Search Results (128)

Colorectal cancer (CRC) pathogenesis is driven by complex protein–protein interactions (PPIs) between the host and the gut microbiome, yet these molecular dialogs remain largely unmapped. This study utilizes a Deep Learning framework, enhanced by protein structure embeddings, to predict approximately 8.9 billion interspecies PPIs from clinical metagenomic data. The model achieved high accuracy with an AUROC of 0.9960, identifying a high-confidence interactome representing roughly 16% of evaluated protein pairs. Phenotype-specific analysis revealed that while microbial hubs shift—transitioning from metabolic enzymes in healthy states to transport and regulatory proteins in CRC—the primary human targets remain remarkably consistent across both cohorts. These core human interactors are predominantly metalloproteins and regulators of ubiquitination, apoptosis, and zinc transport, suggesting these pathways are primary focal points for microbial manipulation regardless of disease state. Furthermore, co-occurring bacterial genera exhibit over 99% overlap in host target profiles, indicating significant functional redundancy in microbial engagement with the host. These findings suggest that CRC probably arises from network-level perturbations of stable host signaling hubs, offering a blueprint for identifying novel therapeutic targets and biomarkers. Full article

Iron (Fe) and nickel (Ni) were both foundational to early metabolism, yet their biological trajectories diverged as Earth’s surface redox state changed. Here, we integrate mineral chemistry network analysis, protein metal-site coordination-sphere analysis, and curated redox comparisons to test how geochemistry and metalloprotein architecture co-evolved. Mineral network analyses show broader electronegativity variation and network diversity for Fe-bearing minerals through time relative to Ni-bearing minerals. In structural analyses of protein metal centers in a combined Fe/Ni protein structure set, it is shown that Fe- and Ni-associated environments differ in amino-acid composition, hydropathy structure, and cysteine representation. The greater chemical diversity and electronegativity variation in Fe minerals mirror the higher redox and structural versatility of Fe-binding proteins. The presence of Fe in a broader range of mineral and protein environments demonstrates the chemical adaptability of the metal, from the anoxic Archean to oxidative Earth surface conditions following the Great Oxidation Event. Iron, with its broad redox potential range in Fe-oxidoreductases, has a central role in both anaerobic and aerobic metabolisms. Nickel, by contrast, is less widespread in biology. Today, Ni is predominantly employed in deeply branching anaerobic pathways and by proteins with narrower redox potential ranges. Our results show that evolutionary processes, constrained by metal chemistry, habitually utilize Fe as a redox generalist while retaining Ni in specialized roles. The divergent paths of Ni and Fe, from rocks to proteins, demonstrate the intimate relationship between planetary geochemistry and metabolic origins on Earth and suggest that Fe/Ni geochemistry may inform habitability assessments in extraterrestrial environments when interpreted within specific planetary environmental contexts. Full article

Members of the genus Streptomyces possess large genomes, a vast and largely unexplored metabolic potential, and a distinctive life cycle characterized by pronounced morphological differentiation. However, despite extensive molecular, genomic, and microbiological research, the functions of many genes in this genus remain poorly characterized. In this study, 929 complete Streptomyces genomes were analyzed. From the predicted proteomes of these genomes, proteins conserved in at least 75% of strains and lacking annotation in the KEGG GENES database were identified and clustered. To expand the annotation, synteny and co-occurrence analyses were performed between these unannotated proteins and annotated genes. A total of 330 conserved clusters were identified; 284 out of 330 clusters contain proteins encoded by genes that are syntenic with those associated with transcriptional regulation, fatty acid metabolism, two-component signaling systems, and morphological development. Additional clusters included metalloproteins and enzymes such as dehydrogenases, suggesting a wide functional spectrum. The conserved yet uncharacterized proteins identified in this analysis represent promising targets for future research, both for elucidating the molecular biology of Streptomyces and for expanding the range of secondary metabolites produced by these ecologically and industrially significant microorganisms Full article

Metalloprotein-based nanomedicines integrate the multifunctionality of metal centers with the engineerability of proteins to construct advanced nanoplatforms for targeted delivery, diagnostic imaging, and multimodal therapy. In these nanomedicines, metal ions or clusters act as functional cores, enabling imaging contrast enhancement, catalytic reactions, and modulation of pathological microenvironments, while protein frameworks provide structural stability, intrinsic biocompatibility, and programmable bio-interfaces. This review summarizes the design principles of three major metalloprotein-based nanomedicines, including native metalloproteins, engineered metalloproteins, and metal–protein hybrid nanostructures, with a focus on ferritin, transferrin, and heme/cytochrome proteins in the contexts of cancer therapy, imaging diagnostics, antimicrobial, and anti-resistance applications. Through discussion of representative metal- and metalloprotein-based nanomedicine candidates, this review highlights the current challenges and outlines opportunities brought by emerging technologies such as artificial intelligence-guided protein design. Collectively, these advances underscore metal- and metalloprotein-based nanomedicines as multifunctional, tunable, and clinically promising platforms that are poised to become an important pillar of future nanomedicine. Full article

Antibiotic resistance is an escalating global health problem that calls for new types of treatments beyond standard antibiotics. This review examines how targeting bacterial metalloproteins, especially those involved in siderophore-driven iron uptake and manganese-based oxidative defense, could lead to more selective antibacterial drugs that are less toxic to humans. Recent research shows that metals and metal-containing compounds can act as antimicrobials, but many of their biological roles are still not well understood. By synthesizing current evidence, this article critically evaluates translational strategies targeting bacterial metalloproteins. These include siderophore–antibiotic conjugates, metal trafficking inhibitors, and catalytic metallodrugs. The review suggests that therapies using receptor-mediated uptake and guided by genomic data deserve priority in clinical development. The review also highlights unresolved challenges in selectivity, toxicity, and resistance mechanisms, offering a roadmap for future research. This review integrates evidence from multiple databases to provide a comprehensive framework for targeting bacterial metalloproteins, combining narrative synthesis with systematic methodology. Full article

Copper transporter 1 (CTR1) is the primary high affinity importer for Cu(I) in eukaryotic cells. CTR1 plays an essential role in maintaining copper homeostasis which is crucial for diverse biological processes. Since its discovery in 1997, research on human CTR1 (hCTR1) has progressed from foundational biochemical characterization to detailed structural and functional elucidation, expanding our understanding of its involvement in human diseases. Here we summarize the current understanding of hCTR1, including its structural features, copper-binding motifs, regulation, trafficking pathways, and roles in disease. We also highlight emerging evidence implicating hCTR1 in cancer, neurodegenerative disorders, and inherited copper metabolism syndromes, emphasizing its potential as a therapeutic target and drug delivery facilitator. Finally, we discuss recent studies and outline future directions, aimed at fully harnessing the biomedical potential of hCTR1. Full article

Analysis of the EPR of dilute transition-ion complexes and metalloproteins in random phases, such as frozen solutions, powders, glasses, and gels, requires a model for the spectral ‘powder’ shape. Such a model comprises a description of the line shape and the linewidth of individual molecules as well as a notion of their physical origin. Spectral features sharpen up with decreasing temperature until the limit of constant linewidth of inhomogeneous broadening. At and below this temperature limit, each molecule has a linewidth that slightly differs from those of its congeners, and which is not related in a simple way to lifetime broadening. Choice of the model not only affects precise assignment of g-values, but also concentration determination (‘spin counting’), and therefore, calculation of stoichiometries in multi-center complexes. Forty years ago, the theoretically and experimentally well-founded statistical theory of g-strain was developed as a prime model for EPR powder patterns. In the intervening years until today, this model was universally ignored in favor of models that are incompatible with physical reality, resulting in many mistakes in EPR spectral interpretation. The purpose of this review is to outline the differences between the models, to reveal where analyses went astray, and thus to turn a very long standstill in EPR powder shape understanding into a new start towards proper methodology. Full article

The ReAV enzyme from Rhizobium etli, a representative of Class 3 L-asparaginases, is sequentially and structurally different from other known L-asparaginases. This distinctiveness makes ReAV a candidate for novel antileukemic therapies. ReAV is a homodimeric protein, with each subunit containing a highly specific zinc-binding site created by two cysteines, a lysine, and a water molecule. Two Ser-Lys tandems (Ser48-Lys51, Ser80-Lys263) are located in the close proximity of the metal binding site, with Ser48 hypothesized to be the catalytic nucleophile. To further investigate the catalytic process of ReAV, site-directed mutagenesis was employed to introduce alanine substitutions at residues from the Ser-Lys tandems and at Arg47, located near the Ser48-Lys51 tandem. These mutational studies, along with enzymatic assays and X-ray structure determinations, demonstrated that substitution of each of these highly conserved residues abolished the catalytic activity, confirming their essential role in enzyme mechanism. Full article

Azurin is a small blue copper protein that participates in redox reactions during anaerobic respiration in Pseudomonas aeruginosa, and there are a significant number of studies employing this model to investigate the electron transfer (ET) processes or coordination sphere of metal ion in metalloproteins. Azurin naturally contains Cu(II/I) as a central ion and is redox-active for a single electron ET. Moreover, azurin with no central ion (apo-azurin) is capable of binding other metal cofactors—e.g., Zn(II)—forming redox-inactive Zn-form and many others impacting the redox potential and structural variation in the active site’s arrangement. Also, mutations of amino acid residues in the immediate vicinity of the metal ion can influence the structure and functionality of a particular metalloprotein. Therefore, this review aims to summarize the abundant information about selected topics related to redox reactions and blue copper proteins, particularly azurin, and is structured as follows: (i) introduction to the structure, properties, and physiological role of this group of metalloproteins, (ii) the role of the equatorial and axial ligands of the central metal ions, or metal species, in the active site on the metal coordination sphere’s structure and related determination of the particular azurin form’s redox potentials, and (iii) the effects of the particular amino acid’s moiety (Phe, Tyr and Trp residues together with acceleration employing Trp-Trp π-π stacking interactions contrary to ET distance dependence) on the preferable type of long-range ET mechanism in an azurin-mediated model biomolecule. We assume that azurin is a suitable model to study the structural functionality of a particular central metal ion or individual amino acid residues in the central ion coordination sphere for studying the redox potential and ET reactions in metalloproteins. Full article

Ultra-high magnetic fields and high-sensitivity cryoprobes permit the achievement of a high S/N ratio in ¹³C detection experiments, thus making a ¹³C superWEFT (Super water eliminated Fourier transform) experiment feasible. ¹³C signals that are not visible using ¹H observed heteronuclear experiments, nor with established 2D ¹³C direct detection experiments, become easily observable when a ¹³C relaxation-based filter is used. Within this frame, optimal control pulses (OC pulses) have been, for the first time, applied to paramagnetic systems. Although the duration of OC pulses competes with relaxation, their application to paramagnetic signals has been successfully tested. OC pulses are much more efficient with respect to the phase- and amplitude-modulated ones routinely used at lower fields while providing bandwidth excitation profiles that are sufficient to meet the need to cover up to an 80 ppm spectral region. On the other hand, when paramagnetic relaxation is shorter than the duration of OC pulses, the use of hard, rectangular pulses is, at the present state of the art, the best approach to minimize the loss of signal intensity. Full article

Diabetes mellitus (DM) has reached pandemic prevalence, significantly impacting global health. Accumulating evidence has highlighted a bidirectional relationship between diabetes and depression, with blood–brain barrier (BBB) disruption playing a pivotal role in the pathogenesis of and therapeutic approaches to both disorders. Mesenchymal stem cells (MSCs) have emerged as a promising cell-based therapeutic strategy for DM; however, their potential to mitigate DM-associated emotional deficits remains unclear. This study investigates whether MSCs can restore BBB integrity and improve emotional deficits in a diabetic mouse model via matrix metalloprotein-9 (MMP-9) inhibition. We used biochemical, molecular, and behavioral analyses to assess BBB function, inflammation, and emotional behavior. Our results demonstrated that diabetic conditions induce BBB dysfunction, characterized by the MMP-9-mediated degradation of tight junction (TJ) proteins claudin-5 (Cldn5) and occludin (Ocln), alongside neuroinflammation and emotional impairments. Notably, MSC administration restored BBB integrity and attenuated neuroinflammation by suppressing MMP-9 activity and upregulating TJ proteins. Importantly, MSC treatment not only alleviated anxiety- and depressive-like behaviors but also enhanced glycemic control in DMmodels. These findings elucidate the mechanistic basis of MSC therapy for DM-related neuropsychiatric complications and, crucially, reveal its dual therapeutic efficacy in concurrently ameliorating both neuropsychiatric symptoms and metabolic dysfunction in DM models. This synergistic therapeutic effect provides a translational rationale for advancing MSC-based therapies into clinical applications. Full article

The world obeys quantum physics and quantum computing presents an alternative way to map physical problems to systems that follow the same laws. Such computation fundamentally constitutes a better way to understand the most challenging quantum problems. One such problem is the accurate simulation of highly correlated quantum systems. Still, modern-day quantum hardware has limitations and only allows for the modeling of simple systems. Here, we present for the first time a quantum computer model simulation of a complex hemocyanin molecule, which is an important respiratory protein involved in various physiological processes and is also used as a key component in therapeutic vaccines for cancer. To characterize the mechanism by which hemocyanin transports oxygen, variational quantum eigensolver (VQE) and quantum embedding methods are used in the context of dynamic mean field theory to solve the Anderson impurity model (AIM). Finally, it is concluded that the magnetic structure of hemocyanin is largely influenced by the many-body correction and that the computational effort for solving correlated electron systems could be substantially reduced with the introduction of quantum computing algorithms. We encourage the use of the Hamiltonian systems presented in this paper as a benchmark for testing quantum computing algorithms’ efficiency for chemistry applications. Full article

Long-range electron transfer (ET) is an essential component of all biological systems. Reactions of metalloproteins are important in this context. Recent work on protein “charge ladders” has revealed how the redox state of embedded metal ions can influence the ionization of amino acid residues at protein surface sites. Inspired by these observations, we carried out a variable pH investigation of intramolecular ET reactions in a ruthenium-modified protein system built on azurin from Pseudomonas aeruginosa. We also generate a Pourbaix diagram that describes the variable pH redox behavior of a Ru model complex, Ru(2,2′-bipyridyl)₂(imidazole)₂(PF₆)₂. The intramolecular ET rate constants for the oxidation of azurin-Cu⁺ by flash-quench-generated Ru³⁺ oxidants do not follow the predictions of the semi-classical ET rate expression with fixed values of reorganization energy (λ) and electronic coupling (H_DA). Based on the pH dependence of the Ru^3+/2+ redox couple, we propose a model where pure ET is operative at acidic pH values (≤ 7) and the mechanism changes to proton-coupled electron transfer at pH ≥ 7.5. The implications of this mechanistic proposal are discussed in the context of biological redox reactions and with respect to other examples of intramolecular ET reactions in the literature. Full article

Precise binding free-energy predictions for ligands targeting metalloproteins, especially zinc-containing histone deacetylase (HDAC) enzymes, require specialized computational approaches due to the unique interactions at metal-binding sites. This study evaluates a docking algorithm optimized for zinc coordination to determine whether it could accurately differentiate between protonated and deprotonated states of hydroxamic acid ligands, a key functional group in HDAC inhibitors (HDACi). By systematically analyzing both protonation states, we sought to identify which state produces docking poses and binding energy estimates most closely aligned with experimental values. The docking algorithm was applied across HDAC 2, 4, and 8, comparing protonated and deprotonated ligand correlations to experimental data. The results demonstrate that the deprotonated state consistently yielded stronger correlations with experimental data, with R² values for deprotonated ligands outperforming protonated counterparts in all HDAC targets (average R² = 0.80 compared to the protonated form where R² = 0.67). These findings emphasize the significance of proper ligand protonation in molecular docking studies of zinc-binding enzymes, particularly HDACs, and suggest that deprotonation enhances predictive accuracy. The study’s methodology provides a robust foundation for improved virtual screening protocols to evaluate large ligand libraries efficiently. This approach supports the streamlined discovery of high-affinity, zinc-binding HDACi, advancing therapeutic exploration of metalloprotein targets. A comprehensive, step-by-step tutorial is provided to facilitate a thorough understanding of the methodology and enable reproducibility of the results. Full article

Epigallocatechin gallate (EGCg), an abundant phytochemical in green tea, is an antioxidant that also binds proteins and complex metals. After gastrointestinal absorption, EGCg binds to serum albumin in the hydrophobic pocket between domains IIA and IIIA and overlaps with the Sudlow I site. Serum albumin also has two metal binding sites, a high-affinity N-terminal site (NTS) site that selectively binds Cu(II), and a low-affinity, less selective multi-metal binding site (MBS). We proposed to determine whether EGCg binds or reacts with Cu(II)-serum albumin using fluorescence, UV–Visible and electron paramagnetic resonance (EPR) spectroscopy. Our results suggest that when serum albumin is loaded with Cu(II) in both sites, EGCg binds to the MBS-Cu(II) and reduces the copper to Cu(I). EGCg does not bind to or react with Cu(II) in the high-affinity NTS site. Potential consequences include changes in copper homeostasis and damage from pro-oxidative Fenton reactions. Full article