Is there a difference in metal ion-based inhibition between members of thionin family: Molecular dynamics simulation study

Thionins have a considerable potential as antimicrobial compounds although their application may be restricted by metal ion-based inhibition of membrane permeabilizing activity. We previously reported the properties associated with the proposed mechanism of metal ion-based inhibition of beta-purothionin. In this study, we investigated the effects of metal ions on alpha-hordothionin which differs from beta-purothionin by eight out of 45 residues. Three of the differing residues are thought to be involved in the mechanism of metal ion-based inhibition in beta-purothionin. The structure and dynamics of alpha-hordothionin were explored using unconstrained molecular dynamics (MD) simulations in explicit water as a function of metal ions. Although the global fold is almost identical to that of beta-purothionin, alpha-hordothionin displays reduced fluctuating motions. Moreover, alpha-hordothionin is more resistant to the presence of metal ions than beta-purothionin. Mg(+2) ions do not affect alpha-hordothionin, whereas K(+) ions induce perturbations in the alpha2 helix, modify dynamics and electrostatic properties. Nevertheless, these changes are considerably smaller than those in beta-purothionin. The proposed mechanism of metal ion-based inhibition involves the hydrogen bonding network of Arg5-Arg30-Gly27, which regulates dynamic unfolding of the alpha2 C-end which is similar to beta-purothionin response. The key residues responsible for the increased resistance for alpha-hordothionin are Gly27 and Gly42 which replace Asn27 and Asp42 involved into the mechanism of metal ion-based inhibition in beta-purothionin. Comparison of MD simulations of alpha-hordothionin with beta-purothionin reveals dynamic properties which we believe are intrinsic properties of thionins with four disulphide bonds.     

Electron spin resonance and magnetic relaxation studies of gadolinium(III) complexes with human transferrin

A human serum transferrin complex was prepared in which Gd(III) was substituted for Fe(III) at the two metal-binding sites. Characteristic changes upon metal binding in both the UV absorption of ligated tyrosines and the solvent proton longitudinal magnetic relaxation rates demonstrated 2/1 metal stoichiometry and pH-dependent binding constants. Binding studies were complicated both by binding of Gd(III) to nonspecific sites on transferrin at pH less than or equal to 7 and by complexation of the Gd(III) by the requisite bicarbonate anion at pH greater than or equal to 6.0. A unique Gd(III) electron spin resonance spectrum, with a prominent signal at g = 4.96, was observed for the specific Gd(III)-transferrin complex. The major features of this spectrum were fit successfully by a model Hamiltonian which utilized crystal field parameters similar to those determined for Fe(III) in transferrin [Aasa, R. (1970) J. Chem. Phys. 52, 3919-3924]. The magnetic field dependence of the solvent proton relaxation rate was measured as a function of both pH and metal ion concentration. An observed biphasic dependence of the relaxation rate on metal concentration is attributed to either sequential metal binding to the two iron-binding sites with different relaxation properties or random binding to two sites that are similar but show conformationally induced changes in relaxation properties as the second metal is bound. The increase in the solvent proton relaxation rate with pH is consistent with a model in which a proton of a second coordination sphere water molecule is hydrogen bonded to a metal ligand which becomes deprotonated at pH 8.5.     

Structural basis for metal binding specificity: the N-terminal cadmium binding domain of the P1-type ATPase CadA

In bacteria, P1-type ATPases are responsible for resistance to di- and monovalent toxic heavy metals by taking them out of the cell. These ATPases have a cytoplasmic N terminus comprising metal binding domains defined by a betaalphabetabetaalphabeta fold and a CXXC metal binding motif. To check how the structural properties of the metal binding site in the N terminus can influence the metal specificity of the ATPase, the first structure of a Cd(II)-ATPase N terminus was determined by NMR and its coordination sphere was investigated by X-ray absorption spectroscopy. A novel metal binding environment was found, comprising the two conserved Cys residues of the metal binding motif and a Glu in loop 5. A bioinformatic search identifies an ensemble of highly homologous sequences presumably with the same function. Another group of highly homologous sequences is found which can be referred to as zinc-detoxifying P1-type ATPases with the metal binding pattern DCXXC in the N terminus. Because no carboxylate groups participate in Cu(I) or Ag(I) binding sites, we suggest that the acidic residue plays a key role in the coordination properties of divalent cations, hence conferring a function to the N terminus in the metal specificity of the ATPase.     

Consolidated plasmid Design for Stabilized Heterologous Production of the complex natural product Siderophore Yersiniabactin

Yersiniabactin (Ybt) is a hybrid polyketide-nonribosomal complex natural product also known as a siderophore for its iron chelation properties. The native producer of Ybt, Yersinia pestis, is a priority pathogen responsible for the plague in which the siderophore properties of Ybt are used to sequester iron and other metal species upon host infection. Alternatively, the high metal binding properties of Ybt enable a plethora of potentially valuable applications benefiting from metal remediation and/or recovery. For these applications, a surrogate production source is highly preferred relative to the pathogenic native host. In this work, we present a modification to the heterologous Escherichia coli production system established for Ybt biosynthesis. In particular, the multiple plasmids originally used to express the genetic pathway required for Ybt biosynthesis were consolidated to a single, copy-amplifiable plasmid. In so doing, plasmid stability was improved from ~30% to ≥80% while production values maintained at 20–30% of the original system, which resulted in titers of 0.5–3 mg/L from shake flask vessels.     

Theory of propagation of ordinary surface cyclotron waves

The dispersion properties of ordinary surface cyclotron waves in a semiinfinite nonuniform plasma are investigated. The waves propagate across the external magnetic field directed along the plasma surface in a metal waveguide the internal surface of which is covered with a dielectric. The problem is solved analytically in the framework of a kinetic model for plasma particles under the assumption of weak spatial dispersion. The influence of the parameters of the dielectric layer separating the plasma from the metal wall, the shape of the plasma density profile, and the value of the external magnetic field on the dispersion properties of surface cyclotron waves is studied both numerically and analytically.     

Fluorescence studies of benzo-[a]-pyrene in liposome membrane systems

This investigation concerns the change in the fluorescence properties of benzo-[a]-pyrene when added to membrane systems. The feasibility of the fluorescence quenching technique using metal ions which have specific transport properties to study diffusion processes of carcinogenic benzo-[a]-pyrene molecules in biomembrane systems is demonstrated.     

Evaluation of filler materials used for uniform load distribution at boundaries during structural biomechanical testing of whole vertebrae

This study was designed to compare the compressive mechanical properties of filler materials, Wood's metal, dental stone, and polymethylmethacrylate (PMMA), which are widely used for performing structural testing of whole vertebrae. The effect of strain rate and specimen size on the mechanical properties of the filler materials was examined using standardized specimens and mechanical testing. Because Wood's metal can be reused after remelting, the effect of remelting on the mechanical properties was tested by comparing them before and after remelting. Finite element (FE) models were built to simulate the effect of filler material size and properties on the stiffness of vertebral body construct in compression. Modulus, yield strain, and yield strength were not different between batches (melt-remelt) of Wood's metal. Strain rate had no effect on the modulus of Wood's metal, however, Young's modulus decreased with increasing strain rate in dental stone whereas increased in PMMA. Both Wood's metal and dental stone were significantly stiffer than PMMA (12.7 +/- 1.8 GPa, 10.4 +/- 3.4 GPa, and 2.9 +/- 0.4 GPa, respectively). PMMA had greater yield strength than Wood's metal (62.9 +/- 8.7 MPa and 26.2 +/- 2.6 MPa). All materials exhibited size-dependent modulus values. The FE results indicated that filler materials, if not accounted for, could cause more than 9% variation in vertebral body stiffness. We conclude that Wood's metal is a superior moldable bonding material for biomechanical testing of whole bones, especially whole vertebrae, compared to the other candidate materials.     

金属纳米材料的生物化学制备及在生物医学领域的应用

近40年来,金属纳米材料发展迅猛,因其不同于宏观晶体的特殊性质,逐渐在各行业中起到了不可或缺的作用。当下人类面临资源、环境等日益严重的生态问题,因此金属纳米材料与生物学结合的绿色生态模式是大势所趋。本文重点综述了利用各种植物提取物、微生物以及蛋白质等生物材料作为还原剂,制备金属以及金属氧化物纳米材料的生物化学绿色合成方法。这些方法操作简单,制备的材料形貌尺寸不会产生太大变化。除此之外,生物材料的特定结构与金属纳米材料结合,通常会表现出协同或者新的理化和生理性能,以至于这些金属纳米材料在光热治疗及生物成像、抑菌及康复治愈和生物传感器及检测等生物医学领域产生了重大影响。金属纳米材料的生物化学制备会给未来纳米材料和生物学领域带来更多的交叉,会有更多跨学科工作者对其现存挑战来进行努力工作,并且在未来的医疗领域定会有金属纳米材料不可或缺的身影。     

Metal ions in biological catalysis: from enzyme databases to general principles

We analysed the roles and distribution of metal ions in enzymatic catalysis using available public databases and our new resource Metal-MACiE (). In Metal-MACiE, a database of metal-based reaction mechanisms, 116 entries covering 21% of the metal-dependent enzymes and 70% of the types of enzyme-catalysed chemical transformations are annotated according to metal function. We used Metal-MACiE to assess the functions performed by metals in biological catalysis and the relative frequencies of different metals in different roles, which can be related to their individual chemical properties and availability in the environment. The overall picture emerging from the overview of Metal-MACiE is that redox-inert metal ions are used in enzymes to stabilize negative charges and to activate substrates by virtue of their Lewis acid properties, whereas redox-active metal ions can be used both as Lewis acids and as redox centres. Magnesium and zinc are by far the most common ions of the first type, while calcium is relatively less used. Magnesium, however, is most often bound to phosphate groups of substrates and interacts with the enzyme only transiently, whereas the other metals are stably bound to the enzyme. The most common metal of the second type is iron, which is prevalent in the catalysis of redox reactions, followed by manganese, cobalt, molybdenum, copper and nickel. The control of the reactivity of redox-active metal ions may involve their association with organic cofactors to form stable units. This occurs sometimes for iron and nickel, and quite often for cobalt and molybdenum. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Spectroscopic characterization of the artificial Siderophore pyridinochelin

Siderophores play a very important role in the uptake process of iron by bacteria. Due to the so-called active transport the uptake of siderophores by bacteria is very specific, which makes the use of siderophores as effective shuttles for antibiotics in the treatment of infections and other diseases caused by bacteria highly attractive. In order to further investigate the transport and incorporation of siderophores into the bacteria cells, distinct molecular probes are needed. Especially artificial siderophores, that show a specific intrinsic fluorescence, are highly attractive for such monitoring purposes. A promising candidate of such a fluorescent artificial siderophore is bis-2,3-dihydroxybenzoyl-2,6-dimethylamino-pyridine (pyridinochelin, PY). The fluorescence properties of PY were investigated in different solvents and in the presence of different metal ions. It was found that PY in its free form shows a complex fluorescence behavior. In methanol a clear dual fluorescence is observed. In aqueous solution intermolecular interactions with water molecules are determining the intrinsic fluorescence. Upon complexation with metal ions (Me3+ = Eu3+, Tb3+, Al3+, Fe3+) the fluorescence characteristics changed. The fluorescence quantum yield of PY decreased upon addition of Me3+--except for Al3+, which showed no fluorescence quenching. The fluorescence decay of PY loaded with metal ions showed a nicely mono-exponential fluorescence decay, which was in contrast to PY in the absence of metal ions. This drastic change in the fluorescence properties of PY upon metal ion complexation makes PY highly attractive as a fluorescence probe for the investigation of siderophore action and siderophore-mediated transport processes.     

The effect of metal ions on the synthesis of extracellular enzymes by sporulating bacteria]

The action of metal ions which are present in nutritious medium on the synthesis of extracellular enzymes by sporulating bacteria is analysed. An important role of these ions in post-secretory modification of protein molecules and formation of functionally active molecules of enzyme is shown. The effect of metal ions on some cell envelope properties and extracellular enzyme secretion is under discussion.     

Physicochemical characterisation of the ubiquitous bracken fern as useful biomaterial for preconcentration of heavy metals

Batch experiments with dry bracken fern have been done to determine cadmium and lead sequestering capacity of this biomaterial. Biomass characterisation was done by infrared spectroscopy and potentiometric analysis. The effect of pH of the metal containing solution, contact time and initial metal concentration has been studied, together with the acid-base properties of the biomaterial. Results obtained have been analysed using mathematical and modelling techniques. Effect of pH on metal sequestration has been correlated with observed acid-base properties of the natural substrate. Kinetic data analysis provided relevant information about metal sequestration rate, showing important differences between lead and cadmium. Maximum uptake was found to be the same for both metals 0.410 mmol/g. This value was also clearly correlated to the number of acidic groups determined for this material which was found to be 0.432 mmol of acidic groups per gram of fern. Results obtained indicate that acidic groups are the functional groups responsible of the sequestration of metal ions and that bracken fern is a promising material for metal preconcentration.     

Marginal Magnesium Doping for High‐Performance Lithium Metal Batteries

Due to unparalleled theoretical capacity and operation voltage, metallic Li is considered as the most attractive candidate for lithium‐ion battery anodes. However, Li metal electrodes suffer from uncontrolled dendrite growth and consequent interfacial instability, which result in an unacceptable level of performance in cycling stability and safety. Herein, it is reported that a marginal amount (1.5 at%) of magnesium (Mg) doping alters the surface properties of Li metal foil drastically in such a way that upon Li plating, a highly dense Li whisker layer is induced, instead of sharp dendrites, with enhanced interfacial stability and cycling performance. The effect of Mg doping is explained in terms of increased surface energy, which facilitates plating of Li onto the main surface over the existing whiskers. The present study offers a useful guideline for Li metal batteries, as it largely resolves the longstanding shortcoming of Li metal electrodes without significantly sacrificing their main advantages.     

Metal ion binding properties of <Emphasis Type="Italic">Tricium aestivum</Emphasis> E<Subscript>c</Subscript>-1 metallothionein: evidence supporting two separate metal thiolate clusters

Metallothioneins are ubiquitous low molecular mass, cysteine-rich proteins with an extraordinary high metal ion content. In contrast to the situation for the vertebrate forms, information regarding the properties of members of the plant metallothionein family is still scarce. We present the first spectroscopic investigation aiming to elucidate the metal ion binding properties and metal thiolate cluster formation of the Tricium aestivum (common wheat) early cysteine-labeled plant metallothionein (E_c-1). For this, the protein was overexpressed recombinantly in Escherichia coli. Recombinant E_c-1 is able to bind a total of six divalent d ¹⁰ metal ions in a metal thiolate cluster arrangement. The pH stability of the zinc and cadmium clusters investigated is comparable to stabilities found for mammalian metallothioneins. Using cobalt(II) as a paramagnetic probe, we were able to show the onset of cluster formation taking place with the addition of a fourth metal ion equivalent to the apo protein. Limited proteolytic digestion experiments complemented with mass spectrometry and amino acid analysis provide clear evidence for the presence of two separate metal thiolate clusters. One cluster consists of four metal ions and is made up by a part of the protein containing 11 cysteine residues, comparable to the situation found in the mammalian counterparts. The second cluster features two metal ions coordinated by six cysteine residues. The occurrence of the latter cluster is unprecedented in the metallothionein superfamily so far. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. This article is dedicated to Prof. Bernhard Lippert on the occasion of his 60th birthday.     

Review of Some Interesting Surface Plasmon Resonance-enhanced Properties of Noble Metal Nanoparticles and Their Applications to Biosystems

Noble metal, especially gold (Au) and silver (Ag) nanoparticles exhibit unique and tunable optical properties on account of their surface plasmon resonance (SPR). In this review, we discuss the SPR-enhanced optical properties of noble metal nanoparticles, with an emphasis on the recent advances in the utility of these plasmonic properties in molecular-specific imaging and sensing, photo-diagnostics, and selective photothermal therapy. The strongly enhanced SPR scattering from Au nanoparticles makes them useful as bright optical tags for molecular-specific biological imaging and detection using simple dark-field optical microscopy. On the other hand, the SPR absorption of the nanoparticles has allowed their use in the selective laser photothermal therapy of cancer. We also discuss the sensitivity of the nanoparticle SPR frequency to the local medium dielectric constant, which has been successfully exploited for the optical sensing of chemical and biological analytes. Plasmon coupling between metal nanoparticle pairs is also discussed, which forms the basis for nanoparticle assembly-based biodiagnostics and the plasmon ruler for dynamic measurement of nanoscale distances in biological systems.     

Electronic coupling and photochemical stability of O,N bound mononuclear Ru(II) and Os(II) – Hydroquinone complexes

The synthesis, spectroscopic and electrochemical characterisation of a series of optically tuneable, ruthenium (II) and osmium (II) polypyridyl complexes, O,N coordinated to electroactive donor ligand, bis-2,5-(2-benzoxazolyl)-hydroquinone (bbhq) is described. The complexes exhibit a rich optical spectroscopy which can be controlled through the redox state of the metal and bbhq ligand. The influence of both the metal and counter-ligand identity on the optical properties of these hydroquinone-based complexes is addressed.Regardless of the identity of metal or counter-ligand, it is the bbhq which is the site of the most facile oxidation and hydroquinone, semiquinone (bbsq) and quinone (bbq) can be generated electrochemically. In each instance, the semiquinone is strongly stabilised with respect to disproportionation, reflected in large stability constants for this moiety. The levels of orbital mixing between metal and ligand are discussed on the basis of the optical properties of the complex and the nature of the metal and counter-ligand. In addition, we address, for the first time, the effect of metal and counter-ligand on the photostability, of Ru(II) and Os(II) hydroquinone bound complexes. We find that like other ruthenium (II) complexes containing strong σ-bonding ligands, the M(bpy)₂ containing complexes are photostable, but the [Ru(biq)₂(bbhq)]⁺ complex is relatively photolabile.     

Radiative decay engineering 5: metal-enhanced fluorescence and plasmon emission

Metallic particles and surfaces display diverse and complex optical properties. Examples include the intense colors of noble metal colloids, surface plasmon resonance absorption by thin metal films, and quenching of excited fluorophores near the metal surfaces. Recently, the interactions of fluorophores with metallic particles and surfaces (metals) have been used to obtain increased fluorescence intensities, to develop assays based on fluorescence quenching by gold colloids, and to obtain directional radiation from fluorophores near thin metal films. For metal-enhanced fluorescence it is difficult to predict whether a particular metal structure, such as a colloid, fractal, or continuous surface, will quench or enhance fluorescence. In the present report we suggest how the effects of metals on fluorescence can be explained using a simple concept, based on radiating plasmons (RPs). The underlying physics may be complex but the concept is simple to understand. According to the RP model, the emission or quenching of a fluorophore near the metal can be predicted from the optical properties of the metal structures as calculated from electrodynamics, Mie theory, and/or Maxwell's equations. For example, according to Mie theory and the size and shape of the particle, the extinction of metal colloids can be due to either absorption or scattering. Incident energy is dissipated by absorption. Far-field radiation is created by scattering. Based on our model small colloids are expected to quench fluorescence because absorption is dominant over scattering. Larger colloids are expected to enhance fluorescence because the scattering component is dominant over absorption. The ability of a metal's surface to absorb or reflect light is due to wavenumber matching requirements at the metal-sample interface. Wavenumber matching considerations can also be used to predict whether fluorophores at a given distance from a continuous planar surface will be emitted or quenched. These considerations suggest that the so called "lossy surface waves" which quench fluorescence are due to induced electron oscillations which cannot radiate to the far-field because wavevector matching is not possible. We suggest that the energy from the fluorophores thought to be lost by lossy surface waves can be recovered as emission by adjustment of the sample to allow wavevector matching. The RP model provides a rational approach for designing fluorophore-metal configurations with the desired emissive properties and a basis for nanophotonic fluorophore technology.     

Binding of metal ions to apoalkaline phosphatase from E. Coli: Effect of ionic radius

Binding of metal ions to $\text{E. Coli}$ apoalkaline phosphatase causes 1) chromophoric changes in tyrosine absorption, 2) changes in enzymatic activity and 3) the release of protons from the enzyme. Investigation of these effects for a selection of metal ions from the Group 11A, Group 11B and transition series revealed that only those ions having crystal ionic radii in the range of 0.72 – 0.99A are able to produce changes in these three properties. The hydrated ionic radii, which are in the range of 4.0 – 4.5A for the ions examined do not correlate well with the ability of the ion to affect the three properties studied here. The size requirement therefore would seem not to apply to the initial binding step which undoubtedly involves the hydrated ion. Rather, the size requirement reflects the size range of a binding site generated by the folding of the protein around the metal ion with concomitant displacement of water molecules from the coordination sphere of the metal.     

Does the accumulation of trace metals in crustaceans affect their ecology—the amphipod example?

Crustaceans, like all aquatic invertebrates, take up and accumulate metals from a wide range of sources and the trace metal concentrations within their tissues and bodies show great variability. Trace metal uptake in crustaceans occurs from the water and food, either of which may be affected by the physico-chemical properties of the sediment. Accumulated metal concentrations in amphipods are contrasted with those of other crustaceans and examples are given to show how external and internal factors affect bioaccumulation. One of the major pathways for the uptake of trace metals is from solution directly through permeable surfaces including the gills. Changes in salinity and oxygen tension can modify the uptake characteristics from solution particularly in the case of interstitial water within sediments. Infaunal amphipods have direct contact with the sediment and the bioavailabilities of trace metals depend on the strength of the metal binding which is determined by a combination of properties including grain size, organic content, the presence of metals such as lead and iron as well as other ambient environmental conditions. Metal concentrations within amphipod bodies reflect the bioavailabilities of trace metals in their habitat. Body size is one of the major factors contributing to individual variability in trace metal concentrations within species. For some amphipod species, there are differences in trace metal accumulation with gender, breeding and developmental stage. In amphipods, accumulated body metal concentrations are the best biomarkers for environmental metal availabilities. Metal accumulation affects the ecology of crustaceans as a consequence of the energy costs associated with excreting and/or detoxifying the incoming metals. If the costs are significant, then this may result in reduced growth and reproduction. The effects of accumulated metals on communities have yet to be determined. Accumulated metals in crustacean prey species may be transferred along the food chain, but biomagnification in fish appears unlikely. One of the main ecological challenges is the need to link molecular biomarkers with ecologically relevant life history characteristics including growth, survival, reproduction and recruitment.