Role of Na+and K+in Enzyme Function

The unexplored role of alkali and alkaline earth elements (ALAEs) on the structure, processing, and biological effects of bioactive glasses

Bioactive glass has been employed in several medical applications since its inception in 1969. The compositions of these materials have been investigated extensively with emphasis on glass network formers, therapeutic transition metals, and glass network modifiers. Through these experiments, several commercial and experimental compositions have been developed with varying chemical durability, induced physiological responses, and hydroxyapatite forming abilities. In many of these studies, the concentrations of each alkali and alkaline earth element have been altered to monitor changes in structure and biological response. This review aims to discuss the impact of each alkali and alkaline earth element on the structure, processing, and biological effects of bioactive glass. We explore critical questions regarding these elements from both a glass science and biological perspective. Should elements with little biological impact be included? Are alkali free bioactive glasses more promising for greater biological responses? Does this mixed alkali effect show increased degradation rates and should it be employed for optimized dissolution? Each of these questions along with others are evaluated comprehensively and discussed in the final section where guidance for compositional design is provided.

Co-metabolism of Na+/K+ ion regulated physiological enhancement on selenium-accumulation in Saccharomyces yeasts

BACKGROUND

Selenium is an important nutritional supplement that mainly exists naturally in soil as inorganic selenium. Saccharomyces cerevisiae cells are excellent medium for converting inorganic selenium in nature into organic selenium.

RESULTS

Under the co-stimulation of sodium selenite (Na2SeO3) and potassium selenite (K2SeO3), the activity of selenophosphate synthetase (SPS) was improved up to about five folds more than conventional Na2SeO3 group with the total selenite salts content of 30 mg/L. Transcriptome analysis first revealed that due to the sharing pathway between sodium ion (Na+) and potassium ion (K+), the K+ largely regulates the metabolisms of amino acid and glutathione under the accumulation of selenite salt. Furthermore, K+ could improve the tolerance performance and selenium-biotransformation yields of Saccharomyces cerevisiae cells under Na2SeO3 salt stimulation.

CONCLUSION

The important role of K+ in regulating the intracellular selenium accumulation especially in terms of amino acid metabolism and glutathione, suggested a new direction for the development of selenium-enrichment supplements with Saccharomyces cerevisiae cell factory. © 2024 Society of Chemical Industry.

Balancing Group I Monatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field

Molecular dynamics (MD) simulations are a commonly used method for investigating molecular behavior at the atomic level. Achieving reliable MD simulation results necessitates the use of an accurate force field. In the present work, we present a protocol to enhance the quality of group 1 monatomic ions (specifically Li+, Na+, K+, Rb+, and Cs+) with respect to their interactions with common polar model compounds in biomolecules in condensed phases in the context of the Drude polarizable force field. Instead of adjusting preexisting individual parameters for ions, model compounds, and water, we employ atom-pair specific Lennard-Jones (LJ) (known as NBFIX in CHARMM) and through-space Thole dipole screening (NBTHOLE) terms to fine-tune the balance of ion-model compound, ion-water, and model compound-water interactions. This involved establishing a protocol for the optimization of NBFIX and NBTHOLE parameters targeting the difference between molecular mechanical (MM) and quantum mechanical (QM) potential energy scans (PES). It is shown that targeting PES involving complexes that include multiple model compounds and/or ions as trimers and tetramers yields parameters that produce condensed phase properties in agreement with experimental data. Validation of this protocol involved the reproduction of experimental thermodynamic benchmarks, including solvation free energies of ions in methanol and N-methylacetamide, osmotic pressures, ionic conductivities, and diffusion coefficients within the condensed phase. These results show the importance of including more complex ion-model compound complexes beyond dimers in the QM target data to account for many-body effects during parameter fitting. The presented parameters represent a significant refinement of the Drude polarizable force field, which will lead to improved accuracy for modeling ion-biomolecular interactions.

Exploring the significance of potassium homeostasis in copper ion binding to human αB-Crystallin

αB-Crystallin (αB-Cry) is a small heat shock protein known for its protective role, with an adaptable structure that responds to environmental changes through oligomeric dynamics. Cu(II) ions are crucial for cellular processes but excessive amounts are linked to diseases like cataracts and neurodegeneration. This study investigated how optimal and detrimental Cu(II) concentrations affect αB-Cry oligomers and their chaperone activity, within the potassium-regulated ionic-strength environment. Techniques including isothermal titration calorimetry, differential scanning calorimetry, fluorescence spectroscopy, inductively coupled plasma atomic emission spectroscopy, cyclic voltammetry, dynamic light scattering, circular dichroism, and MTT assay were employed and complemented by computational methods. Results showed that potassium ions affected αB-Cry's structure, promoting Cu(II) binding at multiple sites and scavenging ability, and inhibiting ion redox reactions. Low concentrations of Cu(II), through modifications of oligomeric interfaces, induce regulation of surface charge and hydrophobicity, resulting in an increase in chaperone activity. Subunit dynamics were regulated, maintaining stable interfaces, thereby inhibiting further aggregation and allowing the functional reversion to oligomers after stress. High Cu(II) disrupted charge/hydrophobicity balance, sewing sizable oligomers together through subunit-subunit interactions, suppressing oligomer dissociation, and reducing chaperone efficiency. This study offers insights into how Cu(II) and potassium ions influence αB-Cry, advancing our understanding of Cu(II)-related diseases.

L-fucose and fucoidan alleviate high-salt diet-promoted acute inflammation

Excessive salt intake is a widespread health issue observed in almost every country around the world. A high salt diet (HSD) has a strong correlation with numerous diseases, including hypertension, chronic kidney disease, and autoimmune disorders. However, the mechanisms underlying HSD-promotion of inflammation and exacerbation of these diseases are not fully understood. In this study, we observed that HSD consumption reduced the abundance of the gut microbial metabolite L-fucose, leading to a more substantial inflammatory response in mice. A HSD led to increased peritonitis incidence in mice, as evidenced by the increased accumulation of inflammatory cells and elevated levels of inflammatory cytokines, such as tumor necrosis factor alpha (TNF-α), interleukin 6 (IL-6), and monocyte chemotactic protein-1 (MCP-1, also known as C-C motif chemokine ligand 2 or CCL2), in peritoneal lavage fluid. Following the administration of broad-spectrum antibiotics, HSD-induced inflammation was abolished, indicating that the proinflammatory effects of HSD were not due to the direct effect of sodium, but rather to HSD-induced alterations in the composition of the gut microbiota. By using untargeted metabolomics techniques, we determined that the levels of the gut microbial metabolite L-fucose were reduced by a HSD. Moreover, the administration of L-fucose or fucoidan, a compound derived from brown that is rich in L-fucose, normalized the level of inflammation in mice following HSD induction. In addition, both L-fucose and fucoidan inhibited LPS-induced macrophage activation in vitro. In summary, our research showed that reduced L-fucose levels in the gut contributed to HSD-exacerbated acute inflammation in mice; these results indicate that L-fucose and fucoidan could interfere with HSD-promotion of the inflammatory response.

Synergetic effect of matrine on the catalytic scFv antibody HS72 in vitro and in mice with Alzheimer disease pathology

Single-chain variable fragment (scFv) HS72 is a catalytic antibody that specifically degrades amyloid β-protein 1-42 (Aβ42) aggregates in vitro or reduces the level or burden of Aβ42 deposits/plaques in the brains of mice with Alzheimer disease pathology. Its efficacy has been shown in protecting neural cells in vitro and improving the morphology of the cell population in the brain of mice with AD pathology (AD mice). Matrine (Mat) is a natural product capable of binding to Aβ42 or its aggregates and blocking their neurotoxicity at concentrations of at least 10 μM or greater. However, this study revealed a synergistic effect of Mat on the catalytic effect of HS72 at low concentrations (0.01-2.5 μM). This is evidenced by the fact that Mat synergistically enhances HS72's ability to degrade Aβ42 aggregates and protect neural cells (SH-SY5Y and HT22 cells, and brain cells of AD mice). The molecular docking models and characterization of Mat's action both indicated that the mechanism of Mat's synergistic impact on HS72 catalysis is to increase the turnover number (or molecular activity) of HS72 by enhancing the catalytic power of the HS72's catalytic groups and encouraging the release of the degradation products (Aβ fragments). The study's results suggest a natural synergy between Mat-like small molecules and the catalytic anti-oligomeric Aβ42 antibody HS72, enabling more effective reduction or removal of Aβ42 aggregates or plaques than the antibody alone. These findings provide novel insights into the effectiveness of anti-oligomeric Aβ42 antibodies in AD immunotherapy.

Potent inhibition of human tyrosinase inhibitor by verproside from the whole plant of Pseudolysimachion rotundum var. subintegrum

Affinity-based ultrafiltration-mass spectrometry coupled with ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry was utilised for the structural identification of direct tyrosinase ligands from a crude Pseudolysimachion rotundum var. subintegrum extract. False positives were recognised by introducing time-dependent inhibition in the control for comparison. The P. rotundum extract contained nine main metabolites in the UPLC-QTOF-MS chromatogram. However, four metabolites were reduced after incubation with tyrosinase, indicating that these metabolites were bound to tyrosinase. The IC50 values of verproside (1) were 31.2 µM and 197.3 µM for mTyr and hTyr, respectively. Verproside showed 5.6-fold higher efficacy than that of its positive control (kojic acid in hTyr). The most potent tyrosinase inhibitor, verproside, features a 3,4-dihydroxybenzoic acid moiety on the iridoid glycoside and inhibits tyrosinase in a time-dependent and competitive manner. Among these three compounds, verproside is bound to the active site pocket with a docking energy of -6.9 kcal/mol and four hydrogen bonding interactions with HIS61 and HIS85.

Multifunctional regulation of NADPH oxidase in growth, microsclerotia formation and virulence in Metarhizium rileyi

OBJECTIVES

Microsclerotia (MS), anti-stress structures produced by many filamentous fungi, have been proven to be a great substitute for conidia in the production of insecticides within entomogenous fungi. NADPH oxidase (Nox) is a highly conserved ROS-response protein family that is widespread in eukaryotes and plays distinct roles in environmental fitness among various filamentous fungi. However, it is not clear whether the formation of MS and pathogenicity in entomogenous fungi is regulated by the Nox inside. In this study, we reported the presence of NADPH oxidase homologs in a great potential biocontrol fungus, Metarhizium rileyi, and further showed multiple biological functions.

RESULTS

Three Nox homologous genes in M. rileyi showed high expression throughout the entire process of MS formation. Targeted deletion of MrNoxA, MrNoxB and MrNoxR all led to a decrease in MS yield and impaired morphology. Moreover, the anti-adversity assay showed that they are indispensable for growth, osmotic pressure and oxidative stress regulation in Metarhizium rileyi. Most importantly, △MrNoxR and △MrNoxA but not △MrNoxB showed a dramatic reduction in virulence via inoculation. The normality of appressoria might be unaffected in mutants since there are no striking differences in virulence compared with WT by topical injections.

CONCLUSION

Our results revealed that NADPH oxidase plays important roles in growth regulation, MS formation and pathogenicity in M. rileyi, perhaps in the ROS response and hyphal polarity.

Cyanophycin and its biosynthesis: not hot but very cool

Covering: 1878 to early 2023Cyanophycin is a biopolymer consisting of a poly-aspartate backbone with arginines linked to each Asp sidechain through isopeptide bonds. Cyanophycin is made by cyanophycin synthetase 1 or 2 through ATP-dependent polymerization of Asp and Arg, or β-Asp-Arg, respectively. It is degraded into dipeptides by exo-cyanophycinases, and these dipeptides are hydrolyzed into free amino acids by general or dedicated isodipeptidase enzymes. When synthesized, chains of cyanophycin coalesce into large, inert, membrane-less granules. Although discovered in cyanobacteria, cyanophycin is made by species throughout the bacterial kingdom, and cyanophycin metabolism provides advantages for toxic bloom forming algae and some human pathogens. Some bacteria have developed dedicated schemes for cyanophycin accumulation and use, which include fine temporal and spatial regulation. Cyanophycin has also been heterologously produced in a variety of host organisms to a remarkable level, over 50% of the host's dry mass, and has potential for a variety of green industrial applications. In this review, we summarize the progression of cyanophycin research, with an emphasis on recent structural studies of enzymes in the cyanophycin biosynthetic pathway. These include several unexpected revelations that show cyanophycin synthetase to be a very cool, multi-functional macromolecular machine.

The Na+,K+-ATPase and its stoichiometric ratio: some thermodynamic speculations

 Almost seventy years after its discovery, the sodium-potassium adenosine triphosphatase (the sodium pump) located in the cell plasma membrane remains a source of novel mechanistic and physiologic findings. A noteworthy feature of this enzyme/transporter is its robust stoichiometric ratio under physiological conditions: it sequentially counter-transports three sodium ions and two potassium ions against their electrochemical potential gradients per each hydrolyzed ATP molecule. Here we summarize some present knowledge about the sodium pump and its physiological roles, and speculate whether energetic constraints may have played a role in the evolutionary selection of its characteristic stoichiometric ratio.

Metal-binding peptides and their potential to enhance the absorption and bioavailability of minerals

Minerals including calcium, iron, zinc, magnesium, and copper have several human nutritional functions due to their metabolic activities. Body tissues require sufficient levels of a variety of micronutrients to maintain their health. To achieve these micronutrient needs, dietary consumption must be adequate. Dietary proteins may regulate the biological functions of the body in addition to acting as nutrients. Some peptides encoded in the native protein sequences are primarily responsible for the absorption and bioavailability of minerals in physiological functions. Metal-binding peptides (MBPs) were discovered as potential agents for mineral supplements. Nevertheless, sufficient studies on how MBPs affect the biological functions of minerals are lacking. The hypothesis is that the absorption and bioavailability of minerals are significantly influenced by peptides, and these properties are further enhanced by the configuration and attribute of the metal-peptide complex. In this review, the production of MBPs is discussed using various key parameters such as the protein sources and amino acid residues, enzymatic hydrolysis, purification, sequencing and synthesis and in silico analysis of MBPs. The mechanisms of metal-peptide complexes as functional food ingredients are elucidated, including metal-peptide ratio, precursors and ligands, complexation reaction, absorbability and bioavailability. Finally, the characteristics and application of different metal-peptide complexes are also described.

Quantitative elemental imaging in eukaryotic algae

All organisms, fundamentally, are made from the same raw material, namely the elements of the periodic table. Biochemical diversity is achieved by how these elements are utilized, for what purpose, and in which physical location. Determining elemental distributions, especially those of trace elements that facilitate metabolism as cofactors in the active centers of essential enzymes, can determine the state of metabolism, the nutritional status, or the developmental stage of an organism. Photosynthetic eukaryotes, especially algae, are excellent subjects for quantitative analysis of elemental distribution. These microbes utilize unique metabolic pathways that require various trace nutrients at their core to enable their operation. Photosynthetic microbes also have important environmental roles as primary producers in habitats with limited nutrient supplies or toxin contaminations. Accordingly, photosynthetic eukaryotes are of great interest for biotechnological exploitation, carbon sequestration, and bioremediation, with many of the applications involving various trace elements and consequently affecting their quota and intracellular distribution. A number of diverse applications were developed for elemental imaging, allowing subcellular resolution, with X-ray fluorescence microscopy (XFM, XRF) being at the forefront, enabling quantitative descriptions of intact cells in a non-destructive method. This Tutorial Review summarizes the workflow of a quantitative, single-cell elemental distribution analysis of a eukaryotic alga using XFM.

Physicochemical and Biochemical Properties of Trypsin-like Enzyme from Two Sturgeon Species

This work aimed to determine the physicochemical and biochemical properties of trypsin from beluga Huso huso and sevruga Acipenser stellatus, two highly valuable sturgeon species. According to the results obtained from the methods of casein-zymogram and inhibitory activity staining, the molecular weight of trypsin for sevruga and beluga was 27.5 and 29.5 kDa, respectively. Optimum pH and temperature values for both trypsins were recorded at 8.5 and 55 °C by BAPNA (a specific substrate), respectively. The stability of both trypsins was well-preserved at pH values from 6.0 to 11.0 and temperatures up to 50 °C. TLCK and SBTI, two specific trypsin inhibitors, showed a significant inhibitory effect on the enzymatic activity of both trypsins (p < 0.05). The enzyme activity was significantly increased in the presence of Ca⁺² and surfactants and decreased by oxidizing agents, Cu⁺², Zn⁺², and Co⁺² (p < 0.05). However, univalent ions Na⁺ and K⁺ did not show any significant effect on the activity of both trypsins (p > 0.05). The results of our study show that the properties of trypsin from beluga and sevruga are in agreement with data reported in bony fish and can contribute to the clear understanding of trypsin activity in these primitive species.

Sodium/(calcium + potassium) exchanger NCKX4 optimizes KLK4 activity in the enamel matrix microenvironment to regulate ECM modeling

Enamel development is a process in which extracellular matrix models from a soft proteinaceous matrix to the most mineralized tissue in vertebrates. Patients with mutant NCKX4, a gene encoding a K+-dependent Na+/Ca2+-exchanger, develop a hypomineralized and hypomature enamel. How NCKX4 regulates enamel protein removal to achieve an almost protein-free enamel is unknown. We characterized the upregulation pattern of Nckx4 in the progressively differentiating enamel-forming ameloblasts by qPCR, and as well as confirmed NCKX4 protein to primarily localize at the apical surface of wild-type ruffle-ended maturation ameloblasts by immunostaining of the continuously growing mouse incisors, posing the entire developmental trajectory of enamel. In contrast to the normal mature enamel, where ECM proteins are hydrolyzed and removed, we found significant protein retention in the maturation stage of Nckx4 -/- mouse enamel. The Nckx4 -/- enamel held less Ca2+ and K+ but more Na+ than the Nckx4 +/+ enamel did, as measured by EDX. The alternating acidic and neutral pH zones at the surface of mineralizing Nckx4 +/+ enamel were replaced by a largely neutral pH matrix in the Nckx4 -/- enamel. In situ zymography revealed a reduced kallikrein-related peptidase 4 (KLK4) activity in the Nckx4 -/- enamel. We showed that KLK4 took on 90% of proteinase activity in the maturation stage of normal enamel, and that recombinant KLK4 as well as native mouse enamel KLK4 both performed less effectively in a buffer with increased [Na+] and pH, conditions found in the Nckx4 -/- developing enamel. This study, for the first time to our knowledge, provides evidence demonstrating the impaired in situ KLK4 activity in Nckx4 -/- enamel and suggests a novel function of NCKX4 in facilitating KLK4-mediated hydrolysis and removal of ECM proteins, warranting the completion of enamel matrix modeling.

A perspective on the discovery of enzyme activators

Enzyme activation remains a largely under-represented and poorly exploited area of drug discovery despite some key literature examples of the successful application of enzyme activators by various mechanisms and their importance in a wide range of therapeutic interventions. Here we describe the background nomenclature, present the current position of this field of drug discovery and discuss the challenges of hit identification for enzyme activation, as well as our perspectives on the approaches needed to overcome these challenges in early drug discovery.

Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions

The reliability of molecular mechanics simulations to predict effects of ion binding to proteins depends on their ability to simultaneously describe ion-protein, ion-water, and protein-water interactions. Force fields (FFs) to describe protein-water and ion-water interactions have been constructed carefully and have also been refined routinely to improve accuracy. Descriptions for ion-protein interactions have also been refined, although in an a posteriori manner through the use of "nonbonded-fix (NB-fix)" approaches in which parameters from default Lennard-Jones mixing rules are replaced with those optimized against some reference data. However, even after NB-fix corrections, there remains a significant need for improvement. This is also true for polarizable FFs that include self-consistent inducible moments. Our recent studies on the polarizable AMOEBA FF suggested that the problem associated with modeling ion-protein interactions could be alleviated by recalibrating polarization models of cation-coordinating functional groups so that they respond better to the high electric fields present near ions. Here, we present such a recalibration of carbonyls, carboxylates, and hydroxyls in the AMOEBA protein FF and report that it does improve predictions substantially─mean absolute errors in Na⁺-protein and K⁺-protein interaction energies decrease from 8.7 to 5.3 and 9.6 to 6.3 kcal/mol, respectively. Errors are computed with respect to estimates from van der Waals-inclusive density functional theory benchmarked against high-level quantum mechanical calculations and experiments. While recalibration does improve ion-protein interaction energies, they still remain underestimated, suggesting that further improvements can be made in a systematic manner through modifications in classical formalism. Nevertheless, we show that by applying our many-body NB-fix correction to Lennard-Jones components, these errors are further reduced to 2.7 and 2.6 kcal/mol, respectively, for Na⁺ and K⁺ ions. Finally, we show that the recalibrated AMOEBA protein FF retains its intrinsic reliability in predicting protein structure and dynamics in the condensed phase.

Development of semi-quantitative urinary sodium test strip

Excessive salt consumption has been associated with greater risk of hypertension. Therefore, monitoring of dietary sodium consumption should be prioritized. As sodium is mainly excreted through urine, 24-hours urine sample can be used to estimate individual sodium intake. Thus, a simple and inexpensive semi-quantitative urinary sodium detection test strip was developed based on the enzymatic reaction between β-galactosidase and chlorophenol red-β-D-galactopyranoside. When tested, colour formation was distinguished at 0 M (chartreuse yellow), 0.05 M (sunflower), 0.1-0.15 M (mango tango), and 0.2-0.25 M (persimmon) sodium. Analysis from ImageJ showed a linear result (r² >0.9), low SD, and significant increase in magenta difference (p<0.01) between 0 M and 0.05-0.25 M sodium. Test strip can detect 0.03 M sodium at minimum but did not last for >2 days in adverse storage conditions (laboratory conditions, ∼80% relative humidity, 40°C, and direct light exposure) when stored in test strip bottles, and even shorter when exposed to the environment. The presence of urinary potassium, urea, and glucose did not affect test strip performance. Test strip produced comparable results to flame photometry with <15% variation when tested on overnight, random spot, and 24-hours urine samples. Overall, the developed test strip can be used to enzymatically semi-quantify 0.05-0.25 M sodium. Test strip was developed by using β-galactosidase and chlorophenol red-β-D-galactopyranoside for the enzymatic detection of urinary sodium. Test strip could perform urinary sodium monitoring by providing colour indicator based on the concentration of sodium tested in the urine sample at a quicker timing in comparison to current quantification methods. The developed test strip could be used by hypertensive and normotensive users conveniently and repeatably wherever and whenever possible without additional equipment. This article is protected by copyright. All rights reserved.

Production, purification, characterization, and applications of -galactosidase from Bacillus flexus JS27 isolated from Manikaran hot springs

α-Galactosidase hydrolyzes the α-1,6-linkage present at the non-reducing end of the sugars and results in the release of galactosyl residue from oligosaccharides like melibiose, raffinose, stachyose, etc. In the present study we report, α-galactosidase from Bacillus flexus isolated from Manikaran hot springs (India). Maximum enzyme production was obtained in guar gum and soybean meal after 72 h at 150 rpm. While, the temperature/pH of production was optimized at 50 °C and 7.0, respectively. Isoenzymes (α-gal I and II) were obtained and characterized based on temperature/pH optima along with their stability profile. JS27 α-Gal II was purified with a final purification fold of 11.54. Native and SDS-PAGE were used to determine the molecular weight of the enzyme as 86 and 41 kDa, respectively, indicating its homodimeric form. JS27 α-Gal II showed optimum enzyme activity at 55 °C and pH 7 (10 min). The enzyme displayed K_m value of 2.3809 mM and V_max of 2.0 × 10⁴ µmol/min/ml with pNPG as substrate. JS27 α-Gal II demonstrated substrate hydrolysis and simultaneous formation of transgalactosylation products (α-GOS) with numerous substrates (sugar/sugar alcohols, oligosaccharides, and complex carbohydrates) which were verified by TLC and HPLC analysis. α-GOS are significant functional food ingredients and can be explored as prebiotics.

Perspective on fluorescence cell imaging with ionophore-based ion-selective nano-optodes

Inorganic ions are ubiquitous in all kinds of cells with highly dynamic spatial and temporal distribution. Taking advantage of different types of fluorescent probes, fluorescence microscopic imaging and quantitative analysis of ion concentrations in cells have rapidly advanced. A family of fluorescent nanoprobes based on ionophores has emerged in recent years with the potential to establish a unique platform for the analysis of common biological ions including Na⁺, K⁺, Ca²⁺, Cl^-, and so on. This article aims at providing a retrospect and outlook of ionophore-based ion-selective nanoprobes and the applications in cell imaging.

Effect of Na+ and K+ on the cucurbituril-mediated hydrolysis of a phenyl acetate

The environment around the active site affects the catalytic activity of enzymes. Studying the cucurbit[7]uril-promoted acid hydrolysis of a cationic phenyl acetate derivative, we found that the hydrophobic cavity of the macrocycle screens the reaction centre from the positively charged neighbouring group. Moreover, the chelation of alkali metal cations with the cucurbit[7]uril portal and acetyl group of the substrate reduces the hydrolysis rate of the encapsulated ester in an aqueous solution. This type of inhibition corresponds to a rare uncompetitive model in contrast to the more common competitive model that relies on substrate displacement.

Effects of improved sodium uptake ability on grain yields of rice plants under low potassium supply

Sodium uptake is a factor that determines potassium use efficiency in plants as sodium can partially replace potassium in plant cells. Rice (Oryza sativa) roots usually exclude sodium but actively take it up when the plant is deficient in potassium. In rice roots, a sodium transporter OsHKT2;1 mediates active sodium uptake. We previously revealed that variation in the expression of OsHKT2;1 underlies the variation in sodium accumulation between a low-sodium-accumulating indica cultivar, IR64, and a high-sodium-accumulating japonica cultivar, Koshihikari. In the present study, we evaluated IR64 and its near-isogenic line IR64-K carrying OsHKT2;1 and neighboring genes inherited from Koshihikari for grain yield. IR64-K had a greater average grain yield and harvest index than IR64 in a pot culture experiment with three levels of potassium fertilizer. The differences were most significant under treatment without the potassium fertilizer. IR64-K also showed a slightly higher grain yield than IR64 when grown in a paddy field without applying the potassium fertilizer. These results suggest that enhanced sodium uptake ability improves the grain yield of rice plants under low-potassium-input conditions.

Activation and thermal stabilization of a recombinant γ-glutamyltranspeptidase from Bacillus licheniformis ATCC 27811 by monovalent cations

The regulation of enzyme activity through complexation with certain metal ions plays an important role in many biological processes. In addition to divalent metals, monovalent cations (MVCs) frequently function as promoters for efficient biocatalysis. Here, we examined the effect of MVCs on the enzymatic catalysis of a recombinant γ-glutamyltranspeptidase (BlrGGT) from Bacillus licheniformis ATCC 27,811 and the application of a metal-activated enzyme to L-theanine synthesis. The transpeptidase activity of BlrGGT was enhanced by Cs⁺ and Na⁺ over a broad range of concentrations with a maximum of 200 mM. The activation was essentially independent of the ionic radius, but K⁺ contributed the least to enhancing the catalytic efficiency. The secondary structure of BlrGGT remained mostly unchanged in the presence of different concentrations of MVCs, but there was a significant change in its tertiary structure under the same conditions. Compared with the control, the half-life (t_1/2) of the Cs⁺-enriched enzyme at 60 and 65 °C was shown to increase from 16.3 and 4.0 min to 74.5 and 14.3 min, respectively. The simultaneous addition of Cs⁺ and Mg²⁺ ions exerted a synergistic effect on the activation of BlrGGT. This was adequately reflected by an improvement in the conversion of substrates to L-theanine by 3.3-15.1% upon the addition of 200 mM MgCl₂ into a reaction mixture comprising the freshly desalted enzyme (25 μg/mL), 250 mM L-glutamine, 600 mM ethylamine, 200 mM each of the MVCs, and 50 mM borate buffer (pH 10.5). Taken together, our results provide interesting insights into the complexation of MVCs with BlrGGT and can therefore be potentially useful to the biocatalytic production of naturally occurring γ-glutamyl compounds. KEY POINTS: • The transpeptidase activity of B. licheniformis γ-glutamyltranspeptidase can be activated by monovalent cations. • The thermal stability of the enzyme was profoundly increased in the presence of 200 mM Cs⁺. • The simultaneous addition of Cs⁺and Mg²⁺ions to the reaction mixture improves L-theanine production.

Application of cellulosic materials as supports for single-step purification and immobilization of a recombinant β-galactosidase via cellulose-binding domain

This study aimed to develop single-step purification and immobilization processes on cellulosic supports of β-galactosidase from Kluyveromyces sp. combined with the Cellulose-Binding Domain (CBD) tag. After 15 min of immobilization, with an enzymatic load of 150 U/g_support, expressed activity values reached 106.88 (microcrystalline cellulose), 115.03 (alkaline nanocellulose), and 108.47 IU/g (acid nanocellulose). The derivatives produced were less sensitive to the presence of galactose in comparison with the soluble purified enzyme. Among the cations assessed (Na⁺, K⁺, Mg²⁺, and Ca²⁺), magnesium provided the highest increase in the enzymatic activity of β-galactosidases immobilized on cellulosic supports. Supports and derivatives showed no cytotoxic effect on the investigated cell cultures (HepG2 and Vero). Derivatives showed high operational stability in the hydrolysis of milk lactose and retained from 53 to 64% of their hydrolysis capacity after 40 reuse cycles. This study obtained biocatalyzers with promising characteristics for application in the food industry. Biocatalyzers were obtained through a low-cost one-step sustainable bioprocess of purification and immobilization of a β-galactosidase on cellulose via CBD.

Halogen-Bonded Driven Tetra-Substituted Benzene Dimers and Trimers: Potential Hosts for Metal Ions

Cyclic dimers and trimers of tetra-substituted benzenes, ((HOOC)2-C6H2-(NHI)2), are selected as convenient model systems for investigating NI…O=C halogen bond strength and cooperativity. The four substituents in benzene are chosen so that two of them act as halogen bond acceptors (COOH) and two act as halogen bond donors (NHI), as shown in the graphical abstract below. The potential for metal ion binding by each of the halogen-bonded aggregates is also investigated using the monoatomic sodium ion, Na+. Density functional theory calculations performed using the wB97XD functional and the DGDZVP basis set confirmed the ability of halogen bonding to drive the formation of the cyclic dimers and trimers of the model system chosen for this study. Evidence of halogen bond cooperativity is seen, for example, in a 9% shortening of each NI…O=C halogen bond distance with a corresponding 53% increase in the respective critical point density value, ρNI…O=C. Cooperativity also results in a 36% increase in the magnitude of the complexation energy per halogen-bond of the trimer relative to that of the dimer. The results of this study confirm the potential for binding a single Na+ ion by either the dimer or the trimer through their respective halogen-bond networks. Binding of two metal ions was shown to be possible by the dimer. Likewise, the trimer was also found to bind three metal ions. Lastly, the overall structure of the halogen-bonded dimer or trimer endured after complexation of the Na+ ions.

Potassium at the Origins of Life: Did Biology Emerge from Biotite in Micaceous Clay?

Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral mica. The best mica for life’s origins is the black mica, biotite, because it has a high content of Mg++ and because it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged. Here, a scenario for life’s origins is presented, in which the necessary processes and components for life arise in niches between mica sheets; vesicle membranes encapsulate these processes and components; the resulting vesicles fuse, forming protocells; and eventually, all of the necessary components and processes are encapsulated within individual cells, some of which survive to seed the early Earth with life. This paper presents three new foci for the hypothesis of life’s origins between mica sheets: (1) that potassium is essential for life’s origins on Earth; (2) that biotite mica has advantages over muscovite mica; and (3) that micaceous clay is a better environment than isolated mica for life’s origins.

The K+-Dependent and -Independent Pyruvate Kinases Acquire the Active Conformation by Different Mechanisms

Eukarya pyruvate kinases possess glutamate at position 117 (numbering of rabbit muscle enzyme), whereas bacteria have either glutamate or lysine. Those with E117 are K⁺-dependent, whereas those with K117 are K⁺-independent. In a phylogenetic tree, 80% of the sequences with E117 are occupied by T113/K114/T120 and 77% of those with K117 possess L113/Q114/(L,I,V)120. This work aims to understand these residues’ contribution to the K⁺-independent pyruvate kinases using the K⁺-dependent rabbit muscle enzyme. Residues 117 and 120 are crucial in the differences between the K⁺-dependent and -independent mutants. K⁺-independent activity increased with L113 and Q114 to K117, but L120 induced structural differences that inactivated the enzyme. T120 appears to be key in folding the protein and closure of the lid of the active site to acquire its active conformation in the K⁺-dependent enzymes. E117K mutant was K⁺-independent and the enzyme acquired the active conformation by a different mechanism. In the K⁺-independent apoenzyme of Mycobacterium tuberculosis, K72 (K117) flips out of the active site; in the holoenzyme, K72 faces toward the active site bridging the substrates through water molecules. The results provide evidence that two different mechanisms have evolved for the catalysis of this reaction.

The active site region plays a critical role in Na+ binding to thrombin

The catalytic activity of thrombin and other enzymes of the blood coagulation and complement cascades is enhanced significantly by binding of Na+ to a site >15 Å away from the catalytic residue S195, buried within the 180 and 220 loops that also contribute to the primary specificity of the enzyme. Rapid kinetics support a binding mechanism of conformational selection where the Na+-binding site is in equilibrium between open (N) and closed (N∗) forms and the cation binds selectively to the N form. Allosteric transduction of this binding step produces enhanced catalytic activity. Molecular details on how Na+ gains access to this site and communicates allosterically with the active site remain poorly defined. In this study, we show that the rate of the N∗→N transition is strongly correlated with the analogous E∗→E transition that governs the interaction of synthetic and physiologic substrates with the active site. This correlation supports the active site as the likely point of entry for Na+ to its binding site. Mutagenesis and structural data rule out an alternative path through the pore defined by the 180 and 220 loops. We suggest that the active site communicates allosterically with the Na+ site through a network of H-bonded water molecules that embeds the primary specificity pocket. Perturbation of the mobility of S195 and its H-bonding capabilities alters interaction with this network and influences the kinetics of Na+ binding and allosteric transduction. These findings have general mechanistic relevance for Na+-activated proteases and allosteric enzymes.

Effects of piperazine and EDTA in garden snail towards electrolytic variation and antimicrobial activities

The present study has been carried out to evaluate the effects of piperazine and EDTA (ethylenediaminetetraacetic acid) in the garden snail, Cornu aspersum. EDTA and piperazine-like chemicals are widely used in various pharmaceutical, household, and industrial applications. The snails after collection were kept in different earthen pots and treated with these chemicals at different concentrations. A higher concentration of these chemicals led to a change in foot color from light to dark brown and loss in average weight with time. It has been found that a 10-fold increase in piperazine and EDTA concentration reduces weight by approximately 12.7- and 11.6-fold, respectively. Further, the study provides an insight into the altered antimicrobial activity of crude extract when treated with ligands. Additionally, the variations in the electrolytes in the mucus sample have been observed with the mean standard deviation (± SD) of 6.4 and 2.4 for Na⁺ and K⁺ ions, respectively.

Potassium dependency of enzymes in plant primary metabolism

Potassium is a macroelement essential to many aspects of plant life, such as photosynthesis, phloem transport or cellular electrochemistry. Many enzymes in animals or microbes are known to be stimulated or activated by potassium (K⁺ ions). Several plant enzymes are also strictly K⁺-dependent, and this can be critical when plants are under K deficiency and thus intracellular K⁺ concentration is low. Although metabolic effects of low K conditions have been documented, there is presently no review focusing on roles of K⁺ for enzyme catalysis or activation in plants. In this mini-review, we compile the current knowledge on K⁺-requirement of plant enzymes and take advantage of structural data to present biochemical roles of K⁺. This information is instrumental to explain direct effects of low K⁺ content on metabolism and this is illustrated with recent metabolomics data.

Beet Molasses Enhance Salinity Tolerance in Thymus serpyllum-A Study under Greenhouse Condition

The growing demand for Thymus serpyllum biomass to produce drugs, cosmetics and spices necessitates the search for innovative methods mitigating the negative effects of environmental stressors in order to improve its yield under unfavorable conditions. Due to the exposure of plants to salinity stress (SS), we investigated the effect of sugar beet molasses (SBM) on the growth and biochemical parameters related to plants’ response to SS. Wild thyme plants were treated for 5 weeks to sodium chloride and 3% molasses solution using two modes of application (soil irrigation or foliar sprays). Plants irrigated by SBM showed slighter stem growth inhibition than control plants, high stress tolerance index and maintained a constant root water content under salt stress. Moreover plants treated with 100 mM NaCl and soil-applied SBM had lower lipid peroxidation level, showed lower POD activity, higher total soluble protein content and maintained a more even free amino acids level, compared to the control treatments. The concentration of potassium ions was higher in the case of plant roots irrigation with sugar beet molasses compared to control plants. In this experiment, most of the growth and biochemical parameters from foliar molasses-sprayed plants did not differ significantly from the control. We provided evidence that soil-applied SBM beneficially changed the plant’s biochemical response to salt stress. On the basis of the obtained results, we conclude that this soil amendment contributes to the strengthening of plant protection against this harmful environmental factor.

Sodium Binding Interactions with Aliphatic Amino Acids: A Guided Ion Beam and Computational Study

Metal binding affinities play a vital role in medicinal, biological, and industrial applications. In particular, metal cation-amino acid (AA) interactions contribute to protein stability such that analyzing analogous prototypical interactions is important. Here, we present a full description of the interactions of sodium cations (Na⁺) and six aliphatic amino acids (AA), where AA = glycine (Gly), alanine (Ala), homoalanine (hAla), valine (Val), leucine (Leu), and isoleucine (Ile). Experimentally, these interactions are evaluated using threshold collision-induced dissociation carried out in a guided ion beam tandem mass spectrometer, allowing for the determination of the kinetic-energy-dependent behavior of Na⁺-AA dissociation. Analysis of these dissociation cross sections, after accounting for multiple ion-molecule collisions, internal energy of reactant ions, and unimolecular decay rates, allows the determination of absolute Na⁺-AA bond dissociation energies (BDEs) in kJ/mol of Gly (164.0), Ala (166.9), hAla (167.9), Val (172.7), Leu (173.7), and Ile (174.6). These are favorably compared to quantum chemical calculations conducted at the B3LYP, B3P86, MP2(full), B3LYP-GD3BJ, and M06-2X levels of theory. Our combination of structural and energetic analyses provides information regarding the specific factors responsible for Na⁺ interactions with amino acids. Specifically, we find that the BDEs increase linearly with increasing polarizability of the amino acid.

IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria

Metal ions are essential for life and represent the second most abundant constituent (after water) of any living cell. While the biological importance of inorganic ions has been appreciated for over a century, we are far from a comprehensive understanding of the functional roles that ions play in cells and organisms. In particular, recent advances are challenging the traditional view that cells maintain constant levels of ion concentrations (ion homeostasis). In fact, the ionic composition (metallome) of cells appears to be purposefully dynamic. The scientific journey that started over 60 years ago with the seminal work by Hodgkin and Huxley on action potentials in neurons is far from reaching its end. New evidence is uncovering how changes in ionic composition regulate unexpected cellular functions and physiology, especially in bacteria, thereby hinting at the evolutionary origins of the dynamic metallome. It is an exciting time for this field of biology, which we discuss and refer to here as IonoBiology.

Potassium and Sodium Salt Stress Characterization in the Yeasts Saccharomyces cerevisiae, Kluyveromyces marxianus, and Rhodotorula toruloides

Biotechnology requires efficient microbial cell factories. The budding yeast Saccharomyces cerevisiae is a vital cell factory, but more diverse cell factories are essential for the sustainable use of natural resources. Here, we benchmarked nonconventional yeasts Kluyveromyces marxianus and Rhodotorula toruloides against S. cerevisiae strains CEN.PK and W303 for their responses to potassium and sodium salt stress. We found an inverse relationship between the maximum growth rate and the median cell volume that was responsive to salt stress. The supplementation of K⁺ to CEN.PK cultures reduced Na⁺ toxicity and increased the specific growth rate 4-fold. The higher K⁺ and Na⁺ concentrations impaired ethanol and acetate metabolism in CEN.PK and acetate metabolism in W303. In R. toruloides cultures, these salt supplementations induced a trade-off between glucose utilization and cellular aggregate formation. Their combined use increased the beta-carotene yield by 60% compared with that of the reference. Neural network-based image analysis of exponential-phase cultures showed that the vacuole-to-cell volume ratio increased with increased cell volume for W303 and K. marxianus but not for CEN.PK and R. toruloides in response to salt stress. Our results provide insights into common salt stress responses in yeasts and will help design efficient bioprocesses. IMPORTANCE Characterization of microbial cell factories under industrially relevant conditions is crucial for designing efficient bioprocesses. Salt stress, typical in industrial bioprocesses, impinges upon cell volume and affects productivity. This study presents an open-source neural network-based analysis method to evaluate volumetric changes using yeast optical microscopy images. It allows quantification of cell and vacuole volumes relevant to cellular physiology. On applying salt stress in yeasts, we found that the combined use of K⁺ and Na⁺ improves the cellular fitness of Saccharomyces cerevisiae strain CEN.PK and increases the beta-carotene productivity in Rhodotorula toruloides, a commercially important antioxidant and a valuable additive in foods.

The design and evolution of fluorescent protein-based sensors for monoatomic ions in biology

Living cells rely on a finely tuned symphony of inorganic ion gradients composed of both cations and anions. This delicate balance is maintained by biological receptors all acting in concert to selectively recognize and position ions for homeostasis. These dynamic processes can be intercepted and visualized with optical microscopy at the organismal, tissue, cellular and subcellular levels using fluorescent protein-based biosensors. Since the first report of such tool for calcium (Ca2+) in 1997, outstanding biological questions and innovations in protein engineering along with associated fields have driven the development of new biosensors for Ca2+ and beyond. In this Review, we summarize a workflow that can be used to generate fluorescent protein-based biosensors to study monoatomic ions in biology. To showcase the scope of this approach, we highlight recent advances reported for Ca2+ biosensors and in detail discuss representative case studies of biosensors reported in the last four years for potassium (K+), magnesium (Mg2+), copper (Cu2+/+), lanthanide (Ln3+) and chloride (Cl-) ions.

Perspectives of fast magic-angle spinning 87 Rb NMR of organic solids at high magnetic fields

We report solid-state ⁸⁷ Rb NMR spectra from two Rb-ionophore complexes obtained with fast magic-angle spinning (MAS) (up to 60 kHz) at 21.1 T. These Rb-ionophore complexes containing macrocycles such as benzo-15-crown-5 and cryptand [2.2.2] are typical of organic Rb salts that exhibit very large ⁸⁷ Rb quadrupole coupling constants (close to 20 MHz). We have also obtained static ⁸⁷ Rb NMR spectra for these two compounds and determined both ⁸⁷ Rb quadrupole coupling and chemical shift tensors. The experimental ⁸⁷ Rb NMR tensor parameters are compared with those obtained by quantum chemical computations. Our results demonstrate that the combination of fast MAS (60 kHz or higher) and a high magnetic field (21.1 T or higher) is sufficient to produce high-quality solid-state ⁸⁷ Rb NMR spectra for organic Rb solids at the natural abundance level. We anticipate that, with additional ⁸⁷ Rb isotope enrichment (up to 99%), the sensitivity of solid-state ⁸⁷ Rb NMR will be 400 times higher than ³⁹ K NMR, which makes the former an attractive surrogate probe for studying K⁺ ion binding in biological systems.

Improved description of ligand polarization enhances transferability of ion-ligand interactions

The reliability of molecular mechanics (MM) simulations in describing biomolecular ion-driven processes depends on their ability to accurately model interactions of ions simultaneously with water and other biochemical groups. In these models, ion descriptors are calibrated against reference data on ion-water interactions, and it is then assumed that these descriptors will also satisfactorily describe interactions of ions with other biochemical ligands. The comparison against the experiment and high-level quantum mechanical data show that this transferability assumption can break down severely. One approach to improve transferability is to assign cross terms or separate sets of non-bonded descriptors for every distinct pair of ion type and its coordinating ligand. Here, we propose an alternative solution that targets an error-source directly and corrects misrepresented physics. In standard model development, ligand descriptors are never calibrated or benchmarked in the high electric fields present near ions. We demonstrate for a representative MM model that when the polarization descriptors of its ligands are improved to respond to both low and high fields, ligand interactions with ions also improve, and transferability errors reduce substantially. In our case, the overall transferability error reduces from 3.3 kcal/mol to 1.8 kcal/mol. These improvements are observed without compromising on the accuracy of low-field interactions of ligands in gas and condensed phases. Reference data for calibration and performance evaluation are taken from the experiment and also obtained systematically from "gold-standard" CCSD(T) in the complete basis set limit, followed by benchmarked vdW-inclusive density functional theory.

K+ promotes the favorable effect of polyamine on gene expression better than Na

BACKGROUND

Polyamines are involved in a wide variety of biological processes including a marked effect on the structure and function of DNA. During our study on the interaction of polyamines with DNA, we found that K+ enhanced in vitro gene expression in the presence of polyamine more strongly than Na+. Thus, we sought to clarify the physico-chemical mechanism underlying this marked difference between the effects of K+ and Na+.

PRINCIPAL FINDINGS

It was found that K+ enhanced gene expression in the presence of spermidine, SPD(3+), much more strongly than Na+, through in vitro experiments with a Luciferase assay on cell extracts. Single-DNA observation by fluorescence microscopy showed that Na+ prevents the folding transition of DNA into a compact state more strongly than K+. 1H NMR measurement revealed that Na+ inhibits the binding of SPD to DNA more strongly than K+. Thus, SPD binds to DNA more favorably in K+-rich medium than in Na+-rich medium, which leads to favorable conditions for RNA polymerase to access DNA by decreasing the negative charge.

CONCLUSION AND SIGNIFICANCE

We found that Na+ and K+ exhibit markedly different effects through competitive binding with a cationic polyamine, SPD, to DNA, which causes a large difference in the higher-order structure of genomic DNA. It is concluded that the larger favorable effect of Na+ than K+ on in vitro gene expression observed in this study is well attributable to the significant difference between Na+ and K+ on the competitive binding inducing conformational transition of DNA.

Potassium starvation induces autophagy in yeast

Autophagy is a conserved process that recycles cellular contents to promote survival. Although nitrogen limitation is the canonical inducer of autophagy, recent studies have revealed several other nutrients important to this process. In this study, we used a quantitative, high-throughput assay to identify potassium starvation as a new and potent inducer of autophagy in the yeast Saccharomyces cerevisiae We found that potassium-dependent autophagy requires the core pathway kinases Atg1, Atg5, and Vps34, and other components of the phosphatidylinositol 3-kinase complex. Transmission EM revealed abundant autophagosome formation in response to both stimuli. RNA-Seq indicated distinct transcriptional responses: nitrogen affects transport of ions such as copper, whereas potassium targets the organization of other cellular components. Thus, nitrogen and potassium share the ability to influence molecular supply and demand but do so in different ways. Both inputs promote catabolism through bulk autophagy, but result in distinct mechanisms of cellular remodeling and synthesis.

Roles for intracellular cation transporters in respiratory growth of yeast

Potassium is involved in copper and iron metabolism in eukaryotic Golgi apparatus, but it is not clear yet whether potassium distributions in other vesicles also affect copper and iron metabolism. Here we show that respiratory growth and iron acquisition by the yeast Saccharomyces cerevisiae relies on potassium (K+) compartmentalization to the mitochondria, as well as the vacuole and late endosome via K+/H+ exchangers Mdm38p, Vnx1p and Nhx1p, respectively. The data indicate that NHX1 and VNX1 knock-out cells grow better than wild type cells on non-fermentable YPEG media, while MDM38 knock-out cells display a growth defect on YPEG media. The over expression of the KHA1 gene located on the Golgi apparatus partially compensates for the growth defect of the MDM38 knock-out strain. The results suggest that the vacuole and late endosome are important potassium storage vesicles and Mdm38p affects the mitochondrial function by regulating copper and iron metabolism. Our study reveals potassium compartmentalization to the subcellular vesicles is relevant for respiratory growth by improving copper utilization and promoting iron absorption.

Zinc and cadmium complexation of L-methionine: An infrared multiple photon dissociation spectroscopy and theoretical study

Methionine (Met) cationized with Zn2+ , forming Zn (Met-H)+ (ACN) where ACN = acetonitrile, Zn (Met-H)+ , and ZnCl+ (Met), as well as Cd2+ , forming CdCl+ (Met), were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from the FELIX free electron laser. A series of low-energy conformers for each complex was found using quantum-chemical calculations in order to identify the structures formed experimentally. For all four complexes, spectral comparison indicated that the main binding motif observed is a charge solvated, tridentate structure where the metal center binds to the backbone amino group nitrogen, backbone carbonyl oxygen (where the carboxylic acid is deprotonated in two of the Zn2+ complexes), and side-chain sulfur. For all species, the predicted ground structures reproduce the experimental spectra well, although low-lying conformers characterized by similar binding motifs may also contribute in each system. The current work provides valuable information regarding the binding interaction between Met and biologically relevant metals. Further, the comparison between the current work and previous analyses involving alkali metal cationized Met as well as cysteine (the other sulfur containing amino acid) cationized with Zn2+ and Cd2+ allows for the elucidation of important metal dependent trends associated with physiologically important metal-sulfur binding.

Evaluation of the biocompatibility of the GSH-coated Ag2S quantum dots in vitro: a perfect example for the non-toxic optical probes

Near-infrared quantum dots (NIR QDs) are promising candidate for the fluorescent probes due to their better penetration depth, long-lived luminescence with size-tunable photoluminescence wavelengths. Glutathione-coated silver sulfide quantum dots (GSH-Ag₂S QDs) were synthesized using AgNO₃ and Na₂S in the aqueous media and they can give reaction with glutathione reductase (GR) and glutathione-s transferase (GST) enzymes as acting substrate analogue in vitro. Investigation of the toxicity of the nanomaterials are necessary to use them in the medical field and biomedical applications. Thus, in this study we investigated biocompatibility of the GSH-Ag₂S QDs in vitro using 293 T and CFPAC-1 cell lines. Cell viability by MTT assay, light microscopy, fluorescence microscopy, oxidative stress enzyme activities and ICP-MS analysis were performed to evaluate the cytotoxicity and internalization of the GSH-Ag₂S QDs. GSH-Ag₂S QDs showed great biocompatibility with both cell lines and did not cause imbalance in the oxidative stress metabolism. The ultralow solubility product constant of Ag₂S QDs (K_sp = 6.3 × 10^-50) prevents release of Ag ions into the biological systems that is in agreement with data obtained by ICP-MS. In conclusion, this data prove potential of GSH-Ag₂S QDs as a biocompatible optical probe to be used for the detection and/or targeting of GSH impaired diseases including cancer.

Phosphoenolpyruvate carboxylase from the cyanobacterium Synechocystis sp. PCC 6803 is under global metabolic control by PII signaling

Phosphoenolpyruvate carboxylase (PEPC) is the second major carbon-fixing enzyme in photoautotrophic organisms. PEPC is required for the synthesis of amino acids of the glutamate and aspartate family by replenishing the TCA cycle. Furthermore, in cyanobacteria, PEPC, together with malate dehydrogenase and malic enzyme, forms a metabolic shunt for the synthesis of pyruvate from PEP. During this process, CO₂ is first fixed and later released again. Due to its central metabolic position, it is crucial to fully understand the regulation of PEPC. Here, we identify PEPC from the cyanobacterium Synechocystis sp. PCC 6803 (PEPC) as a novel interaction partner for the global signal transduction protein P_II . In addition to an extensive characterization of PEPC, we demonstrate specific P_II -PEPC complex formation and its enzymatic consequences. PEPC activity is tuned by the metabolite-sensing properties of P_II : Whereas in the absence of P_II, PEPC is subjected to ATP inhibition, it is activated beyond its basal activity in the presence of P_II . Furthermore, P_II -PEPC complex formation is inhibited by ADP and PEPC activation by P_II -ATP is mitigated in the presence of 2-OG, linking PEPC regulation to the cell's global carbon/nitrogen status. Finally, physiological relevance of the in vitro measurements was proven by metabolomic analyses of Synechocystis wild-type and P_II -deficient cells.

Assessment of changes in physiological and biochemical traits in four pistachio rootstocks under drought, salinity and drought + salinity stresses

In this study, 7-month-old UCB-1, Badami, Ghazvini and Kale-Ghouchi pistachio rootstocks were exposed to control, drought, salinity and drought + salinity environments for 60 d. Total chlorophyll and total carotenoid contents decreased in all cultivars under drought, salinity and drought + salinity stresses. Under drought and salinity stresses, alone or in combination, Na⁺ and Cl^- ions increased in all four pistachio rootstocks, while K⁺ ion decreased only in Ghazvini and Kaleh-Ghouchi cultivars. The enzyme activities of ascorbate peroxidase, polyphenol oxidase, catalase and guaiacol peroxidase increased in all cultivars when subjected to all three stresses with the exception of the ascorbate peroxidase activity in Kale-Ghouchi cultivar during drought stress. Oxidative stress parameters including electrolyte leakage, malondialdehyde, other aldehydes and hydrogen peroxide increased under all three stress conditions in all genotypes. The content of proline, total free amino acids and total soluble carbohydrates were enhanced under drought, salinity and drought + salinity stresses, whereas the protein content decreased in all pistachio rootstocks. In all evaluated traits, except for the K⁺ ion content and APX activity, the highest impacts was seen for drought + salinity > salinity > drought stresses, respectively. For the first time, we have proven that K⁺ ion content has a positive correlation with the ascorbate peroxidase, polyphenol oxidase, catalase and guaiacol peroxidase enzymes activities under drought + salinity stress. Finally, based on the bi-plot and cluster analyses, we have selected the UCB-1 > Badami > Ghazvini > Kale-Ghouchi cultivars as the most tolerant pistachio rootstocks under drought + salinity stress, respectively.

Effects of Castration on miRNA, lncRNA, and mRNA Profiles in Mice Thymus

Thymic degeneration and regeneration are regulated by estrogen and androgen. Recent studies have found that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are involved in organ development. In this study, RNA sequencing (RNA-seq) results showed that ovariectomy significantly affected 333 lncRNAs, 51 miRNAs, and 144 mRNAs levels (p < 0.05 and |log2fold change| > 1), and orchiectomy significantly affected 165 lncRNAs, 165 miRNAs, and 208 mRNA levels in the thymus. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differentially expressed genes (DEGs) were closely related to cell development and immunity. Next, we constructed two lncRNA–miRNA–mRNA networks using Cytoscape based on the targeting relationship between differentially expressed miRNAs (DEMs) and DEGs and differentially expressed lncRNAs (DELs) analyzed by TargetScan and miRanda. Besides, we screened DEGs that were significantly enriched in GO and in ceRNA networks to verify their expression in thymocytes and thymic epithelial cells (TECs). In addition, we analyzed the promoter sequences of DEGs, and identified 25 causal transcription factors. Finally, we constructed transcription factor-miRNA-joint target gene networks. In conclusion, this study reveals the effects of estrogen and androgen on the expression of miRNAs, lncRNAs, and mRNAs in mice thymus, providing new insights into the regulation of thymic development by gonadal hormones and non-coding RNAs.

Thunbergia laurifolia Leaf Extract Increased Levels of Antioxidant Enzymes and Protected Human Cell-Lines In Vitro Against Cadmium

Thunbergia laurifolia or Rang Jued has been used as an herbal tea and in folk medicine as a detoxifying agent. Cd contamination is globally widespread and a serious public health problem. The aim of this study was to determine the endogenous antioxidant enzyme activities and malondialdehyde (MDA) production of the crude dried extract (CDE) of T. laurifolia leaves, using human embryonic kidney (HEK293) and human liver (HepG2) cells as in vitro models. Moreover, the cytotoxicity including anti-cadmium (Cd) toxicity in both cells were measured. The experimental design had 3 treatment groups with combined, pre-, and post-treatments for investigating the anti-Cd toxicity, and cell viability was determined with MTT test (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide). The CDE showed low cytotoxicity and increased catalase (CAT) and glutathione peroxidase (GPx) activities with decreased malondialdehyde (MDA) levels in both cell types. It was found that the CDE protected against Cd-induced toxicity in both cell types, and a synergistic combination therapy effect was seen when CaNa₂EDTA, a chelating agent, was applied. Therefore, CDE can protect against Cd-induced oxidative stress in cells, possibly due to its antioxidant properties. Moreover, using the extract or drinking the herbal tea together with chelating agent should have an efficacy advantage over using the CDE or the chelating agent singly.