtained from the X-ray photoelectron spectra. To belief that each of the zinc group ions possesses several binding sites in human- and bovine serum albumin and is bound to the deprotonated thiol group (-RS - ) of the cysteinyl residues to form tetrahedral and linear metal centers has been further confirmed by the treatment of ligand to metal charge transfer data with Jorgensen's method. According to these results, it was inferred that these binding sites may be located at the 17 disulfide bridges, most likely at the 7 pairs of adjacent disulfide bridges between positions 75 and 567, in the serum albumin. (author). 42 refs.; 5 figs

Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA

International Nuclear Information System (INIS)

Torigoe, Hidetaka; Miyakawa, Yukako; Ono, Akira; Kozasa, Tetsuo

2012-01-01

Highlights: ► Hg 2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio. ► The binding constant between Hg 2+ and the T:T mismatched base pair was 10 6 M −1 . ► The binding constant was larger than those for nonspecific metal–DNA interactions. ► The binding constant for the second Hg 2+ was larger than that for the first Hg 2+ . ► The positive cooperative binding was observed between Hg 2+ and multiple T:T. - Abstract: Metal-mediated base pairs by the interaction between metal ions and artificial bases in oligonucleotides have been developed for their potential applications in nanotechnology. We recently found that a natural T:T mismatched base pair bound with Hg 2+ ion to form a novel T–Hg–T base pair. Here, we examined the thermodynamic properties of the binding between Hg 2+ and each of the single and double T:T mismatched base pair duplex DNAs by isothermal titration calorimetry. Hg 2+ specifically bound with the T:T mismatched base pair at 1:1 molar ratio with 10 6 M −1 binding constant, which was significantly larger than those for nonspecific metal ion–DNA interactions. In the Hg 2+ –double T:T mismatched base pair interaction, the affinity for the second Hg 2+ binding was significantly larger than that for the first Hg 2+ binding. The positively cooperative binding may be favorable to align multiple Hg 2+ in duplex DNA for the application of the metal-mediated base pairs in nanotechnology.

Self-organization in metal complexes

International Nuclear Information System (INIS)

Radecka-Paryzek, W.

1999-01-01

Inorganic self-organization involves the spontaneous generation of well-defined supramolecular architectures from metal ions and organic ligands. The basic concept of supramolecular chemistry is a molecular recognition. When the substrate are metal ions, recognition is expressed in the stability and selectivity of metal ion complexation by organic ligands and depends on the geometry of the ligand and on their binding sites that it contains. The combination of the geometric features of the ligand units and the coordination geometries of the metal ions provides very efficient tool for the synthesis of novel, intriguing and highly sophisticated species such as catenanes, box structures, double and triple helicates with a variety of interesting properties. The article will focus on the examples of inorganic self-organization involving the templating as a first step for the assembly of supramolecular structures of high complexity. (author)

Nanoscale orientation and lateral organization of chimeric metal-binding green fluorescent protein on lipid membrane determined by epifluorescence and atomic force microscopy

International Nuclear Information System (INIS)

Prachayasittikul, Virapong; Isarankura Na Ayudhya, Chartchalerm; Tantimongcolwat, Tanawut; Galla, Hans-Joachim

2005-01-01

Epifluorescence microscopy as well as atomic force microscopy was successfully applied to explore the orientation and lateral organization of a group of chimeric green fluorescent proteins (GFPs) on lipid membrane. Incorporation of the chimeric GFP carrying Cd-binding region (His6CdBP4GFP) to the fluid phase of DPPC monolayer resulted in a strong fluorescence intensity at the air-water interface. Meanwhile, non-specific adsorption of the GFP having hexahistidine (His6GFP) led to the perturbation of the protein structure in which very low fluorescence was observed. Specific binding of both of the chimeric GFPs to immobilized zinc ions underneath the metal-chelating lipid membrane was revealed. This specific binding could be reversibly controlled by addition of metal ions or metal chelator. Binding of the chimeric GFPs to the metal-chelating lipid membrane was proven to be the end-on orientation while the side-on adsorption was contrarily noted in the absence of metal ions. Increase of lateral mobility owing to the fluidization effect on the chelating lipid membrane subsequently facilitated crystal formation. All these findings have opened up a potential approach for a specific orientation of immobilization of protein at the membrane interface. This could have accounted for a better opportunity of sensor development

Metal-binding silica materials for wastewater cleanup

Energy Technology Data Exchange (ETDEWEB)

Kroh, F.O. [TPL, Inc., Albuquerque, NM (United States)

1997-10-01

In this Phase I Small Business Innovation Research program, TPL, Inc. is developing two series of high-efficiency covalently modified silica materials for removing heavy metal ions from wastewater. These materials have metal ion capacities greatly exceeding those of commercial ion exchange resins. One series, containing thiol groups, has high capacity for {open_quotes}soft{close_quotes} heavy metal ions such as Hg, Pb, Ag, and Cd; the other, containing quaternary ammonium groups, has high capacity for anionic metal ions such as pertechnetate, arsenate, selenite, and chromate. These materials have high selectivity for the contaminant metals and will function well in harsh systems that inactivate other systems.

Dansyl-naphthalimide dyads as molecular probes: effect of spacer group on metal ion binding properties.

Science.gov (United States)

Shankar, Balaraman H; Ramaiah, Danaboyina

2011-11-17

Interaction of a few dansyl-naphthalimide conjugates 1a-e linked through polymethylene spacer groups with various metal ions was investigated through absorption, fluorescence, NMR, isothermal calorimetric (ITC), and laser flash photolysis techniques. The characteristic feature of these dyads is that they exhibit competing singlet-singlet energy transfer (SSET) and photoinduced electron transfer (PET) processes, both of which decrease with the increase in spacer length. Depending on the spacer group, these dyads interact selectively with divalent Cu(2+) and Zn(2+) ions, as compared to other mono- and divalent metal ions. Jobs plot analysis showed that these dyads form 2:3 complexes with Cu(2+) ions, while 1:1 complexes were observed with Zn(2+) ions. The association constants for the Zn(2+) and Cu(2+) complexes were determined and are found to be in the order 10(3)-10(5) M(-1). Irrespective of the length of the spacer group, these dyads interestingly act as fluorescence ratiometric molecular probes for Cu(2+) ions by altering the emission intensity of both dansyl and naphthalimide chromophores. In contrast, only the fluorescence intensity of the naphthalimide chromophore of the lower homologues (n = 1-3) was altered by Zn(2+) ions. (1)H NMR and ITC measurements confirmed the involvement of both sulfonamide and dimethylamine groups in the complexation with Cu(2+) ions, while only the latter group was involved with Zn(2+) ions. Laser excitation of the dyads 1a-e showed formation of a transient absorption which can be attributed to the radical cation of the naphthalimide chromophore, whereas only the triplet excited state of the dyads 1a-e was observed in the presence of Cu(2+) ions. Uniquely, the complexation of 1a-e with Cu(2+) ions affects both PET and SSET processes, while only the PET process was partially inhibited by Zn(2+) ions in the lower homologues (n = 1-3) and the higher homologues exhibited negligible changes in their emission properties. Our results

Difference in brain distributions of carbon 11-labeled 4-hydroxy-2(1H)-quinolones as PET radioligands for the glycine-binding site of the NMDA ion channel

Energy Technology Data Exchange (ETDEWEB)

Fuchigami, Takeshi [Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582 (Japan); Photon Medical Research Center, Hamamatsu University School of Medicine, Hamamatsu 431-3192 (Japan); Haradahira, Terushi [Molecular Imaging Center, National Institute of Radiological Sciences, Inage-ku, Chiba 263-8555 (Japan)], E-mail: terushi@niu.ac.jp; Fujimoto, Noriko [Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582 (Japan); Okauchi, Takashi; Maeda, Jun; Suzuki, Kazutoshi; Suhara, Tetsuya [Molecular Imaging Center, National Institute of Radiological Sciences, Inage-ku, Chiba 263-8555 (Japan); Yamamoto, Fumihiko; Sasaki, Shigeki; Mukai, Takahiro [Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582 (Japan); Yamaguchi, Hiroshi [Molecular Imaging Frontier Research Center, Hamamatsu University School of Medicine, Hamamatsu 431-3192 (Japan); Ogawa, Mikako [Photon Medical Research Center, Hamamatsu University School of Medicine, Hamamatsu 431-3192 (Japan); Magata, Yasuhiro [Photon Medical Research Center, Hamamatsu University School of Medicine, Hamamatsu 431-3192 (Japan); Molecular Imaging Frontier Research Center, Hamamatsu University School of Medicine, Hamamatsu 431-3192 (Japan); Maeda, Minoru [Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582 (Japan)

2008-02-15

High-affinity iodine- and ethyl-C-5 substituted analogs of 4-hydroxy-3-(3-[{sup 11}C]methoxyphenyl)-2(1H)-quinolone ([{sup 11}C]4HQ) were synthesized as new positron emission tomography radioligands for the glycine-binding sites of the N-methyl-D-aspartate (NMDA) ion channel. Although both radioligands showed high in vitro specific binding to rat brain slices, their binding characteristics were quite different from each other. 5-Ethyl-[{sup 11}C]4HQ (5Et-[{sup 11}C]4HQ) showed higher in vitro binding in the forebrain regions than in the cerebellum, bindings that were strongly inhibited by both glycine-site agonists and antagonists. In contrast, 5-iodo-[{sup 11}C]4HQ (5I-[{sup 11}C]4HQ) showed a homogeneous in vitro binding throughout the brain, which was inhibited by antagonists but not by agonists. This difference in in vitro binding between 5Et-[{sup 11}C]4HQ and 5I-[{sup 11}C]4HQ was quite similar to that previously observed between [{sup 11}C]L-703,717 and [{sup 11}C]4HQ, both glycine-site antagonists. In vivo brain uptakes of these {sup 11}C-labeled 4-hydroxyquinolones were examined in mice. Initial brain uptakes of 5Et- and 5I-[{sup 11}C]4HQ at 1 min after intravenous injections were comparable to that of [{sup 11}C]4HQ, but they were 1.3-2.1 times higher than that of [{sup 11}C]L-703,717. The treatment with an anticoagulant, warfarin, only slightly increased the initial uptakes of [{sup 11}C]4HQ and 5Et-[{sup 11}C]4HQ in contrast to [{sup 11}C]L-703,717. The in vivo regional brain distributions were slightly different between the two radioligands. Pretreatment with nonradioactive ligand (2 mg/kg) slightly inhibited the binding of 5Et-[{sup 11}C]4HQ (16-36% inhibition) but not that of 5I-[{sup 11}C]4HQ. In this study, it was found that a small structural change in [{sup 11}C]4HQ resulted in a major change in binding characteristics and distributions, suggesting the existence of two binding sites for [{sup 11}C]4-hydroxyquinolones on the NMDA ion channel

Calcium ion binding properties and the effect of phosphorylation on the intrinsically disordered Starmaker protein.

Science.gov (United States)

Wojtas, Magdalena; Hołubowicz, Rafał; Poznar, Monika; Maciejewska, Marta; Ożyhar, Andrzej; Dobryszycki, Piotr

2015-10-27

Starmaker (Stm) is an intrinsically disordered protein (IDP) involved in otolith biomineralization in Danio rerio. Stm controls calcium carbonate crystal formation in vivo and in vitro. Phosphorylation of Stm affects its biomineralization properties. This study examined the effects of calcium ions and phosphorylation on the structure of Stm. We have shown that CK2 kinase phosphorylates 25 or 26 residues in Stm. Furthermore, we have demonstrated that Stm's affinity for calcium binding is dependent on its phosphorylation state. Phosphorylated Stm (StmP) has an estimated 30 ± 1 calcium binding sites per protein molecule with a dissociation constant (KD) of 61 ± 4 μM, while the unphosphorylated protein has 28 ± 3 sites and a KD of 210 ± 22 μM. Calcium ion binding induces a compaction of the Stm molecule, causing a significant decrease in its hydrodynamic radius and the formation of a secondary structure. The screening effect of Na(+) ions on calcium binding was also observed. Analysis of the hydrodynamic properties of Stm and StmP showed that Stm and StmP molecules adopt the structure of native coil-like proteins.

Simple molecular model for the binding of antibiotic molecules to bacterial ion channels

Science.gov (United States)

Mafé, Salvador; Ramírez, Patricio; Alcaraz, Antonio

2003-10-01

A molecular model aimed at explaining recent experimental data by Nestorovich et al. [Proc. Natl. Acad. Sci. USA 99, 9789 (2002)] on the interaction of ampicillin molecules with the constriction zone in a channel of the general bacterial porin, OmpF (outer membrane protein F), is presented. The model extends T. L. Hill's theory for intermolecular interactions in a pair of binding sites [J. Am. Chem. Soc. 78, 3330 (1956)] by incorporating two binding ions and two pairs of interacting sites. The results provide new physical insights on the role of the complementary pattern of the charge distributions in the ampicillin molecule and the narrowest part of the channel pore. Charge matching of interacting sites facilitates drug binding. The dependence of the number of ampicillin binding events per second with the solution pH and salt concentration is explained qualitatively using a reduced number of fundamental concepts.

How Native and Alien Metal Cations Bind ATP: Implications for Lithium as a Therapeutic Agent

Science.gov (United States)

Dudev, Todor; Grauffel, Cédric; Lim, Carmay

2017-02-01

Adenosine triphosphate (ATP), the major energy currency of the cell, exists in solution mostly as ATP-Mg. Recent experiments suggest that Mg2+ interacts with the highly charged ATP triphosphate group and Li+ can co-bind with the native Mg2+ to form ATP-Mg-Li and modulate the neuronal purine receptor response. However, it is unclear how the negatively charged ATP triphosphate group binds Mg2+ and Li+ (i.e. which phosphate group(s) bind Mg2+/Li+) and how the ATP solution conformation depends on the type of metal cation and the metal-binding mode. Here, we reveal the preferred ATP-binding mode of Mg2+/Li+ alone and combined: Mg2+ prefers to bind ATP tridentately to each of the three phosphate groups, but Li+ prefers to bind bidentately to the terminal two phosphates. We show that the solution ATP conformation depends on the cation and its binding site/mode, but it does not change significantly when Li+ binds to Mg2+-loaded ATP. Hence, ATP-Mg-Li, like Mg2+-ATP, can fit in the ATP-binding site of the host enzyme/receptor, activating specific signaling pathways.

(/sup 3/H)diprenorphine binding to kappa-sites in guinea-pig and rat brain: Evidence for apparent heterogeneity

Energy Technology Data Exchange (ETDEWEB)

Wood, M.S.; Traynor, J.R.

1989-07-01

The binding of the unselective opioid antagonist (/sup 3/H)diprenorphine to homogenates prepared from rat brain and from guinea-pig brain and cerebellum has been studied in HEPES buffer containing 10 mM Mg2+ ions. Sequential displacement of bound (/sup 3/H)diprenorphine by ligands with selectivity for mu-, delta-, and kappa-opioid receptors uncovers the multiple components of binding. In the presence of cold ligands that occupy all mu-, delta-, and kappa-sites, opioid binding still remains. This binding represents 20% of total specific sites and is displaced by naloxone. The nature of these undefined opioid binding sites is discussed.

Interaction analysis of chimeric metal-binding green fluorescent protein and artificial solid-supported lipid membrane by quartz crystal microbalance and atomic force microscopy

International Nuclear Information System (INIS)

Prachayasittikul, Virapong; Na Ayudhya, Chartchalerm Isarankura; Hilterhaus, Lutz; Hinz, Andreas; Tantimongcolwat, Tanawut; Galla, Hans-Joachim

2005-01-01

Non-specific adsorption and specific interaction between a chimeric green fluorescent protein (GFP) carrying metal-binding region and the immobilized zinc ions on artificial solid-supported lipid membranes was investigated using the quartz crystal microbalance technique and the atomic force microscopy (AFM). Supported lipid bilayer, composed of octanethiol and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-[N- (5-amino-1-carboxypentyl iminodiacetic acid)succinyl] (NTA-DOGS)-Zn 2+ , was formed on the gold electrode of quartz resonator (5 MHz). Binding of the chimeric GFP to zinc ions resulted in a rapid decrease of resonance frequency. Reversibility of the process was demonstrated via the removal of metal ions by EDTA. Nanoscale structural orientation of the chimeric GFP on the membrane was imaged by AFM. Association constant of the specific binding to metal ions was 2- to 3-fold higher than that of the non-specific adsorption, which was caused by the fluidization effect of the metal-chelating lipid molecules as well as the steric hindrance effect. This infers a possibility for a further development of biofunctionalized membrane. However, maximization is needed in order to attain closer advancement to a membrane-based sensor device

Copper-zinc superoxide dismutase is activated through a sulfenic acid intermediate at a copper ion entry site.

Science.gov (United States)

Fetherolf, Morgan M; Boyd, Stefanie D; Taylor, Alexander B; Kim, Hee Jong; Wohlschlegel, James A; Blackburn, Ninian J; Hart, P John; Winge, Dennis R; Winkler, Duane D

2017-07-21

Metallochaperones are a diverse family of trafficking molecules that provide metal ions to protein targets for use as cofactors. The copper chaperone for superoxide dismutase (Ccs1) activates immature copper-zinc superoxide dismutase (Sod1) by delivering copper and facilitating the oxidation of the Sod1 intramolecular disulfide bond. Here, we present structural, spectroscopic, and cell-based data supporting a novel copper-induced mechanism for Sod1 activation. Ccs1 binding exposes an electropositive cavity and proposed "entry site" for copper ion delivery on immature Sod1. Copper-mediated sulfenylation leads to a sulfenic acid intermediate that eventually resolves to form the Sod1 disulfide bond with concomitant release of copper into the Sod1 active site. Sod1 is the predominant disulfide bond-requiring enzyme in the cytoplasm, and this copper-induced mechanism of disulfide bond formation obviates the need for a thiol/disulfide oxidoreductase in that compartment. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Studies on indigenous ion exchange resins: alkali metal ions-hydrogen ion exchange equilibria

International Nuclear Information System (INIS)

Shankar, S.; Kumar, Surender; Venkataramani, B.

2001-01-01

With a view to select a suitable ion exchange resin for the removal of radionuclides (such as cesium, strontium etc.) from low level radioactive effluents, alkali metal ion -H' exchanges on nine indigenous gel- and macroporous-type and nuclear grade resins have been studied at a total ionic strength of 0.1 mol dm .3 (in the case ofCs' -H' exchange it was 0.05 mol dm .3 ). The expected theoretical capacities were not attained by all the resins for the alkali metal ions. The water content (moles/equiv.) of the fully swollen resins for different alkali metal ionic forms do not follow the usual sequence of greater the tendency of the cation to hydrate the higher the water uptake, but a reverse trend. The ion exchange isotherms (plots of equivalent fractions of the ion in resin phase, N M1 to that in solution, N M ) were not satisfactory and sorption of cations, for most of the resins, was possible only when the acidity of the solution was lowered. The variations of the selectivity coefficient, K, with N M show that the resins are highly cross linked and the selectivity sequence: Cs + >K + >Na + >Li + , obtained for all the resins indicate that hydrated ions were involved in the exchange process. However, the increase in the selectivity was not accompanied by the release of water, but unusual uptake of water, during the exchange process. The characteristics of macroporous resins were not significantly different from those of the gel-type resins. The results are discussed in terms of heterogeneity in the polymer net work, improper sulphonation process resulting in the formation of functional groups at inaccessible sites with weak acidic character and the overall lack of control in the preparation of different resins. (author)

Thioredoxin binding site of phosphoribulokinase overlaps the catalytic site

International Nuclear Information System (INIS)

Porter, M.A.; Hartman, F.C.

1986-01-01

The ATP-regulatory binding site of phosphoribulokinase was studied using bromoacetylethanolamine phosphate (BrAcNHEtOP). BrAcNHEtOP binds to the active-regulatory binding site of the protein. Following trypsin degradation of the labeled protein, fragments were separated by HPLC and sequenced. (DT)

Binding of copper and nickel to cavities in silicon formed by helium ion implantation

International Nuclear Information System (INIS)

Myers, S.M.; Follstaedt, D.M.; Bishop, D.M.

1993-01-01

Cavities formed in Si by He ion implantation and annealing are shown to be strong traps for Cu and Ni impurities. Experiments utilizing ion-beam analysis and transmission electron microscopy indicate that Cu is trapped at the internal surfaces of cavities up to ∼1 monolayer coverage with a binding energy of 2.2±0.2 eV relative to solution. This is greater than the heat of solution from the precipitated Cu 3 Si phase, determined to be 1.7 eV in agreement with earlier work. Copper at cavity-wall sites is reversibly replaced by H during heating in H 2 gas, indicating the relative stability of the two surface terminations. Initial results for Ni impurities indicate that trapping at cavities is again energetically preferred to silicide formation. The saturation coverage of Ni on the internal surfaces, however, is an order of magnitude smaller for Ni than Cu, consistent with published studies of external-surface adsorption. These results suggest that cavity trapping may getter metallic impurities in Si more effectively than methods based on silicide precipitation

Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.

Science.gov (United States)

Wahba, Haytham M; Lecoq, Lauriane; Stevenson, Michael; Mansour, Ahmed; Cappadocia, Laurent; Lafrance-Vanasse, Julien; Wilkinson, Kevin J; Sygusch, Jurgen; Wilcox, Dean E; Omichinski, James G

2016-02-23

In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL.

Potentiometric Determination of Phytic Acid and Investigations of Phytate Interactions with Some Metal Ions.

Science.gov (United States)

Marolt, Gregor; Pihlar, Boris

2015-01-01

Determination of correct amount (concentration) of phytic acid is of vital importance when dealing with protonation and/or metal complexation equilibria. A novel approach for precise and reliable assay of phytic acid, based on the difference between end points by potentiometric titration, has been presented. Twelve phytic acid protons are classified into three groups of acidity, which enables detection of 2 to 3 distinct equivalent points (EPs) depending on experimental conditions, e.g. counter-ion concentration. Using the differences between individual EPs enables correct phytate determination as well as identification of potential contamination and/or determination of initial protonation degree. Impact of uncertainty of phytate amount on the calculation of protonation constants has been evaluated using computer simulation program (Hyperquad2013). With the analysis of titration curves different binding sites on phytate ligand have been proposed for complexation of Ca2+ and Fe3+ ions.

Cucumber Metallothionein-Like 2 (CsMTL2 Exhibits Metal-Binding Properties

Directory of Open Access Journals (Sweden)

Yu Pan

2016-11-01

Full Text Available We identified a novel member of the metallothionein (MT family, Cucumis sativus metallothionein-like 2 (CsMTL2, by screening a young cucumber fruit complementary DNA (cDNA library. The CsMTL2 encodes a putative 77-amino acid Class II MT protein that contains two cysteine (Cys-rich domains separated by a Cys-free spacer region. We found that CsMTL2 expression was regulated by metal stress and was specifically induced by Cd2+ treatment. We investigated the metal-binding characteristics of CsMTL2 and its possible role in the homeostasis and/or detoxification of metals by heterologous overexpression in Escherichia coli cells. Furthermore, we produced a deletion mutant form of the protein, CsMTL2m, that contained the two Cys-rich clusters but lacked the spacer region, in E. coli. We compared the metal-binding properties of CsMTL2 with those of CsMTL2m, the β domain of human metallothionein-like protein 1 (HsMTXb, and phytochelatin-like (PCL heterologously expressed in E. coli using metal-binding assays. We found that E. coli cells expressing CsMTL2 accumulated the highest levels of Zn2+ and Cd2+ of the four transformed cell types, with levels being significantly higher than those of control cells containing empty vector. E. coli cells expressing CsMTL2 had a higher tolerance for cadmium than for zinc ions. These findings show that CsMTL2 improves metal tolerance when heterologously expressed in E. coli. Future studies should examine whether CsMTL2 improves metal tolerance in planta.

How metallic is the binding state of indium hosted by excess-metal chalcogenides in ore deposits?

Science.gov (United States)

Ondina Figueiredo, Maria; Pena Silva, Teresa; Oliveira, Daniel; Rosa, Diogo

2010-05-01

Discovered in 1863, indium is nowadays a strategic scarce metal used both in classical technologic fields (like low melting-temperature alloys and solders) and in innovative nano-technologies to produce "high-tech devices" by means of new materials, namely liquid crystal displays (LCDs), organic light emitting diodes (OLEDs) and the recently introduced transparent flexible thin-films manufactured with ionic amorphous oxide semiconductors (IAOS). Indium is a typical chalcophile element, seldom forming specific minerals and occurring mainly dispersed within polymetallic sulphides, particularly with excess metal ions [1]. The average content of indium in the Earth's crust is very low but a further increase in its demand is still expected in the next years, thus focusing a special interest in uncovering new exploitation sites through promising polymetallic sulphide ores - e.g., the Iberian Pyrite Belt (IPB) [2] - and in improving recycling technologies. Indium recovery stands mostly on zinc extraction from sphalerite, the natural cubic sulphide which is the prototype of so-called "tetrahedral sulphides" where metal ions fill half of the available tetrahedral sites within the cubic closest packing of sulphur anions where the double of unfilled interstices are available for further in-filling. It is worth remarking that such packing array is particularly suitable for accommodating polymetallic cations by filling closely located interstitial sites [3] as happens in excess-metal tetrahedral sulphides - e.g. bornite, ideally Cu5FeS4, recognized as an In-carrying mineral [4]. Studying the tendency towards In-In interactions able of leading to the formation of polycations would efficiently contribute to understand indium crystal chemistry and the metal binding state in natural chalcogenides. Accordingly, an X-ray absorption near-edge spectroscopy (XANES) study at In L3-edge was undertaken using the instrumental set-up of ID21 beamline at the ESRF (European Synchrotron

Immunoglobulin classes, metal binding proteins, and trace metals in ...

African Journals Online (AJOL)

, IgA and IgM), metal binding proteins (Transferrin, Caeruloplasmin, Alpha-2- Macroglobulin and Haptoglobin) and nutritionally essential trace metals/heavy metals (Zn, Fe, Se, Cu, Mg, Cd and Pb) in Nigerian cassava processors using single ...

Cholesterol-Binding Sites in GIRK Channels: The Devil is in the Details.

Science.gov (United States)

Rosenhouse-Dantsker, Avia

2018-01-01

In recent years, it has become evident that cholesterol plays a direct role in the modulation of a variety of ion channels. In most cases, cholesterol downregulates channel activity. In contrast, our earlier studies have demonstrated that atrial G protein inwardly rectifying potassium (GIRK) channels are upregulated by cholesterol. Recently, we have shown that hippocampal GIRK currents are also upregulated by cholesterol. A combined computational-experimental approach pointed to putative cholesterol-binding sites in the transmembrane domain of the GIRK2 channel, the primary subunit in hippocampal GIRK channels. In particular, the principal cholesterol-binding site was located in the center of the transmembrane domain in between the inner and outer α-helices of 2 adjacent subunits. Further studies pointed to a similar cholesterol-binding site in GIRK4, a major subunit in atrial GIRK channels. However, a close look at a sequence alignment of the transmembrane helices of the 2 channels reveals surprising differences among the residues that interact with the cholesterol molecule in these 2 channels. Here, we compare the residues that form putative cholesterol-binding sites in GIRK2 and GIRK4 and discuss the similarities and differences among them.

LIBRA: LIgand Binding site Recognition Application.

Science.gov (United States)

Hung, Le Viet; Caprari, Silvia; Bizai, Massimiliano; Toti, Daniele; Polticelli, Fabio

2015-12-15

In recent years, structural genomics and ab initio molecular modeling activities are leading to the availability of a large number of structural models of proteins whose biochemical function is not known. The aim of this study was the development of a novel software tool that, given a protein's structural model, predicts the presence and identity of active sites and/or ligand binding sites. The algorithm implemented by ligand binding site recognition application (LIBRA) is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. The algorithm makes use of two predefined databases for active sites and ligand binding sites, respectively, derived from the Catalytic Site Atlas and the Protein Data Bank. Tests indicate that LIBRA is able to identify the correct binding/active site in 90% of the cases analyzed, 90% of which feature the identified site as ranking first. As far as ligand binding site recognition is concerned, LIBRA outperforms other structure-based ligand binding sites detection tools with which it has been compared. The application, developed in Java SE 7 with a Swing GUI embedding a JMol applet, can be run on any OS equipped with a suitable Java Virtual Machine (JVM), and is available at the following URL: http://www.computationalbiology.it/software/LIBRAv1.zip. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Metal ion implantation: Conventional versus immersion

International Nuclear Information System (INIS)

Brown, I.G.; Anders, A.; Anders, S.; Dickinson, M.R.; MacGill, R.A.

1994-01-01

Vacuum-arc-produced metal plasma can be used as the ion feedstock material in an ion source for doing conventional metal ion implantation, or as the immersing plasma for doing plasma immersion ion implantation. The basic plasma production method is the same in both cases; it is simple and efficient and can be used with a wide range of metals. Vacuum arc ion sources of different kinds have been developed by the authors and others and their suitability as a metal ion implantation tool has been well established. Metal plasma immersion surface processing is an emerging tool whose characteristics and applications are the subject of present research. There are a number of differences between the two techniques, both in the procedures used and in the modified surfaces created. For example, the condensibility of metal plasma results in thin film formation and subsequent energetic implantation is thus done through the deposited layer; in the usual scenario, this recoil implantation and the intermixing it produces is a feature of metal plasma immersion but not of conventional energetic ion implantation. Metal plasma immersion is more suited (but not limited) to higher doses (>10 17 cm -2 ) and lower energies (E i < tens of keV) than the usual ranges of conventional metal ion implantation. These and other differences provide these vacuum-arc-based surface modification tools with a versatility that enhances the overall technological attractiveness of both

Detection of heavy metal ions in drinking water using a high-resolution differential surface plasmon resonance sensor.

Science.gov (United States)

Forzani, Erica S; Zhang, Haiqian; Chen, Wilfred; Tao, Nongjian

2005-03-01

We have built a high-resolution differential surface plasmon resonance (SPR) sensor for heavy metal ion detection. The sensor surface is divided into a reference and sensing areas, and the difference in the SPR angles from the two areas is detected with a quadrant cell photodetector as a differential signal. In the presence of metal ions, the differential signal changes due to specific binding of the metal ions onto the sensing area coated with properly selected peptides, which provides an accurate real-time measurement and quantification of the metal ions. Selective detection of Cu2+ and Ni2+ in the ppt-ppb range was achieved by coating the sensing surface with peptides NH2-Gly-Gly-His-COOH and NH2-(His)6-COOH. Cu2+ in drinking water was tested using this sensor.

Modeling metal binding to soils: the role of natural organic matter.

Science.gov (United States)

Gustafsson, Jon Petter; Pechová, Pavlina; Berggren, Dan

2003-06-15

The use of mechanistically based models to simulate the solution concentrations of heavy metals in soils is complicated by the presence of different sorbents that may bind metals. In this study, the binding of Zn, Pb, Cu, and Cd by 14 different Swedish soil samples was investigated. For 10 of the soils, it was found that the Stockholm Humic Model (SHM) was able to describe the acid-base characteristics, when using the concentrations of "active" humic substances and Al as fitting parameters. Two additional soils could be modeled when ion exchange to clay was also considered, using a component additivity approach. For dissolved Zn, Cd, Ca, and Mg reasonable model fits were produced when the metal-humic complexation parameters were identical for the 12 soils modeled. However, poor fits were obtained for Pb and Cu in Aquept B horizons. In two of the soil suspensions, the Lund A and Romfartuna Bhs, the calculated speciation agreed well with results obtained by using cation-exchange membranes. The results suggest that organic matter is an important sorbent for metals in many surface horizons of soils in temperate and boreal climates, and the necessity of properly accounting for the competition from Al in simulations of dissolved metal concentrations is stressed.

Artificial Metalloproteins for Binding and Stabilization of a Semiquinone Radical

NARCIS (Netherlands)

Segaud, Nathalie; Drienovska, Ivana; Chen, Juan; Browne, Wesley R.; Roelfes, Gerard

2017-01-01

The interaction of a number of first-row transition-metal ions with a 2,2'-bipyridyl alanine (bpyA) unit incorporated into the lactococcal multidrug resistance regulator (LmrR) scaffold is reported. The composition of the active site is shown to influence binding affinities. In the case of Fe(II),

Adaptive evolution of transcription factor binding sites

Directory of Open Access Journals (Sweden)

Berg Johannes

2004-10-01

Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

Bacterial exopolysaccharides as a modern biotechnological tool for modification of fungal laccase properties and metal ion binding.

Science.gov (United States)

Osińska-Jaroszuk, Monika; Jaszek, Magdalena; Starosielec, Magdalena; Sulej, Justyna; Matuszewska, Anna; Janczarek, Monika; Bancerz, Renata; Wydrych, Jerzy; Wiater, Adrian; Jarosz-Wilkołazka, Anna

2018-03-26

Four bacterial EPSs extracted from Rhizobium leguminosarum bv. trifolii Rt24.2, Sinorhizobium meliloti Rm1021, Bradyrhizobium japonicum USDA110, and Bradyrhizobium elkanii USDA76 were determined towards their metal ion adsorption properties and possible modification of Cerrena unicolor laccase properties. The highest magnesium and iron ion-sorption capacity (~ 42 and ~ 14.5%, respectively) was observed for EPS isolated from B. japonicum USDA110. An evident influence of EPSs on the stability of laccase compared to the control values (without EPSs) was shown after 30-day incubation at 25 °C. The residual activity of laccases was obtained in the presence of Rh76EPS and Rh1021EPS, i.e., 49.5 and 41.5% of the initial catalytic activity, respectively. This result was confirmed by native PAGE electrophoresis. The EPS effect on laccase stability at different pH (from 3.8 to 7.0) was also estimated. The most significant changes at the optimum pH value (pH 5.8) was observed in samples of laccase stabilized by Rh76EPS and Rh1021EPS. Cyclic voltamperometry was used for analysis of electrochemical parameters of laccase stabilized by bacterial EPS and immobilized on single-walled carbon nanotubes (SWCNTs) with aryl residues. Laccases with Rh76EPS and Rh1021EPS had an evident shift of the value of the redox potential compared to the control without EPS addition. In conclusion, the results obtained in this work present a new potential use of bacterial EPSs as a metal-binding component and a modulator of laccase properties especially stability of enzyme activity, which can be a very effective tool in biotechnology and industrial applications.

Ion mobility studies of carbohydrates as group I adducts: isomer specific collisional cross section dependence on metal ion radius.

Science.gov (United States)

Huang, Yuting; Dodds, Eric D

2013-10-15

Carbohydrates play numerous critical roles in biological systems. Characterization of oligosaccharide structures is essential to a complete understanding of their functions in biological processes; nevertheless, their structural determination remains challenging in part due to isomerism. Ion mobility spectrometry provides the means to resolve gas phase ions on the basis of their shape-to-charge ratios, thus providing significant potential for separation and differentiation of carbohydrate isomers. Here, we report on the determination of collisional cross sections for four groups of isomeric carbohydrates (including five isomeric disaccharides, four isomeric trisaccharides, two isomeric pentasaccharides, and two isomeric hexasaccharides) as their group I metal ion adducts (i.e., [M + Li](+), [M + Na](+), [M + K](+), [M + Rb](+), and [M + Cs](+)). In all, 65 collisional cross sections were measured, the great majority of which have not been previously reported. As anticipated, the collisional cross sections of the carbohydrate metal ion adducts generally increase with increasing metal ion radius; however, the collisional cross sections were found to scale with the group I cation size in isomer specific manners. Such measurements are of substantial analytical value, as they illustrate how the selection of charge carrier influences carbohydrate ion mobility determinations. For example, certain pairs of isomeric carbohydrates assume unique collisional cross sections upon binding one metal ion, but not another. On the whole, these data suggest a role for the charge carrier as a probe of carbohydrate structure and thus have significant implications for the continued development and application of ion mobility spectrometry for the distinction and resolution of isomeric carbohydrates.

Bitopic Ligands and Metastable Binding Sites

DEFF Research Database (Denmark)

Fronik, Philipp; Gaiser, Birgit I; Sejer Pedersen, Daniel

2017-01-01

of orthosteric binding sites. Bitopic ligands have been employed to address the selectivity problem by combining (linking) an orthosteric ligand with an allosteric modulator, theoretically leading to high-affinity subtype selective ligands. However, it remains a challenge to identify suitable allosteric binding...... that have been reported to date, this type of bitopic ligands would be composed of two identical pharmacophores. Herein, we outline the concept of bitopic ligands, review metastable binding sites, and discuss their potential as a new source of allosteric binding sites....

Protection against Mitochondrial and Metal Toxicity Depends on Functional Lipid Binding Sites in ATP13A2

Directory of Open Access Journals (Sweden)

Shaun Martin

2016-01-01

Full Text Available The late endo-/lysosomal P-type ATPase ATP13A2 (PARK9 is implicated in Parkinson’s disease (PD and Kufor-Rakeb syndrome, early-onset atypical Parkinsonism. ATP13A2 interacts at the N-terminus with the signaling lipids phosphatidic acid (PA and phosphatidylinositol (3,5 bisphosphate (PI(3,5P2, which modulate ATP13A2 activity under cellular stress conditions. Here, we analyzed stable human SHSY5Y cell lines overexpressing wild-type (WT or ATP13A2 mutants in which three N-terminal lipid binding sites (LBS1–3 were mutated. We explored the regulatory role of LBS1–3 in the cellular protection by ATP13A2 against mitochondrial stress induced by rotenone and found that the LBS2-3 mutants displayed an abrogated protective effect. Moreover, in contrast to WT, the LBS2 and LBS3 mutants responded poorly to pharmacological inhibition of, respectively, PI(3,5P2 and PA formation. We further demonstrate that PA and PI(3,5P2 are also required for the ATP13A2-mediated protection against the toxic metals Mn2+, Zn2+, and Fe3+, suggesting a general lipid-dependent activation mechanism of ATP13A2 in various PD-related stress conditions. Our results indicate that the ATP13A2-mediated protection requires binding of PI(3,5P2 to LBS2 and PA to LBS3. Thus, targeting the N-terminal lipid binding sites of ATP13A2 might offer a therapeutic approach to reduce cellular toxicity of various PD insults including mitochondrial stress.

Serum albumin forms a lactoferrin-like soluble iron-binding complex in presence of hydrogen carbonate ions.

Science.gov (United States)

Ueno, Hiroshi M; Urazono, Hiroshi; Kobayashi, Toshiya

2014-02-15

The iron-lactoferrin complex is a common food ingredient because of its iron-solubilizing capability in the presence of hydrogen carbonate ions. However, it is unclear whether the formation of a stable iron-binding complex is limited to lactoferrin. In this study, we investigated the effects of bovine serum albumin (BSA) on iron solubility and iron-catalyzed lipid oxidation in the presence of hydrogen carbonate ions. BSA could solubilize >100-fold molar equivalents of iron at neutral pH, exceeding the specific metal-binding property of BSA. This iron-solubilizing capability of BSA was impaired by thermally denaturing BSA at ≥ 70 °C for 10 min at pH 8.5. The resulting iron-BSA complex inhibited iron-catalyzed oxidation of soybean oil in a water-in-oil emulsion measured using the Rancimat test. Our study is the first to show that BSA, like lactoferrin, forms a soluble iron-binding complex in the presence of hydrogen carbonate ions. Copyright © 2013 Elsevier Ltd. All rights reserved.

New developments in metal ion implantation by vacuum arc ion sources and metal plasma immersion

International Nuclear Information System (INIS)

Brown, I.G.; Anders, A.; Anders, S.

1996-01-01

Ion implantation by intense beams of metal ions can be accomplished using the dense metal plasma formed in a vacuum arc discharge embodied either in a vacuum arc ion source or in a metal plasma immersion configuration. In the former case high energy metal ion beams are formed and implantation is done in a more-or-less conventional way, and in the latter case the substrate is immersed in the plasma and repetitively pulse-biased so as to accelerate the ions at the high voltage plasma sheath formed at the substrate. A number of advances have been made in the last few years, both in plasma technology and in the surface modification procedures, that enhance the effectiveness and versatility of the methods, including for example: controlled increase of the in charge states produced; operation in a dual metal-gaseous ion species mode; very large area beam formation; macroparticle filtering; and the development of processing regimes for optimizing adhesion, morphology and structure. These complementary ion processing techniques provide the plasma tools for doing ion surface modification over a very wide parameter regime, from pure ion implantation at energies approaching the MeV level, through ion mixing at energies in the ∼1 to ∼100 keV range, to IBAD-like processing at energies from a few tens of eV to a few keV. Here the authors review the methods, describe a number of recent developments, and outline some of the surface modification applications to which the methods have been put. 54 refs., 9 figs

Nonequivalence of alpha-bungarotoxin binding sites in the native nicotinic receptor molecule

International Nuclear Information System (INIS)

Conti-Tronconi, B.M.; Tang, F.; Walgrave, S.; Gallagher, W.

1990-01-01

In the native, membrane-bound form of the nicotinic acetylcholine receptor (M-AcChR) the two sites for the cholinergic antagonist alpha-bungarotoxin (alpha-BGT) have different binding properties. One site has high affinity, and the M-AcChR/alpha-BGT complexes thus formed dissociate very slowly, similar to the complexes formed with detergent-solubilized AcChR (S-AcChR). The second site has much lower affinity (KD approximately 59 +/- 35 nM) and forms quickly reversible complexes. The nondenaturing detergent Triton X-100 is known to solubilize the AcChR in a form unable, upon binding of cholinergic ligands, to open the ion channel and to become desensitized. Solubilization of the AcChR in Triton X-100 affects the binding properties of this second site and converts it to a high-affinity, slowly reversible site. Prolonged incubation of M-AcChR at 4 degrees C converts the low-affinity site to a high-affinity site similar to those observed in the presence of Triton X-100. Although the two sites have similar properties when the AcChR is solubilized in Triton X-100, their nonequivalence can be demonstrated by the effect on alpha-BGT binding of concanavalin A, which strongly reduces the association rate of one site only. The Bmax of alpha-BGT to either Triton-solubilized AcChR or M-AcChR is not affected by the presence of concanavalin A. Occupancy of the high-affinity, slowly reversible site in M-AcChR inhibits the Triton X-100 induced conversion to irreversibility of the second site. At difference with alpha-BGT, the long alpha-neurotoxin from Naja naja siamensis venom (alpha-NTX) binds with high affinity and in a very slowly reversible fashion to two sites in the M-AcChR. We confirm here that Triton-solubilized AcChR or M-AcChR binds in a very slowly reversible fashion the same amount of alpha-NTX

Structural and Biochemical Characterization of Organotin and Organolead Compounds Binding to the Organomercurial Lyase MerB Provide New Insights into Its Mechanism of Carbon–Metal Bond Cleavage

Energy Technology Data Exchange (ETDEWEB)

Wahba, Haytham M. [Département; Faculty; Stevenson, Michael J. [Department; Mansour, Ahmed [Département; Sygusch, Jurgen [Département; Wilcox, Dean E. [Department; Omichinski, James G. [Département

2017-01-03

The organomercurial lyase MerB has the unique ability to cleave carbon–Hg bonds, and structural studies indicate that three residues in the active site (C96, D99, and C159 in E. coli MerB) play important roles in the carbon–Hg bond cleavage. However, the role of each residue in carbon–metal bond cleavage has not been well-defined. To do so, we have structurally and biophysically characterized the interaction of MerB with a series of organotin and organolead compounds. Studies with two known inhibitors of MerB, dimethyltin (DMT) and triethyltin (TET), reveal that they inhibit by different mechanisms. In both cases the initial binding is to D99, but DMT subsequently binds to C96, which induces a conformation change in the active site. In contrast, diethyltin (DET) is a substrate for MerB and the SnIV product remains bound in the active site in a coordination similar to that of HgII following cleavage of organomercurial compounds. The results with analogous organolead compounds are similar in that trimethyllead (TML) is not cleaved and binds only to D99, whereas diethyllead (DEL) is a substrate and the PbIV product remains bound in the active site. Binding and cleavage is an exothermic reaction, while binding to D99 has negligible net heat flow. These results show that initial binding of organometallic compounds to MerB occurs at D99 followed, in some cases, by cleavage and loss of the organic moieties and binding of the metal ion product to C96, D99, and C159. The N-terminus of MerA is able to extract the bound PbVI but not the bound SnIV. These results suggest that MerB could be utilized for bioremediation applications, but certain organolead and organotin compounds may present an obstacle by inhibiting the enzyme.

Isolation and characterization of iron chelators from turmeric (Curcuma longa): selective metal binding by curcuminoids.

Science.gov (United States)

Messner, Donald J; Surrago, Christine; Fiordalisi, Celia; Chung, Wing Yin; Kowdley, Kris V

2017-10-01

Iron overload disorders may be treated by chelation therapy. This study describes a novel method for isolating iron chelators from complex mixtures including plant extracts. We demonstrate the one-step isolation of curcuminoids from turmeric, the medicinal food spice derived from Curcuma longa. The method uses iron-nitrilotriacetic acid (NTA)-agarose, to which curcumin binds rapidly, specifically, and reversibly. Curcumin, demethoxycurcumin, and bisdemethoxycurcumin each bound iron-NTA-agarose with comparable affinities and a stoichiometry near 1. Analyses of binding efficiencies and purity demonstrated that curcuminoids comprise the primary iron binding compounds recovered from a crude turmeric extract. Competition of curcuminoid binding to the iron resin was used to characterize the metal binding site on curcumin and to detect iron binding by added chelators. Curcumin-Iron-NTA-agarose binding was inhibited by other metals with relative potency: (>90% inhibition) Cu 2+  ~ Al 3+  > Zn 2+  ≥ Ca 2+  ~ Mg 2+  ~ Mn 2+ (80% by addition of iron to the media; uptake was completely restored by desferoxamine. Ranking of metals by relative potencies for blocking curcumin uptake agreed with their relative potencies in blocking curcumin binding to iron-NTA-agarose. We conclude that curcumin can selectively bind toxic metals including iron in a physiological setting, and propose inhibition of curcumin binding to iron-NTA-agarose for iron chelator screening.

Basis of the detection, assessment and cleaning up of sites contaminated with heavy metals

International Nuclear Information System (INIS)

Calmano, W.; Foerstner, U.

1993-01-01

The cleaning up of sites contaminated with heavy metals is still in its infancy. Depending on the type and extent of the contamination, new methods of treatment must be developed and matched to each situation. A survey is given of the groundwater contamination of soil heavy metals; the binding, availability and mobilisation of heavy metals; geo-chemical concepts for sites contaminated by heavy metals; judging the potential danger; safety measures; cleaning up processes and the reinstatement and renaturing of the soil. (orig.) [de

Alkali-Metal-Ion-Functionalized Graphene Oxide as a Superior Anode Material for Sodium-Ion Batteries.

Science.gov (United States)

Wan, Fang; Li, Yu-Han; Liu, Dai-Huo; Guo, Jin-Zhi; Sun, Hai-Zhu; Zhang, Jing-Ping; Wu, Xing-Long

2016-06-06

Although graphene oxide (GO) has large interlayer spacing, it is still inappropriate to use it as an anode for sodium-ion batteries (SIBs) because of the existence of H-bonding between the layers and ultralow electrical conductivity which impedes the Na(+) and e(-) transformation. To solve these issues, chemical, thermal, and electrochemical procedures are traditionally employed to reduce GO nanosheets. However, these strategies are still unscalable, consume high amounts of energy, and are expensive for practical application. Here, for the first time, we describe the superior Na storage of unreduced GO by a simple and scalable alkali-metal-ion (Li(+) , Na(+) , K(+) )-functionalized process. The various alkali metals ions, connecting with the oxygen on GO, have played different effects on morphology, porosity, degree of disorder, and electrical conductivity, which are crucial for Na-storage capabilities. Electrochemical tests demonstrated that sodium-ion-functionalized GO (GNa) has shown outstanding Na-storage performance in terms of excellent rate capability and long-term cycle life (110 mAh g(-1) after 600 cycles at 1 A g(-1) ) owing to its high BET area, appropriate mesopore, high degree of disorder, and improved electrical conductivity. Theoretical calculations were performed using the generalized gradient approximation (GGA) to further study the Na-storage capabilities of functionalized GO. These calculations have indicated that the Na-O bond has the lowest binding energy, which is beneficial to insertion/extraction of the sodium ion, hence the GNa has shown the best Na-storage properties among all comparatives functionalized by other alkali metal ions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test

Science.gov (United States)

Pandey, Preeti; Srivastava, Rakesh; Bandyopadhyay, Pradipta

2018-03-01

The relative performance of MM-PBSA and MM-3D-RISM methods to estimate the binding free energy of protein-ligand complexes is investigated by applying these to three proteins (Dihydrofolate Reductase, Catechol-O-methyltransferase, and Stromelysin-1) differing in the number of metal ions they contain. None of the computational methods could distinguish all the ligands based on their calculated binding free energies (as compared to experimental values). The difference between the two comes from both polar and non-polar part of solvation. For charged ligand case, MM-PBSA and MM-3D-RISM give a qualitatively different result for the polar part of solvation.

Ion implantation of metals

International Nuclear Information System (INIS)

Dearnaley, G.

1976-01-01

In this part of the paper descriptions are given of the effects of ion implantation on (a) friction and wear in metals; and (b) corrosion of metals. In the study of corrosion, ion implantation can be used either to introduce a constituent that is known to convey corrosion resistance, or more generally to examine the parameters which control corrosion. (U.K.)

Anions mediate ligand binding in Adineta vaga glutamate receptor ion channels.

Science.gov (United States)

Lomash, Suvendu; Chittori, Sagar; Brown, Patrick; Mayer, Mark L

2013-03-05

AvGluR1, a glutamate receptor ion channel from the primitive eukaryote Adineta vaga, is activated by alanine, cysteine, methionine, and phenylalanine, which produce lectin-sensitive desensitizing responses like those to glutamate, aspartate, and serine. AvGluR1 LBD crystal structures reveal an unusual scheme for binding dissimilar ligands that may be utilized by distantly related odorant/chemosensory receptors. Arginine residues in domain 2 coordinate the γ-carboxyl group of glutamate, whereas in the alanine, methionine, and serine complexes a chloride ion acts as a surrogate ligand, replacing the γ-carboxyl group. Removal of Cl(-) lowers affinity for these ligands but not for glutamate or aspartate nor for phenylalanine, which occludes the anion binding site and binds with low affinity. AvGluR1 LBD crystal structures and sedimentation analysis also provide insights into the evolutionary link between prokaryotic and eukaryotic iGluRs and reveal features unique to both classes, emphasizing the need for additional structure-based studies on iGluR-ligand interactions. Copyright © 2013 Elsevier Ltd. All rights reserved.

A review on various electrochemical techniques for heavy metal ions detection with different sensing platforms.

Science.gov (United States)

Bansod, BabanKumar; Kumar, Tejinder; Thakur, Ritula; Rana, Shakshi; Singh, Inderbir

2017-08-15

Heavy metal ions are non-biodegradable and contaminate most of the natural resources occurring in the environment including water. Some of the heavy metals including Lead (Pb), Mercury (Hg), Arsenic (As), Chromium (Cr) and Cadmium (Cd) are considered to be highly toxic and hazardous to human health even at trace levels. This leads to the requirement of fast, accurate and reliable techniques for the detection of heavy metal ions. This review presents various electrochemical detection techniques for heavy metal ions those are user friendly, low cost, provides on-site and real time monitoring as compared to other spectroscopic and optical techniques. The categorization of different electrochemical techniques is done on the basis of different types of detection signals generated due to presence of heavy metal ions in the solution matrix like current, potential, conductivity, electrochemical impedance, and electrochemiluminescence. Also, the recent trends in electrochemical detection of heavy metal ions with various types of sensing platforms including metals, metal films, metal oxides, nanomaterials, carbon nano tubes, polymers, microspheres and biomaterials have been evoked. Copyright © 2017 Elsevier B.V. All rights reserved.

Phase stabilisation of hexagonal barium titanate doped with transition metals: A computational study

International Nuclear Information System (INIS)

Dawson, J.A.; Freeman, C.L.; Harding, J.H.; Sinclair, D.C.

2013-01-01

Interatomic potentials recently developed for the modelling of BaTiO 3 have been used to explore the stabilisation of the hexagonal polymorph of BaTiO 3 by doping with transition metals (namely Mn, Co, Fe and Ni) at the Ti-site. Classical simulations have been completed on both the cubic and hexagonal polymorphs to investigate the energetic consequences of transition metal doping on each polymorph. Ti-site charge compensation mechanisms have been used for the multi-valent transition metal ions and cluster binding energies have been considered. Simulations show a significant energetic gain when doping occurs at Ti sites in the face sharing dimers (Ti 2 sites) of the hexagonal polymorph compared with the doping of the cubic polymorph. This energetic difference between the two polymorphs is true for all transition metals tested and all charge states and in the case of tri- and tetra-valent dopants negative solution energies are found for the hexagonal polymorph suggesting actual polymorph stabilisation occurs with the incorporation of these ions as observed experimentally. Oxidation during incorporation of Ni 2+ and Fe 3+ ions has also been considered. - Graphical abstract: The representation of the strongest binding energy clusters for tri-valent dopants—(a) Ti 2 /O 1 cluster and (b) Ti 2 /O 2 cluster. Highlights: ► Classical simulations show a significant energetic gain when doping occurs at Ti sites in the face sharing dimers (Ti2 sites) of the hexagonal polymorph compared with the doping of the cubic polymorph. ► This energetic difference between the two polymorphs is true for all transition metals tested and all charge states. ► In the case of tri- and tetra- valent dopants negative solution energies are found for the hexagonal polymorph suggesting actual polymorph stabilisation occurs with the incorporation of these ions

The selectivity of the Na(+)/K(+)-pump is controlled by binding site protonation and self-correcting occlusion.

Science.gov (United States)

Rui, Huan; Artigas, Pablo; Roux, Benoît

2016-08-04

The Na(+)/K(+)-pump maintains the physiological K(+) and Na(+) electrochemical gradients across the cell membrane. It operates via an 'alternating-access' mechanism, making iterative transitions between inward-facing (E1) and outward-facing (E2) conformations. Although the general features of the transport cycle are known, the detailed physicochemical factors governing the binding site selectivity remain mysterious. Free energy molecular dynamics simulations show that the ion binding sites switch their binding specificity in E1 and E2. This is accompanied by small structural arrangements and changes in protonation states of the coordinating residues. Additional computations on structural models of the intermediate states along the conformational transition pathway reveal that the free energy barrier toward the occlusion step is considerably increased when the wrong type of ion is loaded into the binding pocket, prohibiting the pump cycle from proceeding forward. This self-correcting mechanism strengthens the overall transport selectivity and protects the stoichiometry of the pump cycle.

Polymer Catalysts Imprinted with Metal Ions as Biomimics of Metalloenzymes

Directory of Open Access Journals (Sweden)

Joanna Czulak

2013-01-01

Full Text Available This work presents the preparation and properties of molecularly imprinted polymers (MIPs with catalytic centers that mimic the active sites of metalloenzymes. The MIP synthesis was based on suspension polymerization of functional monomers (4-vinylpyridine and acrylonitrile with trimethylolpropane trimethacrylate as a crosslinker in the presence of transition metal ions and 4-methoxybenzyl alcohol as a template. Four metal ions have been chosen for imprinting from among the microelements that are the most essential in the native enzymes: Cu2+, Co2+, Mn2+, and Zn2+. To prepare catalysts, the required loading of metal ions was obtained during sorption process. The catalysts imprinted with Cu2+, Co2+, and Zn2+ were successfully used for hydroquinone oxidation in the presence of hydrogen peroxide. The Mn2+-imprinted catalyst showed no activity due to the insufficient metal loading. Cu2+ MIP showed the highest efficiency. In case of Cu- and Co-MIP catalysts, their activity was additionally increased by the use of surface imprinting technique.

Evolutionary Implications of Metal Binding Features in Different Species’ Prion Protein: An Inorganic Point of View

Directory of Open Access Journals (Sweden)

Diego La Mendola

2014-05-01

Full Text Available Prion disorders are a group of fatal neurodegenerative conditions of mammals. The key molecular event in the pathogenesis of such diseases is the conformational conversion of prion protein, PrPC, into a misfolded form rich in β-sheet structure, PrPSc, but the detailed mechanistic aspects of prion protein conversion remain enigmatic. There is uncertainty on the precise physiological function of PrPC in healthy individuals. Several evidences support the notion of its role in copper homeostasis. PrPC binds Cu2+ mainly through a domain composed by four to five repeats of eight amino acids. In addition to mammals, PrP homologues have also been identified in birds, reptiles, amphibians and fish. The globular domain of protein is retained in the different species, suggesting that the protein carries out an essential common function. However, the comparison of amino acid sequences indicates that prion protein has evolved differently in each vertebrate class. The primary sequences are strongly conserved in each group, but these exhibit a low similarity with those of mammals. The N-terminal domain of different prions shows tandem amino acid repeats with an increasing amount of histidine residues going from amphibians to mammals. The difference in the sequence affects the number of copper binding sites, the affinity and the coordination environment of metal ions, suggesting that the involvement of prion in metal homeostasis may be a specific characteristic of mammalian prion protein. In this review, we describe the similarities and the differences in the metal binding of different species’ prion protein, as revealed by studies carried out on the entire protein and related peptide fragments.

Identification and properties of very high affinity brain membrane-binding sites for a neurotoxic phospholipase from the taipan venom

International Nuclear Information System (INIS)

Lambeau, G.; Barhanin, J.; Schweitz, H.; Qar, J.; Lazdunski, M.

1989-01-01

Four new monochain phospholipases were purified from the Oxyuranus scutellatus (taipan) venom. Three of them were highly toxic when injected into mice brain. One of these neurotoxic phospholipases, OS2, was iodinated and used in binding experiments to demonstrate the presence of two families of specific binding sites in rat brain synaptic membranes. The affinities were exceptionally high, Kd1 = 1.5 +/- 0.5 pM and Kd2 = 45 +/- 10 pM, and the maximal binding capacities were Bmax 1 = 1 +/- 0.4 and Bmax 2 = 3 +/- 0.5 pmol/mg of protein. Both binding sites were sensitive to proteolysis and demonstrated to be located on proteins of Mr 85,000-88,000 and 36,000-51,000 by cross-linking and photoaffinity labeling techniques. The binding of 125 I-OS2 to synaptic membranes was dependent on Ca2+ ions and enhanced by Zn2+ ions which inhibit phospholipase activity. Competition experiments have shown that, except for beta-bungarotoxin, a number of known toxic snake or bee phospholipases have very high affinities for the newly identified binding sites. A good correlation (r = 0.80) was observed between toxicity and affinity but not between phospholipase activity and affinity

Ceruloplasmin revisited: structural and functional roles of various metal cation-binding sites

International Nuclear Information System (INIS)

Bento, Isabel; Peixoto, Cristina; Zaitsev, Vjacheslav N.; Lindley, Peter F.

2007-01-01

The three-dimensional molecular structure of human serum ceruloplasmin has been reinvestigated using X-ray synchrotron data collected at 100 K from a crystal frozen to liquid-nitrogen temperature. The three-dimensional molecular structure of human serum ceruloplasmin has been reinvestigated using X-ray synchrotron data collected at 100 K from a crystal frozen to liquid-nitrogen temperature. The resulting model, with an increase in resolution from 3.1 to 2.8 Å, gives an overall improvement of the molecular structure, in particular the side chains. In addition, it enables the clear definition of previously unidentified Ca 2+ -binding and Na + -binding sites. The Ca 2+ cation is located in domain 1 in a configuration very similar to that found in the activated bovine factor Va. The Na + sites appear to play a structural role in providing rigidity to the three protuberances on the top surface of the molecule. These features probably help to steer substrates towards the mononuclear copper sites prior to their oxidation and to restrict the size of the approaching substrate. The trinuclear copper centre appears to differ from the room-temperature structure in that a dioxygen moiety is bound in a similar way to that found in the endospore coat protein CotA from Bacillus subtilis

Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction

Science.gov (United States)

Mir, Aamir; Chen, Ji; Robinson, Kyle; Lendy, Emma; Goodman, Jaclyn; Neau, David; Golden, Barbara L.

2016-01-01

The hammerhead ribozyme is a self-cleaving RNA broadly dispersed across all kingdoms of life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism by which it catalyzes its reaction remains elusive. The nucleobase of G12 is well positioned to be a general base, but it is unclear if or how this guanine base becomes activated for proton transfer. Metal ions have been implicated in the chemical mechanism, but no interactions between divalent metal ions and the cleavage site have been observed crystallographically. To better understand how this ribozyme functions, we have solved crystal structures of wild-type and G12A mutant ribozymes. We observe a pH-dependent conformational change centered around G12, consistent with this nucleotide becoming deprotonated. Crystallographic and kinetic analysis of the G12A mutant reveals a Zn2+ specificity switch suggesting a direct interaction between a divalent metal ion and the purine at position 12. The metal ion specificity switch and the pH–rate profile of the G12A mutant suggest that the minor imino tautomer of A12 serves as the general base in the mutant ribozyme. We propose a model in which the hammerhead ribozyme rearranges prior to the cleavage reaction, positioning two divalent metal ions in the process. The first metal ion, positioned near G12, becomes directly coordinated to the O6 keto oxygen, to lower the pKa of the general base and organize the active site. The second metal ion, positioned near G10.1, bridges the N7 of G10.1 and the scissile phosphate and may participate directly in the cleavage reaction. PMID:26398724

Branchial cadmium and copper binding and intestinal cadmium uptake in wild yellow perch (Perca flavescens) from clean and metal-contaminated lakes

International Nuclear Information System (INIS)

Klinck, J.S.; Green, W.W.; Mirza, R.S.; Nadella, S.R.; Chowdhury, M.J.; Wood, C.M.; Pyle, G.G.

2007-01-01

Branchial binding kinetics and gastro-intestinal uptake of copper and cadmium where examined in yellow perch (Perca flavescens) from a metal-contaminated lake (Hannah Lake, Sudbury, Ontario, Canada) and an uncontaminated lake (James Lake, North Bay, Ontario, Canada). An in vivo approach was taken for gill binding comparisons while an in vitro gut binding assay was employed for gastro-intestinal tract (GIT) uptake analysis. By investigating metal uptake at the gill and the gut we cover the two main routes of metal entry into fish. Comparisons of water and sediment chemistries, metal burdens in benthic invertebrate, and metal burdens in the livers of perch from the two study lakes clearly show that yellow perch from Hannah L. are chronically exposed to a highly metal-contaminated environment compared to a reference lake. We found that metal-contaminated yellow perch showed no significant difference in gill Cd binding compared to reference fish, but they did show significant decreases in new Cd binding and absorption in their GITs. The results show that gill Cd binding may involve low-capacity, high-affinity binding sites, while gastro-intestinal Cd uptake involves binding sites that are high-capacity, low-affinity. From this we infer that Cd may be more critically controlled at the gut rather than gills. Significant differences in branchial Cu binding (increased binding) were observed in metal-contaminated yellow perch. We suggest that chronic waterborne exposure to Cu (and/or other metals) may be the dominant influence in gill Cu binding rather than chronic exposure to high Cu diets. We give supporting evidence that Cd is taken up in the GIT, at least in part, by a similar pathway as Ca 2+ , principally that elevated dietary Ca 2+ reduces Cd binding and uptake. Overall our study reveals that metal pre-exposure via water and diet can alter uptake kinetics of Cu and Cd at the gill and/or the gut

Branchial cadmium and copper binding and intestinal cadmium uptake in wild yellow perch (Perca flavescens) from clean and metal-contaminated lakes

Energy Technology Data Exchange (ETDEWEB)

Klinck, J.S. [Department of Biology, McMaster University, Hamilton, Ont. L8S 4K1 (Canada)], E-mail: klinckjs@mcmaster.ca; Green, W.W.; Mirza, R.S. [Department of Biology, McMaster University, Hamilton, Ont. L8S 4K1 (Canada); Department of Biology, Nipissing University, North Bay, Ont. P1B 8L7 (Canada); Nadella, S.R.; Chowdhury, M.J.; Wood, C.M. [Department of Biology, McMaster University, Hamilton, Ont. L8S 4K1 (Canada); Pyle, G.G. [Department of Biology, Nipissing University, North Bay, Ont. P1B 8L7 (Canada)

2007-08-30

Branchial binding kinetics and gastro-intestinal uptake of copper and cadmium where examined in yellow perch (Perca flavescens) from a metal-contaminated lake (Hannah Lake, Sudbury, Ontario, Canada) and an uncontaminated lake (James Lake, North Bay, Ontario, Canada). An in vivo approach was taken for gill binding comparisons while an in vitro gut binding assay was employed for gastro-intestinal tract (GIT) uptake analysis. By investigating metal uptake at the gill and the gut we cover the two main routes of metal entry into fish. Comparisons of water and sediment chemistries, metal burdens in benthic invertebrate, and metal burdens in the livers of perch from the two study lakes clearly show that yellow perch from Hannah L. are chronically exposed to a highly metal-contaminated environment compared to a reference lake. We found that metal-contaminated yellow perch showed no significant difference in gill Cd binding compared to reference fish, but they did show significant decreases in new Cd binding and absorption in their GITs. The results show that gill Cd binding may involve low-capacity, high-affinity binding sites, while gastro-intestinal Cd uptake involves binding sites that are high-capacity, low-affinity. From this we infer that Cd may be more critically controlled at the gut rather than gills. Significant differences in branchial Cu binding (increased binding) were observed in metal-contaminated yellow perch. We suggest that chronic waterborne exposure to Cu (and/or other metals) may be the dominant influence in gill Cu binding rather than chronic exposure to high Cu diets. We give supporting evidence that Cd is taken up in the GIT, at least in part, by a similar pathway as Ca{sup 2+}, principally that elevated dietary Ca{sup 2+} reduces Cd binding and uptake. Overall our study reveals that metal pre-exposure via water and diet can alter uptake kinetics of Cu and Cd at the gill and/or the gut.

Enhancement of oxygen reduction at Fe tetrapyridyl porphyrin by pyridyl-N coordination to transition metal ions

International Nuclear Information System (INIS)

Maruyama, Jun; Baier, Claudia; Wolfschmidt, Holger; Bele, Petra; Stimming, Ulrich

2012-01-01

One of the promising candidates as noble-metal-free electrode catalysts for polymer electrolyte fuel cells (PEFCs) is a carbon material with nitrogen atoms coordinating iron ions embedded on the surface (Fe-N x moiety) as the active site, although the activity is insufficient compared to conventional platinum-based electrocatalysts. In order to obtain fundamental information on the activity enhancement, a simple model of the Fe-N x active site was formed by adsorbing 5,10,15,20-Tetrakis(4-pyridyl)-21H,23H-porphine iron(III) chloride (FeTPyPCl) on the basal plane of highly oriented pyrolytic graphite (HOPG), and cathodic oxygen reduction was investigated on the surface in 0.1 M HClO 4 . The catalytic activity for oxygen reduction was enhanced by loading transition metal ions (Co 2+ , Ni 2+ , Cu 2+ ) together with FeTPyPCl. The X-ray photoelectron spectrum of the surface suggested that the metal was coordinated by the pyridine-N. The enhancement effect of the transition metals was supported by two different measurements: oxygen reduction at HOPG in 0.1 M HClO 4 dissolving FeTPyPCl and the metal ions; oxygen reduction in 0.1 M HClO 4 at the subsequently well-rinsed and dried HOPG. The ultraviolet–visible spectrum for the solution also suggested the coordination between the pyridyl-N and the metal ions. The oxygen reduction enhancement was attributed to the electronic interaction between the additional transition metal and the Fe center of the porphyrin through the coordination bonds. These results implied that the improvement of the activity of the noble-metal-free catalyst would be possible by the proper introduction of the transition metal ions around the active site.

Hemoglobin Rahere, a human hemoglobin variant with amino acid substitution at the 2,3-diphosphoglycerate binding site. Functional consequences of the alteration and effects of bezafibrate on the oxygen bindings.

OpenAIRE

Sugihara, J; Imamura, T; Nagafuchi, S; Bonaventura, J; Bonaventura, C; Cashon, R

1985-01-01

We encountered an abnormal hemoglobin (Rahere), with a threonine residue replacing the beta 82 (EF6) lysine residue at the binding site of 2,3-diphosphoglycerate, which was responsible for overt erythrocytosis in two individuals of a Japanese family. Hemoglobin Rahere shows a lower oxygen affinity on the binding of 2,3-diphosphoglycerate or chloride ions than hemoglobin A. Although a decrease in the positive charge density at the binding sites of 2,3-diphosphoglycerate in hemoglobin Rahere ap...

Selective removal of heavy metal ions by disulfide linked polymer networks

DEFF Research Database (Denmark)

Ko, Dongah; Sung Lee, Joo; Patel, Hasmukh A.

2017-01-01

Heavy metal contaminated surface water is one of the oldest pollution problems, which is critical to ecosystems and human health. We devised disulfide linked polymer networks and employed as a sorbent for removing heavy metal ions from contaminated water. Although the polymer network material has...... a moderate surface area, it demonstrated cadmium removal efficiency equivalent to highly porous activated carbon while it showed 16 times faster sorption kinetics compared to activated carbon, owing to the high affinity of cadmium towards disulfide and thiol functionality in the polymer network. The metal...... sorption mechanism on polymer network was studied by sorption kinetics, effect of pH, and metal complexation. We observed that the metal ions―copper, cadmium, and zinc showed high binding affinity in polymer network, even in the presence of competing cations like calcium in water....

Binding energy effects in cascade evolution and sputtering

International Nuclear Information System (INIS)

Robinson, M.T.

1995-06-01

The MARLOWE model was extended to include a binding energy dependent on the local crystalline order, so that atoms are bound less strongly to their lattice sites near surfaces or associated damage. Sputtering and cascade evolution were studied on the examples of self-ion irradiations of Cu and Au monocrystals. In cascades, the mean binding energy is reduced ∼8% in Cu with little dependence on the initial recoil energy; in Au, it is reduced ∼9% at 1 keV and ∼15% at 100 keV. In sputtering, the mean binding energy is reduced ∼8% in Cu and ∼15% in Au with little energy dependence; the yields are increased about half as much. Most sites from which sputtered atoms originate are isolated in both metals. Small clusters of such sites occur in Cu, but there are some large clusters in Au, especially in [111] targets. There are always more large clusters with damage-dependent binding than with a constant binding energy, but only a few clusters are compact enough to be regarded as pits

The attachment of metal-chelating groups to proteins: tagging of albumin by diazonium coupling and use of the products as radiopharmaceuticals

International Nuclear Information System (INIS)

Leung, C.S.H.; Meares, C.F.; Goodwin, D.A.

1978-01-01

The ability to attach firmly chelated metal ions or powerful chelating agents to sites on biological molecules can enhance the utility of a number of physical techniques now used in the study of biological systems. A 'bifunctional' chelating agent, containing both an EDTA group and a diazonium group, has been prepared and coupled to human serum albumin. The extent of labeling under various conditions and the amino-acid sidechains labeled have been investigated. The reaction of protein-bound chelating groups with added metal ions has been studied, with the finding that only about 40-50% of these groups are available to bind metal ions. Proteolysis of the products leads to recovery of full metal-binding capacity. Properties of the products in vivo are discussed. (author)

The conserved potassium channel filter can have distinct ion binding profiles: structural analysis of rubidium, cesium, and barium binding in NaK2K.

Science.gov (United States)

Lam, Yee Ling; Zeng, Weizhong; Sauer, David Bryant; Jiang, Youxing

2014-08-01

Potassium channels are highly selective for K(+) over the smaller Na(+). Intriguingly, they are permeable to larger monovalent cations such as Rb(+) and Cs(+) but are specifically blocked by the similarly sized Ba(2+). In this study, we used structural analysis to determine the binding profiles for these permeant and blocking ions in the selectivity filter of the potassium-selective NaK channel mutant NaK2K and also performed permeation experiments using single-channel recordings. Our data revealed that some ion binding properties of NaK2K are distinct from those of the canonical K(+) channels KcsA and MthK. Rb(+) bound at sites 1, 3, and 4 in NaK2K, as it does in KcsA. Cs(+), however, bound predominantly at sites 1 and 3 in NaK2K, whereas it binds at sites 1, 3, and 4 in KcsA. Moreover, Ba(2+) binding in NaK2K was distinct from that which has been observed in KcsA and MthK, even though all of these channels show similar Ba(2+) block. In the presence of K(+), Ba(2+) bound to the NaK2K channel at site 3 in conjunction with a K(+) at site 1; this led to a prolonged block of the channel (the external K(+)-dependent Ba(2+) lock-in state). In the absence of K(+), however, Ba(2+) acts as a permeating blocker. We found that, under these conditions, Ba(2+) bound at sites 1 or 0 as well as site 3, allowing it to enter the filter from the intracellular side and exit from the extracellular side. The difference in the Ba(2+) binding profile in the presence and absence of K(+) thus provides a structural explanation for the short and prolonged Ba(2+) block observed in NaK2K. © 2014 Lam et al.

Studies of metal binding by the iron transport protein transferrin using time differential perturbed angular correlation spectroscopy

International Nuclear Information System (INIS)

Then, G.M.

1987-01-01

The binding of the transition metal hafnium to transferrin was studied under various chemical conditions using time differential perturbed γγ angular correlation spectroscopy (TDPAC). Observing the electric quadrupole interaction of the 181 Hf probe nuclei size and symmetry of the electric field gradient induced by the ligands of the metal ions can be determined. The experimental data suggest how homogeneous the binding conditions are and to which extend relaxation phenomena are involved. Due to the excellent time resolution obtained with new BaF 2 detectors the quadrupole coupling parameters of 181 Hf-transferrin could be determined very accurately. Under nearly physiological conditions different binding configurations were quantitatively characterized by spectroscopic means and distinguished with high specificity. (orig./PW) [de

X-ray Absorption Spectroscopy of the Zinc-Binding Sites in the Class B2 Metallo-B-lactamsase ImiS from Aeromonas veronii bv. sobria

Energy Technology Data Exchange (ETDEWEB)

Costello,A.; Sharma, N.; Yang, K.; Crowder, M.; Tierney, D.

2006-01-01

X-ray absorption spectroscopy was used to investigate the metal-binding sites of ImiS from Aeromonas veronii bv. sobria in catalytically active (1-Zn), product-inhibited (1-Zn plus imipenem), and inactive (2-Zn) forms. The first equivalent of zinc(II) was found to bind to the consensus Zn{sub 2} site. The reaction of 1-Zn ImiS with imipenem leads to a product-bound species, coordinated to Zn via a carboxylate group. The inhibitory binding site of ImiS was examined by a comparison of wild-type ImiS with 1 and 2 equiv of bound zinc. 2-Zn ImiS extended X-ray absorption fine structure data support a binding site that is distant from the active site and contains both one sulfur donor and one histidine ligand. On the basis of the amino acid sequence of ImiS and the crystal structure of CphA [Garau et al. (2005) J. Mol. Biol. 345, 785-795], we propose that the inhibitory binding site is formed by M146, found on the B2-distinct {alpha}3 helix, and H118, a canonical Zn{sub 1} ligand, proposed to help activate the nucleophilic water. The mutation of M146 to isoleucine abolishes metal inhibition. This is the first characterization of ImiS with the native metal Zn and establishes, for the first time, the location of the inhibitory metal site.

Identification of cation-binding sites on actin that drive polymerization and modulate bending stiffness

Science.gov (United States)

Kang, Hyeran; Bradley, Michael J.; McCullough, Brannon R.; Pierre, Anaëlle; Grintsevich, Elena E.; Reisler, Emil; De La Cruz, Enrique M.

2012-01-01

The assembly of actin monomers into filaments and networks plays vital roles throughout eukaryotic biology, including intracellular transport, cell motility, cell division, determining cellular shape, and providing cells with mechanical strength. The regulation of actin assembly and modulation of filament mechanical properties are critical for proper actin function. It is well established that physiological salt concentrations promote actin assembly and alter the overall bending mechanics of assembled filaments and networks. However, the molecular origins of these salt-dependent effects, particularly if they involve nonspecific ionic strength effects or specific ion-binding interactions, are unknown. Here, we demonstrate that specific cation binding at two discrete sites situated between adjacent subunits along the long-pitch helix drive actin polymerization and determine the filament bending rigidity. We classify the two sites as “polymerization” and “stiffness” sites based on the effects that mutations at the sites have on salt-dependent filament assembly and bending mechanics, respectively. These results establish the existence and location of the cation-binding sites that confer salt dependence to the assembly and mechanics of actin filaments. PMID:23027950

Detection of heavy metal ions in contaminated water by surface plasmon resonance based optical fibre sensor using conducting polymer and chitosan.

Science.gov (United States)

Verma, Roli; Gupta, Banshi D

2015-01-01

Optical fibre surface plasmon resonance (SPR) based sensor for the detection of heavy metal ions in the drinking water is designed. Silver (Ag) metal and indium tin oxide (ITO) are used for the fabrication of the SPR probe which is further modified with the coating of pyrrole and chitosan composite. The sensor works on the wavelength interrogation technique and is capable of detecting trace amounts of Cd(2+), Pb(2+), and Hg(2+) heavy metal ions in contaminated water. Four types of sensing probes are fabricated and characterised for heavy metal ions out of these pyrrole/chitosan/ITO/Ag coated probe is found to be highly sensitive among all other probes. Further, the cadmium ions bind strongly to the sensing surface than other ions and due to this the sensor is highly sensitive for Cd(2+) ions. The sensor's performance is best for the low concentrations of heavy metal ions and its sensitivity decreases with the increasing concentration of heavy metal ions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Pesticides Curbing Soil Fertility: Effect of Complexation of Free Metal Ions

Science.gov (United States)

Kaur, Sukhmanpreet; Kumar, Vijay; Chawla, Mohit; Cavallo, Luigi; Poater, Albert; Upadhyay, Niraj

2017-07-01

Researchers have suggested that the reason behind infertility is pernicious effect of broad spectrum pesticides on non target, beneficial microorganism of soil. Here, studying the chelating effect of selective organophosphate and carbamate pesticides with essential metal ions, at all possible combinations of three different pH (4±0.05, 7±0.05 and 9±0.05) and three different temperatures (15±0.5°C, 30±0.5°C and 45±0.5°C), shows very fast rate of reaction which further increases with increase of pH and temperature. Carbonyl oxygen of carbamate and phosphate oxygen of organophosphate were found to be common ligating sites among all the complexes. Formed metal complexes were found to be highly stable and water insoluble on interaction with essential metal ions in solvent medium as well as over silica. Density functional theory (DFT) calculations not only reinforced the experimental observations, but, after a wide computational conformational analysis, unraveled the nature of the high stable undesired species that consist of pesticides complexed by metal ions from the soil. All in all, apart from the direct toxicity of pesticides, the indirect effect by means of complexation of free metal ions impoverishes the soil.

Pesticides Curbing Soil Fertility: Effect of Complexation of Free Metal Ions

KAUST Repository

Kaur, Sukhmanpreet

2017-07-04

Researchers have suggested that the reason behind infertility is pernicious effect of broad spectrum pesticides on non target, beneficial microorganism of soil. Here, studying the chelating effect of selective organophosphate and carbamate pesticides with essential metal ions, at all possible combinations of three different pH (4 ± 0.05, 7 ± 0.05 and 9 ± 0.05) and three different temperatures (15 ± 0.5°C, 30 ± 0.5°C and 45 ± 0.5°C), shows very fast rate of reaction which further increases with increase of pH and temperature. Carbonyl oxygen of carbamate and phosphate oxygen of organophosphate were found to be common ligating sites among all the complexes. Formed metal complexes were found to be highly stable and water insoluble on interaction with essential metal ions in solvent medium as well as over silica. Density functional theory (DFT) calculations not only reinforced the experimental observations, but, after a wide computational conformational analysis, unraveled the nature of the high stable undesired species that consist of pesticides complexed by metal ions from the soil. All in all, apart from the direct toxicity of pesticides, the indirect effect by means of complexation of free metal ions impoverishes the soil.

Pesticides Curbing Soil Fertility: Effect of Complexation of Free Metal Ions

KAUST Repository

Kaur, Sukhmanpreet; Kumar, Vijay; Chawla, Mohit; Cavallo, Luigi; Poater, Albert; Upadhyay, Niraj

2017-01-01

Researchers have suggested that the reason behind infertility is pernicious effect of broad spectrum pesticides on non target, beneficial microorganism of soil. Here, studying the chelating effect of selective organophosphate and carbamate pesticides with essential metal ions, at all possible combinations of three different pH (4 ± 0.05, 7 ± 0.05 and 9 ± 0.05) and three different temperatures (15 ± 0.5°C, 30 ± 0.5°C and 45 ± 0.5°C), shows very fast rate of reaction which further increases with increase of pH and temperature. Carbonyl oxygen of carbamate and phosphate oxygen of organophosphate were found to be common ligating sites among all the complexes. Formed metal complexes were found to be highly stable and water insoluble on interaction with essential metal ions in solvent medium as well as over silica. Density functional theory (DFT) calculations not only reinforced the experimental observations, but, after a wide computational conformational analysis, unraveled the nature of the high stable undesired species that consist of pesticides complexed by metal ions from the soil. All in all, apart from the direct toxicity of pesticides, the indirect effect by means of complexation of free metal ions impoverishes the soil.

Removal of the metal ions from aqueous solutions by nanoscaled low molecular pectin isolated from seagrass Phyllospadix iwatensis

International Nuclear Information System (INIS)

Khozhaenko, Elena; Kovalev, Valeri; Podkorytova, Elena; Khotimchenko, Maksim

2016-01-01

Pectins from sea grasses are considered as promising substances with pronounced metal-binding activity. Due to the high molecular weight and heterogeneous structure, the use of pectins for removal of metal ions is difficult. Technology of directed pectin degradation was developed and homogenous degraded nanoscaled pectin polymers were synthesized. Experimental samples of degraded pectin isolated from Phyllospadix iwatensis were tested for their metal binding activity in comparison with native pectin from this seagrass and commercial citrus pectin. The metal uptake of all pectin compounds was highest within the pH range from 4.0 to 6.0. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants. Results showed that depolymerized pectin exerts highest lead and cadmium binding activity with pronounced affinity. All pectin compounds were suggested to be favorable sorbents. Therefore, it can be concluded that degraded pectin is a prospective material for creation of metal-removing water treatment systems. - Highlights: • Low molecular nanoscaled pectin was obtained using original hydrolysis method • Metal binding activity of pectin compounds was studied in a batch sorption system • Pectins exert highest metal binding activity at pH 6.0 • Metal binding isotherms of all pectins are best described by the Langmuir equation • Low molecular pectin from seagrasses is more effective than high-molecular pectins

Removal of the metal ions from aqueous solutions by nanoscaled low molecular pectin isolated from seagrass Phyllospadix iwatensis

Energy Technology Data Exchange (ETDEWEB)

Khozhaenko, Elena [Far Eastern Federal University, School of Biomedicine, 8, Sukhanova str., Vladivostok 690091 (Russian Federation); A.V. Zhirmunsky Institute of Marine Biology Far Eastern Branch of Russian Academy of Sciences, 17, Palchevskgo str., Vladivostok 690059 (Russian Federation); Kovalev, Valeri; Podkorytova, Elena [A.V. Zhirmunsky Institute of Marine Biology Far Eastern Branch of Russian Academy of Sciences, 17, Palchevskgo str., Vladivostok 690059 (Russian Federation); Khotimchenko, Maksim, E-mail: maxkhot@yandex.ru [Far Eastern Federal University, School of Biomedicine, 8, Sukhanova str., Vladivostok 690091 (Russian Federation); A.V. Zhirmunsky Institute of Marine Biology Far Eastern Branch of Russian Academy of Sciences, 17, Palchevskgo str., Vladivostok 690059 (Russian Federation)

2016-09-15

Pectins from sea grasses are considered as promising substances with pronounced metal-binding activity. Due to the high molecular weight and heterogeneous structure, the use of pectins for removal of metal ions is difficult. Technology of directed pectin degradation was developed and homogenous degraded nanoscaled pectin polymers were synthesized. Experimental samples of degraded pectin isolated from Phyllospadix iwatensis were tested for their metal binding activity in comparison with native pectin from this seagrass and commercial citrus pectin. The metal uptake of all pectin compounds was highest within the pH range from 4.0 to 6.0. The Langmuir, Freundlich and BET sorption models were applied to describe the isotherms and constants. Results showed that depolymerized pectin exerts highest lead and cadmium binding activity with pronounced affinity. All pectin compounds were suggested to be favorable sorbents. Therefore, it can be concluded that degraded pectin is a prospective material for creation of metal-removing water treatment systems. - Highlights: • Low molecular nanoscaled pectin was obtained using original hydrolysis method • Metal binding activity of pectin compounds was studied in a batch sorption system • Pectins exert highest metal binding activity at pH 6.0 • Metal binding isotherms of all pectins are best described by the Langmuir equation • Low molecular pectin from seagrasses is more effective than high-molecular pectins.

Obtaining sorbents of metal ions based on yeast cells Rhodotorula glutinis

Directory of Open Access Journals (Sweden)

Zh. Tattibayeva

2013-05-01

Full Text Available Ability to separate Cu2+ and Pb2+ ions from solution using yeast cells Rhodotorulа glutinis were considered. The degree of water purification in this case is of 60-70%. To increase the degree of binding of metal ions with cells and facilitate separation processes of water sorbents their immobilization on the surface of the water in the presence of polyethyleneimine was carried out. It is shown that under optimal conditions on the surface of 1 g diatomite 18 ∙ 106 cells is adsorbed. The high sorption capacity of diatomite justified its porosity. IR spectroscopic study of the interaction of the ions Cu2+ and Pb2+ with cell surface showed that high affinity Pb2 + ions to the surface of yeast cells is connected with form of slightly soluble compounds with the phosphate ions.

Synthesis, Characterizations, and Applications of Metal-Ions Incorporated High Quality MCM-41 Catalysts

International Nuclear Information System (INIS)

Lim, Steven S.; Haller, Gary L.

2013-01-01

Various metal ions (transition and base metals) incorporated MCM-41 catalysts can be synthesized using colloidal and soluble silica with non-sodium involved process. Transition metal ion-typically V 5+ , Co 2+ , and Ni 2+ -incorporated MCM-41 catalysts were synthesized by isomorphous substitution of Si ions in the framework. Each incorporated metal ion created a single species in the silica framework, single-site solid catalyst, showing a substantial stability in reduction and catalytic activity. Radius of pore curvature effect was investigated with Co-MCM-41 by temperature programmed reduction (TPR). The size of metallic Co clusters, sub-nanometer, could be controlled by a proper reduction treatment of Co-MCM-41 having different pore size and the initial pH adjustment of the Co-MCM-41 synthesis solution. These small metallic clusters showed a high stability under a harsh reaction condition without serious migration, resulting from a direct anchoring of small metallic clusters to the partially or unreduced metal ions on the surface. After a complete reduction, partial occlusion of the metallic cluster surface by amorphous silica stabilized the particles against aggregations. As a probe reaction of particle size sensitivity, carbon single wall nanotubes (SWNT) were synthesized using Co-MCM-41. A metallic cluster stability test was performed by CO methanation using Co- and Ni-MCM-41. Methanol and methane partial oxidations were carried out with V-MCM-41, and the radius of pore curvature effect on the catalytic activity was investigated

Gamma-aminobutyric acid-modulated benzodiazepine binding sites in bacteria

International Nuclear Information System (INIS)

Lummis, S.C.R.; Johnston, G.A.R.; Nicoletti, G.; Holan, G.

1991-01-01

Benzodiazepine binding sites, which were once considered to exist only in higher vertebrates, are here demonstrated in the bacteria E. coli. The bacterial [ 3 H]diazepam binding sites are modulated by GABA; the modulation is dose dependent and is reduced at high concentrations. The most potent competitors of E.Coli [ 3 H]diazepam binding are those that are active in displacing [ 3 H]benzodiazepines from vertebrate peripheral benzodiazepine binding sites. These vertebrate sites are not modulated by GABA, in contrast to vertebrate neuronal benzodiazepine binding sites. The E.coli benzodiazepine binding sites therefore differ from both classes of vertebrate benzodiazepine binding sites; however the ligand spectrum and GABA-modulatory properties of the E.coli sites are similar to those found in insects. This intermediate type of receptor in lower species suggests a precursor for at least one class of vertebrate benzodiazepine binding sites may have existed

Metal ion coordination in the E. coli Nudix hydrolase dihydroneopterin triphosphate pyrophosphatase: New clues into catalytic mechanism

Energy Technology Data Exchange (ETDEWEB)

Hill, Shannon E.; Nguyen, Elaine; Ukachukwu, Chiamaka U.; Freeman, Dana M.; Quirk, Stephen; Lieberman, Raquel L.; Boggon, Titus J.

2017-07-25

Dihydroneopterin triphosphate pyrophosphatase (DHNTPase), a member of the Mg2+ dependent Nudix hydrolase superfamily, is the recently-discovered enzyme that functions in the second step of the pterin branch of the folate biosynthetic pathway in E. coli. DHNTPase is of interest because inhibition of enzymes in bacterial folate biosynthetic pathways is a strategy for antibiotic development. We determined crystal structures of DHNTPase with and without activating, Mg2+-mimicking metals Co2+ and Ni2+. Four metal ions, identified by anomalous scattering, and stoichiometrically confirmed in solution by isothermal titration calorimetry, are held in place by Glu56 and Glu60 within the Nudix sequence motif, Glu117, waters, and a sulfate ion, of which the latter is further stabilized by a salt bridge with Lys7. In silico docking of the DHNTP substrate reveals a binding mode in which the pterin ring moiety is nestled in a largely hydrophobic pocket, the β-phosphate activated for nucleophilic attack overlays with the crystallographic sulfate and is in line with an activated water molecule, and remaining phosphate groups are stabilized by all four identified metal ions. The structures and binding data provide new details regarding DHNTPase metal requirements, mechanism, and suggest a strategy for efficient inhibition.

Metal ion coordination in the E. coli Nudix hydrolase dihydroneopterin triphosphate pyrophosphatase: New clues into catalytic mechanism.

Directory of Open Access Journals (Sweden)

Shannon E Hill

Full Text Available Dihydroneopterin triphosphate pyrophosphatase (DHNTPase, a member of the Mg2+ dependent Nudix hydrolase superfamily, is the recently-discovered enzyme that functions in the second step of the pterin branch of the folate biosynthetic pathway in E. coli. DHNTPase is of interest because inhibition of enzymes in bacterial folate biosynthetic pathways is a strategy for antibiotic development. We determined crystal structures of DHNTPase with and without activating, Mg2+-mimicking metals Co2+ and Ni2+. Four metal ions, identified by anomalous scattering, and stoichiometrically confirmed in solution by isothermal titration calorimetry, are held in place by Glu56 and Glu60 within the Nudix sequence motif, Glu117, waters, and a sulfate ion, of which the latter is further stabilized by a salt bridge with Lys7. In silico docking of the DHNTP substrate reveals a binding mode in which the pterin ring moiety is nestled in a largely hydrophobic pocket, the β-phosphate activated for nucleophilic attack overlays with the crystallographic sulfate and is in line with an activated water molecule, and remaining phosphate groups are stabilized by all four identified metal ions. The structures and binding data provide new details regarding DHNTPase metal requirements, mechanism, and suggest a strategy for efficient inhibition.

CaMELS: In silico prediction of calmodulin binding proteins and their binding sites.

Science.gov (United States)

Abbasi, Wajid Arshad; Asif, Amina; Andleeb, Saiqa; Minhas, Fayyaz Ul Amir Afsar

2017-09-01

Due to Ca 2+ -dependent binding and the sequence diversity of Calmodulin (CaM) binding proteins, identifying CaM interactions and binding sites in the wet-lab is tedious and costly. Therefore, computational methods for this purpose are crucial to the design of such wet-lab experiments. We present an algorithm suite called CaMELS (CalModulin intEraction Learning System) for predicting proteins that interact with CaM as well as their binding sites using sequence information alone. CaMELS offers state of the art accuracy for both CaM interaction and binding site prediction and can aid biologists in studying CaM binding proteins. For CaM interaction prediction, CaMELS uses protein sequence features coupled with a large-margin classifier. CaMELS models the binding site prediction problem using multiple instance machine learning with a custom optimization algorithm which allows more effective learning over imprecisely annotated CaM-binding sites during training. CaMELS has been extensively benchmarked using a variety of data sets, mutagenic studies, proteome-wide Gene Ontology enrichment analyses and protein structures. Our experiments indicate that CaMELS outperforms simple motif-based search and other existing methods for interaction and binding site prediction. We have also found that the whole sequence of a protein, rather than just its binding site, is important for predicting its interaction with CaM. Using the machine learning model in CaMELS, we have identified important features of protein sequences for CaM interaction prediction as well as characteristic amino acid sub-sequences and their relative position for identifying CaM binding sites. Python code for training and evaluating CaMELS together with a webserver implementation is available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#camels. © 2017 Wiley Periodicals, Inc.

Identification and properties of very high affinity brain membrane-binding sites for a neurotoxic phospholipase from the taipan venom

Energy Technology Data Exchange (ETDEWEB)

Lambeau, G.; Barhanin, J.; Schweitz, H.; Qar, J.; Lazdunski, M. (Centre de Biochimie, Nice (France))

1989-07-05

Four new monochain phospholipases were purified from the Oxyuranus scutellatus (taipan) venom. Three of them were highly toxic when injected into mice brain. One of these neurotoxic phospholipases, OS2, was iodinated and used in binding experiments to demonstrate the presence of two families of specific binding sites in rat brain synaptic membranes. The affinities were exceptionally high, Kd1 = 1.5 +/- 0.5 pM and Kd2 = 45 +/- 10 pM, and the maximal binding capacities were Bmax 1 = 1 +/- 0.4 and Bmax 2 = 3 +/- 0.5 pmol/mg of protein. Both binding sites were sensitive to proteolysis and demonstrated to be located on proteins of Mr 85,000-88,000 and 36,000-51,000 by cross-linking and photoaffinity labeling techniques. The binding of {sup 125}I-OS2 to synaptic membranes was dependent on Ca2+ ions and enhanced by Zn2+ ions which inhibit phospholipase activity. Competition experiments have shown that, except for beta-bungarotoxin, a number of known toxic snake or bee phospholipases have very high affinities for the newly identified binding sites. A good correlation (r = 0.80) was observed between toxicity and affinity but not between phospholipase activity and affinity.

Versatile high current metal ion implantation facility

International Nuclear Information System (INIS)

Brown, I.G.; Dickinson, M.R.; Galvin, J.E.; Godechot, X.; MacGill, R.A.

1992-01-01

A metal ion implantation facility has been developed with which high current beams of practically all the solid metals of the periodic table can be produced. A multicathode, broad-beam, metal vapor vacuum arc ion source is used to produce repetitively pulsed metal ion beams at an extraction voltage of up to 100 kV, corresponding to an ion energy of up to several hundred kiloelectronvolts because of the ion charge state multiplicity, and with a beam current of up to several amps peak pulsed and several tens of milliamps time averaged delivered onto a downstream target. Implantation is done in a broad-beam mode, with a direct line of sight from ion source to target. Here we summarize some of the features of the ion source and the implantation facility that has been built up around it. (orig)

General aspects of metal toxicity.

Science.gov (United States)

Kozlowski, H; Kolkowska, P; Watly, J; Krzywoszynska, K; Potocki, S

2014-01-01

This review is focused on the general mechanisms of metal toxicity in humans. The possible and mainly confirmed mechanisms of their action are discussed. The metals are divided into four groups due to their toxic effects. First group comprises of metal ions acting as Fenton reaction catalyst mainly iron and copper. These types of metal ions participate in generation of the reactive oxygen species. Metals such as nickel, cadmium and chromium are considered as carcinogenic agents. Aluminum, lead and tin are involved in neurotoxicity. The representative of the last group is mercury, which may be considered as a generally toxic metal. Fenton reaction is a naturally occurring process producing most active oxygen species, hydroxyl radical: Fe(2+) + He2O2 ↔ Fe(3+) + OH(-) + OH(•) It is able to oxidize most of the biomolecules including DNA, proteins, lipids etc. The effect of toxicity depends on the damage of molecules i.e. production site of the hydroxyl radical. Chromium toxicity depends critically on its oxidation state. The most hazardous seems to be Cr(6+) (chromates) which are one of the strongest inorganic carcinogenic agents. Cr(6+) species act also as oxidative agents damaging among other nucleic acids. Redox inactive Al(3+), Cd(2+) or Hg(2+) may interfere with biology of other metal ions e.g. by occupying metal binding sites in biomolecules. All these aspects will be discussed in the review.

The selectivity of the Na+/K+-pump is controlled by binding site protonation and self-correcting occlusion

Science.gov (United States)

Rui, Huan; Artigas, Pablo; Roux, Benoît

2016-01-01

The Na+/K+-pump maintains the physiological K+ and Na+ electrochemical gradients across the cell membrane. It operates via an 'alternating-access' mechanism, making iterative transitions between inward-facing (E1) and outward-facing (E2) conformations. Although the general features of the transport cycle are known, the detailed physicochemical factors governing the binding site selectivity remain mysterious. Free energy molecular dynamics simulations show that the ion binding sites switch their binding specificity in E1 and E2. This is accompanied by small structural arrangements and changes in protonation states of the coordinating residues. Additional computations on structural models of the intermediate states along the conformational transition pathway reveal that the free energy barrier toward the occlusion step is considerably increased when the wrong type of ion is loaded into the binding pocket, prohibiting the pump cycle from proceeding forward. This self-correcting mechanism strengthens the overall transport selectivity and protects the stoichiometry of the pump cycle. DOI: http://dx.doi.org/10.7554/eLife.16616.001 PMID:27490484

Phytoremediation: an overview of metallic ion decontamination from soil

Energy Technology Data Exchange (ETDEWEB)

Singh, O.V.; Labana, S.; Pandey, G.; Budhiraja, R.; Jain, R.K. [Inst. of Microbial Technology, Chandigarh (India)

2003-07-01

In recent years, phytoremediation has emerged as a promising ecoremediation technology, particularly for soil and water cleanup of large volumes of contaminated sites. The exploitation of plants to remediate soils contaminated with trace elements could provide a cheap and sustainable technology for bioremediation. Many modern tools and analytical devices have provided insight into the selection and optimization of the remediation process by plant species. This review describes certain factors for the phytoremediation of metal ion decontamination and various aspects of plant metabolism during metallic decontamination. Metal-hyperaccumulating plants, desirable for heavily polluted environments, can be developed by the introduction of novel traits into high biomass plants in a transgenic approach, which is a promising strategy for the development of effective phytoremediation technology. The genetic manipulation of a phytoremediator plant needs a number of optimization processes, including mobilization of trace elements/metal ions, their uptake into the root, stem and other viable parts of the plant and their detoxification and allocation within the plant. This upcoming science is expanding as technology continues to offer new, low-cost remediation options. (orig.)

Coprecipitation of alkali metal ions with calcium carbonate

International Nuclear Information System (INIS)

Okumura, Minoru; Kitano, Yasushi

1986-01-01

The coprecipitation of alkali metal ions Li + , Na + , K + and Rb + with calcium carbonate has been studied experimentally and the following results have been obtained: (1) Alkali metal ions are more easily coprecipitated with aragonite than with calcite. (2) The relationship between the amounts of alkali metal ions coprecipitated with aragonite and their ionic radii shows a parabolic curve with a peak located at Na + which has approximately the same ionic radius as Ca 2+ . (3) However, the amounts of alkali metal ions coprecipitated with calcite decrease with increasing ionic radius of alkali metals. (4) Our results support the hypothesis that (a) alkali metals are in interstitial positions in the crystal structure of calcite and do not substitute for Ca 2+ in the lattice, but (b) in aragonite, alkali metals substitute for Ca 2+ in the crystal structure. (5) Magnesium ions in the parent solution increase the amounts of alkali metal ions (Li + , Na + , K + and Rb + ) coprecipitated with calcite but decrease those with aragonite. (6) Sodium-bearing aragonite decreases the incorporation of other alkali metal ions (Li + , K + and Rb + ) into the aragonite. (author)

Mu opioid receptor binding sites in human brain

International Nuclear Information System (INIS)

Pilapil, C.; Welner, S.; Magnan, J.; Zamir, N.; Quirion, R.

1986-01-01

Our experiments focused on the examination of the distribution of mu opioid receptor binding sites in normal human brain using the highly selective ligand [ 3 H]DAGO, in both membrane binding assay and in vitro receptor autoradiography. Mu opioid binding sites are very discretely distributed in human brain with high densities of sites found in the posterior amygdala, caudate, putamen, hypothalamus and certain cortical areas. Moreover the autoradiographic distribution of [ 3 H]DAGO binding sites clearly reveals the discrete lamination (layers I and III-IV) of mu sites in cortical areas

Metal vapor vacuum arc ion sources

International Nuclear Information System (INIS)

Brown, I.G.; Dickinson, M.R.; Galvin, J.E.; Godechot, X.; MacGill, R.A.

1990-06-01

We have developed a family of metal vapor vacuum are (MEVVA) high current metal ion sources. The sources were initially developed for the production of high current beams of metal ions for heavy ion synchrotron injection for basic nuclear physics research; more recently they have also been used for metal ion implantation. A number of different embodiments of the source have been developed for these specific applications. Presently the sources operate in a pulsed mode, with pulse width of order 1 ms and repetition rate up to 100 pps. Beam extraction voltage is up to 100 kV, and since the ions produced in the vacuum arc plasma are in general multiply ionized the ion energy is up to several hundred keV. Beam current is up to several Amperes peak and around 10 mA time averaged delivered onto target. Nearly all of the solid metals of the Periodic Table have been use to produce beam. A number of novel features have been incorporated into the sources, including multiple cathodes and the ability to switch between up to 18 separate cathode materials simply and quickly, and a broad beam source version as well as miniature versions. here we review the source designs and their performance. 45 refs., 7 figs

Novel metal ion surface modification technique

International Nuclear Information System (INIS)

Brown, I.G.; Godechot, X.; Yu, K.M.

1990-10-01

We describe a method for applying metal ions to the near-surface region of solid materials. The added species can be energetically implanted below the surface or built up as a surface film with an atomically mixed interface with the substrate; the metal ion species can be the same as the substrate species or different from it, and more than one kind of metal species can be applied, either simultaneously or sequentially. Surface structures can be fabricated, including coatings and thin films of single metals, tailored alloys, or metallic multilayers, and they can be implanted or added onto the surface and ion beam mixed. We report two simple demonstrations of the method: implantation of yttrium into a silicon substrate at a mean energy of 70 keV and a dose of 1 x 10 16 atoms/cm 2 , and the formation of a titanium-yttrium multilayer structure with ion beam mixing to the substrate. 17 refs., 3 figs

New Catalytic DNA Biosensors for Radionuclides and Metal ions

International Nuclear Information System (INIS)

Lu, Yi

2003-01-01

The goals of the project are to develop new catalytic DNA biosensors for simultaneous detection and quantification of bioavailable radionuclides and metal ions, and apply the sensors for on-site, real-time assessment of concentration, speciation and stability of the individual contaminants during and after bioremediation. A negative selection strategy was tested and validated. In vitro selection was shown to yield highly active and specific transition metal ion-dependent catalytic DNA/RNA. A fluorescence resonance energy transfer (FRET) study of in vitro selected DNA demonstrated that the trifluorophore labeled system is a simple and powerful tool in studying complex biomolecules structure and dynamics, and is capable of revealing new sophisticated structural changes. New fluorophore/quenchers in a single fluorosensor yielded improved signal to noise ratio in detection, identification and quantification of metal contaminants. Catalytic DNA fluorescent and colorimetric sensors were shown useful in sensing lead in lake water and in leaded paint. Project results were described in two papers and two patents, and won an international prize

Metallic vapor supplying by the electron bombardment for a metallic ion production with an ECR ion source

Energy Technology Data Exchange (ETDEWEB)

Kitagawa, Atsushi; Sasaki, Makoto; Muramatsu, Masayuki [National Inst. of Radiological Sciences, Chiba (Japan); Jincho, Kaoru; Sasaki, Noriyuki; Sakuma, Tetsuya; Takasugi, Wataru; Yamamoto, Mitsugu [Accelerator Engineering Corporation, Chiba (Japan)

2001-11-19

To produce the metallic ion beam for the injection into the Heavy Ion Medical Accelerator in Chiba (HIMAC) at the National Institute of Radiological Sciences (NIRS), a new gas supply method has been developed for an 18 GHz ECR ion source (NIRS-HEC). A metallic target rod at a high positive potential is melted by the electron bombardment technique. The evaporated gas with a maximum flow rate of 50A/sec is supplied into the ECR plasma in case of Fe metal. (author)

Metallic vapor supplying by the electron bombardment for a metallic ion production with an ECR ion source

International Nuclear Information System (INIS)

Kitagawa, Atsushi; Sasaki, Makoto; Muramatsu, Masayuki; Jincho, Kaoru; Sasaki, Noriyuki; Sakuma, Tetsuya; Takasugi, Wataru; Yamamoto, Mitsugu

2001-01-01

To produce the metallic ion beam for the injection into the Heavy Ion Medical Accelerator in Chiba (HIMAC) at the National Institute of Radiological Sciences (NIRS), a new gas supply method has been developed for an 18 GHz ECR ion source (NIRS-HEC). A metallic target rod at a high positive potential is melted by the electron bombardment technique. The evaporated gas with a maximum flow rate of 50A/sec is supplied into the ECR plasma in case of Fe metal. (author)

A control on hydrophobic and hydrophilic interactions between HEWL and metal Schiff-base complexes comprising of different metal ions and ligands

Energy Technology Data Exchange (ETDEWEB)

Koley Seth, Banabithi; Ray, Aurkie; Basu, Samita, E-mail: samita.basu@saha.ac.in

2015-05-15

The structural effects of different copper(II) and nickel(II) Schiff base complexes on hen egg white lysozyme (HEWL) have been investigated through steady state and time resolved absorption and fluorescence, and circular dichroism spectroscopy. The Schiff base ligands with N{sub 4} donor atoms show both hydrophobic and hydrophilic interactions, however hydrophilic interaction prevails with ligands having N{sub 2}O{sub 2} donor atoms. Variation of metal ions from Cu{sup 2+} to Ni{sup 2+} with each type of Schiff base ligand increases the probability of hydrophilic over hydrophobic interactions, which supports their significance in regulating the binding affinity between HEWL and metal complexes. On photo-excitation the complexes comprising of Cu{sup 2+} ion instead of Ni{sup 2+} ion and ligands with N{sub 4} donor system rather than N{sub 2}O{sub 2} donor system, increases the probability of intersystem crossing to populate the corresponding triplet state as observed from laser flash photolysis study. The better binding affinity of nickel complexes with different selectivities compared to copper complexes towards HEWL emphasizes the potentiality of less explored nickel complexes in drug–protein interactions. - Highlights: • Ni{sup II} and Cu{sup II} -Schiff base complexes bind hen egg white lysozyme spontaneously. • Both hydrophobic and hydrophilic interactions are effective for N{sub 4} ligands. • For N{sub 2}O{sub 2} ligands the hydrophilic is predominant over hydrophobic interaction. • Binding affinity and selectivity of Ni{sup II}-complexes are better than Cu{sup II}-complexes. • Replacement of Cu{sup 2+} by Ni{sup 2+} in a ligand enhances chance of hydrophilic interaction.

Ion-beam-mixing in metal-metal systems and metal-silicon systems

International Nuclear Information System (INIS)

Hung, L.

1984-01-01

The influence of energetic ion bombardment on the composition and structure of thin film materials and utilization of ion-beam-mixing techniques to modify interfacial reactions are reported in this thesis. The phase formation in metals by using ion mixing techniques has been studied. Upon ion irradiation of Al/Pt, Al/Pd and Al/Ni thin films, only the simplest intermetallic compounds of PdAl and NiAl were formed in crystalline structure, while the amorphous phase has been observed over a large range of composition. Ion mixing of Au/Cu bilayers resulted in the formation of substitutional solid solutions with no trace of ordered compounds. The formation of the ordered compound CuAu was achieved either by irradiation of bilayers with Ar ions at elevated substrate temperature or by irradiation of the mixed layers with He ions at relatively low temperature. In the Au/Al system several crystal compounds existed in the as-deposited samples. These phases remained crystalline or transformed into other equilibrium compounds upon ion irradiation. The results suggest that the phase formation by ion mixing is dependent on the high quench rate in the collision cascade region and the atomic mobility at the irradiation temperature. The argument can be applied to silicide forming systems. With near-noble metals, the mixed atoms are mobile and form metallurgically distinct phases. With refractory metals, amorphous phases are formed due to lack of atomic mobility

High charge state metal ion production in vacuum arc ion sources

International Nuclear Information System (INIS)

Brown, I.G.; Anders, A.; Anders, S.

1994-01-01

The vacuum arc is a rich source of highly ionized metal plasma that can be used to make a high current metal ion source. Vacuum arc ion sources have been developed for a range of applications including ion implantation for materials surface modification, particle accelerator injection for fundamental nuclear physics research, and other fundamental and applied purposes. Typically the source is repetitively pulsed with pulse length of order a millisecond and duty cycle or order 1% and operation of a dc embodiment has been demonstrated also. Beams have been produced from over 50 of the solid metals of the periodic table, with mean ion energy up to several hundred keV and with peak (pulsed) beam current up to several amperes. The ion charge state distribution has been extensively studied. Ion spectra have been measured for a wide range of metallic cathode materials, including Li, C, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ge, Sr, Y, Zr, Nb, Mo, Pd, Ag, Cd, In, Sn, Sb, Ba, La, Ce, Pr, Nd, Sm, Gd, Dy, Ho, Er, Tm, Yb, Hf, Ta, W, Ir, Pt, Au, Pb, Bi, Th and U, as well as compound and alloy cathode materials such as TiC, SiC, UC, PbS, brass, and stainless steel. The ions generated are in general multiply-stripped with a mean charge state of from 1 to 3, depending on the particular metal species, and the charge state distribution can have components from Q = 1+ to 6+. Here the authors review the characteristics of vacuum arc ion sources from the perspective of their high charge state metal ion production

Entrapment of metal clusters in metal-organic framework channels by extended hooks anchored at open metal sites.

Science.gov (United States)

Zheng, Shou-Tian; Zhao, Xiang; Lau, Samuel; Fuhr, Addis; Feng, Pingyun; Bu, Xianhui

2013-07-17

Reported here are the new concept of utilizing open metal sites (OMSs) for architectural pore design and its practical implementation. Specifically, it is shown here that OMSs can be used to run extended hooks (isonicotinates in this work) from the framework walls to the channel centers to effect the capture of single metal ions or clusters, with the concurrent partitioning of the large channel spaces into multiple domains, alteration of the host-guest charge relationship and associated guest-exchange properties, and transfer of OMSs from the walls to the channel centers. The concept of the extended hook, demonstrated here in the multicomponent dual-metal and dual-ligand system, should be generally applicable to a range of framework types.

Osteopontin: A uranium phosphorylated binding-site characterization

International Nuclear Information System (INIS)

Safi, Samir; Jeanson, Aurelie; Roques, Jerome; Simoni, Eric; Creff, Gaelle; Qi, Lei; Basset, Christian; Vidaud, Claude; Solari, Pier Lorenzo; Den Auwer, Christophe

2013-01-01

Herein, we describe the structural investigation of one possible uranyl binding site inside a non structured protein. This approach couples spectroscopy, thermodynamics, and theoretical calculations (DFT) and studies the interaction of uranyl ions with a phospho-peptide, thus mimicking a possible osteopontin (OPN) hydroxyapatite growth-inhibition site. Although thermodynamical aspects were investigated by using time-resolved laser fluorescence spectroscopy (TRLFS) and isothermal titration calorimetry (ITC), structural characterization was performed by extended X-ray absorption fine structure (EXAFS) at the U L(III)-edge combined with attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. From the vibrational and fluorescence spectra, several structural models of a UO 2 2+ /peptide complex were developed and subsequently refined by using theoretical calculations to fit the experimental EXAFS obtained. The structural effect of the pH value was also considered under acidic to moderately acidic conditions (pH 1.5-5.5). Most importantly, the uranyl/peptide coordination environment was similar to that of the native protein. (authors)

The distribution of iron between the metal-binding sites of transferrin human serum.

Science.gov (United States)

Williams, J; Moreton, K

1980-02-01

The Makey & Seal [(1976) Biochim. Biophys. Acta 453, 250--256] method of polyacrylamide-gel electrophoresis in buffer containing 6 M-urea was used to determine the distribution of iron between the N-terminal and C-terminal iron-binding sites of transferrin in human serum. In fresh serum the two sites are unequally occupied; there is preferential occupation of the N-terminal site. On incubation of the serum at 37 degrees C the preference of iron for the N-terminal site becomes more marked. On storage of serum at -15 degrees C the iron distribution changes so that there is a marked preference for the C-terminal site. Dialysis of serum against buffer at pH 7.4 also causes iron to be bound much more strongly by the C-terminal than by the N-terminal site. The original preference for the N-terminal site can be resroted to the dialysed serum by addition of the diffusible fraction.

Adsorption of heavy metal ions on different clays

International Nuclear Information System (INIS)

Kruse, K.

1992-01-01

The aim of the present dissertation is to study the adsorption of heavy metal ions (Cd 2+ , Cu 2+ , Pb 2+ , Zn 2+ ) and their mixtures on clays. Different clays and bentonites (Ca 2+ -bentonite, activated Na + -bentonite, special heavy metal adsorber bentonite, two organophilic bentonites and a mixed layer clay) were used. The adsorbed metal ions were desorbed by appropriate solutions of HCl, EDTA and dioctadecyl dimethylammonium bromide. High concentrations of the heavy metal ions in the solutions can be reached. The desorption guarantees economical recycling. After desorption the clays were used (up to three times) for purification of contaminated water. The best experimental conditions, i.e. the highest adsorption of heavy metal ions from aqueous solutions was found for the greatest ratio of adsorbent/adsorbate. The adsorption was very fast. Calcium, sodium bentonites and the heavy metal adsorber bentonite attained the highest adsorption and desorption for Cu 2+, Zn 2+ and Pb 2+ ions. Cd 2+ ions were only absorbed by Silitonit, a special heavy metal absorber bentonite. The mixed layer clay (Opalit) ranges in adsorption and desorption properties below the unmodified Ca 2+ -bentonite (Montigel) or the activated Na + -bentonite. Only Tixosorb and Tixogel (organophilic bentonites) reach the lowest value of heavy metal adsorption. Only lead cations which are characterised by good polarizability were adsorbed at higher rates, therefore the organophilic bentonites are not appropriate for adsorption of heavy metal ions from aqueous solutions. Mixing of the metal ions generally decreases the adsorption of Pb 2+ and increases the adsorption of Cd 2+ . From mixtures if heavy metal ions adsorption and desorption of Cu 2+ ions reached a maximum for all clays. (author) figs., tabs., 56 refs

LIGAND-BINDING SITES ON THE MYCOBACTERIUM TUBERCULOSIS UREASE

Directory of Open Access Journals (Sweden)

Lisnyak Yu. V.

2017-10-01

Full Text Available Introduction. Mycobacterium tuberculosis is the causative agent of tuberculosis that remains a serious medical and social health problem. Despite intensive efforts have been made in the past decade, there are no new efficient anti-tuberculosis drugs today, and that need is growing due to the spread of drug-resistant strains of M.tuberculosis. M. tuberculosis urease (MTU, being an important factor of the bacterium viability and virulence, is an attractive target for anti-tuberculosis drugs acting by inhibition of urease activity. However, the commercially available urease inhibitors are toxic and unstable, that prevent their clinical use. Therefore, new more potent anti-tuberculosis drugs inhibiting new targets are urgently needed. A useful tool for the search of novel inhibitors is a computational drug design. The inhibitor design is significantly easier if binding sites on the enzyme are identified in advance. This paper aimed to determine the probable ligand binding sites on the surface of M. tuberculosis urease. Methods. To identify ligand binding sites on MTU surface, сomputational solvent mapping method FTSite was applied by the use of MTU homology model we have built earlier. The method places molecular probes (small organic molecules containing various functional groups on a dense grid defined around the enzyme, and for each probe finds favorable positions. The selected poses are refined by free energy minimization, the low energy conformations are clustered, and the clusters are ranked on the basis of the average free energy. FTSite server outputs the protein residues delineating a binding sites and the probe molecules representing each cluster. To predict allosteric pockets on MTU, AlloPred and AlloSite servers were applied. AlloPred uses the normal mode analysis (NMA and models how the dynamics of a protein would be altered in the presence of a modulator at a specific pocket. Pockets on the enzyme are predicted using the Fpocket

RBPmap: a web server for mapping binding sites of RNA-binding proteins.

Science.gov (United States)

Paz, Inbal; Kosti, Idit; Ares, Manuel; Cline, Melissa; Mandel-Gutfreund, Yael

2014-07-01

Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. We present a new webserver, RBPmap, freely accessible through the website http://rbpmap.technion.ac.il/ for accurate prediction and mapping of RBP binding sites. RBPmap has been developed specifically for mapping RBPs in human, mouse and Drosophila melanogaster genomes, though it supports other organisms too. RBPmap enables the users to select motifs from a large database of experimentally defined motifs. In addition, users can provide any motif of interest, given as either a consensus or a PSSM. The algorithm for mapping the motifs is based on a Weighted-Rank approach, which considers the clustering propensity of the binding sites and the overall tendency of regulatory regions to be conserved. In addition, RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5' and 3' UTRs, non-coding RNA and intergenic regions. RBPmap was tested on high-throughput RNA-binding experiments and was proved to be highly accurate. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Remediation of groundwater containing radionuclides and heavy metals using ion exchange and the AlgaSORB reg-sign biosorbent system

International Nuclear Information System (INIS)

Feiler, H.D.; Darnall, D.W.

1991-01-01

Bio-Recovery Systems, Inc. (BRS) studied the application of an immobilized algal biomass, termed AlgaSORB reg-sign, which has high affinity for heavy metal ions to DOE-contaminated groundwaters. The material can be packed into columns similar to commercial ion exchange resins. Dilute solutions containing heavy metals are passed through columns where metals are absorbed by the AlgaSORB reg-sign resins. Once saturated, metal ions can be stripped from the resin biomass in a highly concentrated solution. Groundwaters contaminated with heavy metal ions from three different Department of Energy (DOE) sites: Savannah River, Hanford and the Oak Ridge Y-12 Plant were studied. The objective was to perform bench-scale treatability studies to establish treatment protocols and to optimize an AlgaSORB reg-sign/ion exchange technology system to remove and recover toxic metal ions from these contaminated groundwaters. The specialty ion exchange/AlgaSORB reg-sign resins tested in these studies show promise for selectively removing chromium, mercury and uranium from contaminated groundwater at DOE sites. The data show that effluents which satisfy the allowable metal ion limits are possible and most likely achievable. The use of these highly selective resins also offer advantages in terms of cost/benefit, risk and scheduling. Their high selectivity allows for high capacity and opportunities for recovery of removed constituents due to high pollutant concentration possible (3 to 4 orders of magnitude). Ion exchange is a proven technology which is easily automated and can be cost-effective, depending on the application

Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory.

Science.gov (United States)

Kucharski, Amir N; Scott, Caitlin E; Davis, Jonathan P; Kekenes-Huskey, Peter M

2016-08-25

Parvalbumin (PV) is a globular calcium (Ca(2+))-selective protein expressed in a variety of biological tissues. Our computational studies of the rat β-parvalbumin (β-PV) isoform seek to elucidate the molecular thermodynamics of Ca(2+) versus magnesium (Mg(2+)) binding at the protein's two EF-hand motifs. Specifically, we have utilized molecular dynamics (MD) simulations and a mean-field electrolyte model (mean spherical approximation (MSA) theory) to delineate how the EF-hand scaffold controls the "local" thermodynamics of Ca(2+) binding selectivity over Mg(2+). Our MD simulations provide the probability density of metal-chelating oxygens within the EF-hand scaffolds for both Ca(2+) and Mg(2+), as well the conformational strain induced by Mg(2+) relative to Ca(2+) binding. MSA theory utilizes the binding domain oxygen and charge distributions to predict the chemical potential of ion binding, as well as their corresponding concentrations within the binding domain. We find that the electrostatic and steric contributions toward ion binding were similar for Mg(2+) and Ca(2+), yet the latter was 5.5 kcal/mol lower in enthalpy when internal strain within the EF hand was considered. We therefore speculate that beyond differences in dehydration energies for the Ca(2+) versus Mg(2+), strain induced in the β-PV EF hand by cation binding significantly contributes to the nearly 10,000-fold difference in binding affinity reported in the literature. We further complemented our analyses of local factors governing cation binding selectivity with whole-protein (global) contributions, such as interhelical residue-residue contacts and solvent exposure of hydrophobic surface. These contributions were found to be comparable for both Ca(2+)- and Mg(2+)-bound β-PV, which may implicate local factors, EF-hand strain, and dehydration, in providing the primary means of selectivity. We anticipate these methods could be used to estimate metal binding thermodynamics across a broad range of

Construction of Insulin 18-mer Nanoassemblies Driven by Coordination to Iron(II) and Zinc(II) Ions at Distinct Sites

DEFF Research Database (Denmark)

Munch, Henrik K.; Nygaard, Jesper; Christensen, Niels Johan

2016-01-01

coordination with two different metal ions. Selective attachment of an abiotic 2,2′-bipyridine (bipy) ligand to HI, yielding HI–bipy, enabled ZnII-binding hexamers to SA into trimers of hexamers, [[HI–bipy]6]3, driven by octahedral coordination to a FeII ion. The structures were studied in solution by small...

A Unified Model of the GABA(A) Receptor Comprising Agonist and Benzodiazepine Binding Sites

DEFF Research Database (Denmark)

Kongsbak, Kristine Grønning; Bergmann, Rikke; Sørensen, Pernille Louise

2013-01-01

We present a full-length a1b2c2 GABA receptor model optimized for agonists and benzodiazepine (BZD) allosteric modulators. We propose binding hypotheses for the agonists GABA, muscimol and THIP and for the allosteric modulator diazepam (DZP). The receptor model is primarily based on the glutamate......-gated chloride channel (GluCl) from C. elegans and includes additional structural information from the prokaryotic ligand-gated ion channel ELIC in a few regions. Available mutational data of the binding sites are well explained by the model and the proposed ligand binding poses. We suggest a GABA binding mode...... of the agonists in the orthosteric site. The carbonyl group of DZP is predicted to interact with two threonines a1T206 and c2T142, similar to the acidic moiety of GABA. The chlorine atom of DZP is placed near the important a1H101 and the N-methyl group near a1Y159, a1T206, and a1Y209. We present a binding mode...

Autoradiographic localization of benzomorphan binding sites in rat brain

Energy Technology Data Exchange (ETDEWEB)

Crain, B.J.; Kwenjen Chang; McNamara, J.O.; Valdes, F.

1985-07-17

The benzomorphan subpopulation of opiate binding sites was labeled by (TH)diprenorphine in the presence of unlabeled ligands selected to quench and delta opiate binding sites. The distribution of benzomorphan binding sites was then localized autoradiographically. The distribution differs from the distributions of , delta and kappa opiate binding and is quite similar to the distribution of US -endorphin immunoreactivity. These observations support the hypothesis, based on biochemical studies in brain membranes, that benzomorphan binding sites may represent the ligand recognition sites of putative epsilon receptors. (Auth.). 34 refs.; 3 figs.

Complexation of metal ions with humic acid: charge neutralization model

International Nuclear Information System (INIS)

Kim, J.I.; Czerwinski, K.R.

1995-01-01

A number of different approaches are being used for describing the complexation equilibrium of actinide ions with humic or fulvic acid. The approach chosen and verified experimentally by Tu Muenchen will be discussed with notable examples from experiment. This approach is based on the conception that a given actinide ion is neutralized upon complexation with functional groups of humic or fulvic acid, e.g. carboxylic and phenolic groups, which are known as heterogeneously cross-linked polyelectrolytes. The photon energy transfer experiment with laser light excitation has shown that the actinide ion binding with the functional groups is certainly a chelation process accompanied by metal ion charge neutralization. This fact is in accordance with the experimental evidence of the postulated thermodynamic equilibrium reaction. The experimental results are found to be independent of origin of humic or fulvic acid and applicable for a broad range of pH. (authors). 23 refs., 7 figs., 1 tab

Cocomplexation of urea and UO22+ in a Schiff base macrocycle: a mimic of an enzyme binding site

International Nuclear Information System (INIS)

van Staveren, C.J.; Fenton, D.E.; Reinhoudt, D.N.; van Eerden, J.; Harkema, S.

1987-01-01

As part of the authors work on the complexation of neutral molecules by macrocyclic ligands, they are particularly interested in the complexation of urea. They have shown that urea can form complexes with (aza-)18-crown but the association constants of these complexes in water are very small (18-crown-6-urea, log K/sub s/ = 0.1). Protonation of urea effects stronger binding especially when the crown ether is sufficiently large to form an encapsulated complex (e.g., the complex benzo-27-crown-9-urea-HClO 4 ). Protonation of the weakly basic urea (pK/sub a/ = 0.1, water, 25 0 C) requires strongly acidic conditions and to avoid this they have introduced a covalently linked carboxylic group in the cavity of the macrocycle. A strong hydrogen bond of urea with 2-carboxyl-1,3-xylyl-30-crown-9 results in an encapsulated complex. The concept of using an electrophilic center to bind urea in the cavity of a crown ether proved to be a more general concept. A metal cation can serve as the electrophile as was shown by the isolation and single-crystal X-ray analysis of the 2,6-pyrido-27-crown-9-urea-LiClO 4 (1:2:1) complex in which one of the urea molecules is encapsulated. In an effort to bind an electrophilic metal ion in the crown ethers irreversibly they have concentrated their work on macrocycles of type 1, since the strong binding of quadridentate (salen type) Schiff bases with soft metal ions is well-known

GABA, depressants and chloride ions affect the rate of dissociation of 35S-t-butylbicyclophosphorothionate binding

International Nuclear Information System (INIS)

Maksay, G.; Ticku, M.K.

1985-01-01

The dissociation of 35 S-TBPS was studied from binding sites of rat cerebral cortex. Monophasic dissociation plots became polyphasic and accelerated in the presence of micromolar concentrations of GABA suggesting the involvement of low (or super-low) affinity GABA receptors. The presence of the depressants etazolate, R(-)MPPB and ethanol resulted in similarly accelerated dissociation patterns. In contrast, the convulsants S(+)MPPB and pentamethylenetetrazol did not significantly affect the dissociation of TBPS. Dissociation initiated by dilution was not affected either by an excess of picrotoxin or by varying the equilibrium occupancy of the TBPS sites. These findings rule out the possibility of a kinetic cooperativity for the binding of convulsants. The removal of chloride ions also enhanced the rate of TBPS dissociation. Kinetic heterogeneity of the TBPS binding sites can be interpreted with allosteric interactions mediated by various sites at the GABA receptor complex coupled to different states of the chloride ionophore. 15 references, 3 figures, 1 table

Laccase Immobilization by Chelated Metal Ion Coordination Chemistry

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Qingqing Wang

2014-09-01

Full Text Available In this work, amidoxime polyacrylonitrile (AOPAN nanofibrous membrane was prepared by a reaction between PAN nanofibers and hydroxylamine hydrochloride. The AOPAN nanofibrous membranes were used for four metal ions (Fe3+, Cu2+, Ni2+, Cd2+ chelation under different conditions. Further, the competition of different metal ions coordinating with AOPAN nanofibrous membrane was also studied. The AOPAN chelated with individual metal ion (Fe3+, Cu2+, Ni2+, Cd2+ and also the four mixed metal ions were further used for laccase (Lac immobilization. Compared with free laccase, the immobilized laccase showed better resistance to pH and temperature changes as well as improved storage stability. Among the four individual metal ion chelated membranes, the stability of the immobilized enzymes generally followed the order as Fe–AOPAN–Lac > Cu–AOPAN–Lac > Ni–AOPAN–Lac > Cd–AOPAN–Lac. In addition, the immobilized enzyme on the carrier of AOPAN chelated with four mixed metal ions showed the best properties.

Chemodynamics of metal ion complexation by charged nanoparticles: a dimensionless rationale for soft, core-shell and hard particle types.

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Duval, Jérôme F L

2017-05-17

Soft nanoparticulate complexants are defined by a spatial confinement of reactive sites and electric charges inside their 3D body. In turn, their reactivity with metal ions differs significantly from that of simple molecular ligands. A revisited form of the Eigen mechanism recently elucidated the processes leading to metal/soft particle pair formation. Depending on e.g. particle size and metal ion nature, chemodynamics of nanoparticulate metal complexes is controlled by metal conductive diffusion to/from the particles, by intraparticulate complex formation/dissociation kinetics, or by both. In this study, a formalism is elaborated to achieve a comprehensive and systematic identification of the rate-limiting step governing the overall formation and dissociation of nanoparticulate metal complexes. The theory covers the different types of spherical particulate complexants, i.e. 3D soft/permeable and core-shell particles, and hard particles with reactive sites at the surface. The nature of the rate-limiting step is formulated by a dynamical criterion involving a power law function of the ratio between particle radius and an intraparticulate reaction layer thickness defined by the key electrostatic, diffusional and kinetic components of metal complex formation/dissociation. The analysis clarifies the intertwined contributions of particle properties (size, soft or hard type, charge, density or number of reactive sites) and aqueous metal ion dehydration kinetics in defining the chemodynamic behavior of nanoparticulate metal complexes. For that purpose, fully parameterized chemodynamic portraits involving the defining features of particulate ligand and metal ion as well as the physicochemical conditions in the local intraparticulate environment, are constructed and thoroughly discussed under conditions of practical interest.

Metallic ion release from biocompatible cobalt-based alloy

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Dimić Ivana D.

2014-01-01

Full Text Available Metallic biomaterials, which are mainly used for the damaged hard tissue replacements, are materials with high strength, excellent toughness and good wear resistance. The disadvantages of metals as implant materials are their susceptibility to corrosion, the elastic modulus mismatch between metals and human hard tissues, relatively high density and metallic ion release which can cause serious health problems. The aim of this study was to examine metallic ion release from Co-Cr-Mo alloy in artificial saliva. In that purpose, alloy samples were immersed into artificial saliva with different pH values (4.0, 5.5 and 7.5. After a certain immersion period (1, 3 and 6 weeks the concentrations of released ions were determined using Inductively Coupled Plasma - Mass Spectrophotometer (ICP-MS. The research findings were used in order to define the dependence between the concentration of released metallic ions, artificial saliva pH values and immersion time. The determined released metallic ions concentrations were compared with literature data in order to describe and better understand the phenomenon of metallic ion release from the biocompatible cobalt-based alloy. [Projekat Ministarstva nauke Republike Srbije, br. III 46010 i br. ON 174004

Nanopore Device for Reversible Ion and Molecule Sensing or Migration

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Pourmand, Nader (Inventor); Vilozny, Boaz (Inventor); Actis, Paolo (Inventor); Seger, R. Adam (Inventor); Singaram, Bakthan (Inventor)

2015-01-01

Disclosed are methods and devices for detection of ion migration and binding, utilizing a nanopipette adapted for use in an electrochemical sensing circuit. The nanopipette may be functionalized on its interior bore with metal chelators for binding and sensing metal ions or other specific binding molecules such as boronic acid for binding and sensing glucose. Such a functionalized nanopipette is comprised in an electrical sensor that detects when the nanopipette selectively and reversibly binds ions or small molecules. Also disclosed is a nanoreactor, comprising a nanopipette, for controlling precipitation in aqueous solutions by voltage-directed ion migration, wherein ions may be directed out of the interior bore by a repulsing charge in the bore.

The Structure of the Iron Binding Protein, FutA1, from Synechocystis 6803*

International Nuclear Information System (INIS)

Koropatkin, Nicole; Randich, Amelia M.; Bhattacharyya-Pakrasi, Maitrayee; Pakrasi, Himadri B.; Smith, Thomas J.

2007-01-01

Cyanobacteria account for a significant percentage of aquatic primary productivity even in areas where the concentrations of essential micronutrients are extremely low. To better understand the mechanism of iron selectivity and transport, the structure of the solute-binding domain of an ABC iron transporter, FutA1, was determined in the presence and absence of iron. The iron ion is bound within the 'C-clamp' structure via four tyrosine and one histidine residues. There are extensive interactions between these ligating residues and the rest of the protein such that the conformations of the side chains remain relatively unchanged as the iron is released by the opening of the metal binding cleft. This is in stark contrast to the zinc binding protein, ZnuA, where the domains of the metal binding protein remain relatively fixed while the ligating residues rotate out of the binding pocket upon metal release. The rotation of the domains in FutA1 is facilitated by two flexible β-strands running along the back of the protein that act like a hinge during domain motion. This motion may require relatively little energy since total contact area between the domains is the same whether the protein is in the open or closed conformation. Consistent with the pH dependency of iron binding, the main trigger for iron release is likely the histidine in the iron-binding site. Finally, neither FutA1 nor FutA2 binds iron as a siderophore complex or in the presence of anions and both preferentially bind ferrous over ferric ions

Five of Five VHHs Neutralizing Poliovirus Bind the Receptor-Binding Site.

Science.gov (United States)

Strauss, Mike; Schotte, Lise; Thys, Bert; Filman, David J; Hogle, James M

2016-01-13

Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In this study, we present high-resolution cryo-electron microscopy reconstructions of poliovirus with five neutralizing VHHs. All VHHs bind the capsid in the canyon at sites that extensively overlap the poliovirus receptor-binding site. In contrast, the interaction involves a unique (and surprisingly extensive) surface for each of the five VHHs. Five regions of the capsid were found to participate in binding with all five VHHs. Four of these five regions are known to alter during the expansion of the capsid associated with viral entry. Interestingly, binding of one of the VHHs, PVSS21E, resulted in significant changes of the capsid structure and thus seems to trap the virus in an early stage of expansion. We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five VHHs bind deep in the virus canyon at similar sites that overlap extensively with the binding site for the receptor (CD155). The binding surfaces on the VHHs are surprisingly extensive, but despite the use of similar binding surfaces on the virus, the binding surface on the VHHs is unique for each VHH. In four of the five complexes, the virus remains essentially unchanged, but for the fifth there are significant changes reminiscent of but smaller in magnitude than the changes associated with cell entry, suggesting that this VHH traps the virus in a previously undescribed early intermediate state. The neutralizing mechanisms of the VHHs and their potential use as quality control agents for the end game of poliovirus eradication are discussed. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Antidepressant Binding Site in a Bacterial Homologue of Neurotransmitter Transporters

International Nuclear Information System (INIS)

Singh, S.; Yamashita, A.; Gouaux, E.

2007-01-01

Sodium-coupled transporters are ubiquitous pumps that harness pre-existing sodium gradients to catalyse the thermodynamically unfavourable uptake of essential nutrients, neurotransmitters and inorganic ions across the lipid bilayer. Dysfunction of these integral membrane proteins has been implicated in glucose/galactose malabsorption, congenital hypothyroidism, Bartter's syndrome, epilepsy, depression, autism and obsessive-compulsive disorder. Sodium-coupled transporters are blocked by a number of therapeutically important compounds, including diuretics, anticonvulsants and antidepressants, many of which have also become indispensable tools in biochemical experiments designed to probe antagonist binding sites and to elucidate transport mechanisms. Steady-state kinetic data have revealed that both competitive and noncompetitive modes of inhibition exist. Antagonist dissociation experiments on the serotonin transporter (SERT) have also unveiled the existence of a low-affinity allosteric site that slows the dissociation of inhibitors from a separate high-affinity site. Despite these strides, atomic-level insights into inhibitor action have remained elusive. Here we screen a panel of molecules for their ability to inhibit LeuT, a prokaryotic homologue of mammalian neurotransmitter sodium symporters, and show that the tricyclic antidepressant (TCA) clomipramine noncompetitively inhibits substrate uptake. Cocrystal structures show that clomipramine, along with two other TCAs, binds in an extracellular-facing vestibule about 11 (angstrom) above the substrate and two sodium ions, apparently stabilizing the extracellular gate in a closed conformation. Off-rate assays establish that clomipramine reduces the rate at which leucine dissociates from LeuT and reinforce our contention that this TCA inhibits LeuT by slowing substrate release. Our results represent a molecular view into noncompetitive inhibition of a sodium-coupled transporter and define principles for the rational

Antidepressant Binding Site in a Bacterial Homologue of Neurotransmitter Transporters

Energy Technology Data Exchange (ETDEWEB)

Singh,S.; Yamashita, A.; Gouaux, E.

2007-01-01

Sodium-coupled transporters are ubiquitous pumps that harness pre-existing sodium gradients to catalyse the thermodynamically unfavourable uptake of essential nutrients, neurotransmitters and inorganic ions across the lipid bilayer. Dysfunction of these integral membrane proteins has been implicated in glucose/galactose malabsorption, congenital hypothyroidism, Bartter's syndrome, epilepsy, depression, autism and obsessive-compulsive disorder. Sodium-coupled transporters are blocked by a number of therapeutically important compounds, including diuretics, anticonvulsants and antidepressants, many of which have also become indispensable tools in biochemical experiments designed to probe antagonist binding sites and to elucidate transport mechanisms. Steady-state kinetic data have revealed that both competitive and noncompetitive modes of inhibition exist. Antagonist dissociation experiments on the serotonin transporter (SERT) have also unveiled the existence of a low-affinity allosteric site that slows the dissociation of inhibitors from a separate high-affinity site. Despite these strides, atomic-level insights into inhibitor action have remained elusive. Here we screen a panel of molecules for their ability to inhibit LeuT, a prokaryotic homologue of mammalian neurotransmitter sodium symporters, and show that the tricyclic antidepressant (TCA) clomipramine noncompetitively inhibits substrate uptake. Cocrystal structures show that clomipramine, along with two other TCAs, binds in an extracellular-facing vestibule about 11 {angstrom} above the substrate and two sodium ions, apparently stabilizing the extracellular gate in a closed conformation. Off-rate assays establish that clomipramine reduces the rate at which leucine dissociates from LeuT and reinforce our contention that this TCA inhibits LeuT by slowing substrate release. Our results represent a molecular view into noncompetitive inhibition of a sodium-coupled transporter and define principles for the

Semi-Interpenetrating Polymer Networks with Predefined Architecture for Metal Ion Fluorescence Monitoring

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Kyriakos Christodoulou

2016-11-01

Full Text Available The development of new synthetic approaches for the preparation of efficient 3D luminescent chemosensors for transition metal ions receives considerable attention nowadays, owing to the key role of the latter as elements in biological systems and their harmful environmental effects when present in aquatic media. In this work, we describe an easy and versatile synthetic methodology that leads to the generation of nonconjugated 3D luminescent semi-interpenetrating amphiphilic networks (semi-IPN with structure-defined characteristics. More precisely, the synthesis involves the encapsulation of well-defined poly(9-anthrylmethyl methacrylate (pAnMMA (hydrophobic, luminescent linear polymer chains within a covalent poly(2-(dimethylaminoethyl methacrylate (pDMAEMA hydrophilic polymer network, derived via the 1,2-bis-(2-iodoethoxyethane (BIEE-induced crosslinking process of well-defined pDMAEMA linear chains. Characterization of their fluorescence properties demonstrated that these materials act as strong blue emitters when exposed to UV irradiation. This, combined with the presence of the metal-binding tertiary amino functionalities of the pDMAEMA segments, allowed for their applicability as sorbents and fluorescence chemosensors for transition metal ions (Fe3+, Cu2+ in solution via a chelation-enhanced fluorescence-quenching effect promoted within the semi-IPN network architecture. Ethylenediaminetetraacetic acid (EDTA-induced metal ion desorption and thus material recyclability has been also demonstrated.

Metallic ions in the upper atmosphere

International Nuclear Information System (INIS)

Kumar, S.

1979-01-01

During the past 20 years considerable progress has been made in establishing the presence of metallic ions in the sporadic E layers at mid latitudes and as discrete patches at high altitudes in the equatorial ionosphere. The E-region observations have been based on rocket flights, which represent local conditions faithfully. But the global distribution of metallic ions and variations relating to changes in season, local time, magnetic activity, etc., which require satellite data, have been largely unexamined. This work presents a few aspects of this missing global distribution over an altitude range of 100 to 1000 km, using the data from AE-C, AE-D, and OGO-6 satellites and the rocket flights 18.117 and 18.118 from Wallops Island on July 12 and 13, 1971. The rocket data provide a day-night pair of vertical profiles that include altitudes not covered by the satellites. Results are presented for Mg + , Al + , Si + and Fe + ions in terms of their detection probabilities, median concentrations and relative abundances with respect to Mg + ions as a function of significant geophysical parameters. Na + and K + ions have been excluded from this study because alkali metal ions driven off the spacecraft hamper the measurement of ambient Na + and K + ions. This study has indicated that in general different metallic ions appear together in comparable concentrations except for Al + , which is an order of magnitude smaller than the others

Competition effects in cation binding to humic acid: Conditional affinity spectra for fixed total metal concentration conditions

Science.gov (United States)

David, Calin; Mongin, Sandrine; Rey-Castro, Carlos; Galceran, Josep; Companys, Encarnació; Garcés, José Luis; Salvador, José; Puy, Jaume; Cecilia, Joan; Lodeiro, Pablo; Mas, Francesc

2010-09-01

Information on the Pb and Cd binding to a purified Aldrich humic acid (HA) is obtained from the influence of different fixed total metal concentrations on the acid-base titrations of this ligand. NICA (Non-Ideal Competitive Adsorption) isotherm has been used for a global quantitative description of the binding, which has then been interpreted by plotting the Conditional Affinity Spectra of the H + binding at fixed total metal concentrations (CAScTM). This new physicochemical tool, here introduced, allows the interpretation of binding results in terms of distributions of proton binding energies. A large increase in the acidity of the phenolic sites as the total metal concentration increases, especially in presence of Pb, is revealed from the shift of the CAScTM towards lower affinities. The variance of the CAScTM distribution, which can be used as a direct measure of the heterogeneity, also shows a significant dependence on the total metal concentration. A discussion of the factors that influence the heterogeneity of the HA under the conditions of each experiment is provided, so that the smoothed pattern exhibited by the titration curves can be justified.

Study of the nucleotide binding site of the yeast Schizosaccharomyces pombe plasma membrane H+-ATPase using formycin triphosphate-terbium complex

International Nuclear Information System (INIS)

Ronjat, M.; Lacapere, J.J.; Dufour, J.P.; Dupont, Y.

1987-01-01

The plasma membrane of yeasts contains an H+-ATPase similar to the other cation transport ATPases of eukaryotic organisms. This enzyme has been purified and shows H+ transport in reconstituted vesicles. In the presence of Mg2+, formycin triphosphate (FTP) is hydrolyzed by the H+-ATPase and supports H+ transport. When combined with terbium ion, FTP (Tb-FTP) and ATP (Tb-ATP) are no longer hydrolyzed. Competition between Mg-ATP and Tb-FTP for ATP hydrolysis indicates that terbium-associated nucleotides bind to the catalytic site of the H+-ATPase. The fluorescent properties of the Tb-FTP complex were used to study the active site of the H+-ATPase. Fluorescence of Tb-FTP is greatly enhanced upon binding into the nucleotide site of H+-ATPase with a dissociation constant of 1 microM. Tb-ATP, Tb-ADP, and Tb-ITP are competitive inhibitors of Tb-FTP binding with Ki = 4.5, 5.0, and 6.0 microM, respectively. Binding of Tb-FTP is observed only in the presence of an excess of Tb3+ with an activation constant Ka = 25 microM for Tb3+. Analysis of the data reveals that the sites for Tb-FTP and Tb3+ binding are independent entities. In standard conditions these sites would be occupied by Mg-ATP and Mg2+, respectively. These findings suggest an important regulatory role of divalent cations on the activity of H+-ATPase. Replacement of H 2 O by D 2 O in the medium suggests the existence of two types of nucleotide binding sites differing by the hydration state of the Tb3+ ion in the bound Tb-FTP complex

Optimization of exopolysaccharide production from Pseudomonas stutzeri AS22 and examination of its metal-binding abilities.

Science.gov (United States)

Maalej, H; Hmidet, N; Boisset, C; Buon, L; Heyraud, A; Nasri, M

2015-02-01

To investigate the effect of culture conditions and medium components on exopolysaccharide (EPS) production by Pseudomonas stutzeri AS22 and to access the EPS performance as a metal-binding exopolysaccharide. The EPS production conditions of Ps. stutzeri AS22 in submerged culture were optimized using two approaches for EPS quantification, and its metal-binding capacity was evaluated using both single and mixed metal ions systems. Maximum EPS level was achieved after 24 h of incubation at 30°C with an initial pH of 8.0, 250 rev min(-1) stirring level and 10% inoculum size. 50 g l(-1) starch, 5 g l(-1) yeast extract, 0.5 g l(-1) NaCl, 1.4 g l(-1) K2 HPO4, 0.4 g l(-1) MgSO4, 0.4 g l(-1) CaCl2 and 1 g l(-1) mannose were found to be the most suitable carbon, nitrogen, mineral and additional carbohydrate sources, respectively. From metal-binding experiments, the crude EPS showed interesting metal adsorption capacity adopting the order Pb > Co > Fe > Cu > Cd. Lead was preferentially biosorbed with a maximal uptake of 460 mg g(-1) crude EPS. Under the optimal culture requirements, EPS level reached 10.2 g l(-1) after 24 h of fermentation, seven times more than the production under initial conditions. According to the metal-binding assay, the crude EPS has potential to be used as a novel biosorbent in the treatment of heavy metals-contaminated water. Our results are interesting in terms of yield as well as efficiency for the potential use of the Ps. stutzeri exopolysaccharide as a metal-absorbent polymer in the bioremediation field. © 2014 The Society for Applied Microbiology.

Opioid binding sites in the guinea pig and rat kidney: Radioligand homogenate binding and autoradiography

Energy Technology Data Exchange (ETDEWEB)

Dissanayake, V.U.; Hughes, J.; Hunter, J.C. (Parke-Davis Research Unit, Addenbrookes Hospital Site, Cambridge (England))

1991-07-01

The specific binding of the selective {mu}-, {delta}-, and {kappa}-opioid ligands (3H)(D-Ala2,MePhe4,Gly-ol5)enkephalin ((3H) DAGOL), (3H)(D-Pen2,D-Pen5)enkephalin ((3H)DPDPE), and (3H)U69593, respectively, to crude membranes of the guinea pig and rat whole kidney, kidney cortex, and kidney medulla was investigated. In addition, the distribution of specific 3H-opioid binding sites in the guinea pig and rat kidney was visualized by autoradiography. Homogenate binding and autoradiography demonstrated the absence of {mu}- and {kappa}-opioid binding sites in the guinea pig kidney. No opioid binding sites were demonstrable in the rat kidney. In the guinea pig whole kidney, cortex, and medulla, saturation studies demonstrated that (3H)DPDPE bound with high affinity (KD = 2.6-3.5 nM) to an apparently homogeneous population of binding sites (Bmax = 8.4-30 fmol/mg of protein). Competition studies using several opioid compounds confirmed the nature of the {delta}-opioid binding site. Autoradiography experiments demonstrated that specific (3H)DPDPE binding sites were distributed radially in regions of the inner and outer medulla and at the corticomedullary junction of the guinea pig kidney. Computer-assisted image analysis of saturation data yielded KD values (4.5-5.0 nM) that were in good agreement with those obtained from the homogenate binding studies. Further investigation of the {delta}-opioid binding site in medulla homogenates, using agonist ((3H)DPDPE) and antagonist ((3H)diprenorphine) binding in the presence of Na+, Mg2+, and nucleotides, suggested that the {delta}-opioid site is linked to a second messenger system via a GTP-binding protein. Further studies are required to establish the precise localization of the {delta} binding site in the guinea pig kidney and to determine the nature of the second messenger linked to the GTP-binding protein in the medulla.

Muscarinic acetylcholine receptors: location of the ligand binding site

International Nuclear Information System (INIS)

Hulme, E.; Wheatley, M.; Curtis, C.; Birdsall, N.

1987-01-01

The key to understanding the pharmacological specificity of muscarinic acetylcholine receptors (mAChR's) is the location within the receptor sequence of the amino acid residues responsible for ligand binding. To approach this problem, they have purified mAChR's from rat brain to homogeneity by sequential ion-exchange chromatography, affinity chromatography and molecular weight fractionation. Following labelling of the binding site with an alkylating affinity label, 3 H-propylbenzilycholine mustard aziridinium ion ( 3 H-PrBCM), the mAChR was digested with a lysine-specific endoproteinase, and a ladder of peptides of increasing molecular weight, each containing the glycosylated N-terminus, isolated by chromatography on wheat-germ agglutinin sepharose. The pattern of labelling showed that a residue in the peptides containing transmembrane helices 2 and/or 3 of the mAChR was alkylated. The linkage was cleaved by 1 M hydroxylamine, showing that 3 H-PrBCM was attached to an acidic residue, whose properties strongly suggested it to be embedded in a hydrophobic intramembrane region of the mAChR. Examination of the cloned sequence of the mAChR reveals several candidate residues, the most likely of which is homologous to an aspartic acid residue thought to protonate the retinal Schiff's base in the congeneric protein rhodopsin

Analysis of metal ion release from biomedical implants

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Ivana Dimić