Uranyl Binding to Proteins and Structural-Functional Impacts

Extraction of uranyl from spent nuclear fuel wastewater via complexation-a local vibrational mode study

CONTEXT

The efficient extraction of uranyl from spent nuclear fuel wastewater for subsequent reprocessing and reuse is an essential effort toward minimization of long-lived radioactive waste. N-substituted amides and Schiff base ligands are propitious candidates, where extraction occurs via complexation with the uranyl moiety. In this study, we extensively probed chemical bonding in various uranyl complexes, utilizing the local vibrational modes theory alongside QTAIM and NBO analyses. We focused on (i) the assessment of the equatorial O-U and N-U bonding, including the question of chelation, and (ii) how the strength of the axial U = O bonds of the uranyl moiety changes upon complexation. Our results reveal that the strength of the equatorial uranium-ligand interactions correlates with their covalent character and with charge donation from O and N lone pairs into the vacant uranium orbitals. We also found an inverse relationship between the covalent character of the equatorial ligand bonds and the strength of the axial uranium-oxygen bond. In summary, our study provides valuable data for a strategic modulation of N-substituted amide and Schiff base ligands towards the maximization of uranyl extraction.

METHOD

Quantum chemistry calculations were performed under the PBE0 level of theory, paired with the relativistic NESCau Hamiltonian, currently implemented in Cologne2020 (interfaced with Gaussian16). Wave functions were expanded in the cc-pwCVTZ-X2C basis set for uranium and Dunning's cc-pVTZ for the remaining atoms. For the bonding properties, we utilized the package LModeA in the local modes analyses, AIMALL in the QTAIM calculations, and NBO 7.0 for the NBO analyses.

Uranium removal in groundwater by Priestia sp. isolated from uranium-contaminated mining soil

Priestia sp. WW1 was isolated from a uranium-contaminated mining soil and identified. The uranium removal characteristics and mechanism of Priestia sp. WW1 were investigated. The results showed that the removal efficiency of uranium decreased with the increase of initial uranium concentration. When the uranium initial concentration was 5 mg/L, the uranium removal efficiency achieved 92.1%. The increase of temperature could promote the uranium removal. Carbon source could affect the removal rate of uranium, which was the fastest when the methanol was used as carbon source. The solution pH had significant effect on the uranium removal efficiency, which reached the maximum under solution pH 5.0. The experimental results and FTIR as well as XPS demonstrated that Priestia sp. WW1 could remove uranium via both adsorption and reduction. The common chloride ions, sulfate ions, Mn(II) and Cu(II) enhanced the uranium removal, while Fe(III) depressed the uranium removal. The Priestia sp. WW1 could effectively remove the uranium in the actual mining groundwater, and the increase of initial biomass could improve the removal efficiency of uranium in the actual mining groundwater. This study provided a promising bacterium for uranium remediation in the groundwater.

Electron Microscopy of Cryptococcus neoformans: Processing Challenges to Avoid Artifacts

This chapter describes methodological details for preparing specimens of Cryptococcus neoformans (although it can be applied to any species of the genus) and their subsequent analysis by scanning and transmission electron microscopy. Adaptations to conventional protocols for better preservation of the sample, as well as to avoid artifacts, are presented. The protocols may be used to examine both the surface ultrastructure and the interior of this pathogenic fungus in detail.

Plant polyphenol surfactant construction with strong surface activity and chelation properties as efficient decontamination of UO22+ on cotton fabric

Chemically synthesized surfactants have promising applications in the treatment of uranium, however, their hazardous environmental effects, non-biodegradability, and numerous drawbacks prevent them from being widely used in practice. Herein, we successfully synthesized a green chelating and foaming integrated surfactant (BTBS) by Mannich reaction and acylation of bayberry tannin for the effective removal of UO22+ from aqueous environments or solid surfaces. The as-prepared surfactant was systematically characterized by FT-IR, showing that the hydrophobic groups were successfully grafted onto tannin. The modified material showed better foaming and emulsifying properties, which proved this method could improve the amphiphilicity of tannin. Moreover, for the first time, a foam fractionation method in conjunction with a tannin-based surfactant was applied for UO22+ removal from water. This surfactant was used as a co-surfactant and could readily remove 90 % of UO22+ (20 mg L-1) from water. The removal of UO22+ could be completed in a short time (30 min), and the maximum adsorption capacity was determined as 175.9 mg g-1. This surfactant can also be used for efficient decontamination of uranium-contaminated cotton cloth with a high removal rate of 94.55 %. In addition, the mechanism studies show that the adsorption of BTBS for UO22+ can be mainly attributed to a chelating mechanism between UO22+ and the adjacent phenolic hydroxyls. The novel biomass-derived BTBS with advantages such as high capture capacity, environmental friendliness, and cost-effectiveness suggests that it plays an important role in the remediation of radionuclide pollution.

In Silico Simulations Reveal Molecular Mechanism of Uranyl Ion Toxicity towards DNA-Binding Domain of PARP-1 Protein

The molecular toxicity of the uranyl ion (UO22+) in living cells is primarily determined by its high affinity to both native and potential metal-binding sites that commonly occur in the structure of biomolecules. Recent advances in computational and experimental research have shed light on the structural properties and functional impacts of uranyl binding to proteins, organic ligands, nucleic acids, and their complexes. In the present work, we report the results of the computational investigation of the uranyl-mediated loss of DNA-binding activity of PARP-1, a eukaryotic enzyme that participates in DNA repair, cell differentiation, and the induction of inflammation. The latest experimental studies have shown that the uranyl ion directly interacts with its DNA-binding subdomains, zinc fingers Zn1 and Zn2, and alters their tertiary structure. Here, we propose an atomistic mechanism underlying this process and compute the free energy change along the suggested pathway. Our Quantum Mechanics/Molecular Mechanics (QM/MM) simulations of the Zn2-UO22+ complex indicate that the uranyl ion replaces zinc in its native binding site. However, the resulting state is destroyed due to the spontaneous internal hydrolysis of the U-Cys162 coordination bond. Despite the enthalpy of hydrolysis being +2.8 kcal/mol, the overall reaction free energy change is -0.6 kcal/mol, which is attributed to the loss of domain's native tertiary structure originally maintained by a zinc ion. The subsequent reorganization of the binding site includes the association of the uranyl ion with the Glu190/Asp191 acidic cluster and significant perturbations in the domain's tertiary structure driven by a further decrease in the free energy by 6.8 kcal/mol. The disruption of the DNA-binding interface revealed in our study is consistent with previous experimental findings and explains the loss of PARP-like zinc fingers' affinity for nucleic acids.

High-efficiency uranium extraction from seawater by low-cost natural protein hydrogel

Utilization of uranium resource in seawater are highly possible to meet the growth demands for the sustainable development of nuclear energy industry. Bio-adsorbents exhibit high performance in terms of adsorption selectivity, equilibrium speed, and environmental friendliness, while the high fabrication cost hinders their practical application. In this study, a low-cost soy protein isolate (SPI) is used to fabricate adsorbent named SPI hydrogel for uranium extraction. This is the first report on applying bio-adsorbents derived from low-cost natural proteins for uranium extraction. The SPI hydrogel showed high uranium adsorption capacity of 53.94 mg g^-1 in simulated nuclear wastewater and 5.29 mg g^-1 is achieved in natural seawater, which is higher than all currently available adsorbents based on non-modified natural biomolecules. The amino and oxygen-containing groups are identified as the functional groups for uranyl binding by providing four oxygen and two nitrogen atoms to form equatorial coordination with uranyl, which guarantees the high binding selectivity and affinity to uranyl ions. The low cost for accessing the raw material together with the environmental friendliness, high salt tolerance, high uranium adsorption ability, and high selectivity to uranium, make SPI hydrogel a promising adsorbent for uranium extraction from seawater and nuclear wastewater.

The plasma membrane-associated cation-binding protein PCaP1 of Arabidopsis thaliana is a uranyl-binding protein

Uranium (U) is a naturally-occurring radionuclide that is toxic to living organisms. Given that proteins are primary targets of U(VI), their identification is an essential step towards understanding the mechanisms of radionuclide toxicity, and possibly detoxification. Here, we implemented a chromatographic strategy including immobilized metal affinity chromatography to trap protein targets of uranyl in Arabidopsis thaliana. This procedure allowed the identification of 38 uranyl-binding proteins (UraBPs) from root and shoot extracts. Among them, UraBP25, previously identified as plasma membrane-associated cation-binding protein 1 (PCaP1), was further characterized as a protein interacting in vitro with U(VI) and other metals using spectroscopic and structural approaches, and in planta through analyses of the fate of U(VI) in Arabidopsis lines with altered PCaP1 gene expression. Our results showed that recombinant PCaP1 binds U(VI) in vitro with affinity in the nM range, as well as Cu(II) and Fe(III) in high proportions, and that Ca(II) competes with U(VI) for binding. U(VI) induces PCaP1 oligomerization through binding at the monomer interface, at both the N-terminal structured domain and the C-terminal flexible region. Finally, U(VI) translocation in Arabidopsis shoots was affected in pcap1 null-mutant, suggesting a role for this protein in ion trafficking in planta.

Uranium extraction from seawater: material design, emerging technologies and marine engineering

Uranium extraction from seawater (UES), a potential approach to securing the long-term uranium supply and sustainability of nuclear energy, has experienced significant progress in the past decade. Promising adsorbents with record-high capacities have been developed by diverse innovative synthetic strategies, and scale-up marine field tests have been put forward by several countries. However, significant challenges remain in terms of the adsorbents' properties in complex marine environments, deployment methods, and the economic viability of current UES systems. This review presents an up-to-date overview of the latest advancements in the UES field, highlighting new insights into the mechanistic basis of UES and the methodologies towards the function-oriented development of uranium adsorbents with high adsorption capacity, selectivity, biofouling resistance, and durability. A distinctive emphasis is placed on emerging electrochemical and photochemical strategies that have been employed to develop efficient UES systems. The most recent achievements in marine tests by the major countries are summarized. Challenges and perspectives related to the fundamental, technical, and engineering aspects of UES are discussed. This review is envisaged to inspire innovative ideas and bring technical solutions towards the development of technically and economically viable UES systems.

Health Effects of Particulate Uranium Exposure

Uranium contamination has become a nonnegligible global health problem. Inhalation of particulate uranium is one of the predominant routes of occupational and environmental exposure. Uranium particle is a complex two-phase flow of matter that is both particulate and flowable. This particular physicochemical property may alter its biological activity. Epidemiological studies from occupationally exposed populations in the uranium industry have concluded that there is a possible association between lung cancer risk and uranium exposure, while the evidence for the risk of other tumors is not sufficient. The toxicological effects of particulate uranium exposure to animals have been shown in laboratory tests to focus on respiratory and central nervous system damage. Fibrosis and tumors can occur in the lung tissue of the respiratory tract. Uranium particles can also induce a concentration-dependent increase in cytotoxicity, targeting mitochondria. The understanding of the health risks and potential toxicological mechanisms of particulate uranium contamination is still at a preliminary stage. The diversity of particle parameters has limited the in-depth exploration. This review summarizes the current evidence on the toxicology of particulate uranium and highlights the knowledge gaps and research prospects.

Assessment of U and As in groundwater of India: A meta-analysis

More than 2.5 billion people depend upon groundwater worldwide for drinking, and giving quality water has become one of the great apprehensions of human culture. The contamination of Uranium (U) and Arsenic (As) in the groundwater of India is gaining global attention. The current review provides state-of-the-art groundwater contamination with U and As in different zones of India based on geology and soil texture. The average concentration of U in different zones of India was in the order: West Zone (41.07 μg/L) > North Zone (37.7 μg/L) > South Zone (13.5 μg/L)> Central Zone (7.4 μg/L) > East Zone (5.7 μg/L) >Southeast Zone (2.4 μg/L). The average concentration of As in groundwater of India is in the order: South Zone (369.7 μg/L)>Central Zone (260.4 μg/L)>North Zone (67.7 μg/L)>East Zone (60.3 μg/L)>North-east zone (9.78 μg/L)>West zone (4.14 μg/L). The highest concentration of U and As were found in quaternary sediments, but U in clay skeletal and As in loamy skeletal. Results of health risk assessment showed that the average health quotient of U in groundwater for children and adults was less than unity. In contrast, it was greater than unity for As posing a harmful impact on human health. This review provides the baseline data regarding the U and As contamination status in groundwater of India, and appropriate, effective control measures need to be taken to control this problem.

Actinide Decorporation: A Review on Chelation Chemistry and Nanocarriers for Pulmonary Administration

Chelation is considered the best method for detoxification by promoting excretion of actinides (Am, Np, Pu, Th, U) from the human body after internal contamination. Chemical agents that possess carboxylic acid or hydroxypyridinonate groups play a vital role in actinide decorporation. In this review article, we provide considerable background details on the chelation chemistry of actinides with an aim to formulate better decorporation agents. Nanocarriers for pulmonary delivery represent an exciting prospect in the development of novel therapies for actinide decorporation that both reduce toxic side effects of the agent and improve its retention in the body. Recent studies have demonstrated the benefits of using a nebulizer or an inhaler to administer chelating agents for the decorporation of actinides. Effective chelation therapy with large groups of internally contaminated people can be a challenge unless both the agent and the nanocarrier are readily available from strategic national stockpiles for radiological or nuclear emergencies. Sunflower lecithin is particularly adept at alleviating the burden of administration when used to form liposomes as a nanocarrier for pulmonary delivery of diethylenetriamine-pentaacetic acid (DTPA) or hydroxypyridinone (HOPO). Better physiologically-based pharmacokinetic models must be developed for each agent in order to minimize the frequency of multiple doses that can overload the emergency response operations.

Uranium chelating ability of decorporation agents in serum evaluated by X-ray absorption spectroscopy

Internal exposure to actinides such as uranium and plutonium has been reduced using chelating agents for decorporation because of their potential to induce both radiological and chemical toxicities. This study measures uranium chemical forms in serum in the presence and absence of chelating agents based on X-ray absorption spectroscopy (XAS). The chelating agents used were 1-hydroxyethane 1,1-bisphosphonate (EHBP), inositol hexaphosphate (IP6), deferoxamine B (DFO), and diethylenetriaminepentaacetate (DTPA). Percentages of uranium-chelating agents and uranium-bioligands (bioligands: inorganic and organic ligands coordinating with uranium) dissolving in the serum were successfully evaluated based on principal component analysis of XAS spectra. The main ligands forming complexes with uranium in the serum were estimated as follows: IP6 > EHBP > bioligands > DFO ≫ DTPA when the concentration ratio of the chelating agent to uranium was 10. Measurements of uranium chemical forms and their concentrations in the serum would be useful for the appropriate treatment using chelating agents for the decorporation of uranium.

Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria

Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO₂²⁺ and Fe³⁺. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.

Hydrophobic core formation and secondary structure elements in uranyl(VI)-binding peptides

Cyclic peptides as well as a modified EF-hand motif of calmodulin have been newly designed to achieve high affinity towards uranyl(VI). Cyclic peptides may be engineered to bind uranyl(VI) to its backbone under acidic conditions, which may enhance its selectivity. For the modified EF-hand motif of calmodulin, strong electrostatic interactions between uranyl(VI) and negatively charged side chains play an important role in achieving high affinity; however, it is also essential to have a secondary structure element and formation of hydrophobic cores in the metal-bound state of the peptide.

Graphene-based materials for the adsorptive removal of uranium in aqueous solutions

Ground water contamination by radioactive elements has become a critical issue that can pose significant threats to human health. Adsorption is the most promising approach for the removal of radioactive elements owing to its simplicity, effectiveness, and easy operation. Among the plethora of functional adsorbents, graphene oxide and its derivatives are recognized for their excellent potential as adsorbent with the unique 2D structure, high surface area, and intercalated functional groups. To learn more about their practical applicability, the procedures involved in their preparation and functionalization are described with the microscopic removal mechanism by GO functionalities across varying solution pH. The performance of these adsorbents is assessed further in terms of the basic performance metrics such as partition coefficient. Overall, this article is expected to provide valuable insights into the current status of graphene-based adsorbents developed for uranium removal with a guidance for the future directions in this research field.

Biosensing with DNAzymes

This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.

Complexation of uranyl (UO2)2+ with bidentate ligands: XRD, spectroscopic, computational, and biological studies

Three new uranyl complexes [(UO₂)(OAc)₂(CMZ)], [(UO₂)(OAc)₂(MP)] and [(UO₂)(OAc)₂(SCZ)] were synthesized and characterized by elemental analysis, FT-IR, UV-Vis spectroscopy, powder XRD analysis, and molar conductivity. The IR analysis confirmed binding to the metal ion by the sulfur and ethoxy oxygen atoms in the carbimazole (CMZ) ligand, while in the 6-mercaptopurine (MP) ligand, the sulfur and the N7 nitrogen atom of a purine coordinated binding to the metal ion. The third ligand showed a 1:1 molar ratio and bound via sulfonamide oxygen and the nitrogen of the pyrimidine ring. Analysis of the synthesized complexes also showed that acetate groups had monodentate binding to the (UO₂²⁺). Density Functional Theory (DFT) calculations at the B3LYP level showed similar structures to the experimental results. Theoretical quantum parameters predicted the reactivity of the complexes in the order, [(UO₂)(OAc)₂(SCZ)] > [(UO₂)(OAc)₂(MP)]> [(UO₂)(OAc)₂(CMZ)]. DNA binding studies revealed that [(UO₂)(OAc)₂(SCZ)] and [(UO₂)(OAc)₂(CMZ)] have the highest binding constant (K_b) among the uranyl complexes. Additionally, strong binding of the MP and CMZ metal complexes to human serum albumin (HSA) were observed by both absorbance and fluorescence approaches. The antibacterial activity of the complexes was also evaluated against four bacterial strains: two gram-negative; Escherichia coli and Klebsiella pneumonia, and two gram-positive; Staphylococcus aureus and Streptococcus mutans. [(UO₂)(OAc)₂(MP)] had the greatest antibacterial activity against Klebsiella pneumonia, the gram-positive bacteria, with even higher activity than the standard antibiotic. In vitro cytotoxicity tests were also performed against three human cancer lines, and revealed the most cytotoxic complexes to be [(UO₂)(OAc)₂(SCZ)], which showed moderate activity against a colon cancer cell line. Thus, uranyl addition enhances the antibacterial and anticancer properties of the free ligands.

Synthesis, characterization and (in vitro and in silico) biological activity of a series of dioxouranium(VI) complexes with non-steroidal anti-inflammatory drugs

The reaction of the dioxouranium(VI) ion with a series of non-steroidal anti-inflammatory drugs (NSAIDs), namely mefenamic acid, indomethacin, diclofenac, diflunisal and tolfenamic acid, as ligands in the absence or presence of diverse N,N'-donors (1,10-phenanthroline,2,2'-bipyridine or 2,2'-bipyridylamine) as co-ligands led to the formation of ten complexes bearing the formulas [UO₂(NSAID-O,O')₂(O-donor)₂] or [UO₂(NSAID-O,O')₂(N,N'-donor)], respectively. The complexes were characterized with diverse spectroscopic techniques and the crystal structures of three complexes were determined by single-crystal X-ray crystallography. The biological profile of the resultant complexes was assessed in vitro and in silico. The in vitro studies include their antioxidant properties (ability to scavenge free radicals 1,1-diphenyl-picrylhydrazyl and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) and to reduce H₂O₂), their interaction with DNA (linear calf-thymus DNA or supercoiled circular pBR322 plasmid DNA) and their affinity for serum albumins (bovine and human serum albumin). In silico molecular docking calculations were performed regarding the behavior of the complexes towards DNA and their binding to both albumins.

X-ray Ptychography Imaging of Human Chromosomes After Low-dose Irradiation

Studies of the structural and functional role of chromosomes in cytogenetics have spanned more than 10 decades. In this work, we take advantage of the coherent X-rays available at the latest synchrotron sources to extract the individual masses of all 46 chromosomes of metaphase human B and T cells using hard X-ray ptychography. We have produced 'X-ray karyotypes' of both heavy metal-stained and unstained spreads to determine the gain or loss of genetic material upon low-level X-ray irradiation doses due to radiation damage. The experiments were performed at the I-13 beamline, Diamond Light Source, Didcot, UK, using the phase-sensitive X-ray ptychography method.

Uranium directly interacts with the DNA repair protein poly (ADP-ribose) polymerase 1

People living in southwest part of United States are exposed to uranium (U) through drinking water, air, and soil. U is radioactive, but independent of this radioactivity also has important toxicological considerations as an environmental metal. At environmentally relevant concentrations, U is both mutagenic and carcinogenic. Emerging evidence shows that U inhibits DNA repair activity, but how U interacts with DNA repair proteins is still largely unknown. Herein, we report that U directly interacts with the DNA repair protein, Protein Poly (ADP-ribose) Polymerase 1 (PARP-1) through direct binding with the zinc finger motif, resulting in zinc release from zinc finger and DNA binding activity loss of the protein. At the peptide level, instead of direct competition with zinc ion in the zinc finger motif, U does not show thermodynamic advantages over zinc. Furthermore, zinc pre-occupied PARP-1 zinc finger is insensitive to U treatment, but U bound to PARP-1 zinc finger can be partially replaced by zinc. These results provide mechanistic basis on molecular level to U inhibition of DNA repair.

Emerging health risks and underlying toxicological mechanisms of uranium contamination: Lessons from the past two decades

Uranium contamination is a global health concern. Regarding natural or anthropogenic uranium contamination, the major sources of concern are groundwater, mining, phosphate fertilizers, nuclear facilities, and military activities. Many epidemiological and laboratory studies have demonstrated that environmental and occupational uranium exposure can induce multifarious health problems. Uranium exposure may cause health risks because of its chemotoxicity and radiotoxicity in natural or anthropogenic scenarios: the former is generally thought to play a more significant role with regard to the natural uranium exposure, and the latter is more relevant to enriched uranium exposure. The understanding of the health risks and underlying toxicological mechanisms of uranium remains at a preliminary stage, and many controversial findings require further research. In order to present state-of-the-art status in this field, this review will primarily focus on the chemotoxicity of uranium, rather than its radiotoxicity, as well as the involved toxicological mechanisms. First, the natural or anthropogenic uranium contamination scenarios will be briefly summarized. Second, the health risks upon natural uranium exposure, for example, nephrotoxicity, bone toxicity, reproductive toxicity, hepatotoxicity, neurotoxicity, and pulmonary toxicity, will be discussed based on the reported epidemiological cases and laboratory studies. Third, the recent advances regarding the toxicological mechanisms of uranium-induced chemotoxicity will be highlighted, including oxidative stress, genetic damage, protein impairment, inflammation, and metabolic disorder. Finally, the gaps and challenges in the knowledge of uranium-induced chemotoxicity and underlying mechanisms will be discussed.