Metal-binding Ability Research Articles

New peptides with metal binding abilities and their use as drug carriers.

Many new designed molecules that target efficiently in vitro bacterial metalloproteases were completely inactive in cellulo against Gram negative bacteria. Their activities were limited by the severe restriction of the penetration/diffusion rate through the outer membrane barrier. To bypass this limitation, we have assayed the strategy of metallodrugs, to improve the delivery of hydroxamic acid inhibitors to peptide deformylase. In this metal-chaperone, to facilitate bacterial uptake, the ancillary ligand tris(2-pyridylmethyl)amine (TPA) or di(picolyl)amine (DPA) was functionalized by a tetrapeptide analogue of antimicrobial peptide, RWRW(OBn) (AA08 with TPA) and/or an efflux pump modulator PAβN (AA09 with TPA and AA27 with DPA). We prepared Co(III), Zn(II), and Cu(II) metallodrugs. Using a fluorescent hydroxamic acid, we showed that, in contrast to Cu(II) metallodrugs, Co(III) metallodrugs were stable in the Mueller Hinton (MH) broth during the time required for bacterial assays. The antibacterial activities were determined against E. coli strain wild-type (AG100) and E. coli strain deleted from acrAB efflux pump (AG100A). While none of the PDFinhs used in this study (SMP289 with an indole scaffold, AT015 and AT019 built on a 1,2,4-oxadiazole scaffold) displayed activity higher than 128 μM, all the metallodrugs were active with MICs around 8 μM both against AG100 and AG100A. However, compared to the activities of equimolar combinations of PDFinhs and the free chelating peptides (AA08, AA09, or AA27), they showed similar activities. A synergistic association between AT019 and AA08 or AA09 was determined using the fractional inhibitory concentration with AG100 and AG100A. Combinations of peptides lacking the chelating group with PDFinhs were inefficient. LC-MS analyses showed that the chelating peptides bind Zn(II) cation when incubated in MH broth. These results support the in situ formation of a zinc metallodrug, but we failed to detect it by LC-MS in MH. Nevertheless, this chelating peptides metalated with zinc act as permeabilizers which are more efficient than PAβN to facilitate the uptake of PDFinhs by Gram(-) bacteria.

Cytotoxic and antigenotoxic activities of phosvitin from egg yolk

Egg yolk phosvitin is one of the most phosphorylated proteins in nature, and thus has a strong metal-binding ability. The objective of this study was to evaluate the cytotoxic and antigenotoxic activities of phosvitin in vitro. Using the 3-[4,5-dimethythiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) assay, the cytotoxicity of phosvitin was evaluated in human cancer cell lines of various tissue origins, including the cervix (HeLa), breast (MCF-7), stomach (AGS), lung (A549 and SK-MES-1), liver (HepG2), and larynx (Hep-2). The growth of all cancer cell lines was inhibited in a dose-dependent manner by phosvitin. Among the cancer cell lines tested, MCF-7 and SK-MES-1 were the least sensitive and HeLa, AGS, and HepG2 were the most sensitive to phosvitin. The 50% inhibition of cell viability values of phosvitin were 5.38, 11.57, 4.78, 6.98, 11.82, 3.93, and 9.97 mg/mL for HeLa, MCF-7, AGS, A549, SK-MES-1, HepG2, and Hep-2, respectively. The protective effects of phosvitin against DNA damage in human leukocytes indicated that phosvitin showed protective effects against the oxidative stress-induced DNA damages in human leukocytes. These results suggested that phosvitin has a high potential to be used as an anticancer agent for humans.

Specific binding of Zn2+, Cd2+ and Ni2+ ions by a cyclic four-cysteinyl peptide.

The metal binding abilities of the GCASCDNCRACKK cyclic peptide towards Zn(2+), Cd(2+) and Ni(2+) ions were studied by potentiometric and spectroscopic methods. The aim of this work was to understand the impact of cyclization on the peptide binding mode and the stability of the formed metal complexes when compared to its linear Ac-GCASCDNCRACKK-NH2 analogue. The obtained results clearly indicate that in the case of Cd(2+) and Ni(2+) complexes, the cyclization of the coordinating peptide distinctly increases the complex stability in the whole pH range studied. Surprisingly, different results were obtained for Zn(2+) complexes. The peptide cyclization seems to prevent the binding of all four available cysteinyl residues to the Zn(2+) ion, resulting in the reduced stability of the respective complexes.

Abiotic stress response in yeast and metal-binding ability of a type 2 metallothionein-like protein (PutMT2) from Puccinellia tenuiflora.

Metallothioneins are low-molecular weight and cysteine-rich metal-binding proteins that play predominant cellular roles in the scavenging of reactive oxygen species and in mediating metal metabolism. To evaluate the role of a type-2 metallothionein-like gene from Puccinellia tenuiflora (PutMT2), the gene was over-expressed in yeast, and growth was assessed under a variety of abiotic stress conditions including peroxide (H2O2), salinity (NaCl and NaHCO3), and metal stress. PutMT2 overexpression in yeast improved the tolerance of cells to H2O2, NaCl, NaHCO3, Zn(2+), Fe(2+), Fe(3+), Cd(2+), Cr(6+), and Ag(+), but increased the sensitivity of cells to Mn(2+), Co(2+), Cu(2+), and Ni(2+) compared with control cells. PutMT2 was then expressed in Escherichia coli BL21as a glutathione S-transferase (GST) fusion protein (GST-PutMT2), and the metal-binding ability of GST-PutMT2 was analyzed and compared with GST alone using inductively coupled plasma atomic emission spectroscopy. Results showed that PutMT2 could bind to Cr, Cd, Co, Ag, Ba, Pb, Mn, Zn, Fe, Cu, P, Al, and Mg, but not Ni and As. There was no evidence to suggest that PutMT2 exhibited a specific or selective binding tendency to any individual metal ion. PutMT2 protein bound to Zn, Na, and Cu in vivo, perhaps with the highest affinity for Cu. Taken together, our results suggest that PutMT2 protein could play an important role in improving metal tolerance by metal binding in yeast. However, additional studies are required to confirm these results and to clarify the function of PutMT2 in transgenic plants.

How does it kill?: understanding the candidacidal mechanism of salivary histatin 5.

Histatins are salivary cationic peptides that provide the first line of defense against oral candidiasis caused by Candida albicans. This minireview presents a critical evaluation of our knowledge of the candidacidal mechanism of histatin 5 (Hst 5). Hst 5 is the most potent among all histatin family members with regard to its antifungal activity. The mode of action of Hst 5 has been a subject of intense debate. Unlike other classical host innate immune proteins, pore formation or membrane lysis by Hst 5 has largely been disproven, and it is now known that all targets of Hst 5 are intracellular. Hst 5 binds C. albicans cell wall proteins (Ssa1/2) and glycans and is taken up by the cells through fungal polyamine transporters in an energy-dependent manner. Once inside the fungal cells, Hst 5 may affect mitochondrial functions and cause oxidative stress; however, the ultimate cause of cell death is by volume dysregulation and ion imbalance triggered by osmotic stress. Besides these diverse targets, a novel mechanism based on the metal binding abilities of Hst 5 is discussed. Finally, translational approaches for Hst 5, based on peptide design and synergy with other known drugs, are considered a step forward for bench-to-bed application of Hst 5.

Purification, crystallization and preliminary X-ray analysis of a putative nucleotide phosphohydrolase, YpgQ, fromBacillus subtilis

The histidine-aspartate (HD) domain exerts phosphohydrolase activity on nucleotides and functions in nucleotide metabolism. Sequence analysis suggested that YpgQ from Bacillus subtilis contains the HD domain, but the structure and function of YpgQ remain to be revealed. The recombinant YpgQ protein was overexpressed in an Escherichia coli cell expression system and was purified to homogeneity by Ni-NTA affinity and anion-exchange chromatography. Crystals in space group P2₁ were obtained in PEG 600 solutions and diffracted X-rays to 2.3 Å resolution. Moreover, X-ray fluorescence scans on YpgQ crystals demonstrated the metal-binding ability of YpgQ.

Genetic Incorporation of a Phenanthroline-Containing Amino Acid in Escherichia coli

A simple and general method that selectively introduces metal binding sites into a protein can greatly increase the ability to design and biosynthesize artificial metalloproteins. Here, we report the incorporation of a phenanthroline-containing amino acid (Phen-Ala) into proteins in Escherichia coli by using the tRNACUA and tyrosyl aminoacyl-tRNA synthetase pair (BpyRS) from Methanococcus jannaschii, which was originally developed for a bipyridine-containing amino acid (Bpy-Ala). The incorporation efficiency of BpyRS for PhenAla was comparable to that for Bpy-Ala. Because of its high metal-binding ability and characteristic spectral properties, Phen-Ala can be a useful alternative to the existing metal-chelating amino acids for the design and synthesis of artificial metalloproteins.

Probing the equatorial groove of the hookworm protein and vaccine candidate antigen, Na-ASP-2

Hookworm activation-associated secreted proteins can be structurally classified into at least three different groups. The hallmark feature of Group 1 activation-associated secreted proteins is a prominent equatorial groove, which is inferred to form a ligand binding site. Furthermore, a conserved tandem histidine motif is located in the centre of the groove and believed to provide or support a yet to be determined catalytic activity.Here, we report three-dimensional crystal structures of Na-ASP-2, an L3-secreted activation-associated secreted protein from the human hookworm Necator americanus, which demonstrate transition metal binding ability of the conserved tandem histidine motif. We further identified moderate phosphohydrolase activity of recombinant Na-ASP-2, which relates to the tandem histidine motif. By panning a random 12-mer peptide phage library, we identified a peptide with high similarity to the human calcium-activated potassium channel SK3, and confirm binding of the synthetic peptide to recombinant Na-ASP-2 by differential scanning fluorimetry. Potential binding modes of the peptide to Na-ASP-2 were studied by molecular dynamics simulations which clearly identify a preferred topology of the Na-ASP-2:SK3 peptide complex.

Supramolecular assembling of molecular ion-ligands on graphite-based solid materials directed to specific binding of metal ions

Molecular ligands with a particular topology, based on a polar heteroaromatic nucleus linked to hydrophilic (metal-complexing) substituents, form very stable assemblies with activated carbons (ACs) due to strong π–π interactions between the planar pyrimidine moiety and the arene centers of the AC surfaces. Heteroatomic functions at the edges of the AC graphitic sheets do not alter the interaction mode with the ligands nor the stability of the assemblies. That results in the formation of stable hybrids, AC/ligand, whose surface chemical properties, specially the acid base behavior and the affinity to metal ions, reflect those of the non-conjugated, hydrophilic moieties of the ligands. Consequently, such hybrid materials show metal ion adsorptivities that are superior to those of the parent AC and correlate with the metal-binding abilities of the non-conjugated substituents. Significant amounts of meso- and macropores are required in the parent AC to efficiently transfer the chemical properties of the ligand non-conjugated substituents to the hybrid AC/ligand. After adsorption of metal ions, new hybrids, AC/ligand/metal, emerge with interesting potential applications. Thus, an AC/triamine ligand/Pd(II) hybrid showed high catalytic activity in hydrogenation reactions due to the formation of highly stable Pd nanoparticles at the AC surface during the first reaction cycle.

Rapid Ni, Zn, and Cu Ion-Promoted Alcoholysis of N,N-Bis(2-picolyl)- and N,N-Bis((1H-benzimidazol-2-yl)methyl)-p-nitrobenzamides in Methanol and Ethanol

The methanolysis and ethanolysis of the Ni(II), Zn(II), and Cu(II) complexes of N,N-bis(2-picolyl)-p-nitrobenzamide (1) and N,N-bis((1H-benzimidazol-2-yl)methyl)-p-nitrobenzamide (2) were studied under pH-controlled conditions at 25 °C. Details of the mechanism were obtained from plots of the kobs values for the reaction under pseudo-first-order conditions as a function of [M2+]. Such plots give saturation kinetics for the Cu(II)-promoted reactions of 1 and 2 in both solvents, the Zn(II)-promoted reaction of 1 in methanol, and the Zn(II)- and Ni(II)-promoted reactions of 2 in methanol and ethanol. Logs of the maximal observed rate constants obtained from the latter plots, (kobs(max)), when plotted versus s(s)pH, are curved downward only for the Cu(II) complexes of 1 and 2 in both solvents and the Zn(II) complex of 1 in methanol. Despite differences in the metal-binding abilities and pKa values for formation of the active form, there is a common reaction mechanism, with the active form being 1:M(II):(–OR) and 2:M(II):(–OR), where M(II):(–OR) is the metal-bound alkoxide. The acceleration provided by the metal ion is substantial, being 10(14)–10(19) relative to the k2(¯OMe) value for the alkoxide-promoted alcoholysis of the uncomplexed amide.

Integrated analysis of seaweed components during seasonal fluctuation by data mining across heterogeneous chemical measurements with network visualization.

Biological information is intricately intertwined with several factors. Therefore, comprehensive analytical methods such as integrated data analysis, combining several data measurements, are required. In this study, we describe a method of data preprocessing that can perform comprehensively integrated analysis based on a variety of multimeasurement of organic and inorganic chemical data from Sargassum fusiforme and explore the concealed biological information by statistical analyses with integrated data. Chemical components including polar and semipolar metabolites, minerals, major elemental and isotopic ratio, and thermal decompositional data were measured as environmentally responsive biological data in the seasonal variation. The obtained spectral data of complex chemical components were preprocessed to isolate pure peaks by removing noise and separating overlapping signals using the multivariate curve resolution alternating least-squares method before integrated analyses. By the input of these preprocessed multimeasurement chemical data, principal component analysis and self-organizing maps of integrated data showed changes in the chemical compositions during the mature stage and identified trends in seasonal variation. Correlation network analysis revealed multiple relationships between organic and inorganic components. Moreover, in terms of the relationship between metal group and metabolites, the results of structural equation modeling suggest that the structure of alginic acid changes during the growth of S. fusiforme, which affects its metal binding ability. This integrated analytical approach using a variety of chemical data can be developed for practical applications to obtain new biochemical knowledge including genetic and environmental information.

Full characterization of the Cu-, Zn-, and Cd-binding properties of CnMT1 and CnMT2, two metallothioneins of the pathogenic fungus Cryptococcus neoformans acting as virulence factors

We report here the full characterization of the metal binding abilities of CnMT1 and CnMT2, two Cryptococcus neoformans proteins recently identified as metallothioneins (MTs), which have been shown to play a crucial role in the virulence and pathogenicity of this human-infecting fungus. In this work, we first performed a thorough in silico study of the CnMT1 and CnMT2 genes, cDNAs and corresponding encoded products. Subsequently, the Zn(II)-, Cd(II)- and Cu(I) binding abilities of both proteins were fully determined through the analysis of the metal-to-protein stoichiometries and the structural features (determined by ESI-MS, CD, ICP-AES and UV-vis spectroscopies) of the corresponding recombinant Zn-, Cd- and Cu-MT preparations synthesized in metal-enriched media. Finally, the analysis of the Zn/Cd and Zn/Cu replacement processes of the respective Zn-MT complexes when allowed to react with Cd(II) or Cu(I) aqueous solutions was performed. Comprehensive consideration of all gathered results allows us to consider both isoforms as genuine copper-thioneins, and led to the identification of unprecedented Cu5-core clusters in MTs. CnMT1 and CnMT2 polypeptides appear to be evolutionarily related to the small fungal MTs, probably by ancient tandem-duplication events responding to a highly selective pressure to chelate copper, and far from the properties of Zn- and Cd-thioneins. Finally, we propose a modular structure of the Cu-CnMT1 and Cu-CnMT2 complexes on the basis of Cu5 clusters, concordantly with the modular structure of the sequence of CnMT1 and CnMT2, constituted by three and five Cys-rich units, respectively.

Changes in Spectral Characteristics and Copper (II)-Binding of Dissolved Organic Matter in Leachate from Different Water-Treatment Processes

The aim of the present study was to investigate the fluorescence properties of dissolved organic matter (DOM) from four leachate samples, which were disposed by regulating tank (RTK), anaerobic treatment (ATT), oxidation ditch (ODH), and membrane bioreactor and to assess their binding capacities and stability constants by Cu(II). The results showed that five fluorescent peaks, including three humic-like peaks (peaks A, C, and E) and two protein-like peaks (peaks B and D), were identified. Most fluorescent components can be degraded after ODH. Fluorescence-quenching titration showed that the modified Stern-Volmer model can be used to fit the quenching data and calculate conditional stability constants (log K) and the % of fluorophores (f %) between DOM and Cu(II). DOM-Cu(II) complexes had relatively high log K values in the RTK and ATT disposals. After the ODH-treatment process, log K values showed a marked decrease. The f % values of protein-like materials were evidently greater than those of humic-like substances. The results showed the impact of the water treatment on the metal-binding ability of various fractions.

Immobilization of the enzyme GpdQ on magnetite nanoparticles for organophosphate pesticide bioremediation

Annually thousands of people die or suffer from organophosphate (pesticide) poisoning. In order to remove these toxic compounds from the environment, the use of enzymes as bioremediators has been proposed. We report here a Ser127Ala mutant based on the enzyme glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes. The mutant, with improved metal binding abilities, has been immobilized using glutaraldehyde on PAMAM dendrimer-modified magnetite nanoparticles. The immobilized system was characterized using elemental analysis as well as infrared, transmission electron and X-ray photoelectron spectroscopies. The amount of GpdQ that was immobilized with the optimized procedure was 1.488nmol per g MNP. A kinetic assay has been designed to evaluate the activity of the system towards organophosphoester substrates. The specific activity towards BPNPP directly after immobilization was 3.55μmolmg−1min−1, after one week 3.39μmolmg−1min−1 and after 120days 3.36μmolmg−1min−1, demonstrating that the immobilized enzyme was active for multiple cycles and could be stored on the nanoparticles for a prolonged period.

Metal-Binding Ability of VIP1: A bZIP Protein in Arabidopsis thaliana

VirE2-interacting protein 1 (VIP1) is an Arabidopsis thaliana bZIP transcription factor which regulates pathogen responses and rehydration responses. VIP1 has transcriptional activation potential, DNA-binding ability, and a nuclear-cytoplasmic shuttling property. These functions are possibly regulated by cofactors and/or post-translational modifications. During an investigation of the functions of VIP1, we discovered that VIP1 can react with an Ni²⁺-activated derivative of horseradish peroxidase, HisProbe-HRP, suggesting that VIP1 can bind Ni²⁺. Using truncated versions and mutated versions of VIP1, the Ni²⁺-binding region was narrowed. Using VIP1 H145Q and H145R mutants, which have H → Q and H → R mutations at the amino acid position 145 of VIP1, a trihistidine site at the amino acid position 144-146 was confirmed to be responsible for the Ni²⁺-binding ability. Immobilized-metal affinity chromatography (IMAC) suggested that VIP1 can bind Zn²⁺ and Co²⁺ as well as Ni²⁺, which is consistent with the known metal-chelating property of polyhistidine. In IMAC, the levels of purified VIP1 were not significantly different between denaturing and non-denaturing conditions, suggesting that the trihistidine is located on the surface of the native form of VIP1. In gel shift assays, VIP1-dependent decreases of electrophoretic mobilities of DNA probes were further decreased by Co²⁺. Among wild-type VIP1 and the H145Q and H145R mutants, H145R was the least sensitive to the effect of Co²⁺ in the gel shift assays. These results suggest that the Co²⁺ and the metal-binding site of VIP1 affect the interaction between VIP1 and DNA.

New Peptide-based antimicrobials for tackling drug resistance in bacteria: single-cell fluorescence imaging.

New peptide molecules with metal binding abilities proved to be active against multidrug resistant clinical isolates. One of them labeled with a dansylated lysine has been imaged inside single-multidrug resistant bacteria cells by deep ultraviolet fluorescence, showing a heterogeneous subcellular localization. The fluorescence intensity is clearly related to the accumulation of the drug inside the bacteria, being dependent both on its concentration and on the incubation time with cells.

Cadmium detection by a thermally responsive elastin copolymer with metal-binding functionality

Heavy metals are of great concern to environmental safety because of their adverse effects on the environment and human health, even at very low levels. In particular, cadmium and several cadmium-containing compounds are carcinogens and induce many types of cancer. Biological extracts of cadmium have been given greater attention recently because they are considered to be environmentally benign and economically acceptable. Among promising candidates, one emerging technology is the use of tunable, metal-binding biopolymers based on elastin-like polypeptides (ELPs). An ELP consists of the repeating pentapeptide of specific amino acids, Val-Pro-Gly-Xaa-Gly (where the “guest residue” Xaa is any amino except proline) that undergoes a reversible phase transition at a specific temperature (transition temperature, Tt). However, the ELP itself is relatively non-selective. A biopolymer with metal-binding domains that have stronger affinity, capacity, and selectivity would have distinct advantages. We investigated the use of a new generation of ELP biopolymers, EC18-ELP containing synthetic phytochelatin (EC), which is a metal-binding protein with a repetitive motif (Glu-Cys)nGly, as the metal-binding domain. In this study, an EC18-ELP fusion protein was expressed in Escherichia coli and the metal binding ability of EC to cadmium was examined quantitatively. In addition, transition temperature variation was analyzed when the fusion protein bound to cadmium.

Sialorphin and its analog as ligands for copper(II) ions

In this study the sialorphin (Gln-His-Asn-Pro-Arg) and its analog (Glp-His-Asn-Pro-Arg) were analyzed in terms of metal binding ability. Both peptides were synthesized using the solid-phase method. The application of number analytical methods: potentiometry, spectroscopy (UV–Vis, CD, NMR) and mass spectrometry allowed for a detailed characterization of the coordination abilities of presented peptides. The analysis of the obtained results has shown that both peptides are able to form a series of complexes. However due to the presence of free N-terminal amino group the sialorphin is more effective in metal ion binding. Nevertheless, in basic conditions both peptides involve the amide nitrogen belonging to the side chain of Asn3 moiety and form 4N complex with square planar structure. This unusual ability has been confirmed by the results obtained from the NMR studies.

Density functional theory investigation of the VIIIB transition metal atoms deposited on (5,5) single-walled carbon nanotubes

The binding of VIIIB transition metals i.e. Fe, Ru, Os, Co, Rh, Ir, Ni, Pd, and Pt single atoms to single-walled carbon nanotube (SWCNT) was investigated using the density functional theory method. The B3LYP/LanL2DZ calculation shows that all these transition metal atoms have strong binding abilities to SWCNT. The binding abilities of these transition metals onto SWCNT are in following order: Os>Ru>Ir>Fe>Rh>Pt>Ni>Co>Pd. The Os single atom binding on SWCNT is the strongest binding of which the binding energy is −240.66kcal/mol. The partial charge transfers from transition metal to SWCNT, density of states and energy gaps of metal atoms deposited on SWCNTs were analyzed and reported.

Structural Consequences of the N7 and C8 Translocation on the Metal Binding Behavior of Adenine

7-Deaza-8-aza-adenine, namely 4-aminopyrazolo[3,4-d]pyrimidine (H4app), is a bioisoster of adenine (Hade) resulting from the translocation of N7 and C8 atoms on the purine moiety. With the aim of studying the influence of this translocation on the metal binding abilities of H4app, we have prepared and structurally characterized two ternary copper(II) complexes having H4app and one N-benzyl-iminodiacetate chelator (MEBIDA or FBIDA, with a methyl or fluoro group in para- of the benzyl aromatic ring): [Cu(2)(MEBIDA)(2)(μ(2)-N1,N8-H4app)(H(2)O)(2)]·4H(2)O (1) and [Cu(4)(FBIDA)(4)(μ(2)-N8,N9-H4app)(2)(H(2)O)]·3.5H(2)O (2). Furthermore, thermal, spectral, and magnetic properties have been also investigated. In 1, H(N9)4app is disordered over two equally pondered positions and the μ(2)-N1,N8 coordination mode is assisted by N6-H···O and N9-H···O intramolecular interactions, respectively. The acyclic nonlinear molecular topology of 2 is strongly influenced by two intramolecular H-bonding interactions (O-H···O-carboxylate) involving the apical aqua ligand of a terminal Cu(II) atom. Thus, both compounds have in common the Cu-N8 bond. In order to better understand our limited structural information, DFT calculations for the individual tautomers of H4app as well as mononuclear Cu(II) model systems have been carried out. According to previous results, we conclude that H(N9)4app is the most stable tautomer followed by H(N8)4app. When N9 and N8 are metalated, then the tautomer H(N1)4app can come into play as observed in compound 2. Likewise, the findings concerning compound 1 suggest that the formation of a Cu-N1 bond in H4app results was favored compared to neutral adenine, for which only one case has been reported with such coordination despite the large variety of related Cu(II)-Hade described in the literature.