Active sites of transition-metal enzymes with a focus on nickel

Since 1995, crystal structures have been determined for many transition-metal enzymes, in particular those containing the rarely used transition metals vanadium, molybdenum, tungsten, manganese, cobalt and nickel. Accordingly, our understanding of how an enzyme uses the unique properties of a specific transition metal has been substantially increased in the past few years. The different functions of nickel in catalysis are highlighted by describing the active sites of six nickel enzymes — methyl-coenzyme M reductase, urease, hydrogenase, superoxide dismutase, carbon monoxide dehydrogenase and acetyl-coenzyme A synthase.     

Trace Metal Imaging of Sulfate-Reducing Bacteria and Methanogenic Archaea at Single-Cell Resolution by Synchrotron X-Ray Fluorescence Imaging

Metal cofactors are required for many enzymes in anaerobic microbial respiration. This study examined iron, cobalt, nickel, copper, and zinc in cellular and abiotic phases at the single-cell scale for a sulfate-reducing bacterium (Desulfococcus multivorans) and a methanogenic archaeon (Methanosarcina acetivorans) using synchrotron X-ray fluorescence microscopy. Relative abundances of cellular metals were also measured by inductively coupled plasma mass spectrometry. For both species, zinc and iron were consistently the most abundant cellular metals. M. acetivorans contained higher nickel and cobalt content than D. multivorans, likely due to elevated metal requirements for methylotrophic methanogenesis. Cocultures contained spheroid zinc sulfides and cobalt/copper sulfides.     

A high-performance liquid chromatography method for determining transition metal content in proteins

Transition metals are common components of cellular proteins and the detailed study of metalloproteins necessitates the identification and quantification of bound metal ions. Screening for metals is also an informative step in the initial characterization of the numerous unknown and unclassified proteins now coming through the proteomic pipeline. We have developed a high-performance liquid chromatography method for the quantitative determination of the most prevalent biological transition metals: manganese, iron, cobalt, nickel, copper, and zinc. The method is accurate and simple and can be adapted for automated high-throughput studies. The metal analysis involves acid hydrolysis to release the metal ions into solution, followed by ion separation on a mixed-bead ion-exchange column and absorbance detection after postcolumn derivatization with the metallochromic indicator 4-(2-pyridylazo)resorcinol. The potential interferences by common components of protein solutions were investigated. The metal content of a variety of metalloproteins was analyzed and the data were compared to data obtained from inductively coupled plasma-atomic emission spectroscopy. The sensitivity of the assay allows for the detection of 0.1-0.8 nmol, depending on the metal. The amount of protein required is governed by the size of the protein and the fraction of protein with metal bound. For routine analysis 50 microg was used but for many proteins 10 microg would be sufficient. The advantages, disadvantages, and possible applications of this method are discussed.     

Synthesis of redox-active ferrocene pyrazole conjugates and their cytotoxicity in human mammary adenocarcinoma MCF-7 cells

The redox-active ferrocenoyl modified pyrazole ligand (3-Fc-AMP) readily coordinates to a variety of transition metal ions. Here, we describe our findings regarding the synthesis and structural characterization of iron and cobalt complexes of Fc-AMP, and the cytotoxicity profiles of these chemicals in vitro. Using the human mammary adenocarcinoma MCF-7 cell line we show that the free ligand and three metal complexes induced cytotoxicity with calculated LC₅₀s ranging from 45.8 to 73.2 μM. The toxicity of the complexes decreased as the redox potential increased. The present study demonstrates the potential chemotherapeutic promise of metal complexes of a redox-active ferrocenoyl modified pyrazole ligand on human cancer cells.     

Effect of metal binding and posttranslational lysine carboxylation on the activity of recombinant hydantoinase

Bacterial hydantoinase possesses a binuclear metal center in which two metal ions are bridged by a posttranslationally carboxylated lysine. How the carboxylated lysine and metal binding affect the activity of hydantoinase was investigated. A significant amount of iron was always found in Agrobacterium radiobacter hydantoinase purified from unsupplemented cobalt-, manganese-, or zinc-amended Escherichia coli cell cultures. A titration curve for the reactivation of apohydantoinase with cobalt indicates that the first metal was preferentially bound but did not give any enzyme activity until the second metal was also attached to the hydantoinase. The pH profiles of the metal-reconstituted hydantoinase were dependent on the specific metal ion bound to the active site, indicating a direct involvement of metal in catalysis. Mutation of the metal binding site residues, H57A, H59A, K148A, H181A, H237A, and D313A, completely abolished hydantoinase activity but preserved about half of the metal content, except for K148A, which lost both metals in its active site. However, the activity of K148A could be chemically rescued by short-chain carboxylic acids in the presence of cobalt, indicating that the carboxylated lysine was needed to coordinate the binuclear ion within the active site of hydantoinase. The mutant D313E enzyme was also active but resulted in a pH profile different from that of wild-type hydantoinase. A mechanism for hydantoinase involving metal, carboxylated K148, and D313 was proposed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters

The transition metals nickel and cobalt, essential components of many enzymes, are taken up by specific transport systems of several different types. We integrated in silico and in vivo methods for the analysis of various protein families containing both nickel and cobalt transport systems in prokaryotes. For functional annotation of genes, we used two comparative genomic approaches: identification of regulatory signals and analysis of the genomic positions of genes encoding candidate nickel/cobalt transporters. The nickel-responsive repressor NikR regulates many nickel uptake systems, though the NikR-binding signal is divergent in various taxonomic groups of bacteria and archaea. B(12) riboswitches regulate most of the candidate cobalt transporters in bacteria. The nickel/cobalt transporter genes are often colocalized with genes for nickel-dependent or coenzyme B(12) biosynthesis enzymes. Nickel/cobalt transporters of different families, including the previously known NiCoT, UreH, and HupE/UreJ families of secondary systems and the NikABCDE ABC-type transporters, showed a mosaic distribution in prokaryotic genomes. In silico analyses identified CbiMNQO and NikMNQO as the most widespread groups of microbial transporters for cobalt and nickel ions. These unusual uptake systems contain an ABC protein (CbiO or NikO) but lack an extracytoplasmic solute-binding protein. Experimental analysis confirmed metal transport activity for three members of this family and demonstrated significant activity for a basic module (CbiMN) of the Salmonella enterica serovar Typhimurium transporter.     

Transition metal homeostasis: from yeast to human disease

Transition metal ions are essential nutrients to all forms of life. Iron, copper, zinc, manganese, cobalt and nickel all have unique chemical and physical properties that make them attractive molecules for use in biological systems. Many of these same properties that allow these metals to provide essential biochemical activities and structural motifs to a multitude of proteins including enzymes and other cellular constituents also lead to a potential for cytotoxicity. Organisms have been required to evolve a number of systems for the efficient uptake, intracellular transport, protein loading and storage of metal ions to ensure that the needs of the cells can be met while minimizing the associated toxic effects. Disruptions in the cellular systems for handling transition metals are observed as a number of diseases ranging from hemochromatosis and anemias to neurodegenerative disorders including Alzheimer??s and Parkinson??s disease. The yeast Saccharomyces cerevisiae has proved useful as a model organism for the investigation of these processes and many of the genes and biological systems that function in yeast metal homeostasis are conserved throughout eukaryotes to humans. This review focuses on the biological roles of iron, copper, zinc, manganese, nickel and cobalt, the homeostatic mechanisms that function in S. cerevisiae and the human diseases in which these metals have been implicated.     

Neuromelanin associated redox-active iron is increased in the substantia nigra of patients with Parkinson's disease

Degeneration of dopaminergic neurones during Parkinson's disease is most extensive in the subpopulation of melanized-neurones located in the substantia nigra pars compacta. Neuromelanin is a dark pigment produced in the dopaminergic neurones of the human substantia nigra and has the ability to bind a variety of metal ions, especially iron. Post-mortem analyses of the human brain have established that oxidative stress and iron content are enhanced in association with neuronal death. As redox-active iron (free Fe2+ form) and other transition metals have the ability to generate highly reactive hydroxyl radicals by a catalytic process, we investigated the redox activity of neuromelanin (NM)-aggregates in a group of parkinsonian patients, who presented a statistically significant reduction (- 70%) in the number of melanized-neurones and an increased non-heme (Fe3+) iron content as compared with a group of matched-control subjects. The level of redox activity detected in neuromelanin-aggregates was significantly increased (+ 69%) in parkinsonian patients and was highest in patients with the most severe neuronal loss. This change was not observed in tissue in the immediate vicinity of melanized-neurones. A possible consequence of an overloading of neuromelanin with redox-active elements is an increased contribution to oxidative stress and intraneuronal damage in patients with Parkinson's disease.     

大肠杆菌拓扑异构酶I结合重金属的特性及功能影响

【背景】大肠杆菌拓扑异构酶Ⅰ(Escherichia coli topoisomerase I,E.coli TopA)在DNA复制、转录、重组和基因表达调控等过程发挥关键作用。研究表明E.coli TopA只有结合锌离子才具有活性,然而E.coli TopA能否结合其他金属离子尤其是重金属离子,以及结合其他金属后是否具有活性,目前仍不清楚。【目的】探究大肠杆菌拓扑异构酶Ⅰ是否结合环境中常见重金属离子,研究重金属离子结合E.coli TopA蛋白后对其活性的影响。【方法】在分别添加有锌、钴、镍、镉、铁、汞、砷、铬、铅、铜离子的M9基础培养中表达、纯化出E.coli TopA蛋白,并对纯化得到的蛋白用电感耦合等离子体质谱仪进行相应金属离子含量的测定;利用表达E.coli TopA锌指结构的突变体蛋白鉴定重金属离子的结合位点;通过体外超螺旋DNA松弛实验测定不同金属结合E.coli TopA的拓扑异构酶活性;通过测定蛋白内源性荧光推测不同金属结合E.coli TopA的空间构象差异。【结果】E.coli TopA在体内除了能结合锌和铁之外,还能够结合钴、镍、镉3种离子,但是不能结合汞、砷、铬、铅、铜离子。钴、镍、镉结合形式的E.coli TopA,每个蛋白分子最多可以结合3个相应的金属离子,他们与TopA蛋白的结合位点也是位于3个锌指结构域,而且每个锌指结构域结合1个金属离子。此外,E.coli TopA结合钴、镍、镉离子后,其DNA拓扑异构酶活性并未受到影响,可能是由于钴、镍、镉离子结合形式的E.coli TopA蛋白,其空间构象与锌结合形式相比并未发生显著变化。【结论】由于DNA拓扑异构酶在维持细胞正常生理功能中发挥关键作用,研究表明E.coli TopA的功能不会受到常见重金属的干扰(不结合或者结合后活性无影响),这也有可能是大肠杆菌在进化过程中产生的对抗环境中重金属离子毒害作用的一种自我保护和耐受机制,具有重要的生理意义。     

Release of Metal Ions from Orthodontic Appliances: An In Vitro Study

In this paper, we report the results of an in vitro experiment on the release of metal ions from orthodontic appliances composed of alloys containing iron, chromium, nickel, silicon, and molybdenum into artificial saliva. The concentrations of magnesium, aluminum, silicon, phosphorus, sulfur, potassium, calcium, titanium, vanadium, manganese, iron, cobalt, copper, zinc, nickel, and chromium were significantly higher in artificial saliva in which metal brackets, bands, and wires used in orthodontics were incubated. In relation to the maximum acceptable concentrations of metal ions in drinking water and to recommended daily doses, two elements of concern were nickel (573 vs. 15 μg/l in the controls) and chromium (101 vs. 8 μg/l in the controls). Three ion release coefficients were defined: α, a dimensionless multiplication factor; β, the difference in concentrations (in micrograms per liter); and γ, the ion release coefficient (in percent). The elevated levels of metals in saliva are thought to occur by corrosion of the chemical elements in the alloys or welding materials. The concentrations of some groups of dissolved elements appear to be interrelated.     

A note on susceptibility of Branhamella catarrhalis to heavy metals

The susceptibility of 56 strains of Branhamella catarrhalis and ten Neisseria spp. to arsenate, silver, nickel, mercury, lead, cadmium, chromium, manganese, iron, cobalt and molybdenum was tested with an agar dilution technique. All but two strains of B. catarrhalis were resistant to multiple metal ions. There were not sufficient differences in susceptibility, however, to allow the development of a typing scheme based on resistograms. Heavy metal resistance in Branhamella was unrelated to beta-lactamase production. Neisseria spp. were more susceptible to metal ions than B. catarrhalis and this may form the basis of a simple diagnostic test.     

A note on susceptibility of Branhamella catarrhalis to heavy metals

The susceptibility of 56 strains of Branhamella catarrhalis and ten Neisseria spp. to arsenate, silver, nickel, mercury, lead, cadmium, chromium, manganese, iron, cobalt and molybdenum was tested with an agar dilution technique. All but two strains of B. catarrhalis were resistant to multiple metal ions. There were not sufficient differences in susceptibility, however, to allow the development of a typing scheme based on resistograms. Heavy metal resistance in Branhamella was unrelated to beta-lactamase production. Neisseria spp. were more susceptible to metal ions than B. catarrhalis and this may form the basis of a simple diagnostic test.     

Hydrogen binding in coordination compounds of 3(5)-(4-methoxyphenyl)pyrazole

The solid state structures of 3(5)-(4-methoxyphenyl)pyrazole and its coordination compounds with a series of two valent transition metals have been investigated. Since pyrazoles provide not only a nitrogen donor site for the coordination to metal ions, but also an additional N–H function, they are ideal ligands for the formation of hydrogen bound coordination polymers or for the implementation of secondary interactions with other ligands bound to the same central ion, resulting in a rigid ligand environment at the central metal. We chose cobalt, nickel, palladium, copper and zinc as twofold positively charged Lewis acids preferring coordination numbers of four and six to prove the capability of pyrazole to undergo intramolecular hydrogen bonds. In the four-coordinate mode, either tetrahedral (Zn²⁺) or square planar coordination geometries (Pd²⁺) are possible, providing different geometric restrictions for hydrogen bonding.     

Effect of metal ions on HIF-1α and Fe homeostasis in human A549 cells

Several metals are carcinogenic but little is known about the mechanisms by which they cause cancer. A pathway that may contribute to metal ion induced carcinogenesis is by hypoxia signaling, which involves a disruption of cellular iron homeostasis by competition with iron transporters or iron-regulated enzymes. To examine the involvement of iron in the hypoxia signaling activity of these metal ions we investigated HIF-1α protein stabilization, IRP-1 activity, and ferritin protein levels in human lung carcinoma A459 cells exposed to various agents in serum- and iron-free salt–glucose medium (SGM) or in normal complete medium. We also studied the effects of excess exogenous iron on these responses induced by nickel ion exposure. Our results show the following: (1) SGM enhanced metals-induced HIF-1α stabilization and IRP-1 activation (e.g., nickel and cobalt ions). (2) If SGM was reconstituted with a slight excess level (25 μM of FeSO₄) of iron, this enhancing ability was significantly decreased. (3) The effect of a high level of exogenous iron (500 μM of FeSO₄) on metal-induced hypoxia and iron metabolism was highly dependent on the order of addition. If treatment with the Fe and metal ions was simultaneous (co-treatment), the effects of nickel ion exposure were overwhelmed, since the added Fe reversed HIF-1α stabilization, decreased IRP-1 activity, and increased ferritin level. Pre-treatment with iron was not able to reverse the responses caused by nickel ion exposure. These results imply that it is important to consider the available iron concentration and suitable exposure design when studying metal-induced hypoxia or metal-induced disruption of Fe homeostasis.     

Metallic ion content and damage to the DNA in oral mucosa cells of children with fixed orthodontic appliances

Although the metal devices used in orthodontic treatments are manufactured highly resistance to corrosion, they may still suffer some localized corrosion resulting from the oral cavity conditions. The corrosion causes the release of metals from the alloys used for their manufacture. In this report, we evaluated the in vivo metal ions release of three alloys (stainless steel, titanium and nickel-free) usually used in the orthodontics treatments and its genotoxicity. We applied to 15 patients, between 12 and 16 years, 4 tubes and 20 brackets. Samples from oral mucosa were taken before the treatment and 30 days later. The concentration of the titanium, chromium, manganese, cobalt, nickel, molybdenum and iron were detected using inductively coupled plasma mass spectrometry (ICP-MS). The genotoxicity was measured with a comet assay (Olive moment). The oral mucosa cells in contact with the stainless steel alloy displayed the greatest titanium and manganese concentrations and those in contact with the nickel-free alloy presented the greatest concentration of chromium and iron. Both alloys, stainless steel and nickel-free, induced a higher DNA damage in the oral mucosa cells than the titanium alloy, in which the Olive moment was similar to controls. Based on the results of our study, we can conclude that titanium brackets and tubes are the most biocompatible of the three alloys.     

Predicted metal binding sites for phytoremediation

Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. The objective of the study is to design and analyze metal binding motifs against the genes involved in phytoremediation. This is being done on the basis of certain pre-requisite amino-acid residues known to bind metal ions/metal complexes in medicinal and aromatic plants (MAP''s). Earlier work on MAP''s have shown that heavy metals accumulated by aromatic and medicinal plants do not appear in the essential oil and that some of these species are able to grow in metal contaminated sites. A pattern search against the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases yielded true positives in each case showing the high specificity of the motifs designed for the ions of nickel, lead, molybdenum, manganese, cadmium, zinc, iron, cobalt and xenobiotic compounds. Motifs were also studied against PDB structures. Results of the study suggested the presence of binding sites on the surface of protein molecules involved. PDB structures of proteins were finally predicted for the binding sites functionality in their respective phytoremediation usage. This was further validated through CASTp server to study its physico-chemical properties. Bioinformatics implications would help in designing strategy for developing transgenic plants with increased metal binding capacity. These metal binding factors can be used to restrict metal update by plants. This helps in reducing the possibility of metal movement into the food chain.     

Dihydrolipoic acid lowers the redox activity of transition metal ions but does not remove them from the active site of enzymes

Alpha-lipoic acid (LA) and its reduced form, dihydrolipoic acid (DHLA), have been suggested to chelate transition metal ions and, hence, mitigate iron- and copper-mediated oxidative stress in biological systems. However, it remains unclear whether LA and DHLA chelate transition metal ions in a redox-inactive form, and whether they remove metal ions from the active site of enzymes. Therefore, we investigated the effects of LA and DHLA on iron- or copper-catalyzed oxidation of ascorbate, a sensitive assay for the redox activity of these metal ions. We found that DHLA, but not LA, significantly inhibited ascorbate oxidation mediated by Fe(III)-citrate, suggesting that reduced thiols are required for iron binding. DHLA also strongly inhibited Cu(II)(histidine)(2)-mediated ascorbate oxidation in a concentration-dependent manner, with complete inhibition at a DHLA:Cu(II) molar ratio of 3:1. In contrast, no inhibition of copper-catalyzed ascorbate oxidation was observed with LA. To investigate whether LA and DHLA remove copper or iron from the active site of enzymes, Cu,Zn superoxide dismutase and the iron-containing enzyme aconitase were used. We found that neither LA nor DHLA, even at high, millimolar concentrations, altered the activity of these enzymes. Our results suggest that DHLA chelates and inactivates redox-active transition metal ions in small-molecular, biological complexes without affecting iron- or copper-dependent enzyme activities.     

Growth-modulating tripeptide (glycylhistidyllysine): association with copper and iron in plasma, and stimulation of adhesiveness and growth of hepatoma cells in culture by tripeptide-metal ion complexes

The tripeptide H-Gly-His-Lys-OH (GHL) is a human plasma constituent which has been previously shown to modulate the growth and viability of a variety of cell types and organisms. Experimental observations presented herein indicate that GHL is complexed with the transition metal ions Cu++ and Fe++ in vivo and may exert its biological effects as a peptide-metal chelate. At physiological pH in vitro, GHL associates with ionic copper, cobalt, iron, molybdenum, manganese, nickel, and zinc, but has no affinity for calcium, manganese, potassium, and sodium. GHL acts synergistically with copper, iron, cobalt, and zinc to alter patterns of cell growth in monolayer cultures of a tumorigenic hepatoma cell line (HTC4). These transition metals induce cellular flattening and adhesion to support surfaces, and inhibit DNA synthesis and lactic acid production when growth is limited by reduction of serum concentrations in medium. These inhibitory effects are neutralized, and intercellular adhesion and growth are stimulated by GHL in medium at nanomolar concentrations. Cu and Fe are the most active metals when combined with GHL. The results suggest that the inability of HTC4 cultures to replicate without adequate concentrations of serum in medium may reflect deficiency of GHL and transition metals, which appear to form complexes prior to interaction with cells. Chelation of transition metals with GHL and, potentially, with other growth-modulating peptide factors in plasma or medium, may provide a mechanism for expression and regulation of biological activities influenced by transition metals and polypeptide growth factors. The observed effects of GHL-metal complexes, including stimulation of cellular adhesiveness to substratum (flattening) and intercellular attachment (monolayer formation), appear to satisfy requirements for growth of hepatoma cells in monolayer culture.     

Transformation of Fe,Mn, Co,and Ni compounds in humic podzols at different moisture

Incubation of humic podzol at soil moisture of 60 and 100% field capacity (FC) and after addition of peat and glucose increased the content of nickel and cobalt compounds in the water-soluble, exchangeable, organic matter-bound, and amorphous iron-bound fractions. At the same time, the content of elements bound to crystallized iron compounds decreased twofold and fourfold at 60 and 100% FC, respectively. The content of cobalt and nickel decreased in the residual fraction by 25 and 50%, respectively. The transformation of cobalt and nickel in soil is closely related to the transformation of iron and manganese compounds as well as to redox processes. The lowest pH and redox potential (RP) as well as the highest increase in the mobility of the elements was observed after soil incubation with glucose at 100% FC.     

Effect of metal ions on HIF-1alpha and Fe homeostasis in human A549 cells

Several metals are carcinogenic but little is known about the mechanisms by which they cause cancer. A pathway that may contribute to metal ion induced carcinogenesis is by hypoxia signaling, which involves a disruption of cellular iron homeostasis by competition with iron transporters or iron-regulated enzymes. To examine the involvement of iron in the hypoxia signaling activity of these metal ions we investigated HIF-1alpha protein stabilization, IRP-1 activity, and ferritin protein levels in human lung carcinoma A459 cells exposed to various agents in serum- and iron-free salt-glucose medium (SGM) or in normal complete medium. We also studied the effects of excess exogenous iron on these responses induced by nickel ion exposure. Our results show the following: (1) SGM enhanced metals-induced HIF-1alpha stabilization and IRP-1 activation (e.g., nickel and cobalt ions). (2) If SGM was reconstituted with a slight excess level (25 microM of FeSO(4)) of iron, this enhancing ability was significantly decreased. (3) The effect of a high level of exogenous iron (500 microM of FeSO(4)) on metal-induced hypoxia and iron metabolism was highly dependent on the order of addition. If treatment with the Fe and metal ions was simultaneous (co-treatment), the effects of nickel ion exposure were overwhelmed, since the added Fe reversed HIF-1alpha stabilization, decreased IRP-1 activity, and increased ferritin level. Pre-treatment with iron was not able to reverse the responses caused by nickel ion exposure. These results imply that it is important to consider the available iron concentration and suitable exposure design when studying metal-induced hypoxia or metal-induced disruption of Fe homeostasis.