Recent Advances in Metalloproteomics

Interactions between proteins and metal ions and their complexes are important in many areas of the life sciences, including physiology, medicine, and toxicology. Despite the involvement of essential elements in all major processes necessary for sustaining life, metalloproteomes remain ill-defined. This is not only owing to the complexity of metalloproteomes, but also to the non-covalent character of the complexes that most essential metals form, which complicates analysis. Similar issues may also be encountered for some toxic metals. The review discusses recently developed approaches and current challenges for the study of interactions involving entire (sub-)proteomes with such labile metal ions. In the second part, transition metals from the fourth and fifth periods are examined, most of which are xenobiotic and also tend to form more stable and/or inert complexes. A large research area in this respect concerns metallodrug-protein interactions. Particular attention is paid to separation approaches, as these need to be adapted to the reactivity of the metal under consideration.

Mitochondrial ATP synthase as a direct molecular target of chromium(III) to ameliorate hyperglycaemia stress

Chromium(III) is extensively used as a supplement for muscle development and the treatment of diabetes mellitus. However, its mode of action, essentiality, and physiological/pharmacological effects have been a subject of scientific debate for over half a century owing to the failure in identifying the molecular targets of Cr(III). Herein, by integrating fluorescence imaging with a proteomic approach, we visualized the Cr(III) proteome being mainly localized in the mitochondria, and subsequently identified and validated eight Cr(III)-binding proteins, which are predominately associated with ATP synthesis. We show that Cr(III) binds to ATP synthase at its beta subunit via the catalytic residues of Thr213/Glu242 and the nucleotide in the active site. Such a binding suppresses ATP synthase activity, leading to the activation of AMPK, improving glucose metabolism, and rescuing mitochondria from hyperglycaemia-induced fragmentation. The mode of action of Cr(III) in cells also holds true in type II diabetic male mice. Through this study, we resolve the long-standing question of how Cr(III) ameliorates hyperglycaemia stress at the molecular level, opening a new horizon for further exploration of the pharmacological effects of Cr(III).

Fluorescent proteins and genetically encoded biosensors

The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.

Cisplatin Binding to Human Serum Transferrin: A Crystallographic Study

The molecular mechanism of how human serum transferrin (hTF) recognizes cisplatin at the atomic level is still unclear. Here, we report the molecular structure of the adduct formed upon the reaction of hTF with cisplatin. Pt binds the side chain of Met256 (at the N-lobe), without altering the protein overall conformation.

Quantifying In Situ Structural Stabilities of Human Blood Plasma Proteins Using a Novel Iodination Protein Stability Assay

Many of the diseases that plague society today are driven by a loss of protein quality. One method to quantify protein quality is to measure the protein folding stability (PFS). Here, we present a novel mass spectrometry (MS)-based approach for PFS measurement, iodination protein stability assay (IPSA). IPSA quantifies the PFS by tracking the surface-accessibility differences of tyrosine, histidine, methionine, and cysteine under denaturing conditions. Relative to current methods, IPSA increases protein coverage and granularity to track the PFS changes of a protein along its sequence. To our knowledge, this study is the first time the PFS of human serum proteins has been measured in the context of the blood serum (in situ). We show that IPSA can quantify the PFS differences between different transferrin iron-binding states in near in vivo conditions. We also show that the direction of the denaturation curve reflects the in vivo surface accessibility of the amino acid residue and reproducibly reports a residue-specific PFS. Along with IPSA, we introduce an analysis tool Chalf that provides a simple workflow to calculate the residue-specific PFS. The introduction of IPSA increases the potential to use protein structural stability as a structural quality metric in understanding the etiology and progression of human disease. Data is openly available at Chorusproject.org (project ID 1771).

Identification and Tetramer Structure of Hemin-Binding Protein SPD_0310 Linked to Iron Homeostasis and Virulence of Streptococcus pneumoniae

Iron and iron-containing compounds are essential for bacterial virulence and host infection. Hemin is an important supplement compound for bacterial survival in an iron-deficient environment. Despite strong interest in hemin metabolism, the detailed mechanism of hemin transportation in Gram-positive bacteria is yet to be reported. The results of our study revealed that the homologous proteins of SPD_0310 were significantly conservative in Gram-positive bacteria (P < 0.001), and these proteins were identified as belonging to an uncharacterized protein family (UPF0371). The results of thermodynamic and kinetic studies have shown that SPD_0310 has a high hemin-binding affinity. Interestingly, we found that the crystal structure of SPD_0310 presented a homotetramer conformation, which is required for hemin binding. SPD_0310 can interact with many hemin-binding proteins (SPD_0090, SPD_1609, and GAPDH) located on the cell surface, which contributes to hemin transfer to the cytoplasm. It also has a high affinity with other iron transporters in the cytoplasm (SPD_0226 and SPD_0227), which facilitates iron redistribution in cells. More importantly, the knockout of the spd_0310 gene (Δspd_0310) resulted in a decrease in the iron content and protein expression levels of many bacterial adhesion factors. Moreover, the animal model showed that the Δspd_0310 strain has a lower virulence than the wild type. Based on the crystallographic and biochemical studies, we inferred that SPD_0310 is a hemin intermediate transporter which contributes to iron homeostasis and further affects the virulence of Streptococcus pneumoniae in the host. Our study provides not only an important theoretical basis for the in-depth elucidation of the hemin transport mechanism in bacteria but also an important candidate target for the development of novel antimicrobial agents based on metal transport systems. IMPORTANCE Iron is an essential element for bacterial virulence and infection of the host. The detailed hemin metabolism in Gram-positive bacteria has rarely been studied. SPD_0310 belongs to the UPF0371 family of proteins, and results of homology analysis and evolutionary tree analysis suggested that it was widely distributed and highly conserved in Gram-positive bacteria. However, the function of the UPF0371 family remains unknown. We successfully determined the crystal structure of apo-SPD_0310, which is a homotetramer. We found that cytoplasmic protein SPD_0310 with a special tetramer structure has a strong hemin-binding ability and interacts with many iron transporters, which facilitates hemin transfer from the extracellular space to the cytoplasm. The results of detailed functional analyses indicated that SPD_0310 may function as a hemin transporter similar to hemoglobin in animals and contributes to bacterial iron homeostasis and virulence. This study provides a novel target for the development of antimicrobial drugs against pathogenic Gram-positive bacteria.

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. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The proteomic profiling of multiple tissue damage in chickens for a selenium deficiency biomarker discovery

Over the past decades, substantial advances have been made in both the early diagnosis and accurate prognosis of numerous cancers because of the impressive development of novel proteomic strategies. Selenium (Se) is an essential trace element in humans and animals. Se deficiency could lead to Keshan disease in humans, mulberry heart disease in pigs and damage of tissues including cardiac injury, apoptosis in the liver, reduction in the immune responses in spleen and cerebral lesions in chickens. However, it is well know that plasma biomarkers are not specific and also show alterations in various diseases including those caused by Se deficiency. Therefore, new definition biomarkers are needed to improve disease surveillance and reduce unnecessary chicken losses due to Se deficiency. To identify new biomarkers for Se deficiency, we performed exploratory heart, liver, spleen, muscle, vein, and artery proteomic screens to further validate the biomarkers using Venn analysis, GO enrichment, heatmap analysis, and IPA analysis. Based on the bioinformatics methods mentioned above, we found that differentially expressed genes and proteins are enriched to the PI3K/AKT/mTOR signal pathway and insulin pathway. We further used western blot to detect the expression of proteins related to the two pathways. Results showed that the components of the PI3K/AKT/mTOR signal pathway were definitely decreased in heart, liver, spleen, muscle, vein and artery tissues in the Se deficient group. Expression IGF and IGFBP2 of the insulin pathway were differentially increased in the heart, liver, and spleen in Se deficient group samples and decreased in muscle and artery. In conclusion, 5 proteins, namely PI3K, AKT, mTOR, IGF, and IGFBP2, were differentially expressed, which could be potentially useful Se deficient biomarkers. In the present study, proteomic profiling was used to elucidate protein biomarkers that distinguished Se deficient samples from the controls, which might provide a new direction for the diagnosis and targeted treatment induced by Se deficiency in chickens.

Bismuth drugs tackle Porphyromonas gingivalis and attune cytokine response in human cells

Periodontitis is the leading cause of severe tooth loss and edentulism in adults worldwide and is closely linked to systemic conditions such as diabetes and cardiovascular disease. Porphyromonas gingivalis is the key pathogen in periodontitis. Herein, we provided the first evidence that bismuth drugs suppress P. gingivalis in its planktonic, biofilm, and intracellular states. In total, 42 bismuth-associated proteins were identified including its major virulent factors (e.g., gingipains, hemagglutinin HagA, and fimbriae). Bismuth perturbed its iron acquisition, disturbed the energy metabolism and virulence, and deactivated multiple key enzymes (e.g., superoxide dismutase and thioredoxins). Moreover, bismuth inhibited its biofilm formation and disrupted the 3-day matured biofilms. Notably, the internalized P. gingivalis in various human cells (e.g., human gingival epithelium progenitors, HGEPs) was oppressed by bismuth but not the commonly used antibiotic metronidazole. Importantly, bismuth drugs enabled the counteraction of immuno-inflammatory responses in different host cells perturbed by P. gingivalis. The production of IL-6 and IL-8 attenuated by P. gingivalis in both of native and IL-1β-stimulated HGEPs was restored, while the bacterium-enhanced expression of IL-6, IL-1β, and TNFα in THP-1 macrophages was alleviated. This proof-of-concept study brings prospects for the potential reposition of the routinely used anti-Helicobacter pylori bismuth drugs to better manage inflammatory diseases such as periodontitis and P. gingivalis-related complex systemic disorders.

Recognition of Proteins by Metal Chelation-Based Fluorescent Probes in Cells

Fluorescent probes such as thiol-reactive and Ni2+-nitrilotriacetate (NTA) based probes provide a powerful toolbox for real-time visualization of a protein and a proteome in living cells. Herein, we first went through basic principles and applications of thiol-reactive based probes in protein imaging and recognition. We then summarize a family of metal-NTA based fluorescence probes in the visualization of His6-tagged protein and identification of metalloproteins at proteome-wide scale. The pros and cons of the probes, as well as ways to optimize them, are discussed.

Systems Approaches for Unveiling the Mechanism of Action of Bismuth Drugs: New Medicinal Applications beyond Helicobacter Pylori Infection

Metallodrugs have been widely used as diagnostic and therapeutic agents. Understanding their mechanisms of action may lead to advances in rational drug design. However, to achieve this, diversified approaches are required because of the complexity of metal-biomolecule interactions. Bismuth drugs in combination with antibiotics as a quadruple therapy show excellent success rates in the eradication of Helicobacter pylori, even for antibiotic-resistant strains, and in fact, they have been used in the clinic for decades for the treatment of infection. Understanding the mechanism of action of bismuth drugs may extend their medicinal application beyond the treatment of H. pylori infection. This Account describes several general strategies for mechanistic studies of metallodrugs, including system pharmacology and metalloproteomics approaches. The application of these approaches is exemplified using bismuth drugs. Through a system pharmacology approach, we showed that glutathione- and multidrug-resistance-associated protein 1-mediated self-propelled disposal of bismuth in human cells might explain the selective toxicity of bismuth drugs to H. pylori but not the human host. The development of metalloproteomics has enabled extensive studies of the putative protein targets of metallodrugs with a dynamic range of affinity. Continuous-flow GE-ICP-MS allows simultaneous monitoring of metals and their associated proteins with relatively high affinity on a proteome-wide scale. The fluorescence approach relies on unique M ⁿ⁺-NTA-based fluorescence probes and is particularly applicable for mining those proteins that bind to metals/metallodrugs weakly or transiently. Integration of these methods with quantitative proteomics makes it possible to maximum coverage of bismuth-associated proteins, and the sustained efficacy of bismuth drugs lies in their ability to disrupt multiple biological pathways through binding and functional perturbation of key enzymes. The knowledge acquired by mechanistic studies of bismuth drugs led to the discovery of UreG as a new target for the development of urease inhibitors. The ability of Bi(III) to inhibit metallo-β-lactamase (MBL) activity through displacement of the Zn(II) cofactor renders bismuth drugs new potential as broad-spectrum inhibitors of MBLs. Therefore, bismuth drugs could be repurposed together with clinically used antibiotics as a cotherapy to cope with the current antimicrobial resistance crisis. We anticipate that the methodologies described in this Account are generally applicable for understanding the (patho)physiological roles of metals/metallodrugs. Our mechanism-guided discovery of new druggable targets as well as new medicinal applications of bismuth drugs will inspire researchers in relevant fields to engage in the rational design of drugs and reuse of existing drugs, eventually leading to the development of new effective therapeutics.