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Protein Science : a Publication of the... Sep 2017Protein crystallization is one of the major bottlenecks in protein structure elucidation with new strategies being constantly developed to improve the chances of... (Review)
Review
Protein crystallization is one of the major bottlenecks in protein structure elucidation with new strategies being constantly developed to improve the chances of crystallization. Generally, well-ordered epitopes possessing complementary surface and capable of producing stable inter-protein interactions generate a regular three-dimensional arrangement of protein molecules which eventually results in a crystal lattice. Metals, when used for crystallization, with their various coordination numbers and geometries, can generate such epitopes mediating protein oligomerization and/or establish crystal contacts. Some examples of metal-mediated oligomerization and crystallization together with our experience on metal-mediated crystallization of a putative rRNA methyltransferase from Sinorhizobium meliloti are presented. Analysis of crystal structures from protein data bank (PDB) using a non-redundant data set with a 90% identity cutoff, reveals that around 67% of proteins contain at least one metal ion, with ∼14% containing combination of metal ions. Interestingly, metal containing conditions in most commercially available and popular crystallization kits generally contain only a single metal ion, with combinations of metals only in a very few conditions. Based on the results presented in this review, it appears that the crystallization screens need expansion with systematic screening of metal ions that could be crucial for stabilizing the protein structure or for establishing crystal contact and thereby aiding protein crystallization.
Topics: Crystallization; Crystallography, X-Ray; Metals; Models, Molecular; Proteins
PubMed: 28643473
DOI: 10.1002/pro.3214 -
Chemosphere Jul 2023Water pollution has jeopardized human health, and a safe supply of drinking water has been recognized as a worldwide issue. The increase in the accumulation of heavy... (Review)
Review
Water pollution has jeopardized human health, and a safe supply of drinking water has been recognized as a worldwide issue. The increase in the accumulation of heavy metals in water from different sources has led to the search for efficient and environmentally friendly treatment methods and materials for their removal. Natural zeolites are promising materials for removing heavy metals from different sources contaminating the water. It is important to know the structure, chemistry, and performance of the removal of heavy metals from water, of the natural zeolites to design water treatment processes. This review focuses on critical analyses of the application of distinct natural zeolites for the adsorption of heavy metals from water, specifically, arsenic (As(III), As(V)), cadmium (Cd(II)), chromium (Cr(III), Cr(VI)), lead (Pb(II)), mercury(Hg(II)) and nickel (Ni(II)). The reported results of heavy-metal removal by natural zeolites are summarized, and the chemical modification of natural zeolites by acid/base/salt reagent, surfactants, and metallic reagents has been analyzed, compared, and described. Furthermore, the adsorption/desorption capacity, systems, operating parameters, isotherms, and kinetics for natural zeolites were described and compared. According to the analysis, clinoptilolite is the most applied natural zeolite to remove heavy metals. It is effective in removing As, Cd, Cr, Pb, Hg, and Ni. Additionally, an interesting fact is a variation between the natural zeolites from different geological origins regarding the sorption properties and capacities for heavy metals suggesting that natural zeolites from different regions of the world are unique.
Topics: Humans; Cadmium; Zeolites; Adsorption; Lead; Water Pollutants, Chemical; Metals, Heavy; Mercury; Kinetics
PubMed: 36972873
DOI: 10.1016/j.chemosphere.2023.138508 -
Environmental Research Jul 2019Electronic cigarettes (E-cigarettes) generate aerosol containing metal contaminants. Our goals were to quantify aerosol metal concentrations and to compare the effects...
BACKGROUND
Electronic cigarettes (E-cigarettes) generate aerosol containing metal contaminants. Our goals were to quantify aerosol metal concentrations and to compare the effects of power setting and device type (closed-system vs. open-system) on metal release.
METHODS
Aerosol samples were collected from two closed-system devices (a cigalike and pod) and two open-system devices (mods). Each open-system device was operated at three different power settings to examine the effect of device power on metal release. Concentrations of 14 metals in e-cigarette aerosol collected via droplet deposition were measured using inductively coupled plasma mass spectroscopy. Aerosol metal concentrations were reported as mass fractions (μg/kg) in the e-liquid.
RESULTS
For open-system device 1 (OD1), median arsenic (As), chromium (Cr), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), antimony (Sb), tin (Sn), and zinc (Zn) concentrations increased 14, 54, 17, 30, 41, 96, 14, 81, 631, and 7-fold when the device power was increased from low (20 W) to intermediate (40 W) setting. When the power was further increased from intermediate (40 W) to high (80 W) setting, concentrations of As, Cr, Cu, Mn, Ni, and Sb did not change significantly. For open-system device 2 (OD2), Cr and Mn concentrations increased significantly when device power was increased from low (40 W) to intermediate (120 W) setting, and then decreased significantly when power was further increased from intermediate (120 W) to high (200 W) setting. Among the four devices, aerosol metal concentrations were higher for the open-system than the closed-system devices, except for aluminum (Al) and uranium (U). For Cr, median (interquartile range) concentrations (μg/kg) from the open-system devices were 2.51 (1.55, 4.23) and 15.6 (7.88, 54.5) vs. 0.39 (0.05, 0.72) and 0.41 (0.34, 0.57) for the closed-system devices. For Ni, concentrations (μg/kg) from the open-system devices were 793 (508, 1169) and 2148 (851, 3397) vs. 1.32 (0.39, 3.35) and 11.9 (10.7, 22.7) from the closed-system devices. Inhalation of 0% and 100% of samples from OD1, 7.4% and 88.9% from OD2 by typical e-cigarette users would exceed chronic minimum risk levels (MRL) of Mn and Ni, respectively. No MRL exceedance was predicted for the closed-system devices. A large fraction of users of OD1 (100%) and OD2 (77.8%) would be exposed to Ni levels higher than those from reference tobacco cigarette 3R4F.
CONCLUSIONS
Our findings suggest that power setting and device type affect metal release from devices to aerosol which would subsequently be inhaled by users. Metal concentrations from open-system devices first increased with device power, and then leveled off for most metals. Open-system devices generate aerosol with higher metal concentrations than closed-system devices. These findings inform tobacco regulatory science, policy makers and health professionals on potential metal health risks associated with e-cigarette use, design and manufacturing.
Topics: Aerosols; Chromium; Electronic Nicotine Delivery Systems; Environmental Monitoring; Metals; Metals, Heavy; Nickel
PubMed: 31071493
DOI: 10.1016/j.envres.2019.04.003 -
MAbs 2023Transition metals can be introduced in therapeutic protein drugs at various steps of the manufacturing process (e.g. manufacturing raw materials, formulation, storage),...
Transition metals can be introduced in therapeutic protein drugs at various steps of the manufacturing process (e.g. manufacturing raw materials, formulation, storage), and can cause a variety of modifications on the protein. These modifications can potentially influence the efficacy, safety, and stability of the therapeutic protein, especially if critical quality attributes (CQAs) are affected. Therefore, it is meaningful to understand the interactions between proteins and metals that can occur during the manufacturing process, formulation, and storage of biotherapeutics. Here, we describe a novel strategy to differentiate between ultra-trace levels of transition metals (cobalt, chromium, copper, iron, and nickel) interacting with therapeutic proteins and free metal in solution in the drug formulation using size exclusion chromatography coupled to inductively coupled plasma mass spectrometry (SEC-ICP-MS). Two monoclonal antibodies (mAbs) were coformulated and stored up to nine days in a scaled down model to mimic metal exposure from manufacturing tanks. The samples containing the mAbs were first analyzed by ICP-MS for bulk metal analysis, then studied using SEC-ICP-MS to measure the extent of metal-protein interactions. The SEC separation was used to differentiate metal associated with the mAbs from free metal in solution. Relative quantitation of metal-protein interaction was then calculated using the relative peak areas of protein-associated metal to free metal in solution and weighting it to the total metal concentration in the mixture as measured by bulk metal analysis by ICP-MS. The SEC-ICP-MS method offers an informative means of measuring metal-protein interactions during drug development.
Topics: Antibodies, Monoclonal; Mass Spectrometry; Metals; Copper; Iron
PubMed: 37032437
DOI: 10.1080/19420862.2023.2199466 -
Journal of Fluorescence Jul 2004We report recent achievements in metal-enhanced fluorescence from our laboratory. Several fluorophore systems have been studied on metal particle-coated surfaces and in... (Review)
Review
We report recent achievements in metal-enhanced fluorescence from our laboratory. Several fluorophore systems have been studied on metal particle-coated surfaces and in colloid suspensions. In particular, we describe a distance dependent enhancement on silver island films (SIFs), release of self-quenching of fluorescence near silver particles, and the applications of fluorescence enhancement near metalized surfaces to bioassays. We discuss a number of methods for various shaped silver particle deposition on surfaces.
Topics: Algorithms; Avidin; Biotin; Colloids; DNA; Electrochemistry; Fluorescence; Fluorescence Resonance Energy Transfer; Fluorescent Dyes; Metals; Microscopy, Atomic Force; Nanostructures; Nanotechnology; Nucleic Acid Hybridization; Photochemistry; Serum Albumin, Bovine; Silver; Spectrometry, Fluorescence; Surface Properties
PubMed: 15617385
DOI: 10.1023/b:jofl.0000031824.48401.5c -
FEMS Immunology and Medical Microbiology Feb 2005Metal ions are integral part of some viral proteins and play an important role in their survival and pathogenesis. Zinc, magnesium and copper are the commonest metal ion... (Review)
Review
Metal ions are integral part of some viral proteins and play an important role in their survival and pathogenesis. Zinc, magnesium and copper are the commonest metal ion that binds with viral proteins. Metal ions participate in maturation of genomic RNA, activation and catalytic mechanisms, reverse transcription, initial integration process and protection of newly synthesized DNA, inhibition of proton translocation (M2 protein), minus- and plus-strand transfer, enhance nucleic acid annealing, activation of transcription, integration of viral DNA into specific sites and act as a chaperone of nucleic acid. Metal ions are also required for nucleocapsid protein-transactivation response (TAR)-RNA interactions. In certain situations more than one metal ion is required e.g. RNA cleavage by RNase H. This review underscores the importance of metal ions in the survival and pathogenesis of a large group of viruses and studies on structural basis for metal binding should prove useful in the early design and development of viral inhibitors.
Topics: Coenzymes; Ions; Metalloproteins; Metals; Protein Binding; Viral Proteins; Virus Physiological Phenomena
PubMed: 15681139
DOI: 10.1016/j.femsim.2004.11.004 -
Molecules (Basel, Switzerland) Mar 2021Bacterial infections of medical devices present severe problems connected with long-term antibiotic treatment, implant failure, and high hospital costs. Therefore, there... (Review)
Review
Bacterial infections of medical devices present severe problems connected with long-term antibiotic treatment, implant failure, and high hospital costs. Therefore, there are enormous demands for innovative techniques which would improve the surface properties of implantable materials. Plasma technologies present one of the compelling ways to improve metal's antibacterial activity; plasma treatment can significantly alter metal surfaces' physicochemical properties, such as surface chemistry, roughness, wettability, surface charge, and crystallinity, which all play an important role in the biological response of medical materials. Herein, the most common plasma treatment techniques like plasma spraying, plasma immersion ion implantation, plasma vapor deposition, and plasma electrolytic oxidation as well as novel approaches based on gaseous plasma treatment of surfaces are gathered and presented. The latest results of different surface modification approaches and their influence on metals' antibacterial surface properties are presented and critically discussed. The mechanisms involved in bactericidal effects of plasma-treated surfaces are discussed and novel results of surface modification of metal materials by highly reactive oxygen plasma are presented.
Topics: Anti-Bacterial Agents; Bacterial Adhesion; Biofilms; Humans; Metals; Nanostructures; Oxidation-Reduction; Plasma Gases; Pressure; Prostheses and Implants; Prosthesis-Related Infections; Surface Properties; Wettability
PubMed: 33808010
DOI: 10.3390/molecules26051418 -
Nature Ecology & Evolution May 2023Evolution creates functional diversity of proteins, the essential building blocks of all biological systems. However, studies of natural proteins sampled across the tree...
Evolution creates functional diversity of proteins, the essential building blocks of all biological systems. However, studies of natural proteins sampled across the tree of life and evaluated in a single experimental system are lacking. Almost half of enzymes require metals, and metalloproteins tend to optimally utilize the physicochemical properties of a specific metal co-factor. Life must adapt to changes in metal bioavailability, including those during the transition from anoxic to oxic Earth or pathogens' exposure to nutritional immunity. These changes can challenge the ability of metalloenzymes to maintain activity, presumptively driving their evolution. Here we studied metal-preference evolution within the natural diversity of the iron/manganese superoxide dismutase (SodFM) family of reactive oxygen species scavengers. We identified and experimentally verified residues with conserved roles in determining metal preference that, when combined with an understanding of the protein's evolutionary history, improved prediction of metal utilization across the five SodFM subfamilies defined herein. By combining phylogenetics, biochemistry and structural biology, we demonstrate that SodFM metal utilization can be evolutionarily fine tuned by sliding along a scale between perfect manganese and iron specificities. Over the history of life, SodFM metal preference has been modulated multiple independent times within different evolutionary and ecological contexts, and can be changed within short evolutionary timeframes.
Topics: Metals; Iron; Metalloproteins
PubMed: 37037909
DOI: 10.1038/s41559-023-02012-0 -
Nature Communications Mar 2023High-entropy multimetallic nanopatterns with controlled morphology, composition and uniformity hold great potential for developing nanoelectronics, nanophotonics and...
High-entropy multimetallic nanopatterns with controlled morphology, composition and uniformity hold great potential for developing nanoelectronics, nanophotonics and catalysis. Nevertheless, the lack of general methods for patterning multiple metals poses a limit. Here, we develop a DNA origami-based metallization reaction system to prescribe multimetallic nanopatterns with peroxidase-like activities. We find that strong coordination between metal elements and DNA bases enables the accumulation of metal ions on protruding clustered DNA (pcDNA) that are prescribed on DNA origami. As a result of the condensation of pcDNA, these sites can serve as nucleation site for metal plating. We have synthesized multimetallic nanopatterns composed of up to five metal elements (Co, Pd, Pt, Ag and Ni), and obtained insights on elemental uniformity control at the nanoscale. This method provides an alternative pathway to construct a library of multimetallic nanopatterns.
Topics: Alloys; Entropy; Metal Nanoparticles; Metals; DNA
PubMed: 36990981
DOI: 10.1038/s41467-023-37333-y -
Journal of Environmental Sciences... Feb 2024Heavy metals from mica waste not only deteriorate the soil quality but also results in the uptake of metals in the crop. The present investigation was conducted to...
Heavy metals from mica waste not only deteriorate the soil quality but also results in the uptake of metals in the crop. The present investigation was conducted to evaluate the effects of different fractions of metals on the uptake in rice, soil microbial and biochemical properties in mica waste-contaminated soils of Jharkhand, India. From each active mine, soil samples were randomly collected at distances of < 50 m (zone 1), 50-100 m (zone 2), and >100 m (zone 3). Sequential metal extraction was used to determine the fractions of different metals (nickel (Ni), cadmium (Cd), chromium (Cr) and lead (Pb)) including water-soluble (Ws) and exchangeable metals (Ex), carbonate-bound metals (CBD), Fe/Mn oxide (OXD) bound metals, organically bound metals (ORG), and residues (RS). The Ni, Cr, Cd and Pb in rice grain were 0.83±0.41, 0.41±0.19, 0.21±0.14 and 0.17±0.08 mg/kg respectively. From the variable importance plot of the random forest (RF) algorithm, the Ws fraction of Ni, Cr and Cd and Ex fraction of Pb was the most important predictor for rice grain metal content. Further, the partial dependence plots (PDP) give us an insight into the role of the two most important metal fractions on rice grain metal content. The microbial and enzyme activity was significantly and negatively correlated with Ws and Ex metal fractions, indicating that water-soluble and exchangeable fractions exert a strong inhibitory effect on the soil microbiological parameters and enzyme activities.
Topics: Cadmium; Oryza; Lead; Metals, Heavy; Nickel; Chromium; Soil; Water; Soil Pollutants
PubMed: 37923441
DOI: 10.1016/j.jes.2022.10.038