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.

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.

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.

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.

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.

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.

Design principles of heterointerfacial redox chemistry for highly reversible lithium metal anode.

High electrochemical reversibility is required for the application of high-energy-density lithium (Li) metal batteries; however, inactive Li formation and SEI (solid electrolyte interface)-instability-induced electrolyte consumption cause low Coulombic efficiency (CE). The prior interfacial chemical designs in terms of alloying kinetics have been used to enhance the CE of Li metal anode; however, the role of its redox chemistry at heterointerfaces remains a mystery. Herein, the relationship between heterointerfacial redox chemistry and electrochemical transformation reversibility is investigated. It is demonstrated that the lower redox potential at heterointerface contributes to higher CE, and this enhancement in CE is primarily due to the regulation of redox chemistry to Li deposition behavior rather than the formation of SEI films. Low oxidation potential facilitates the formation of the surface with the highly electrochemical binding feature after Li stripping, and low reduction potential can maintain binding ability well during subsequent Li plating, both of which homogenize Li deposition and thus optimize CE. In particular, Mg hetero-metal with ultra-low redox potential enables Li metal anode with significantly improved CE (99.6%) and stable cycle life for 700 cycles at 3.0 mA cm-2. This work provides insight into the heterointerfacial design principle of next-generation negative electrodes for highly reversible metal batteries.

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.

Ultrafast generation of hidden phases via energy-tuned electronic photoexcitation in magnetite.

Phase transitions occurring in nonequilibrium conditions can evolve through high-energy intermediate states inaccessible via equilibrium adiabatic conditions. Because of the subtle nature of such hidden phases, their direct observation is extremely challenging and requires simultaneous visualization of matter at subpicoseconds and subpicometer scales. Here, we show that a magnetite crystal in the vicinity of its metal-to-insulator transition evolves through different hidden states when controlled via energy-tuned ultrashort laser pulses. By directly monitoring magnetite's crystal structure with ultrafast electron diffraction, we found that upon near-infrared (800 nm) excitation, the trimeron charge/orbital ordering pattern is destroyed in favor of a phase-separated state made of cubic-metallic and monoclinic-insulating regions. On the contrary, visible light (400 nm) activates a photodoping charge transfer process that further promotes the long-range order of the trimerons by stabilizing the charge density wave fluctuations, leading to the reinforcement of the monoclinic insulating phase. Our results demonstrate that magnetite's structure can evolve through completely different metastable hidden phases that can be reached long after the initial excitation has relaxed, breaking ground for a protocol to control emergent properties of matter.

A tandem activity-based sensing and labeling strategy reveals antioxidant response element regulation of labile iron pools.

Iron is an essential element for life owing to its ability to participate in a diverse array of oxidation-reduction reactions. However, misregulation of iron-dependent redox cycling can also produce oxidative stress, contributing to cell growth, proliferation, and death pathways underlying aging, cancer, neurodegeneration, and metabolic diseases. Fluorescent probes that selectively monitor loosely bound Fe(II) ions, termed the labile iron pool, are potentially powerful tools for studies of this metal nutrient; however, the dynamic spatiotemporal nature and potent fluorescence quenching capacity of these bioavailable metal stores pose challenges for their detection. Here, we report a tandem activity-based sensing and labeling strategy that enables imaging of labile iron pools in live cells through enhancement in cellular retention. Iron green-1 fluoromethyl (IG1-FM) reacts selectively with Fe(II) using an endoperoxide trigger to release a quinone methide dye for subsequent attachment to proximal biological nucleophiles, providing a permanent fluorescent stain at sites of elevated labile iron. IG1-FM imaging reveals that degradation of the major iron storage protein ferritin through ferritinophagy expands the labile iron pool, while activation of nuclear factor-erythroid 2-related factor 2 (NRF2) antioxidant response elements (AREs) depletes it. We further show that lung cancer cells with heightened NRF2 activation, and thus lower basal labile iron, have reduced viability when treated with an iron chelator. By connecting labile iron pools and NRF2-ARE activity to a druggable metal-dependent vulnerability in cancer, this work provides a starting point for broader investigations into the roles of transition metal and antioxidant signaling pathways in health and disease.

Suppressing Zn pulverization with three-dimensional inert-cation diversion dam for long-life Zn metal batteries.

Tremendous attention has been paid to the water-associated side reactions and zinc (Zn) dendrite growth on the electrode-electrolyte interface. However, the Zn pulverization that can cause continuous depletion of active Zn metal and exacerbate hydrogen evolution is severely neglected. Here, we disclose that the excessive Zn feeding that causes incomplete crystallization is responsible for Zn pulverization formation through analyzing the thermodynamic and kinetics process of Zn deposition. On the basis, we introduce 1-ethyl-3-methylimidazolium cations (EMIm+) into the electrolyte to form a Galton-board-like three-dimensional inert-cation (3DIC) region. Modeling test shows that the 3DIC EMIm+ can induce the Zn2+ flux to follow in a Gauss distribution, thus acting as elastic sites to buffer the perpendicular diffusion of Zn2+ and direct the lateral diffusion, thus effectively avoiding the local Zn2+ accumulation and irreversible crystal formation. Consequently, anti-pulverized Zn metal deposition behavior is achieved with an average Coulombic efficiency of 99.6% at 5 mA cm-2 over 2,000 cycles and superb stability in symmetric cell over 1,200 h at -30 °C. Furthermore, the Zn||KVOH pouch cell can stably cycle over 1,200 cycles at 2 A g-1 and maintain a capacity of up to 12 mAh.

Sustainable lithium extraction enabled by responsive metal-organic frameworks with ion-sieving adsorption effects.

Metal-organic frameworks (MOFs) are superior ion adsorbents for selectively capturing toxic ions from water. Nevertheless, they have rarely been reported to have lithium selectivity over divalent cations due to the well-known flexibility of MOF framework and the similar physiochemical properties of Li+ and Mg2+. Herein, we report an ion-sieving adsorption approach to design sunlight-regenerable lithium adsorbents by subnanoporous MOFs for efficient lithium extraction. By integrating the ion-sieving agent of MOFs with light-responsive adsorption sites of polyspiropyran (PSP), the ion-sieving adsorption behaviors of PSP-MOFs with 6.0, 8.5, and 10.0 Å windows are inversely proportional to their pore size. The synthesized PSP-UiO-66 with a narrowest window size of 6.0 Å shows high LiCl adsorption capacity up to 10.17 mmol g-1 and good Li+/Mg2+ selectivity of 5.8 to 29 in synthetic brines with Mg/Li ratio of 1 to 0.1. It could be quickly regenerated by sunlight irradiation in 6 min with excellent cycling performance of 99% after five cycles. This work sheds light on designing selective adsorbents using responsive subnanoporous materials for environmentally friendly and energy-efficient ion separation and purification.

Unraveling the molecular mechanism for enhanced gas adsorption in mixed-metal MOFs via solid-state NMR spectroscopy.

The incorporation of multiple metal ions in metal-organic frameworks (MOFs) through one-pot synthesis can induce unique properties originating from specific atomic-scale spatial apportionment, but the extraction of this crucial information poses challenges. Herein, nondestructive solid-state NMR spectroscopy was used to discern the atomic-scale metal apportionment in a series of bulk Mg1-xCox-MOF-74 samples via identification and quantification of eight distinct arrangements of Mg/Co ions labeled with a 13C-carboxylate, relative to Co content. Due to the structural characteristics of metal-oxygen chains, the number of metal permutations is infinite for Mg1-xCox-MOF-74, making the resolution of atomic-scale metal apportionment particularly challenging. The results were then employed in density functional theory calculations to unravel the molecular mechanism underlying the macroscopic adsorption properties of several industrially significant gases. It is found that the incorporation of weak adsorption sites (Mg2+ for CO and Co2+ for CO2 adsorption) into the MOF structure counterintuitively boosts the gas adsorption energy on strong sites (Co2+ for CO and Mg2+ for CO2 adsorption). Such effect is significant even for Co2+ remote from Mg2+ in the metal-oxygen chain, resulting in a greater enhancement of CO adsorption across a broad composition range, while the enhancement of CO2 adsorption is restricted to Mg2+ with adjacent Co2+. Dynamic breakthrough measurements unambiguously verified the trend in gas adsorption as a function of metal composition. This research thus illuminates the interplay between atomic-scale structures and macroscopic gas adsorption properties in mixed-metal MOFs and derived materials, paving the way for developing superior functional materials.