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1.
Molecules ; 29(13)2024 Jul 07.
Article in English | MEDLINE | ID: mdl-38999173

ABSTRACT

Ovalbumin (OVA), a protein vital for chick embryo nutrition, hydration, and antimicrobial protection, together with other egg-white proteins, migrates to the amniotic fluid and is orally absorbed by the embryo during embryogenesis. Recently, it has been shown that for optimal eggshell quality, the hen diet can be supplemented with manganese. Although essential for embryonic development, manganese in excess causes neurotoxicity. This study investigates whether OVA may be involved in the regulation of manganese levels. The binding of Mn(II) to OVA was investigated using electron paramagnetic resonance (EPR) spectroscopy. The results show that OVA binds a maximum of two Mn(II) ions, one with slightly weaker affinity, even in a 10-fold excess, suggesting it may have a protective role from Mn(II) overload. It seems that the binding of Mn(II), or the presence of excess Mn(II), does not affect OVA's tertiary structure, as evidenced from fluorescence and UV/vis measurements. Comparative analysis with bovine and human serum albumins revealed that they exhibit higher affinities for Mn(II) than OVA, most likely due to their essentially different physiological roles. These findings suggest that OVA does not play a role in the transport and storage of manganese; however, it may be involved in embryo protection from manganese-induced toxicity.


Subject(s)
Embryonic Development , Homeostasis , Manganese , Ovalbumin , Manganese/metabolism , Animals , Chick Embryo , Electron Spin Resonance Spectroscopy/methods , Humans , Protein Binding , Cattle , Chickens
2.
Biotechnol Rep (Amst) ; 42: e00832, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38948352

ABSTRACT

The antioxidant and antiproliferative activity of red tilapia (Oreochromis spp.) viscera hydrolysates (RTVH) was evaluated. For that, the hydrolysates was applied to three cancer cell lines (HepG2, Huh7 and SW480) and the control (CCD-18Co). Finally, the line on which the hydrolysate had the greatest effect (SW480) and the control (CCD-18Co) were subjected to the ApoTox-Glo Triplex Assay to determine apoptosis, toxicity, and cell viability. The result showed that hydrolysate had a dose-dependent cytotoxic effect selective on the three cancer cell lines, compared to the control cells. There is a relationship between the antioxidant capacity of RTVHs and their antiproliferative capacity on cancer cells evaluated, which achieved cell viability by action of RTVH of 34.68 and 41.58 and 25.41 %, to HepG2, Huh7 and SW480, respectively. The action of RTVH on cancer cell line SW480 is not due to the induction of apoptosis but to the rupture of the cell membrane.

3.
J Proteome Res ; 2024 Jul 12.
Article in English | MEDLINE | ID: mdl-38993068

ABSTRACT

Within the intricate landscape of the proteome, approximately 30% of all proteins bind metal ions. This repertoire is even larger when considering all the different forms of a protein, known as proteoforms. Here, we propose the term "metalloforms" to refer to different structural or functional variations of a protein resulting from the binding of various hetero- or homogeneous metal ions. Using human Cu(I)/Zn(II)-metallothionein-3 as a representative model, we developed a chemical proteomics strategy to simultaneously differentiate and map Zn(II) and Cu(I) metal binding sites. In the first labeling step, N-ethylmaleimide reacts with Cysteine (Cys), resulting in the dissociation of all Zn(II) ions while Cu(I) remains bound to the protein. In the second labeling step, iodoacetamide is utilized to label Cu(I)-bound Cys residues. Native mass spectrometry (MS) was used to determine the metal/labeling protein stoichiometries, while bottom-up/top-down MS was used to map the Cys-labeled residues. Next, we used a developed methodology to interrogate an isolated rabbit liver metallothionein fraction containing three metallothionein-2 isoforms and multiple Cd(II)/Zn(II) metalloforms. The approach detailed in this study thus holds the potential to decode the metalloproteoform diversity within other proteins.

4.
Int J Mol Sci ; 25(13)2024 Jun 28.
Article in English | MEDLINE | ID: mdl-39000272

ABSTRACT

In recent years, interest in very small proteins (µ-proteins) has increased significantly, and they were found to fulfill important functions in all prokaryotic and eukaryotic species. The halophilic archaeon Haloferax volcanii encodes about 400 µ-proteins of less than 70 amino acids, 49 of which contain at least two C(P)XCG motifs and are, thus, predicted zinc finger proteins. The determination of the NMR solution structure of HVO_2753 revealed that only one of two predicted zinc fingers actually bound zinc, while a second one was metal-free. Therefore, the aim of the current study was the homologous production of additional C(P)XCG proteins and the quantification of their zinc content. Attempts to produce 31 proteins failed, underscoring the particular difficulties of working with µ-proteins. In total, 14 proteins could be produced and purified, and the zinc content was determined. Only nine proteins complexed zinc, while five proteins were zinc-free. Three of the latter could be analyzed using ESI-MS and were found to contain another metal, most likely cobalt or nickel. Therefore, at least in haloarchaea, the variability of predicted C(P)XCG zinc finger motifs is higher than anticipated, and they can be metal-free, bind zinc, or bind another metal. Notably, AlphaFold2 cannot correctly predict whether or not the four cysteines have the tetrahedral configuration that is a prerequisite for metal binding.


Subject(s)
Archaeal Proteins , Haloferax volcanii , Zinc Fingers , Zinc , Haloferax volcanii/metabolism , Haloferax volcanii/chemistry , Zinc/metabolism , Zinc/chemistry , Archaeal Proteins/chemistry , Archaeal Proteins/metabolism , Protein Binding , Amino Acid Sequence
5.
Adv Protein Chem Struct Biol ; 141: 203-221, 2024.
Article in English | MEDLINE | ID: mdl-38960474

ABSTRACT

The arylsulfatase A (ARSA) gene is observed to be deficient in patients with metachromatic leukodystrophy (MLD), a type of lysosomal storage disease. MLD is a severe neurodegenerative disorder characterized by an autosomal recessive inheritance pattern. This study aimed to map the most deleterious mutations at the metal binding sites of ARSA and the amino acids in proximity to the mutated positions. We utilized an array of computational tools, including PredictSNP, MAPP, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT, SNAP, and ConSurf, to identify the most detrimental mutations potentially implicated in MLD collected from UniProt, ClinVar, and HGMD. Two mutations, D29N and D30H, as being extremely deleterious based on assessments of pathogenicity, conservation, biophysical characteristics, and stability analysis. The D29 and D30 are located at the metal-interacting regions of ARSA and found to undergo post-translational modification, specifically phosphorylation. Henceforth, the in-depth effect of metal binding upon mutation was examined using molecular dynamics simulations (MDS) before and after phosphorylation. The MDS results exhibited high deviation for the D29N and D30H mutations in comparison to the native, and the same was confirmed by significant residue fluctuation and reduced compactness. These structural alterations suggest that such mutations may influence protein functionality, offering potential avenues for personalized therapeutic and providing a basis for potential mutation-specific treatments for severe MLD patients.


Subject(s)
Cerebroside-Sulfatase , Leukodystrophy, Metachromatic , Mutation , Humans , Binding Sites , Cerebroside-Sulfatase/genetics , Cerebroside-Sulfatase/metabolism , Cerebroside-Sulfatase/chemistry , Leukodystrophy, Metachromatic/genetics , Leukodystrophy, Metachromatic/metabolism , Metals/metabolism , Metals/chemistry , Molecular Dynamics Simulation
6.
Eur J Med Chem ; 276: 116639, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38964259

ABSTRACT

Since influenza virus RNA polymerase subunit PAN is a dinuclear Mn2+ dependent endonuclease, metal-binding pharmacophores (MBPs) with Mn2+ coordination has been elucidated as a promising strategy to develop PAN inhibitors for influenza treatment. However, few attentions have been paid to the relationship between the optimal arrangement of the donor atoms in MBPs and anti-influenza A virus (IAV) efficacy. Given that, the privileged hydroxypyridinones fusing a seven-membered lactam ring with diverse side chains, chiral centers or cyclic systems were designed and synthesized. A structure-activity relationship study resulted in a hit compound 16l (IC50 = 2.868 ± 0.063 µM against IAV polymerase), the seven-membered lactam ring of which was fused a pyrrolidine ring. Further optimization of the hydrophobic binding groups on 16l afforded a lead compound (R, S)-16s, which exhibited a 64-fold more potent inhibitory activity (IC50 = 0.045 ± 0.002 µM) toward IAV polymerase. Moreover, (R, S)-16s demonstrated a potent anti-IAV efficacy (EC50 = 0.134 ± 0.093 µM) and weak cytotoxicity (CC50 = 15.35 µM), indicating the high selectivity of (R, S)-16s. Although the lead compound (R, S)-16s exhibited a little weaker activity than baloxavir, these findings illustrated the utility of a metal coordination-based strategy in generating novel MBPs with potent anti-influenza activity.

7.
Environ Sci Pollut Res Int ; 31(30): 43369-43380, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38902445

ABSTRACT

Dissolved organic matter (DOM), the most active component in interstitial waters, determines the stability of heavy metals and secondary release in sediments. However, little is known about the composition and metal-binding patterns of DOM in interstitial water from oligotrophic lakes affected by different anthropogenic perturbations. Here, 18 interstitial water samples were prepared from sediments in agricultural, residential, tourist, and forest regions in an oligotrophic lake (Shengzhong Lake in Sichuan Province, China) watershed. Interstitial water quality and DOM composition, properties, and Cu(II)- and Pb(II)-binding characteristics were measured via physicochemical analysis, UV-vis spectroscopic, fluorescence excitation-emission matrix-parallel factor analysis (EEM-PARAFAC), and fluorescence titration methods. The DOM, which was produced mainly by microbial activities, had low molecular weights, humification degrees, and aromaticity. Based on EEM-PARAFAC results, the DOM was generally composed of tryptophan- (57.7%), terrestrial humic- (18.7%), microbial humic- (15.6%), and tyrosine-like (8.0%) substances. The DOM in the metal complexes was primarily composed of tryptophan-like substances, which accounted for ~42.6% of the DOM-Cu(II) complexes and ~72.0% of the DOM-Pb(II) complexes; however, microbial humic-like substances primarily contributed to the stability of DOM-Cu(II) (logKCu = 3.7-4.6) and DOM-Pb(II) (logKPb = 4.3-4.8). Water quality parameters did not significantly affect the stability of DOM-metal complexes. We demonstrated that the metal-binding patterns of DOM in interstitial water from oligotrophic lakes are highly dependent on microbial DOM composition and are affected by anthropogenic perturbations to a lesser extent.


Subject(s)
Copper , Environmental Monitoring , Geologic Sediments , Lakes , Lead , Water Pollutants, Chemical , Lakes/chemistry , Lead/analysis , Geologic Sediments/chemistry , Copper/analysis , Copper/chemistry , China , Water Pollutants, Chemical/analysis , Humic Substances
8.
Sci Total Environ ; 946: 174245, 2024 Oct 10.
Article in English | MEDLINE | ID: mdl-38925395

ABSTRACT

Dissolved organic matter (DOM) plays an important role in governing metal speciation and migration in aquatic systems. In this study, various DOM samples were collected from Lakes Erhai, Kokonor, and Chaka, and size-fractionated into high molecular weight (HMW, 1 kDa-0.7 µm) and low molecular weight (LMW, <1 kDa) fractions for measurements of dissolved organic carbon (DOC), spectral properties, and metal binding behaviors. Our results demonstrated that samples from Lake Chaka exhibited the highest DOC concentration and fluorescence indices but the lowest percentage of carbohydrates. Regardless of sampling locations, the HMW-DOM fractions contained higher abundances of aromatic DOM, carbohydrates and protein-like substances, but lower abundance of fulvic acid-like substances compared to those in the LMW fractions. Metal titration experiments coupled with the excitation-emission matrix (EEM)-parallel factor (PARAFAC) modeling revealed that the quenching of the PARAFAC-derived fluorescent components was more pronounced in the presence of Cu(II) compared to Pb(II). Humic-like components emerged as a superior model, exhibiting higher binding affinities for Cu(II) than protein-like substances, while the opposite trend was observed for Pb(II). In samples obtained from Lakes Erhai and Kokonor, the condition stability constants (Log KM) for the binding of both Cu(II) and Pb(II) with the HMW-DOM fraction were higher than those with the LMW-DOM fraction. Conversely, a contrasting trend was observed for Lake Chaka. This study highlighted the heterogeneity in spectral properties and metal-binding behaviors of natural DOMs, contributing to an improved understanding of the molecular interactions between DOM components and metal ions and their environmental fate in aquatic ecosystems.

9.
Sci Total Environ ; 946: 174020, 2024 Oct 10.
Article in English | MEDLINE | ID: mdl-38897475

ABSTRACT

Soil contamination by heavy metals represents an important environmental and public health problem of global concern. Biocrust-forming cyanobacteria offer promise for heavy metal immobilisation in contaminated soils due to their unique characteristics, including their ability to grow in contaminated soils and produce exopolysaccharides (EPS). However, limited research has analysed the representativeness of cyanobacteria in metal-contaminated soils. Additionally, there is a lack of studies examining how cyanobacteria adaptation to specific environments can impact their metal-binding capacity. To address this research gap, we conducted a study analysing the bacterial communities of cyanobacteria-dominated biocrusts in a contaminated area from South Sardinia (Italy). Additionally, by using two distinct approaches, we isolated three Nostoc commune strains from cyanobacteria-dominated biocrust and we also evaluated their potential to immobilise heavy metals. The first isolation method involved acclimatizing biocrust samples in liquid medium while, in the second method, biocrust samples were directly seeded onto agar plates. The microbial community analysis revealed Cyanobacteria, Bacteroidota, Proteobacteria, and Actinobacteria as the predominant groups, with cyanobacteria representing between 13.3 % and 26.0 % of the total community. Despite belonging to the same species, these strains exhibited different growth rates (1.1-2.2 g L-1 of biomass) and capacities for EPS production (400-1786 mg L-1). The three strains demonstrated a notable ability for metal immobilisation, removing up to 88.9 % of Cu, 86.2 % of Pb, and 45.3 % of Zn from liquid medium. Cyanobacteria EPS production showed a strong correlation with the removal of Cu, indicating its role in facilitating metal immobilisation. Furthermore, differences in Pb immobilisation (40-86.2 %) suggest possible environmental adaptation mechanisms of the strains. This study highlights the promising application of N. commune strains for metal immobilisation in soils, offering a potential bioremediation tool to combat the adverse effects of soil contamination and promote environmental sustainability.


Subject(s)
Agriculture , Cyanobacteria , Lead , Metals, Heavy , Soil Microbiology , Soil Pollutants , Zinc , Cyanobacteria/growth & development , Soil Pollutants/analysis , Metals, Heavy/analysis , Zinc/analysis , Italy , Lead/analysis , Lead/metabolism , Agriculture/methods , Biodegradation, Environmental , Copper/analysis , Soil/chemistry , Environmental Restoration and Remediation/methods
10.
New Phytol ; 243(1): 314-329, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38730532

ABSTRACT

Effector proteins are central to the success of plant pathogens, while immunity in host plants is driven by receptor-mediated recognition of these effectors. Understanding the molecular details of effector-receptor interactions is key for the engineering of novel immune receptors. Here, we experimentally determined the crystal structure of the Puccinia graminis f. sp. tritici (Pgt) effector AvrSr27, which was not accurately predicted using AlphaFold2. We characterised the role of the conserved cysteine residues in AvrSr27 using in vitro biochemical assays and examined Sr27-mediated recognition using transient expression in Nicotiana spp. and wheat protoplasts. The AvrSr27 structure contains a novel ß-strand rich modular fold consisting of two structurally similar domains that bind to Zn2+ ions. The N-terminal domain of AvrSr27 is sufficient for interaction with Sr27 and triggering cell death. We identified two Pgt proteins structurally related to AvrSr27 but with low sequence identity that can also associate with Sr27, albeit more weakly. Though only the full-length proteins, trigger Sr27-dependent cell death in transient expression systems. Collectively, our findings have important implications for utilising protein prediction platforms for effector proteins, and those embarking on bespoke engineering of immunity receptors as solutions to plant disease.


Subject(s)
Fungal Proteins , Nicotiana , Triticum , Zinc , Zinc/metabolism , Triticum/immunology , Triticum/microbiology , Nicotiana/immunology , Nicotiana/microbiology , Nicotiana/metabolism , Fungal Proteins/metabolism , Fungal Proteins/chemistry , Puccinia , Plant Immunity , Protein Binding , Amino Acid Sequence , Cell Death , Protein Domains , Models, Molecular , Plant Diseases/microbiology , Plant Diseases/immunology
11.
Protein Sci ; 33(6): e5017, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38747382

ABSTRACT

Biparatopic antibodies (bpAbs) are engineered antibodies that bind to multiple different epitopes within the same antigens. bpAbs comprise diverse formats, including fragment-based formats, and choosing the appropriate molecular format for a desired function against a target molecule is a challenging task. Moreover, optimizing the design of constructs requires selecting appropriate antibody modalities and adjusting linker length for individual bpAbs. Therefore, it is crucial to understand the characteristics of bpAbs at the molecular level. In this study, we first obtained single-chain variable fragments and camelid heavy-chain variable domains targeting distinct epitopes of the metal binding protein MtsA and then developed a novel format single-chain bpAb connecting these fragment antibodies with various linkers. The physicochemical properties, binding activities, complex formation states with antigen, and functions of the bpAb were analyzed using multiple approaches. Notably, we found that the assembly state of the complexes was controlled by a linker and that longer linkers tended to form more compact complexes. These observations provide detailed molecular information that should be considered in the design of bpAbs.


Subject(s)
Single-Chain Antibodies , Single-Chain Antibodies/chemistry , Single-Chain Antibodies/genetics , Single-Chain Antibodies/immunology , Animals , Humans , Protein Engineering/methods , Epitopes/chemistry , Epitopes/immunology , Immunoglobulin Heavy Chains/chemistry , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Heavy Chains/immunology
12.
Protein Sci ; 33(5): e4971, 2024 May.
Article in English | MEDLINE | ID: mdl-38591647

ABSTRACT

As protein crystals are increasingly finding diverse applications as scaffolds, controlled crystal polymorphism presents a facile strategy to form crystalline assemblies with controllable porosity with minimal to no protein engineering. Polymorphs of consensus tetratricopeptide repeat proteins with varying porosity were obtained through co-crystallization with metal salts, exploiting the innate metal ion geometric requirements. A single structurally exposed negative amino acid cluster was responsible for metal coordination, despite the abundance of negatively charged residues. Density functional theory calculations showed that while most of the crystals were the most thermodynamically stable assemblies, some were kinetically trapped states. Thus, crystalline porosity diversity is achieved and controlled with metal coordination, opening a new scope in the application of proteins as biocompatible protein-metal-organic frameworks (POFs). In addition, metal-dependent polymorphic crystals allow direct comparison of metal coordination preferences.


Subject(s)
Metal-Organic Frameworks , Proteins , Proteins/genetics , Proteins/chemistry , Metals/chemistry , Crystallization
13.
Acta Crystallogr D Struct Biol ; 80(Pt 5): 362-376, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38682667

ABSTRACT

Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.


Subject(s)
Databases, Protein , Metalloproteins , Metals , Metalloproteins/chemistry , Metals/chemistry , Binding Sites , Models, Molecular , Protein Conformation
14.
Biochemistry (Mosc) ; 89(Suppl 1): S180-S204, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38621750

ABSTRACT

In many proteins, supplementary metal-binding centers appear under stress conditions. They are known as aberrant or atypical sites. Physico-chemical properties of proteins are significantly changed after such metal binding, and very stable protein aggregates are formed, in which metals act as "cross-linking" agents. Supplementary metal-binding centers in proteins often arise as a result of posttranslational modifications caused by reactive oxygen and nitrogen species and reactive carbonyl compounds. New chemical groups formed as a result of these modifications can act as ligands for binding metal ions. Special attention is paid to the role of cysteine SH-groups in the formation of supplementary metal-binding centers, since these groups are the main target for the action of reactive species. Supplementary metal binding centers may also appear due to unmasking of amino acid residues when protein conformation changing. Appearance of such centers is usually considered as a pathological process. Such unilateral approach does not allow to obtain an integral view of the phenomenon, ignoring cases when formation of metal complexes with altered proteins is a way to adjust protein properties, activity, and stability under the changed redox conditions. The role of metals in protein aggregation is being studied actively, since it leads to formation of non-membranous organelles, liquid condensates, and solid conglomerates. Some proteins found in such aggregates are typical for various diseases, such as Alzheimer's and Huntington's diseases, amyotrophic lateral sclerosis, and some types of cancer.


Subject(s)
Metals , Oxidative Stress , Metals/chemistry , Metals/metabolism , Oxidation-Reduction , Protein Processing, Post-Translational
15.
Article in English | MEDLINE | ID: mdl-38573823

ABSTRACT

Escherichia coli were engineered to selectively adsorb and recover lithium from the environment by employing a bacterial cell surface display strategy. Lithium binding peptide (LBP1) was integrated into the Escherichia coli membrane protein OmpC. The effect of environmental conditions on the adsorption of lithium by a recombinant strain was evaluated, and lithium particles on the cellular surface were analyzed by FE-SEM and XRD. To elevate the lithium adsorption, dimeric, trimeric, and tetrameric repeats of the LBP1 peptide were constructed and displayed on the surface of E. coli. The constructed recombinant E. coli displaying the LBP1 trimer was applied to real industrial lithium battery wastewater to recover lithium.


Subject(s)
Escherichia coli , Lithium , Porins , Escherichia coli/genetics , Escherichia coli/metabolism , Adsorption , Industrial Waste , Bacterial Outer Membrane Proteins/genetics , Bacterial Outer Membrane Proteins/metabolism , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Wastewater/microbiology , Electric Power Supplies , Cell Surface Display Techniques , Recombinant Proteins/genetics
16.
Elife ; 132024 Apr 19.
Article in English | MEDLINE | ID: mdl-38640016

ABSTRACT

Mediator of ERBB2-driven cell motility 1 (MEMO1) is an evolutionary conserved protein implicated in many biological processes; however, its primary molecular function remains unknown. Importantly, MEMO1 is overexpressed in many types of cancer and was shown to modulate breast cancer metastasis through altered cell motility. To better understand the function of MEMO1 in cancer cells, we analyzed genetic interactions of MEMO1 using gene essentiality data from 1028 cancer cell lines and found multiple iron-related genes exhibiting genetic relationships with MEMO1. We experimentally confirmed several interactions between MEMO1 and iron-related proteins in living cells, most notably, transferrin receptor 2 (TFR2), mitoferrin-2 (SLC25A28), and the global iron response regulator IRP1 (ACO1). These interactions indicate that cells with high-MEMO1 expression levels are hypersensitive to the disruptions in iron distribution. Our data also indicate that MEMO1 is involved in ferroptosis and is linked to iron supply to mitochondria. We have found that purified MEMO1 binds iron with high affinity under redox conditions mimicking intracellular environment and solved MEMO1 structures in complex with iron and copper. Our work reveals that the iron coordination mode in MEMO1 is very similar to that of iron-containing extradiol dioxygenases, which also display a similar structural fold. We conclude that MEMO1 is an iron-binding protein that modulates iron homeostasis in cancer cells.


Subject(s)
Homeostasis , Iron , Neoplasms , Humans , Cation Transport Proteins/metabolism , Cation Transport Proteins/genetics , Cell Line, Tumor , Ferroptosis , Iron/metabolism , Iron Regulatory Protein 1 , Neoplasms/metabolism , Neoplasms/genetics , Protein Binding , Receptors, Transferrin/metabolism , Receptors, Transferrin/genetics
17.
Molecules ; 29(5)2024 Feb 29.
Article in English | MEDLINE | ID: mdl-38474606

ABSTRACT

Metalloenzymes are ubiquitously present in the human body and are relevant to a variety of diseases. However, the development of metalloenzyme inhibitors is limited by low specificity and poor drug-likeness associated with metal-binding fragments (MBFs). A generalized drug discovery strategy was established, which is characterized by the property characterization of zinc-dependent metalloenzyme inhibitors (ZnMIs). Fifteen potential Zn2+-binding fragments (ZnBFs) were identified, and a customized pharmacophore feature was defined based on these ZnBFs. The customized feature was set as a required feature and applied to a search for novel inhibitors for histone deacetylase 1 (HDAC1). Ten potential HDAC1 inhibitors were recognized, and one of them (compound 9) was a known potent HDAC1 inhibitor. The results demonstrated the effectiveness of our strategy to identify novel inhibitors for zinc-dependent metalloenzymes.


Subject(s)
Histone Deacetylase Inhibitors , Metalloproteins , Humans , Histone Deacetylase Inhibitors/pharmacology , Metalloproteins/chemistry , Drug Discovery , Zinc , Histone Deacetylase 1
18.
FEBS J ; 291(13): 2980-2993, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38555564

ABSTRACT

Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.


Subject(s)
Models, Molecular , Nickel , Protein Binding , Nickel/metabolism , Nickel/chemistry , Binding Sites , Crystallography, X-Ray , Amino Acid Sequence , Phylogeny , Mutation , Mutagenesis, Site-Directed
19.
Int J Biol Macromol ; 263(Pt 2): 130436, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38408578

ABSTRACT

Peptides are recognized as promising adsorbents in metal selective recovery. In this study, the designed gallium-binding peptide H6GaBP was immobilized by the polysaccharide polymer sodium alginate (SA) for gallium recovery. The synthesized H6GaBP@SA microspheres exhibited a maximum adsorption capacity of 127.4 mg/g and demonstrated high selectivity for gallium at lower pH values. The adsorption process aligned well with the pseudo-second-order equation and Langmuir model. To elucidate the adsorption mechanism, a comprehensive characterization including molecular docking, scanning electron microscope coupled with energy-dispersive X-ray spectroscopy (SEM-EDS), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and thermogravimetry analysis (TGA), were conducted. These analyses revealed that gallium ions were initially adsorbed through electrostatic interaction by H6GaBP@SA, followed by a cation exchange reaction between Ga(OH)2+ and Ca2+, as well as coordination between gallium and histidine residues on the peptide. Moreover, the H6GaBP@SA exhibited improved thermal stability compared to sole sodium alginate microspheres, and the coordination of gallium with peptides can also defer the decomposition rate of the adsorbents. Compared to other adsorbents, the peptide-encapsulated hydrogel microspheres exhibited superior gallium selectivity and improved adsorption capacity, offering an environmentally friendly option for gallium recovery.


Subject(s)
Gallium , Water Pollutants, Chemical , Hydrogels/chemistry , Alginates/chemistry , Adsorption , Molecular Docking Simulation , Spectroscopy, Fourier Transform Infrared , Peptides , Hydrogen-Ion Concentration , Kinetics , Water Pollutants, Chemical/chemistry
20.
J Inorg Biochem ; 253: 112500, 2024 04.
Article in English | MEDLINE | ID: mdl-38301386

ABSTRACT

Metallopeptidases are a group of metal-dependent enzymes that hydrolyze peptide bonds. These enzymes found in Streptococcus pneumoniae assist the pathogen in infecting the host by breaking down host tissues and extracellular matrix proteins. Considering metallopeptidases' significant role in bacterial virulence, inhibiting this enzyme represents a promising avenue for research. These enzymes are characterized by the presence of Zn(II) in the active site, proper coordination of which is essential for their catalytic function. This work aims to determine the significance of the specific amino acids in the metal binding domain of metallopeptidase from S. pneumoniae. For this purpose, we investigated the coordination chemistry of Zn(II), Ni(II), and Cu(II) ions with point-mutated peptide models of the metal-binding domain. Mutations were introduced at His-2 (L1) and Glu-1. Studies have shown that at pH 7.14 (pH of infected lungs by S. pneumoniae), point mutation on glutamic acid caused only minor effects on the binding of Zn(II) and Ni(II), while significantly improving Cu(II) binding. The stability of copper complexes is greater with the mutant Glu-1 â†’ Gln-1 than with the original domain due to a hydrogen bonding network created by the Gln backbone with its side chain. Substituting histidine resulted in a significant reduction in metal binding for all metal ions, highlighting the crucial role of His-2 in metal coordination. Introduced mutations at neutral pH did not significantly affect the secondary structure of metal complexes. However, at alkaline pH, the peptides showed a higher percentage of antiparallel ß-sheet structures upon the addition of Cu(II), Ni(II) and Zn(II).


Subject(s)
Copper , Zinc , Copper/chemistry , Catalytic Domain , Zinc/chemistry , Amino Acids , Metals , Peptides/metabolism , Metalloproteases , Chelating Agents , Ions
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