Experimental localization of metal-binding sites reveals the role of metal ions in type II DNA topoisomerases.

Metal ions have important roles in supporting the catalytic activity of DNA-regulating enzymes such as topoisomerases (topos). Bacterial type II topos, gyrases and topo IV, are primary drug targets for fluoroquinolones, a class of clinically relevant antibacterials requiring metal ions for efficient drug binding. While the presence of metal ions in topos has been elucidated in biochemical studies, accurate location and assignment of metal ions in structural studies have historically posed significant challenges. Recent advances in X-ray crystallography address these limitations by extending the experimental capabilities into the long-wavelength range, exploiting the anomalous contrast from light elements of biological relevance. This breakthrough enables us to confirm experimentally the locations of Mg2+ in the fluoroquinolone-stabilized Streptococcus pneumoniae topo IV complex. Moreover, we can unambiguously identify the presence of K+ and Cl- ions in the complex with one pair of K+ ions functioning as an additional intersubunit bridge. Overall, our data extend current knowledge on the functional and structural roles of metal ions in type II topos.

How bacteria actively use passive physics to make biofilms.

Modern molecular microbiology elucidates the organizational principles of bacterial biofilms via detailed examination of the interplay between signaling and gene regulation. A complementary biophysical approach studies the mesoscopic dependencies at the cellular and multicellular levels with a distinct focus on intercellular forces and mechanical properties of whole biofilms. Here, motivated by recent advances in biofilm research and in other, seemingly unrelated fields of biology and physics, we propose a perspective that links the biofilm, a dynamic multicellular organism, with the physical processes occurring in the extracellular milieu. Using Bacillus subtilis as an illustrative model organism, we specifically demonstrate how such a rationale explains biofilm architecture, differentiation, communication, and stress responses such as desiccation tolerance, metabolism, and physiology across multiple scales-from matrix proteins and polysaccharides to macroscopic wrinkles and water-filled channels.

The discovery of a catalytic RNA within RNase P and its legacy.

Sidney Altman's discovery of the processing of one RNA by another RNA that acts like an enzyme was revolutionary in biology and the basis for his sharing the 1989 Nobel Prize in Chemistry with Thomas Cech. These breakthrough findings support the key role of RNA in molecular evolution, where replicating RNAs (and similar chemical derivatives) either with or without peptides functioned in protocells during the early stages of life on Earth, an era referred to as the RNA world. Here, we cover the historical background highlighting the work of Altman and his colleagues and the subsequent efforts of other researchers to understand the biological function of RNase P and its catalytic RNA subunit and to employ it as a tool to downregulate gene expression. We primarily discuss bacterial RNase P-related studies but acknowledge that many groups have significantly contributed to our understanding of archaeal and eukaryotic RNase P, as reviewed in this special issue and elsewhere.

Structure and ion-dependent folding of k-junctions.

k-Junctions are elaborated forms of kink turns with an additional helix on the nonbulged strand, thus forming a three-way helical junction. Two were originally identified in the structures of Arabidopsis and Escherichia coli thiamine pyrophosphate (TPP) riboswitches, and another called DUF-3268 was tentatively identified from sequence information. In this work we show that the Arabidopsis and E. coli riboswitch k-junctions fold in response to the addition of magnesium or sodium ions, and that atomic mutations that should disrupt key hydrogen bonding interactions greatly impair folding. Using X-ray crystallography, we have determined the structure of the DUF-3268 RNA and thus confirmed that it is a k-junction. It also folds upon the addition of metal ions, though requiring a 40-fold lower concentration of either divalent or monovalent ions. The key difference between the DUF-3268 and riboswitch k-junctions is the lack of nucleotides inserted between G1b and A2b in the former. We show that this insertion is primarily responsible for the difference in folding properties. Finally, we show that the DUF-3268 can functionally substitute for the k-junction in the E. coli TPP riboswitch such that the chimera can bind the TPP ligand, although less avidly.

Structure, function, and evolution of the metal-binding domain in the nucleosome.

The eukaryotic nucleosome, the basic unit of chromatin, is thermodynamically stable and plays critical roles in the cell, including the maintenance of DNA topology and regulation of gene expression. At its C2 axis of symmetry, the nucleosome exhibits a domain that can coordinate divalent metal ions. This article discusses the roles of the metal-binding domain in the nucleosome structure, function, and evolution.

Cation Triggered Self-Assembly of α-Lactalbumin Nanotubes.

Metal ions play a dual role in biological systems. Although they actively participate in vital life processes, they may contribute to protein aggregation and misfolding and thus contribute to development of diseases and other pathologies. In nanofabrication, metal ions mediate the formation of nanostructures with diverse properties. Here, we investigated the self-assembly of α-lactalbumin into nanotubes induced by coordination with metal ions, screened among the series Mn2+, Co2+, Ni2+, Zn2+, Cd2+, and Au3+. Our results revealed that the affinity of metal ions toward hydrolyzed α-lactalbumin peptides not only impacts the kinetics of nanotube formation but also influences their length and rigidity. These findings expand our understanding of supramolecular assembly processes in protein-based materials and pave the way for designing novel materials such as metallogels in biochip and biosensor applications.

An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11.

Human cleavage and polyadenylation specificity factor (CPSF)73 (also known as CPSF3) is the endoribonuclease that catalyzes the cleavage reaction for the 3'-end processing of pre-mRNAs. The active site of CPSF73 is located at the interface between a metallo-ß-lactamase domain and a ß-CASP domain. Two metal ions are coordinated by conserved residues, five His and two Asp, in the active site, and they are critical for the nuclease reaction. The metal ions have long been thought to be zinc ions, but their exact identity has not been examined. Here we present evidence from inductively coupled plasma mass spectrometry and X-ray diffraction analyses that a mixture of metal ions, including Fe, Zn, and Mn, is present in the active site of CPSF73. The abundance of the various metal ions is different in samples prepared from different expression hosts. Zinc is present at less than 20% abundance in a sample expressed in insect cells, but the sample is active in cleaving a pre-mRNA substrate in a reconstituted canonical 3'-end processing machinery. Zinc is present at 75% abundance in a sample expressed in human cells, which has comparable endonuclease activity. We also observe a mixture of metal ions in the active site of the CPSF73 homolog INTS11, the endonuclease for Integrator. Taken together, our results provide further insights into the role of metal ions in the activity of CPSF73 and INTS11 for RNA 3'-end processing.

From ferroptosis to cuproptosis, and calcicoptosis, to find more novel metals-mediated distinct form of regulated cell death.

Regulated cell death (RCD), also known as programmed cell death (PCD), plays a critical role in various biological processes, such as tissue injury/repair, development, and homeostasis. Dysregulation of RCD pathways can lead to the development of many human diseases, such as cancer, neurodegenerative disorders, and cardiovascular diseases. Maintaining proper metal ion homeostasis is critical for human health. However, imbalances in metal levels within cells can result in cytotoxicity and cell death, leading to a variety of diseases and health problems. In recent years, new types of metal overload-induced cell death have been identified, including ferroptosis, cuproptosis, and calcicoptosis. This has prompted us to examine the three defined metal-dependent cell death types, and discuss other metals-induced ferroptosis, cuproptosis, and disrupted Ca2+ homeostasis, as well as the roles of Zn2+ in metals' homeostasis and related RCD. We have reviewed the connection between metals-induced RCD and various diseases, as well as the underlying mechanisms. We believe that further research in this area will lead to the discovery of novel types of metal-dependent RCD, a better understanding of the underlying mechanisms, and the development of new therapeutic strategies for human diseases.

Ferroptosis and cuproptposis in kidney Diseases: dysfunction of cell metabolism.

Metal ions play an important role in living organisms and are involved in essential physiological activities. However, the overload state of ions can cause excess free radicals, cell damage, and even cell death. Ferroptosis and cuproptosis are specific forms of cell death that are distinct from apoptosis, necroptosis, and other regulated cell death. These unique modalities of cell death, dependent on iron and copper, are regulated by multiple cellular metabolic pathways, including steady-state metal redox treatment mitochondrial activity of lipid, amino acid and glucose metabolism, and various signaling pathways associated with disease. Although the mechanisms of ferroptosis and cuproptosis are not yet fully understood, there is no doubt that ion overload plays a crucial act in these metal-dependent cell deaths. In this review, we discussed the core roles of ion overload in ferroptosis and cuproptosis, the association between metabolism imbalance and ferroptosis and cuproptosis, the extract the diseases caused by ion overload and current treatment modalities.

1D Anionic Covalent Organic Frameworks With Directed Migration of Alkali Metal Ions for High Ionic Conductivity.

Rational construction of high-performance ionic conductors is a critical challenge in the field of energy storage. In this study, a series of 1D anionic titanium-based covalent organic frameworks (COFs) containing abundant alkali metal ion migration sites, namely, COF-M-R (M = Li, Na, K; R = H, Me, Et), is constructed. The integration of negative TiO6 2- sites on 1D anionic COFs allows alkali metal cations to migrate directly through the channels. Meanwhile, the π-π stacking of 1D chain-to-chain allows the distribution of ion-migration sites in 2D planes. In view of this, multidimensional ionic transport in COFs is realized to achieve high ionic conductivity. COF-M-Rs exhibit an increased ionic conductivity as the counterions change from Li+ to Na+ to K+. Notably, COF-Na-Et has an impressive ionic conductivity as high as 0.81 × 10-3 S cm-1. The different decorated groups (H, Me, and Et) on the skeleton influence the dissociation of the cation from the polyanion. This study offers deep insights into the design of COF-based solid-state electrolytes to achieve high ionic conductivity by increasing the ionic transport dimensions.

Boosting Photoluminescence of Rare-Earth-Based Double Perovskites by Isoelectronic Doping of ns2 Metal Ions.

Doping of ns2 metal ions as an energy transfer (ET) bridge can significantly elevate the photoluminescence properties. Nonetheless, the fundamental influence of ns2 metal ions on the local lattice structures remains unclear, hindering the advancement of functional materials. Herein, Sb3+ doped rare earth double perovskites is employed as a typical case to demonstrate this issue. It is found that the isoelectronic doping of Sb3+ ions not only enhances the ET efficiency but also changes their localized electronic and lattice structures. Both density functional theory (DFT) and Judd-Ofelt (J-O) theory calculations provide unambiguous evidence that the isoelectronic doping of Sb3+ ions enables a more localized charge density in the [LnCl6]3- (Ln: Lanthanide) octahedron and reduces the symmetry of the environment around the Ln3+, facilitating the radiative transition rates of Ln3+ while enhancing their ET efficiency. Compared with Cs2NaScCl6:Ln3+, the ET efficiency of Cs2NaScCl6:Sb3+/Ln3+ is enhanced by 1.5-fold, reaching up to 98.3%. To the best of available knowledge, this work is the first to unravel the intrinsic mechanism of enhanced ET process enabled by isoelectronic doping via DFT and J-O theory. This research sheds light on understanding the mechanism of photophysics and rational design of the functional perovskite materials.

Lattice Engineering via Transition Metal Ions for Boosting Photoluminescence Quantum Yields of Lead-Free Layered Double Perovskite Nanocrystals.

Lead-free layered double perovskite nanocrystals (NCs), i.e., Cs4M(II)M(III)2Cl12, have recently attracted increasing attention for potential optoelectronic applications due to their low toxicity, direct bandgap nature, and high structural stability. However, the low photoluminescence quantum yield (PLQY, <1%) or even no observed emissions at room temperature have severely blocked the further development of this type of lead-free halide perovskites. Herein, two new layered perovskites, Cs4CoIn2Cl12 (CCoI) and Cs4ZnIn2Cl12 (CZnI), are successfully synthesized at the nanoscale based on previously reported Cs4CuIn2Cl12 (CCuI) NCs, by tuning the M(II) site with different transition metal ions for lattice tailoring. Benefiting from the formation of more self-trapped excitons (STEs) in the distorted lattices, CCoI and CZnI NCs exhibit significantly strengthened STE emissions toward white light compared to the case of almost non-emissive CCuI NCs, by achieving PLQYs of 4.3% and 11.4% respectively. The theoretical and experimental results hint that CCoI and CZnI NCs possess much lower lattice deformation energies than that of reference CCuI NCs, which are favorable for the recombination of as-formed STEs in a radiative way. This work proposes an effective strategy of lattice engineering to boost the photoluminescent properties of lead-free layered double perovskites for their future warm white light-emitting applications.

On the Synthesis and Structure of 'Naked' Ga(I) and In(I) Salts and the Surprising Stability of Simple Ga(I) and In(I) Salts in the Coordinating Solvents Ether and Acetonitrile.

In this work, we present the solid-state structures of solvent-free Ga[pf] and In[pf] salts ([pf]-=[Al(ORF)4]-; RF=C(CF3)3), which are very rare examples of salts with truly 'naked' metal cations. Both salts may serve as starting materials for subvalent gallium and indium chemistry with very weakly coordinating ligands providing the freedom of choice for solvents and ligands for the future. On the other hand, we report and rationalize the formation and isolation of [M(OEt2)2][pf] and [M(MeCN)2][pf] (M=Ga, In), underlining the surprising stability of these subvalent group 13 M+ ions against disproportionation. Unexpectedly, dicoordinate and carbene analogous [M(L)2]+ ions with the [pf]- counterion are stable in L=acetonitrile and diethyl ether at room temperature, opening up possible applications for example in organic synthesis and catalysis.

Elevating the Performance of Heterometallic 3d/4f SMMs: The Role of Diamagnetic CoIII and ZnII Ions in Magnetization Dynamics.

Recent advances in the synthesis of 3d/4f Single-Molecule Magnets (SMMs) have revealed the effective role of incorporating diamagnetic CoIII or ZnII ions to enhance the magnetic properties of LnIII ions. This concept highlights notable examples of CoIII/LnIII and ZnII/LnIII SMMs documented in the recent literature, illustrating how the selection of various peripheral and/or bridging ligands can modulate the magnetic anisotropy of 4f metal ions, thereby increasing their energy barriers.

Proton vs Electron: The Dual Role of Redox-Inactive Metal Ions in Permanganate Oxidation Kinetics.

Redox-inactive metal-ion-driven modulation of the oxidation behavior of high-valent metal-oxo complex has garnered significant interest in biological and chemical synthesis; however, their role in permanganate (Mn(VII)) oxidation for the removal of organic pollutants has been largely neglected. Here, we uncover the impact of six metal ions (i.e., Ca2+, Mg2+, Ni2+, Zn2+, Al3+, and Sc3+) presenting in water environments on Mn(VII) activity. These ions uniformly boost the electron and oxygen transfer capabilities of Mn(VII) while impeding proton transfer, as evidenced by electrochemical tests, thioanisole probe analysis, and the kinetic isotope effect. The observed effects are intricately linked to the Lewis acidity of the metal ions. Further mechanistic insights reveal that Mn(VII) can interact with metal ions without direct reduction. Such interactions modify the electronic configuration of Mn(VII) and create an acidic microenvironment, thus increasing its electrophilicity and the energy barrier for the abstraction of proton from organic substrates. More importantly, the efficacy of Mn(VII) in removing phenolic pollutants is regulated by these ions through changing the driving force for proton and electron transfer, i.e., facilitated at pH > 4.5 and inhibited at lower pH. The contribution of active Mn intermediates is also discussed to reveal the oxidative mechanism of the metal ion/Mn(VII) system. These findings not only facilitate the rational design of Mn(VII) oxidation conditions in the presence of metal ions for water decontamination but also offer an alternative paradigm for enhancing electrophilic oxidation.

Speciation Analysis of Metals and Metalloids by Surface Enhanced Raman Spectroscopy.

The presence of metalloids and heavy metals in the environment is of critical concern due to their toxicological impacts. However, not all metallic species have the same risk level. Specifically, the physical, chemical, and isotopic speciation of the metal(loids) dictate their metabolism, toxicity, and environmental fate. As such, speciation analysis is critical for environmental monitoring and risk assessment. In the past two decades, surface-enhanced Raman spectroscopy (SERS) has seen significant developments regarding trace metal(loid) sensing due to its ultrahigh sensitivity, readiness for in situ real-time applications, and cost-effectiveness. However, the speciation of metal(loid)s has not been accounted for in the design and application of SERS sensors. In this Perspective, we examine the potential of SERS for metal(loid) speciation analysis and highlight the advantages, progress, opportunities, and challenges of this application.

The Impact of Metal Ions on MXene Membranes: Critical Role of Titanium Vacancies.

Two-dimensional transition metal carbides and nitrides (MXenes) and MXene-based membranes hold promise for applications including water purification and seawater desalination; however, their environmental behavior and fate in these matrices remain unknown. In this study, we systematically assessed the reaction efficiencies of Ti3C2Tx at varying important environmental conditions. Our experiments revealed that copper and iron ions accelerated the oxidation rate of Ti3C2Tx 55.4 and 33.4 times, respectively. TiO2 and amorphous carbon were identified as the primary solid products. Based on in situ water-phase atomic force microscopy, atomic high-angle annular dark-field scanning transmission electron microscopy, and theoretical results, we postulate that metal ions enhance Ti3C2Tx oxidation by spontaneously migrating and anchoring at Ti vacancies, which then become active sites for this reaction. This process increases the adsorption of H2O and oxygen, making the Ti vacancy-rich surface convex area the most vulnerable site to attack. The findings in this study provide useful information for a comprehensive understanding of the interaction between MXene structural defects and metal ions as well as for the design and modification of MXene membranes resistant to metal ion impact.

Insights into the Mechanism of Selective Removal of Heavy Metal Ions by the Pulsed/Direct Current Electrochemical Method.

Heavy metal pollution treatment in industrial wastewater is crucial for protecting biological and environmental safety. However, the highly efficient and selective removal of heavy metal ions from multiple cations in wastewater is a significant challenge. This work proposed a pulse electrochemical method with a low-/high-voltage periodic appearance to selectively recover heavy metal ions from complex wastewater. It exhibited a higher recovery efficiency for heavy metal ions (100% for Pb2+ and Cd2+, >98% for Mn2+) than other alkali and alkaline earth metal ions (Na+, Ca2+, and Mg2+ were kept below 3.6, 1.3, and 2.6%, respectively) in the multicomponent solution. The energy consumption was only 34-77% of that of the direct current electrodeposition method. The results of characterization and experiment unveil the mechanism that the low-/high-voltage periodic appearance can significantly suppress the water-splitting reaction and break the mass-transfer limitation between heavy metal ions and electrodes. In addition, the plant study demonstrates the feasibility of treated wastewater for agricultural use, further proving the high sustainability of the method. Therefore, it provides new insights into the selective recovery of heavy metals from industrial wastewater.

Nanoscale Insights into the Interaction Mechanism Underlying the Adsorption and Retention of Heavy Metal Ions by Humic Acid.

The mobility and distribution of heavy metal ions (HMs) in aquatic environments are significantly influenced by humic acid (HA), which is ubiquitous. A quantitative understanding of the interaction mechanism underlying the adsorption and retention of HMs by HA is of vital significance but remains elusive. Herein, the interaction mechanism between HA and different types of HMs (i.e., Cd(II), Pb(II), arsenate, and chromate) was quantitatively investigated at the nanoscale. Based on quartz crystal microbalance with dissipation tests, the adsorption capacities of Pb(II), Cd(II), As(V), and Cr(VI) ionic species on the HA surface were measured as ∼0.40, ∼0.25, ∼0.12, and ∼0.02 nmol cm-2, respectively. Atomic force microscopy force results showed that the presence of Pb(II)/Cd(II) cations suppressed the electrostatic double-layer repulsion during the approach of two HA surfaces and the adhesion energy during separation was considerably enhanced from ∼2.18 to ∼5.05/∼4.18 mJ m-2. Such strong adhesion stems from the synergistic metal-HA complexation and cation-π interaction, as evidenced by spectroscopic analysis and theoretical simulation. In contrast, As(V)/Cr(VI) oxo-anions could form only weak hydrogen bonds with HA, resulting in similar adhesion energies for HA-HA (∼2.18 mJ m-2) and HA-As(V)/Cr(VI)-HA systems (∼2.26/∼1.96 mJ m-2). This work provides nanoscale insights into quantitative HM-HA interactions, improving the understanding of HMs biogeochemical cycling.

Peptides and metal ions: A successful marriage for developing artificial metalloproteins.

The mutual relationship between peptides and metal ions enables metalloproteins to have crucial roles in biological systems, including structural, sensing, electron transport, and catalytic functions. The effort to reproduce or/and enhance these roles, or even to create unprecedented functions, is the focus of protein design, the first step toward the comprehension of the complex machinery of nature. Nowadays, protein design allows the building of sophisticated scaffolds, with novel functions and exceptional stability. Recent progress in metalloprotein design has led to the building of peptides/proteins capable of orchestrating the desired functions of different metal cofactors. The structural diversity of peptides allows proper selection of first- and second-shell ligands, as well as long-range electrostatic and hydrophobic interactions, which represent precious tools for tuning metal properties. The scope of this review is to discuss the construction of metal sites in de novo designed and miniaturized scaffolds. Selected examples of mono-, di-, and multi-nuclear binding sites, from the last 20 years will be described in an effort to highlight key artificial models of catalytic or electron-transfer metalloproteins. The authors' goal is to make readers feel like guests at the marriage between peptides and metal ions while offering sources of inspiration for future architects of innovative, artificial metalloproteins.