Search Results (234)

Background: This study aimed to investigate rapid oxidation in poultry and fish myoglobin compared to livestock myoglobin using protein structural differences and bioinformatics tools. Methods: Myoglobins from beef (Bos taurus), bison (Bos bison), sheep (Ovis aries), goat (Capra hircus), red deer (Cervus elaphus), pork (Sus scrofa), chicken (Gallus gallus), turkey (Meleagris gallopavo), yellowfin tuna (Thunnus albacares), and tilapia (Oreochromis niloticus) were analyzed to understand differences in structure and function that may influence oxidative behavior. Results: Fish and poultry had shorter or absent D-helix in their myoglobin structure than other species. Tilapia showed the largest heme cavity surface area, indicating significant internal void space, while yellowfin tuna had the largest heme cavity volume, which could affect ligand binding dynamics compared with poultry and other livestock species. However, the heme solvent-accessible area was greater in chicken and turkey than in fish and other livestock species. Tuna myoglobin contains a cysteine and fish myoglobins have fewer amino acids compared to other species. Limited knowledge is currently available on the effects of proteoform, especially post-translational modifications, on the oxidation of myoglobin from different species. Conclusions: The bioinformatics approach used in this study suggests that, in addition to physiological reasons, shorter D-helix, larger heme cavity in tilapia and yellowfin tuna, and greater solvent-accessible area in poultry contribute to increased oxidation in myoglobin from poultry and fish compared with myoglobin from livestock species. Full article

Class 1 phytoglobins (Pgbs) are known for their multifunctional roles in plant stress responses, with recent studies suggesting broader interactions involving metabolic and transcriptional regulation. Interestingly, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) moonlights in many roles in colocalized spaces during cellular stress that are strikingly suitable for supporting Pgb function. This study investigates the molecular interactions of class 1 Pgb from sugar beet (Beta vulgaris), BvPgb 1.2, and an alanine-substituted mutant (C86A), focusing on their ability to bind GAPDH and DNA. Using dual-emission isothermal spectral shift (SpS) analysis, we report strong binding interactions with GAPDH, with dissociation constants (K_D) of 260 ± 50 nM for the recombinant wild-type protein (rWT) and a significantly stronger affinity for C86A (120 ± 40 nM), suggesting that the cysteine residue limits the interaction. Remarkably strong DNA-binding affinities were also observed for both variants, displaying biphasic binding. This behavior is characteristic of hexacoordinated globins and reflects the presence of two distinct species: a fast-reacting open pentacoordinated form and a slow-reacting closed hexacoordinated form with high apparent affinity. Here, the K_D in the open configuration was 120 ± 50 nm and 50 ± 20 nM for rWT and C86A, respectively. In the closed configuration, however, the cysteine appears to support the interaction, as the K_D was measured at 100 ± 10 pM and 230 ± 60 pM for rWT and C86A, respectively. Protein–protein docking studies reinforced these findings, revealing electrostatically driven interactions between BvPgb 1.2 and GAPDH, characterized by a substantial buried surface area indicative of a stable, biologically relevant complex. Protein–DNA docking similarly confirmed energetically favorable binding near the heme pocket without obstructing ligand accessibility. Together, these findings indicate a potential regulatory role for BvPgb 1.2 through its interaction with GAPDH and DNA. Full article

The bark of Dillenia indica L. is a rich source of phenolic and triterpenoid compounds, including betulinic acid (BA), known for their antioxidant and anti-aging properties. This study investigated the antioxidant potential of a BA-enriched extract through a multidisciplinary approach combining computational, experimental, and cell-based evaluations. Molecular docking and molecular dynamics simulations revealed that BA binds stably to Kelch-like ECH-associated protein 1 (KEAP1), suggesting activation of the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway. Extraction conditions were optimized using response surface methodology (RSM) and artificial neural network (ANN) modeling, yielding the maximum total phenolic content (TPC; 85.33 ± 2.26 mg gallic acid equivalents/g) and total flavonoid content (TFC; 75.60 ± 1.66 mg catechin equivalents/g), with ANN demonstrating superior predictive performance compared to RSM. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) confirmed the presence of BA in the optimized extract. Simulated gastrointestinal digestion revealed reductions in TPC, TFC, and radical scavenging activity during the gastric phase. In ultraviolet B (UVB)-irradiated human keratinocyte (HaCaT) cells, the optimized extract significantly reduced intracellular reactive oxygen species (ROS) and upregulated the KEAP1-Nrf2-heme oxygenase-1 (HO-1) pathway, confirming its antioxidant mechanism. These findings highlight the extract’s stability, bioactivity, and mechanistic efficacy, supporting its application as a nutraceutical ingredient for combating oxidative stress and skin aging. Full article

Heme enzymes that bind and reduce O₂ are susceptible to poisoning by NO. The high reactivity and affinity of NO for ferrous heme produces stable ferrous-NO complexes, which in theory should preclude O₂ binding and turnover. However, NO inhibition is often competitive with respect to O₂ and rapidly reversible, thus providing cellular and organismal survival advantages. This kinetic paradox has prompted a search for mechanisms for reversal and hence resistance. Here, I critically review proposed resistance mechanisms for NO dioxygenase (NOD) and cytochrome c oxidase (CcO), which substantiate reduction or oxidation of the tightly bound NO but nevertheless fail to provide kinetically viable solutions. A ferrous heme intermediate is clearly not available during rapid steady-state turnover. Reversible inhibition can be attributed to NO competing with O₂ in transient low-affinity interactions with either the ferric heme in NOD or the ferric heme-cupric center in CcO. Toward resolution, I review the underlying principles and evidence for kinetic control of ferric heme reduction via an O₂-triggered ferric heme spin crossover and an electronically-forced motion of the heme and structurally-linked protein side chains that elicit electron transfer and activate O₂ in the flavohemoglobin-type NOD. For CcO, kinetics, structures, and density functional theory point to the existence of an analogous O₂ and reduced oxygen intermediate-controlled electron-transfer gate with a linked proton pump function. A catalytic cycle and mechanism for CcO is finally at hand that links each of the four O₂-reducing electrons to each of the four pumped protons in time and space. A novel proton-conducting tunnel and channel, electron path, and pump mechanism, most notably first hypothesized by Mårten Wikström in 1977 and pursued since, are laid out for further scrutiny. In both models, low-energy spin-orbit couplings or ‘spintronic’ interactions with O₂ and NO or copper trigger the electronic motions within heme that activate electron transfer to O₂, and the exergonic reactions of transient reactive oxygen intermediates ultimately drive all enzyme, electron, and proton motions. Full article

Background/Objectives: Giardiasis is one of the oldest-reported infectious diseases worldwide. It affects individuals with weakened immune systems and progresses into chronic infection if untreated. Morphological analysis and visualization of cell shapes using unlabeled or fluorophore-labeled samples are commonly employed to identify the parasite. Methods: To distinguish molecular content variations between trophozoites and infectious type I cysts, the current research presents an alternative approach based on label-free Raman microscopy. Results: Constituents responsible for plasma membrane thickening and cyst wall formation during encystation, such as N-acetylgalactosamine (GalNAc) and N-acetylglucosamine (GlcNAc) were detected. Although these two coexisting compounds have similar molecular structures, their spectroscopic distinction and visual localization through Raman microscopy are achievable. While immature and non-viable cysts contain a larger amount of GlcNAc, a potential transition of this moiety to GalNAc might occur as the cysts mature and become infectious. Other Raman results revealed changes in the oxidation states of heme-binding proteins and in lipid–protein metabolism, each serving as an additional protection mechanism that the parasite employs for survival. Complementary bright field and confocal fluorescence microscopy results corroborate the Raman outcomes. Conclusions: The molecular-level findings of this work, which presents a detailed spectroscopic analysis of Giardia’s encystation and excystation stages, substantiate the need to use complementary methods for monitoring the parasite’s dynamics and efficacy in terms of self-protection. This alternative method provides accurate insights for further understanding the multifaceted factors involved in Giardia’s encystation process and its acquired resistance to external stimuli. Full article

Phytoglobins (Pgbs) are plant hemoglobin-like proteins with key roles in nitric oxide (NO) scavenging, oxygen sensing, and hypoxic stress responses. Their typical hexacoordination results in unusually high affinities for gaseous ligands such as NO and carbon monoxide (CO), complicating measurement using conventional methods. Standard assays often require large sample volumes and lack sensitivity for high-affinity, low-abundance proteins like hexacoordinated Pgbs. Here, we present a microscale capillary-based fluorescence assay for the high-precision measurement of protein–gas binding. Fluorophore-labeled proteins are loaded into gas-saturated capillaries and analyzed via dual-wavelength fluorescence to monitor isothermal spectral shifts upon ligand binding. Phosphate-buffered saline with Tween20 (PBS-T20) ensures gas stability and minimizes nonspecific adsorption. Using this approach, we characterized CO and NO binding to the recombinant wildtype (rWT) of Beta vulgaris Pgb 1.2 (BvPgb 1.2) and its C86A mutant. CO titrations revealed biphasic binding, with EC₅₀ ~400 nM and ~700 μM (rWT) and ~500 nM and ~400 μM (C86A). NO binding showed K_D values of ~1600 nM (rWT) and ~400 nM (C86A), implicating Cys86 in ligand affinity. This assay provides a robust, low-volume method for high-affinity protein–gas studies and shows biphasic dynamics in BvPgbs. Full article

Oxidative stress significantly contributes to the exacerbation of brain damage during cerebral ischemia-reperfusion injury (CIR/I). In our previous study, purified cornel iridoid glycoside (PCIG), consisting of morroniside (MOR) and loganin (LOG), showed neuroprotective effects against CIR/I. To further explore the antioxidative effects and underlying molecular mechanisms, we applied PCIG, MOR, and LOG to rats injured by middle cerebral artery occlusion/reperfusion (MCAO/R) as well as H₂O₂-stimulated PC12 cells. Additionally, the molecular docking analysis was performed to assess the interaction between the PCIG constituents and Kelch-like ECH-associated protein 1 (Keap1). The results showed that the treated rats experienced fewer neurological deficits, reduced lesion volumes, and lower cell death accompanied by decreased levels of malondialdehyde (MDA) and protein carbonyl, as well as increased activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px). In H₂O₂-stimulated PC12 cells, the treatments decreased reactive oxygen species (ROS) production, mitigated mitochondrial dysfunction, and inhibited mitochondrial-dependent apoptosis. Moreover, the treatments facilitated Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) translocation into the nucleus and selectively increased the expression of NAD(P)H quinone oxidoreductase 1 (NQO-1) and heme oxygenase 1 (HO-1) through MOR and LOG, respectively. Both MOR and LOG demonstrated strong binding affinity to Keap1. These findings suggested that PCIG, rather than any individual components, might serve as a valuable treatment for ischemic stroke by activating the Nrf2/NQO-1 and Nrf2/HO-1 signaling pathway. Full article

The Spodoptera litura, a Lepidopteran pest known for its high fecundity, undergoes a complete metamorphosis, including a distinctive process during which the male testes fuse from two separate organs into a single entity, significantly enhancing its fertility. To elucidate the molecular mechanisms underlying this testicular fusion, this study employed an integrated multi-omics approach to investigate concurrent changes at the transcriptomic and proteomic levels. We identified a series of synchronized alterations on the peritestic larval membrane, including heme binding, peptidase activity, hydrolase activity, metal ion transport, redox reactions, and chitin metabolism, all of which are substantially enriched at specific temporal points during testicular fusion. Nine genes/proteins co-expressed at the mRNA and protein levels were selected for targeted quantitative proteomics (PRM) and quantitative PCR (qPCR) validation, leading to the identification of five genes potentially involved in the testicular fusion process: Sl3030, ARCP, PSLRE, Obstructor-E, and Osris9B. Notably, the gene Sl3030, once knocked out, not only disrupted the normal fusion process but also resulted in reduced testis size, thickened peritestic membranes, and abnormal sperm development. Transcriptomic sequencing of the Sl3030 knockout mutant revealed its primary influence on the fusion process by affecting the assembly of the microtubule system and cytoskeleton. This research, for the first time, provides a multi-omics perspective on the response of key signaling pathways and molecular changes during the testicular fusion of S. litura and validates the role of the previously uncharacterized gene Sl3030 in this process, offering valuable insights into the complex mechanisms of testicular fusion in this species. Full article

Frataxin is a component of the iron–sulfur (Fe-S) cluster assembly complex in mitochondria, and deficiency is associated with Friedreich ataxia (FA). The yeast homolog Yfh1 resembles and cross-complements with its human equivalent, and frataxin bypass scenarios are of particular interest because they may point to strategies for treating FA. Here, we describe frataxin/Yfh1 bypass by overexpression of Rsm22, an assembly factor for the mitochondrial ribosome. Rsm22 overexpression in Yfh1-depleted yeast cells restored critical processes in mitochondria, including Fe-S cluster assembly, lipoic acid synthesis, iron homeostasis, and heme synthesis, to a significant extent. Formation of cytoplasmic Fe-S proteins was also restored, suggesting recovery of the mitochondrial ability to generate the (Fe-S)_int intermediate that is exported from mitochondria and is utilized for cytoplasmic Fe-S cluster assembly. Importantly, an essential component of the mitochondrial iron–sulfur cluster machinery, namely ferredoxin, was virtually absent in mitochondria lacking Yfh1, but it was recovered with Rsm22 overexpression. Interestingly, ferredoxin overexpression could offset some of the effects of Yfh1 depletion. Ferredoxin has recently been shown to bind to the cysteine desulfurase protein Nfs1 at the same site as Yfh1, in a conserved arginine patch on Nfs1, such that ferredoxin binding at this site may confer frataxin-bypass activity. Full article

Hepcidin is a key regulator of systemic iron homeostasis, which is essential for maintaining iron balance and cellular health. To investigate its role in zebrafish, we empolyed a hepcidin knockout model. Morphological and histological analyses revealed pale livers and significant iron accumulation in hep^−/− zebrafish, particularly in liver, skin, and egg tissues. RNA sequencing identified 1,424 differentially expressed genes (DEGs) between wild-type (WT) and hep^−/− zebrafish, with significant enrichment in pathways related to ferroptosis, fatty acid degradation, and heme binding. Western blot analysis showed reduced levels of key iron-related proteins, including GPX4, Fth1, and ferroportin (FPN), indicating impaired iron transport and increased oxidative stress. Gene Ontology (GO) and KEGG analyses highlighted disruptions in iron metabolism and lipid oxidation, linking iron overload to ferroptosis in the absence of hepcidin. These findings demonstrate that hepcidin deficiency leads to profound dysregulation of iron homeostasis, driving lipid peroxidation and ferroptosis in the zebrafish liver. Our study provides mechanistic insights into the molecular consequences of hepcidin loss, advancing our understanding of iron-related oxidative damage and its physiological impacts. Full article

Background: Intestinal ischemia reperfusion injury (IRI) is a harmful process that occurs during intestinal infarction and intestinal transplantation (ITx). It is characterized by severe inflammation which disrupts the mucosal barrier, causing bacterial translocation and sepsis. Tranilast (N-[3,4-dimethoxycinnamoyl]-anthranilic acid) (TL) is a synthetic compound with powerful anti-inflammatory properties. Objective: To investigate the effect of pretreatment with TL in a validated rat model of intestinal IRI (60 min of ischemia). Methods: TL (650 mg/kg) was administered by oral gavage 24 and 2 h before the onset of ischemia. Experiment 1 examined 7-day survival in 3 study groups (sham, vehicle+IRI and TL+IRI, n = 10/group). In Experiment 2, the effects on the intestinal wall integrity and inflammation were studied after 60 min of reperfusion using 3 groups (sham, IRI and TL+IRI, n = 6/group). The following end-points were studied: L-lactate, intestinal fatty acid-binding protein (I-FABP), histology, intestinal permeability, endotoxin translocation, pro- and anti-inflammatory cytokines and heme oxygenase-1 (HO-1) levels. Experiment 3 examined the role of HO-1 upregulation in TL pretreatment, by blocking its expression using Zinc protoporphyrin (ZnPP) at 20 mg/kg vs. placebo (n = 6/group). Results: Intestinal IRI resulted in severe damage of the intestinal wall and a 10% 7-day survival. These alterations led to endotoxin translocation and upregulation of pro-inflammatory cytokines. TL pretreatment improved survival up to 50%, significantly reduced inflammation and protected the intestinal barrier. The HO-1 inhibitor ZnPP, abolished the protective effect of TL. Conclusions: TL pretreatment improves survival by protecting the intestinal barrier function, decreasing inflammation and endotoxin translocation, through upregulation of HO-1.This rat study of severe intestinal ischemia reperfusion injury demonstrates a novel role for Tranilast as a potential therapy. Administration of Tranilast led to a marked reduction in mortality, inflammation and intestinal permeability and damage. The study proved that Tranilast functions through upregulation of heme oxygenase-1. Full article

Currently, various types of myoglobins and hemoglobins are widely used in the fields of food additives and biocatalytic applications. However, the limited availability of heme constrains the biosynthesis of these high-activity hemoproteins in microbial chassis cells. In this work, a new heme synthetic pathway was reconstructed in the mitochondria by eliminating the spatial barrier during heme synthesis in Saccharomyces cerevisiae, resulting in a significant enhancement in intracellular heme supply. To further enhance the supply of the essential precursor for heme synthesis (5-aminolevulinate, ALA), the special ALA exporter in the mitochondrial membrane (Ort1p) was identified and knocked out. Moreover, the mitochondrial heme exporter (Ygr127wp) was overexpressed to promote the transport of heme to the cytoplasm to participate in the synthesis of various myoglobins and hemoglobins. Based on these strategies in the engineered strain, the binding ratios of heme in porcine myoglobin (52.4 ± 4.9%) and soybean hemoglobin (75.5 ± 2.8%) were, respectively, increased by 2.4-fold and 3.6-fold, and the titers of porcine myoglobin (130.5 ± 2.8 mg·L⁻¹) and soybean hemoglobin (152.8 ± 2.6 mg·L⁻¹), respectively, increased by 31.1% and 42.1%. Furthermore, the engineered strain presents great potential in the efficient synthesis of other heme-binding proteins and enzymes in S. cerevisiae. Full article

The discovery of carbon monoxide releasing molecules (CORMs) was one of the most impactful innovations in biochemistry, affecting multiple disciplines for the past few decades. Sixteen years ago, a ruthenium dimer-containing CORM, CORM-2, enhanced coagulation and diminished fibrinolysis in human plasma by modulation of fibrinogen, plasmin, and α₂-antiplasmin via CO binding to putative heme groups attached to these proteins. This finding linked CO exposure in settings involving heme oxygenase-1 upregulation during inflammation or environmental exposure to thromboembolic disease in hundreds of subsequent manuscripts. However, CO-independent effects of CORM-2 involving a putative ruthenium radical (Ru•) formed during CO release was found to be responsible for many of effects by CORM-2 in other works. Using a novel approach with human plasmatic coagulation kinetic methods, Ru• was posited to bind to critical histidines and other amino acids to modulate function, and excess histidine to quench CORM-2-mediated effects. This paradigm of histidine addition would definitively address if CO or Ru• was responsible for CORM-2-mediated effects. Thus, plasma coagulation/fibrinolytic kinetic data were assessed via thrombelastography ±CORM-2, ±histidine added. Histidine nearly completely abrogated CORM-2-mediated hypercoagulation in a concentration-dependent fashion; further, histidine also nearly eliminated all kinetic effects on fibrinolysis. In conclusion, CORM-2 Ru• formation, not CO release, is the true molecular mechanism modulating coagulation and fibrinolysis. Full article

Ferrochelatase is the terminal enzyme in heme biosynthesis. Bacillus thuringiensis (Bt) 97-27 contains two ferrochelatases, HemH1 and HemH2, but their regulatory mechanisms and functional differences under virous environmental stimuli remain unclear. This study confirmed that the iron uptake regulator protein (Fur) bound to the promoters of hemH1 and hemH2, with Fe²⁺ or Fe³⁺ enhancing this binding. Heterologous expression of HemH1 and HemH2 in Escherichia coli showed that pEH2/BL grew better than pEH1/BL under different 2,2′-Bipyridyl, Fe²⁺, and Fe³⁺ concentrations. Under iron limitation, the heme precursor ALA production decreased significantly in both strains. The heme production of pEH2/BL decreased sharply under iron-limited conditions, while that of pEH1/BL decreased significantly under iron-rich conditions. The H₂O₂ sensitivity experiment revealed that E. coli pEH1/BL was more tolerant to H₂O₂ than pEH2/BL. In Bt, ΔhemH2 was most sensitive to H₂O₂ stress, but complementation of hemH1 or hemH2 partially restored H₂O₂ resistance, with the overexpressed strain pHH2/Bt being most tolerant. β-galactosidase assays indicated that Fur positively regulated hemH1 and negatively regulated hemH2 under normal conditions, but this regulation reversed with 2.5 mM Fe³⁺. qRT-PCR showed upregulation of genes related to heme synthesis, oxidative stress, and ferrous iron transport. This study reveals the functional differentiation of HemH1 and HemH2 under the joint regulation of Fur and environmental factors, highlighting their synergistic roles in heme synthesis, heavy metal detoxification, and oxidative stress resistance to maintain bacterial physiological homeostasis. Full article

Cytochromes P450 are a superfamily of heme-containing monooxygenases involved in a variety of oxidative metabolic reactions, primarily catalyzing the insertion of an oxygen atom into a C-H bond. CYP102 represents the first example of a bacterial P450 that can be classified as a type II (eukaryotic-like) P450 and functions as a catalytically self-sufficient enzyme. These unique features have made CYP102 an attractive system for studying P450 structure and function. However, an overall picture of the specific amino acid residues that are crucial to the functioning of CYP102 and the effect of mutations on the P450 structure and catalysis is yet to be reported. Such an approach will aid protein engineering approaches used to improve this enzyme. To address this research knowledge gap, we have investigated 105 CYP102 crystal structures in this study. We demonstrate that the CYP102 active site is highly dynamic and flexible. Amino acid residues that play critical roles in substrate binding, orientation, and anchoring were identified. Mutational studies highlighted the roles of amino acids and provided possible bioengineering improvement strategies for CYP102. Decoy molecules are a promising agent for deceiving CYP102 and permitting non-native substrates into the active site. Ru(II)-diimine photosensitizers and zinc/cobalt (III) sepulchrate (Co(III)Sep) could be used as alternative electron sources. The present study serves as a reference for understanding the structure–functional analysis of CYP102 family members precisely and of P450 enzymes in general. Significantly, this work contributes to the effort to develop an improved CYP102 enzyme, thereby advancing the field of P450 research and potentially leading to new industrial applications. Full article