Metalloproteomics for Biomedical Research: Methodology and Applications.

Metals are essential components in life processes and participate in many important biological processes. Dysregulation of metal homeostasis is correlated with many diseases. Metals are also frequently incorporated into diagnosis and therapeutics. Understanding of metal homeostasis under (patho)physiological conditions and the molecular mechanisms of action of metallodrugs in biological systems has positive impacts on human health. As an emerging interdisciplinary area of research, metalloproteomics involves investigating metal-protein interactions in biological systems at a proteome-wide scale, has received growing attention, and has been implemented into metal-related research. In this review, we summarize the recent advances in metalloproteomics methodologies and applications. We also highlight emerging single-cell metalloproteomics, including time-resolved inductively coupled plasma mass spectrometry, mass cytometry, and secondary ion mass spectrometry. Finally, we discuss future perspectives in metalloproteomics, aiming to attract more original research to develop more advanced methodologies, which could be utilized rapidly by biochemists or biologists to expand our knowledge of how metal functions in biology and medicine.

The Crystal Structure of a Biological Insulated Transmembrane Molecular Wire.

A growing number of bacteria are recognized to conduct electrons across their cell envelope, and yet molecular details of the mechanisms supporting this process remain unknown. Here, we report the atomic structure of an outer membrane spanning protein complex, MtrAB, that is representative of a protein family known to transport electrons between the interior and exterior environments of phylogenetically and metabolically diverse microorganisms. The structure is revealed as a naturally insulated biomolecular wire possessing a 10-heme cytochrome, MtrA, insulated from the membrane lipidic environment by embedding within a 26 strand ß-barrel formed by MtrB. MtrAB forms an intimate connection with an extracellular 10-heme cytochrome, MtrC, which presents its hemes across a large surface area for electrical contact with extracellular redox partners, including transition metals and electrodes.

Transition Metal Sequestration by the Host-Defense Protein Calprotectin.

In response to microbial infection, the human host deploys metal-sequestering host-defense proteins, which reduce nutrient availability and thereby inhibit microbial growth and virulence. Calprotectin (CP) is an abundant antimicrobial protein released from neutrophils and epithelial cells at sites of infection. CP sequesters divalent first-row transition metal ions to limit the availability of essential metal nutrients in the extracellular space. While functional and clinical studies of CP have been pursued for decades, advances in our understanding of its biological coordination chemistry, which is central to its role in the host-microbe interaction, have been made in more recent years. In this review, we focus on the coordination chemistry of CP and highlight studies of its metal-binding properties and contributions to the metal-withholding innate immune response. Taken together, these recent studies inform our current model of how CP participates in metal homeostasis and immunity, and they provide a foundation for further investigations of a remarkable metal-chelating protein at the host-microbe interface and beyond.

Gating movements and ion permeation in HCN4 pacemaker channels.

The HCN1-4 channel family is responsible for the hyperpolarization-activated cation current If/Ih that controls automaticity in cardiac and neuronal pacemaker cells. We present cryoelectron microscopy (cryo-EM) structures of HCN4 in the presence or absence of bound cAMP, displaying the pore domain in closed and open conformations. Analysis of cAMP-bound and -unbound structures sheds light on how ligand-induced transitions in the channel cytosolic portion mediate the effect of cAMP on channel gating and highlights the regulatory role of a Mg2+ coordination site formed between the C-linker and the S4-S5 linker. Comparison of open/closed pore states shows that the cytosolic gate opens through concerted movements of the S5 and S6 transmembrane helices. Furthermore, in combination with molecular dynamics analyses, the open pore structures provide insights into the mechanisms of K+/Na+ permeation. Our results contribute mechanistic understanding on HCN channel gating, cyclic nucleotide-dependent modulation, and ion permeation.

Protein lipoylation: mitochondria, cuproptosis, and beyond.

Protein lipoylation, a crucial post-translational modification (PTM), plays a pivotal role in mitochondrial function and emerges as a key player in cell death through cuproptosis. This novel copper-driven cell death pathway is activated by excessive copper ions binding to lipoylated mitochondrial proteins, disrupting energy production and causing lethal protein aggregation and cell death. The intricate relationship among protein lipoylation, cellular energy metabolism, and cuproptosis offers a promising avenue for regulating essential cellular functions. This review focuses on the mechanisms of lipoylation and its significant impact on cell metabolism and cuproptosis, emphasizing the key genes involved and their implications for human diseases. It offers valuable insights into targeting dysregulated cellular metabolism for therapeutic purposes.

Characterizing metal-biomolecule interactions by mass spectrometry.

Metal micronutrients are essential for life and exist in a delicate balance to maintain an organism's health. The labile nature of metal-biomolecule interactions clouds the understanding of metal binders and metal-mediated conformational changes that are influential to health and disease. Mass spectrometry (MS)-based methods and technologies have been developed to better understand metal micronutrient dynamics in the intra- and extracellular environment. In this review, we describe the challenges associated with studying labile metals in human biology and highlight MS-based methods for the discovery and study of metal-biomolecule interactions.

Gene-Environment Interactions: My Unique Journey.

I am deeply honored to be invited to write this scientific autobiography. As a physician-scientist, pediatrician, molecular biologist, and geneticist, I have authored/coauthored more than 600 publications in the fields of clinical medicine, biochemistry, biophysics, pharmacology, drug metabolism, toxicology, molecular biology, cancer, standardized gene nomenclature, developmental toxicology and teratogenesis, mouse genetics, human genetics, and evolutionary genomics. Looking back, I think my career can be divided into four distinct research areas, which I summarize mostly chronologically in this article: (a) discovery and characterization of the AHR/CYP1 axis, (b) pharmacogenomics and genetic prediction of response to drugs and other environmental toxicants, (c) standardized drug-metabolizing gene nomenclature based on evolutionary divergence, and (d) discovery and characterization of the SLC39A8 gene encoding the ZIP8 metal cation influx transporter. Collectively, all four topics embrace gene-environment interactions, hence the title of my autobiography.

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.

Endonuclease V (EndoV) cleaves the second phosphodiester bond 3' to a deaminated adenosine (inosine). Although highly conserved, EndoV homologs change substrate preference from DNA in bacteria to RNA in eukaryotes. We have characterized EndoV from six different species and determined crystal structures of human EndoV and three EndoV homologs from bacteria to mouse in complex with inosine-containing DNA/RNA hybrid or double-stranded RNA (dsRNA). Inosine recognition is conserved, but changes in several connecting loops in eukaryotic EndoV confer recognition of 3 ribonucleotides upstream and 7 or 8 bp of dsRNA downstream of the cleavage site, and bacterial EndoV binds only 2 or 3 nt flanking the scissile phosphate. In addition to the two canonical metal ions in the active site, a third Mn2+ that coordinates the nucleophilic water appears necessary for product formation. Comparison of EndoV with its homologs RNase H1 and Argonaute reveals the principles by which these enzymes recognize RNA versus DNA.

Phosphorescent metallaknots of Au(I)-bis(acetylide) strands directed by Cu(I) π-coordination.

Knots containing metal atoms as part of their continuous strand backbone are termed as metallaknots. While several metallaknots have been synthesized through one-pot self-assembly, the designed synthesis of metallaknots by controlling the arrangement of entanglements and strands connectivity remains unexplored. Here, we report the synthesis of metallaknots composed with Au(I)-bis(acetylide) linkages and templated by Cu(I) ions. Varying the ratio of the building blocks results in the switchable formation of two trefoil knots with different stoichiometries and symmetries (C2 or D3) and an entangled metalla-complex. While the entangled complex formed serendipitously, the strand ends can be subsequently linked through coordinative closure to generate a 41 metallaknot in a highly designable fashion. The comparable structural characteristics of resulting metalla-complexes allow us to probe the correlations between their topologies and photophysical properties, showing the backbone rigidity of knots endows complexes with excellent phosphorescent properties. This strategy, in conjunction with the coordinative closure approach, provides a straightforward route for the formation of highly phosphorescent metallaknots that were previously challenging to access.

Cu(II) complex that synergistically potentiates cytotoxicity and an antitumor immune response by targeting cellular redox homeostasis.

Developing anticancer drugs with low side effects is an ongoing challenge. Immunogenic cell death (ICD) has received extensive attention as a potential synergistic modality for cancer immunotherapy. However, only a limited set of drugs or treatment modalities can trigger an ICD response and none of them have cytotoxic selectivity. This provides an incentive to explore strategies that might provide more effective ICD inducers free of adverse side effects. Here, we report a metal-based complex (Cu-1) that disrupts cellular redox homeostasis and effectively stimulates an antitumor immune response with high cytotoxic specificity. Upon entering tumor cells, this Cu(II) complex enhances the production of intracellular radical oxidative species while concurrently depleting glutathione (GSH). As the result of heightening cellular oxidative stress, Cu-1 gives rise to a relatively high cytotoxicity to cancer cells, whereas normal cells with low levels of GSH are relatively unaffected. The present Cu(II) complex initiates a potent ferroptosis-dependent ICD response and effectively inhibits in vivo tumor growth in an animal model (c57BL/6 mice challenged with colorectal cancer). This study presents a strategy to develop metal-based drugs that could synergistically potentiate cytotoxic selectivity and promote apoptosis-independent ICD responses through perturbations in redox homeostasis.

Microbes vary strategically in their metalation of mononuclear enzymes.

Studies have determined that nonredox enzymes that are cofactored with Fe(II) are the most oxidant-sensitive targets inside Escherichia coli. These enzymes use Fe(II) cofactors to bind and activate substrates. Because of their solvent exposure, the metal can be accessed and oxidized by reactive oxygen species, thereby inactivating the enzyme. Because these enzymes participate in key physiological processes, the consequences of stress can be severe. Accordingly, when E. coli senses elevated levels of H2O2, it induces both a miniferritin and a manganese importer, enabling the replacement of the iron atom in these enzymes with manganese. Manganese does not react with H2O2 and thereby preserves enzyme activity. In this study, we examined several diverse microbes to identify the metal that they customarily integrate into ribulose-5-phosphate 3-epimerase, a representative of this enzyme family. The anaerobe Bacteroides thetaiotaomicron, like E. coli, uses iron. In contrast, Bacillus subtilis and Lactococcus lactis use manganese, and Saccharomyces cerevisiae uses zinc. The latter organisms are therefore well suited to the oxidizing environments in which they dwell. Similar results were obtained with peptide deformylase, another essential enzyme of the mononuclear class. Strikingly, heterologous expression experiments show that it is the metal pool within the organism, rather than features of the protein itself, that determine which metal is incorporated. Further, regardless of the source organism, each enzyme exhibits highest turnover with iron and lowest turnover with zinc. We infer that the intrinsic catalytic properties of the metal cannot easily be retuned by evolution of the polypeptide.

Magnetism and metallicity in moiré transition metal dichalcogenides.

The ability to control the properties of twisted bilayer transition metal dichalcogenides in situ makes them an ideal platform for investigating the interplay of strong correlations and geometric frustration. Of particular interest are the low energy scales, which make it possible to experimentally access both temperature and magnetic fields that are of the order of the bandwidth or the correlation scale. In this manuscript, we analyze the moiré Hubbard model, believed to describe the low energy physics of an important subclass of the twisted bilayer compounds. We establish its magnetic and the metal-insulator phase diagram for the full range of magnetic fields up to the fully spin-polarized state. We find a rich phase diagram including fully and partially polarized insulating and metallic phases of which we determine the interplay of magnetic order, Zeeman-field, and metallicity, and make connection to recent experiments.

Interfacial solvation-structure regulation for stable Li metal anode by a desolvation coating technique.

Rechargeable lithium (Li) metal batteries face challenges in achieving stable cycling due to the instability of the solid electrolyte interphase (SEI). The Li-ion solvation structure and its desolvation process are crucial for the formation of a stable SEI on Li metal anodes and improving Li plating/stripping kinetics. This research introduces an interfacial desolvation coating technique to actively modulate the Li-ion solvation structure at the Li metal interface and regulate the participation of the electrolyte solvent in SEI formation. Through experimental investigations conducted using a carbonate electrolyte with limited compatibility to Li metal, the optimized desolvation coating layer, composed of 12-crown-4 ether-modified silica materials, selectively displaces strongly coordinating solvents while simultaneously enriching weakly coordinating fluorinated solvents at the Li metal/electrolyte interface. This selective desolvation and enrichment effect reduce solvent participation to SEI and thus facilitate the formation of a LiF-dominant SEI with greatly reduced organic species on the Li metal surface, as conclusively verified through various characterization techniques including XPS, quantitative NMR, operando NMR, cryo-TEM, EELS, and EDS. The interfacial desolvation coating technique enables excellent rate cycling stability (i.e., 1C) of the Li metal anode and prolonged cycling life of the Li||LiCoO2 pouch cell in the conventional carbonate electrolyte (E/C 2.6 g/Ah), with 80% capacity retention after 333 cycles.

Achieving metal-like catalysis from semiconductor for on-surface synthesis.

Free of posttransfer, on-surface synthesis (OSS) of single-atomic-layer nanostructures directly on semiconductors holds considerable potential for next-generation devices. However, due to the high diffusion barrier and abundant defects on semiconductor surfaces, extended and well-defined OSS on semiconductors has major difficulty. Furthermore, given semiconductors' limited thermal catalytic activity, initiating high-barrier reactions remains a significant challenge. Herein, using TiO2(011) as a prototype, we present an effective strategy for steering the molecule adsorption and reaction processes on semiconductors, delivering lengthy graphene nanoribbons with extendable widths. By introducing interstitial titanium (Tiint) and oxygen vacancies (Ov), we convert TiO2(011) from a passive supporting template into a metal-like catalytic platform. This regulation shifts electron density and surface dipoles, resulting in tunable catalytic activity together with varied molecule adsorption and diffusion. Cyclodehydrogenation, which is inefficient on pristine TiO2(011), is markedly improved on Tiint/Ov-doped TiO2. Even interribbon cyclodehydrogenation is achieved. The final product's dimensions, quality, and coverage are all controllable. Tiint doping outperforms Ov in producing regular and prolonged products, whereas excessive Tiint compromises molecule landing and coupling. This work demonstrates the crucial role of semiconductor substrates in OSS and advances OSS on semiconductors from an empirical trial-and-error methodology to a systematic and controllable paradigm.

Parallel ecological and evolutionary responses to selection in a natural bacterial community.

Evolution can occur over ecological timescales, suggesting a potentially important role for rapid evolution in shaping community trait distributions. However, evidence of concordant eco-evolutionary dynamics often comes from in vitro studies of highly simplified communities, and measures of ecological and evolutionary dynamics are rarely directly comparable. Here, we quantified how ecological species sorting and rapid evolution simultaneously shape community trait distributions by tracking within- and between-species changes in a key trait in a complex bacterial community. We focused on the production of siderophores; bacteria use these costly secreted metabolites to scavenge poorly soluble iron and to detoxify environments polluted with toxic nonferrous metals. We found that responses to copper-imposed selection within and between species were ultimately the same-intermediate siderophore levels were favored-and occurred over similar timescales. Despite being a social trait, this level of siderophore production was selected regardless of whether species evolved in isolation or in a community context. Our study suggests that evolutionary selection can play a pivotal role in shaping community trait distributions within natural, highly complex, bacterial communities. Furthermore, trait evolution may not always be qualitatively affected by interactions with other community members.

Iron: Life's primeval transition metal.

Modern life requires many different metal ions, which enable diverse biochemical functions. It is commonly assumed that metal ions' environmental availabilities controlled the evolution of early life. We argue that evolution can only explore the chemistry that life encounters, and fortuitous chemical interactions between metal ions and biological compounds can only be selected for if they first occur sufficiently frequently. We calculated maximal transition metal ion concentrations in the ancient ocean, determining that the amounts of biologically important transition metal ions were orders of magnitude lower than ferrous iron. Under such conditions, primitive bioligands would predominantly interact with Fe(II). While interactions with other metals in certain environments may have provided evolutionary opportunities, the biochemical capacities of Fe(II), Fe-S clusters, or the plentiful magnesium and calcium could have satisfied all functions needed by early life. Primitive organisms could have used Fe(II) exclusively for their transition metal ion requirements.

Steering lithium and potassium storage mechanism in covalent organic frameworks by incorporating transition metal single atoms.

Organic electrodes mainly consisting of C, O, H, and N are promising candidates for advanced batteries. However, the sluggish ionic and electronic conductivity limit the full play of their high theoretical capacities. Here, we integrate the idea of metal-support interaction in single-atom catalysts with π-d hybridization into the design of organic electrode materials for the applications of lithium (LIBs) and potassium-ion batteries (PIBs). Several types of transition metal single atoms (e.g., Co, Ni, Fe) with π-d hybridization are incorporated into the semiconducting covalent organic framework (COF) composite. Single atoms favorably modify the energy band structure and improve the electronic conductivity of COF. More importantly, the electronic interaction between single atoms and COF adjusts the binding affinity and modifies ion traffic between Li/K ions and the active organic units of COFs as evidenced by extensive in situ and ex situ characterizations and theoretical calculations. The corresponding LIB achieves a high reversible capacity of 1,023.0 mA h g-1 after 100 cycles at 100 mA g-1 and 501.1 mA h g-1 after 500 cycles at 1,000 mA g-1. The corresponding PIB delivers a high reversible capacity of 449.0 mA h g-1 at 100 mA g-1 after 150 cycles and stably cycled over 500 cycles at 1,000 mA g-1. This work provides a promising route to engineering organic electrodes.

Regulation of the d-band center of metal-organic frameworks for energy-saving hydrogen generation coupled with selective glycerol oxidation.

The hybrid electrolyzer coupled glycerol oxidation (GOR) with hydrogen evolution reaction (HER) is fascinating to simultaneously generate H2 and high value-added chemicals with low energy input, yet facing a challenge. Herein, Cu-based metal-organic frameworks (Cu-MOFs) are reported as model catalysts for both HER and GOR through doping of atomically dispersed precious and nonprecious metals. Remarkably, the HER activity of Ru-doped Cu-MOF outperformed a Pt/C catalyst, with its Faradaic efficiency for formate formation at 90% at a low potential of 1.40 V. Furthermore, the hybrid electrolyzer only needed 1.36 V to achieve 10 mA cm-2, 340 mV lower than that for splitting pure water. Theoretical calculations demonstrated that electronic interactions between the host and guest (doped) metals shifted downward the d-band centers (εd) of MOFs. This consequently lowered water adsorption and dissociation energy barriers and optimized hydrogen adsorption energy, leading to significantly enhanced HER activities. Meanwhile, the downshift of εd centers reduced energy barriers for rate-limiting step and the formation energy of OH*, synergistically enhancing the activity of MOFs for GOR. These findings offered an effective means for simultaneous productions of hydrogen fuel and high value-added chemicals using one hybrid electrolyzer with low energy input.

Electroluminescent vertical tunneling junctions based on WSe2 monolayer quantum emitter arrays: Exploring tunability with electric and magnetic fields.

We experimentally demonstrate the creation of defects in monolayer WSe2 via nanopillar imprinting and helium ion irradiation. Based on the first method, we realize atomically thin vertical tunneling light-emitting diodes based on WSe2 monolayers hosting quantum emitters at deterministically specified locations. We characterize these emitters by investigating the evolution of their emission spectra in external electric and magnetic fields, as well as by inducing electroluminescence at low temperatures. We identify qualitatively different types of quantum emitters and classify them according to the dominant electron-hole recombination paths, determined by the mechanisms of intervalley mixing occurring in fundamental conduction and/or valence subbands.

Large Fermi surface in pristine kagome metal CsV3Sb5 and enhanced quasiparticle effective masses.

The kagome metal CsV[Formula: see text]Sb[Formula: see text] is an ideal platform to study the interplay between topology and electron correlation. To understand the fermiology of CsV[Formula: see text]Sb[Formula: see text], intensive quantum oscillation (QO) studies at ambient pressure have been conducted. However, due to the Fermi surface reconstruction by the complicated charge density wave (CDW) order, the QO spectrum is exceedingly complex, hindering a complete understanding of the fermiology. Here, we directly map the Fermi surface of the pristine CsV[Formula: see text]Sb[Formula: see text] by measuring Shubnikov-de Haas QOs up to 29 T under pressure, where the CDW order is completely suppressed. The QO spectrum of the pristine CsV[Formula: see text]Sb[Formula: see text] is significantly simpler than the one in the CDW phase, and the detected oscillation frequencies agree well with our density functional theory calculations. In particular, a frequency as large as 8,200 T is detected. Pressure-dependent QO studies further reveal a weak but noticeable enhancement of the quasiparticle effective masses on approaching the critical pressure where the CDW order disappears, hinting at the presence of quantum fluctuations. Our high-pressure QO results reveal the large, unreconstructed Fermi surface of CsV[Formula: see text]Sb[Formula: see text], paving the way to understanding the parent state of this intriguing metal in which the electrons can be organized into different ordered states.