Main Binding Site Research Articles

Polyphenols-Based Nanosheets of Propolis Modulate Cytotoxic Amyloid Fibril Assembly of α-Synuclein.

Natural compounds with anti-aggregation capacity are increasingly recognized as viable candidates against neurodegenerative diseases. Recently, the polyphenolic fraction of propolis (PFP), a complex bee product, has been shown to inhibit amyloid aggregation of a model protein especially in the nanosheet form. Here, we examine the aggregation-modulating effects of the PFP nanosheets on α-synuclein (α-syn), an intrinsically disordered protein involved in the pathogenesis of Parkinson's disease. Based on a range of biophysical data including intrinsic and extrinsic fluorescence, circular dichroism (CD) data, and nuclear magnetic resonance spectroscopy, we propose a model for the interaction of α-syn with PFP nanosheets, where the positively charged N-terminal and the middle non-amyloid component regions of α-syn act as the main binding sites with the negatively charged PFP nanosheets. The Thioflavin T (ThT) fluorescence, Congo red absorbance, and CD data reveal a prominent dose-dependent inhibitory effect of PFP nanosheets on α-syn amyloid aggregation, and the microscopy images and MTT assay data suggest that the PFP nanosheets redirect α-syn aggregation toward nontoxic off-pathway oligomers. When preformed α-syn amyloid fibrils are present, fluorescence images show co-localization of PFP nanosheets and ThT, further confirming the binding of PFP nanosheets with α-syn amyloid fibrils. Taken together, our results demonstrate the binding and anti-aggregation activity of PFP nanosheets in a disease-related protein system and propose them as potential nature-based tools for probing and targeting pathological protein aggregates in neurodegenerative diseases.

Drug–Membrane Interaction as Revealed by Spectroscopic Methods: The Role of Drug Structure in the Example of Rifampicin, Levofloxacin and Rapamycin

We have investigated the nature of the interaction of small organic drug molecules with lipid membranes of various compositions. Using infrared spectroscopy and differential scanning calorimetry methods, we studied the role of the structure of the active molecule in interaction with the membrane using the example of dipalmitoylphosphatidylcholine (DPPC) and dipalmitoylphosphatidylcholine:cardiolipin (DPPC:CL) liposomes. We discovered the key role of the heterocycle in interaction with the polar part of the bilayer and the network of unsaturated bonds in interaction with the hydrophobic part. For rifampicin and levofloxacin, the main binding sites were phosphate and carbonyl groups of lipids, and in the case of anionic liposomes we found a slight penetration of rifampicin into the hydrophobic part of the bilayer. For rapamycin, experimental confirmation of the localization of the molecule in the region of fatty acid chains was obtained, and perturbation in the region of phosphate groups was demonstrated for the first time. The process of phase transition of liposomal forms of rifampicin and levofloxacin was studied. DPPC liposomes accelerate the phase transition when loaded with a drug. DPPC:CL liposomes are less susceptible to changes in the phase transition rate.

Computational Screening of Metal-Organic Frameworks for Ammonia Capture from H2/N2/NH3 Mixtures.

The separation of ammonia from H2/N2/NH3 mixtures is an important step in ammonia decomposition for hydrogen production and ammonia synthesis from H2 and N2 based nonaqueous technologies. Metal–organic frameworks (MOFs) are considered as potential materials for capturing ammonia. In the present work, high-throughput screening of 2932 Computation-Ready Experimental MOFs (CoRE MOFs) was carried out for ammonia capture from H2/N2/NH3 mixtures by Grand Canonical Monte Carlo (GCMC) simulations. It was found that the high-performing MOFs are characterized by tube-like channels, moderate LCD (largest cavity diameter) (4–7.5 Å), and high Qst0(NH3) (the isosteric heat of NH3 adsorption) (>45 kJ/mol). MOFs with high NH3 adsorption capacity often feature moderate surface area, while the surface area of MOFs with high NH3 selectivity is relatively lower, which limits the NH3 adsorption capacity. Qst0 and the Henry’s constant (KH) are two energy descriptors describing the interactions between adsorbents and adsorbates. The former has a stronger correlation with the adsorption selectivity, while the latter has a stronger correlation with the adsorption capacity. By analyzing the molecular density distribution of adsorbates in high-performing MOFs, it was found that unsaturated coordinated metal sites provide the main functional binding sites for NH3. Most MOFs with high NH3 selectivity have multiple different metal nodes or other atoms except C, O, and H, such as N and P. Multiple metal nodes and nonmetallic atoms provide more functional binding sites. Finally, the adsorption behavior with various concentrations of gas mixtures was examined to verify the universality of the screening calculations, and the effect of framework flexibility on adsorption performance was explored.

Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside

Microtubules play important roles in biological functions by forming superstructures, such as doublets and branched structures, in vivo. Despite the importance, it is challenging to construct these superstructures in vitro. Here, we designed a tetrameric fluorescent protein Azami-Green (AG) fused with His-tag and Tau-derived peptide (TP), TP-AG, to generate the superstructures. Main binding sites of TP-AG can be controlled to the inside and outside of microtubules by changing the polymerization conditions. The binding of TP-AG to the inside promoted microtubule formation and generated rigid and stable microtubules. The binding of TP-AG to the outside induced various microtubule superstructures, including doublets, multiplets, branched structures, and extremely long microtubules by recruiting tubulins to microtubules. Motile microtubule aster structures were also constructed by TP-AG. The generation of various microtubule superstructures by a single type of exogenous protein is a new concept for understanding the functions of microtubules and constructing microtubule-based nanomaterials.

The Formation, Structural Characteristics, Absorption Pathways and Bioavailability of Calcium-Peptide Chelates.

Calcium is one of the most important mineral elements in the human body and is closely related to the maintenance of human health. To prevent calcium deficiency, various calcium supplements have been developed, but their application tends to be limited by low calcium content and highly irritating effects on the stomach, among other side effects. Recently, calcium–peptide chelates, which have excellent stability and are easily absorbed, have received attention as an alternative emerging calcium supplement. Calcium-binding peptides (CaBP) are usually obtained via the hydrolysis of animal or plant proteins, and calcium-binding capacity (CaBC) can be further improved through chromatographic purification techniques. In calcium ions, the phosphate group, carboxylic group and nitrogen atom in the peptide are the main binding sites, and the four modes of combination are the unidentate mode, bidentate mode, bridging mode and α mode. The stability and safety of calcium–peptide chelates are discussed in this paper, the intestinal absorption pathways of calcium elements and peptides are described, and the bioavailability of calcium–peptide chelates, both in vitro and in vivo, is also introduced. This review of the research status of calcium–peptide chelates aims to provide a reasonable theoretical basis for their application as calcium supplementation products.

Biophysical Characterization of the Interaction between a Transport Human Plasma Protein and the 5,10,15,20-Tetra(pyridine-4-yl)porphyrin.

The interaction between human serum albumin (HSA) and the non-charged synthetic photosensitizer 5,10,15,20-tetra(pyridine-4-yl)porphyrin (4-TPyP) was evaluated by in vitro assays under physiological conditions using spectroscopic techniques (UV-vis, circular dichroism, steady-state, time-resolved, synchronous, and 3D-fluorescence) combined with in silico calculations by molecular docking. The UV-vis and steady-state fluorescence parameters indicated a ground-state association between HSA and 4-TPyP and the absence of any dynamic fluorescence quenching was confirmed by the same average fluorescence lifetime for HSA without (4.76 ± 0.11 ns) and with 4-TPyP (4.79 ± 0.14 ns). Therefore, the Stern–Volmer quenching (KSV) constant reflects the binding affinity, indicating a moderate interaction (104 M−1) being spontaneous (ΔG°= -25.0 kJ/mol at 296 K), enthalpically (ΔH° = -9.31 ± 1.34 kJ/mol), and entropically (ΔS° = 52.9 ± 4.4 J/molK) driven. Binding causes only a very weak perturbation on the secondary structure of albumin. There is just one main binding site in HSA for 4-TPyP (n ≈ 1.0), probably into the subdomain IIA (site I), where the Trp-214 residue can be found. The microenvironment around this fluorophore seems not to be perturbed even with 4-TPyP interacting via hydrogen bonding and van der Waals forces with the amino acid residues in the subdomain IIA.

Tolerance and Cadmium (Cd) Immobilization by Native Bacteria Isolated in Cocoa Soils with Increased Metal Content

Twelve cadmium native bacteria previously isolated in soils of cocoa farms located in the western Colombian Andes (Santander), and tolerant to 2500 µM CdCl2 (120 mg Cd/L), were chosen in order to test their tolerance and Cd immobilization using liquid culture medium (Nutritive broth) at different concentrations of heavy metals. Furthermore, in the greenhouse experiments, the strains Exiguobacterium sp. (11-4A), Klebsiella variicola sp. (18-4B), and Enterobacter sp. (29-4B) were applied in combined treatments using CCN51 cacao genotype seeds grown in soil with different concentrations of Cd. All bacterial strains’ cell morphologies were deformed in TEM pictures, which also identified six strain interactions with biosorption and four strain capacities for bioaccumulation; FT-IR suggested that the amide, carbonyl, hydroxyl, ethyl, and phosphate groups on the bacteria biomass were the main Cd binding sites. In the pot experiments, the concentration of Cd was distributed throughout the cacao plant, but certain degrees of immobilization of Cd can occur in soil to prevent an increase in this level in roots with the presence of Klebsiella sp.

The Application of the Neuroprotective and Potential Antioxidant Effect of Ergotamine Mediated by Targeting N-Methyl-D-Aspartate Receptors

(1) Background: The N-methyl-D-aspartate receptors (NMDARs) mediate fast excitatory currents leading to depolarization. Postsynaptic NMDARs are ionotropic glutamate receptors that mediate excitatory glutamate or glycine signaling in the CNS and play a primary role in long-term potentiation, which is a major form of use-dependent synaptic plasticity. The overstimulation of NMDARs mediates excessive Ca2+ influx to postsynaptic neurons and facilitates more production of ROS, which induces neuronal apoptosis. (2) Methods: To confirm the induced inward currents by the coapplication of glutamate and ergotamine on NMDARs, a two-electrode voltage clamp (TEVC) was conducted. The ergotamine-mediated inhibitory effects of NR1a/NR2A subunits were explored among four different kinds of recombinant NMDA subunits. In silico docking modeling was performed to confirm the main binding site of ergotamine. (3) Results: The ergotamine-mediated inhibitory effect on the NR1a/NR2A subunits has concentration-dependent, reversible, and voltage-independent properties. The major binding sites were V169 of the NR1a subunit and N466 of the NR2A subunit. (4) Conclusion: Ergotamine effectively inhibited NR1a/NR2A subunit among the subtypes of NMDAR. This inhibition effect can prevent excessive Ca2+ influx, which prevents neuronal death.

Understanding the role of water on temperature-dependent structural modifications of SARS CoV-2 main protease binding sites

Thermally stable and labile proteases are found in microorganisms. Protease mediates the cleavage of polyproteins in the virus replication and transcription process. 6 µs MD simulations were performed for monomer/dimer SARS CoV-2 main protease system in both SPC/E and mTIP3P water model to analyse the temperature-dependent behaviour of the protein. It is found that maximum conformational changes are observed at 348 K which is near the melting temperature. Network distribution of evolved conformations shows an increase in the number of communities with the rise in the temperature. The global conformation of the protein was found to be intact whereas a local conformational space evolved due to thermal fluctuations. The global conformational change in the free energy ΔΔG value for the monomer and the dimer between 278 K and 383 K is found to be 2.51 and 2.10 kJ/mol respectively. A detailed analysis was carried out on the effect of water on the temperature-dependent structural modifications of four binding pockets of SARS CoV-2 main protease namely, catalytic dyad, substrate-binding site, dimerization site and allosteric site. It is found that the water structure around the binding sites is altered with temperature. The water around the dimer sites is more ordered than the monomer sites regardless of the rise in temperature due to structural rigidity. The energy expense of binding the small molecules at substrate binding is less compared to the allosteric site. The water-water hydrogen bond lifetime is found to be more near the cavity of His41. Also, it is observed that mTIP3P water molecules have a similar effect to that of SPC/E water molecules on the main protease.

Crystallographic analysis of interaction between cisplatin and human serum albumin: Effect of fatty acid

Metallodrugs are important for anticancer treatments. They bind mainly to human serum albumin (HSA) in blood circulation, greatly modulating their pharmacokinetics and anticancer efficacy. Fatty acid (FA) is one of the most important endogenous ligands of HSA with tight binding to HSA and affecting its conformation. However, the effect of fatty acids on metallodrugs interaction with HSA is unknown. Here we identify the binding sites of a widely used metallodrug, cisplatin, in HSA in the presence or absence of a representative fatty acid, myristate, by X-ray crystallography. Our crystal structures indicate that the sidechain of residue Met548 becomes more exposed to solvent in the presence of fatty acid, and is the main Pt binding site together with Met329 in HSA:Myr:cisplatin ternary structure. An undoubted new Pt binding site is detected at His338 in the presence of fatty acid, and additional two sites are also identified at His146 and His440 + K436. In addition, we revealed the mechanism of cisplatin-induced HSA aggregation, which is due to the crosslinking between Met298 and His510 of two HSA molecules.

Substrate binding in the mitochondrial ADP/ATP carrier is a step-wise process guiding the structural changes in the transport cycle

Mitochondrial ADP/ATP carriers import ADP into the mitochondrial matrix and export ATP to the cytosol to fuel cellular processes. Structures of the inhibited cytoplasmic- and matrix-open states have confirmed an alternating access transport mechanism, but the molecular details of substrate binding remain unresolved. Here, we evaluate the role of the solvent-exposed residues of the translocation pathway in the process of substrate binding. We identify the main binding site, comprising three positively charged and a set of aliphatic and aromatic residues, which bind ADP and ATP in both states. Additionally, there are two pairs of asparagine/arginine residues on opposite sides of this site that are involved in substrate binding in a state-dependent manner. Thus, the substrates are directed through a series of binding poses, inducing the conformational changes of the carrier that lead to their translocation. The properties of this site explain the electrogenic and reversible nature of adenine nucleotide transport.

Pyridoxal water-soluble cobalt(II) helicates: Synthesis, structural analysis, and interactions with biomacromolecules

Helical complexes composed of organic ligand strands and metallic centers, called helicates, present interactions with biomacromolecules, such as deoxyribonucleic acid, as one of their main biological applications in bioinorganic chemistry. Despite the potential antineoplastic and antibacterial results of the interactions between helicates and biomacromolecules, there is still a gap of research in the literature, primarily in terms of solubility in aqueous media. In this study, we present the synthesis, structural analysis, and interaction with biomacromolecules of two water-soluble cobalt(II) double-stranded helicates: [CoII2L22][CoII(NCS)4]∙9H2O (C1) and [CoII2L42]Cl2∙11H2O (C2). These complexes are obtained from iminic ligands (L2 and L4) derived from pyridoxal, a vitamin B6 aldehyde derivative. Through spectroscopic assays, these helical complexes were shown to have weak and moderate binding capacities with calf-thymus deoxyribonucleic acid and human serum albumin, respectively. The theoretical assays suggest that C1 and C2 interact with the minor groove of deoxyribonucleic acid and have different main binding sites with human serum albumin. Furthermore, Van der Waals and hydrogen bonds were shown to be the main intermolecular forces for these C1-C2:biomacromolecules interactions.

MO660: Medium Chain Fatty Acids used as Binding Competitors of Albumin Improve the Dialytic Clearance of Protein-Bound Uraemic Toxins

Abstract BACKGROUND AND AIMS Protein-bound uraemic toxins (PBUTs) remain a concerning burden in patients with end-stage renal disease (ESRD) since their removal in haemodialysis (HD) is limited by their strong binding to plasma proteins. By increasing their circulating free fraction during HD, "binding competitors" of albumin could be used to increase their dialytic clearance. Medium-chain fatty acids (MCFAs, 4–10 carbon length) are potent candidates for that purpose. The aim of this work was to evaluate the displacing capacities of MCFAs. METHOD Sodium salts of butanoic acid (C4), hexanoic acid (C6), octanoic acid (C8) and decanoic acid (C10) were purchased from Sigma-Aldrich. The interaction between MCFAs and serum albumin was explored using two fluorescent probes: warfarin (specific to Sudlow's site I) and dansylsarcosine (specific to Sudlow's site II). Indoxyl-sulfate (IS, final concentration 212 µM) and p-cresyl sulfate (p-CS, final concentration 250 µM) were added to a 600 µM bovine serum albumin-phosphate buffered saline solution. The free fractions of IS and p-CS were assayed with or without MCFAs (1–2 mM) using ultrafiltration devices. To mimic the removal of PBUTs during an HD session, batches of 2L of fresh bovine blood were loaded with IS and p-CS (final concentration 200 µM). A 2-h closed-loop HD session was performed using a Fresenius 5008 CorDiax HD generator (Fresenius, Germany). A solution of 224 mM of sodium octanoate (C8) was perfused using the electric syringe pump at the rate of 150 µL/min; a solution of saline 0.9% was used as a control. A total of 1 mL of blood was sampled every 15 min through the arterial sampling port and concentrations of IS and pCS were assayed by HPLC coupled with fluorescence detection. The haemolytic effect of MCFAs was evaluated in vitro by assaying the free haemoglobin concentration. RESULTS Among the short-chain fatty acids tested, octanoic (C8) and decanoic (C10), acids were more prone to displace dansylsarcosine from Sudlow's site II of albumin (which is the main binding site of IS and p-CS). In vitro, the incubation with 2 mM of sodium octanoate or decanoate increased the free fraction of PBUTs from 12 to 53% for p-CS (4.4 folds change, P < .05) and from 11 to 45% for IS (4.1 folds change, P < .05). The per-dialytic infusion of sodium octanoate significantly increased the fractional removal of p-CS (from 38 to 88%, P < .001) and IS (from 36 to 91%, P < .001) (Figure 1). No significant haemolysis was observed for the concentration of MCFAs ˂ 2 mmol/L. CONCLUSION MCFAs and especially C8 and C10 are serious candidates to displace the binding of PBUTs such as p-CS and IS. The per-dialytic administration of MCFA significantly increased the removal of PBUTs and could constitute a new strategy to get rid of these compounds and prevent their accumulation in end-stage kidney disease patients. Due to their safeness (toxicity and metabolism profiles in vivo), MCFAs could be better tolerated than other chemical compounds that have already been tested clinically such as ibuprofen. Further in vivo studies are, however needed to carefully evaluate this potentially new therapeutic option.

Treatment of nitrate containing wastewater by adsorption process using polypyrrole-modified plastic-carbon: Characteristic and mechanism

Polypyrrole-modified plastic-carbon (PET-PPy) composite was prepared by using high porosity plastic-carbon materials and a special doping mechanism of polypyrrole to remove nitrate from water to achieve waste recycling. As a result, PET-PPy-500 showed remarkable nitrate adsorption in both acidic and alkaline wastewater. The pseudo-second-order kinetic and Langmuir isotherm models were fit for the nitrate adsorption by PET-PPy-500, and the maximum adsorption capacity predicted by the Langmuir model was 10.04 mg NO3–N/g (45.18 mg NO3−/g) at 30 °C. The ion exchange and electrostatic attraction were the main mechanisms of removing NO3− by PET-PPy-500, which was demonstrated by the interface characterization and theoretical calculation. The doped ions (Cl−) and/or other anions produced by charge transfer interaction were the main exchange ions in the process of NO3− adsorption. The main binding sites in the electrostatic adsorption process were nitrogen-containing functional groups, which can be confirmed by the results of XPS and density functional theory (DFT). Furthermore, DFT results also showed that the adsorption of nitrate by PET-PPy was a spontaneous exothermic process, and the adsorption energy at the nitrogen site was the lowest. The findings of this study provide a feasible strategy for the advanced treatment of nitrate containing wastewater.

The interaction of dengue virus capsid protein with negatively charged interfaces drives the in vitro assembly of nucleocapsid-like particles.

Dengue virus (DENV) causes a major arthropod-borne viral disease, with 2.5 billion people living in risk areas. DENV consists in a 50 nm-diameter enveloped particle in which the surface proteins are arranged with icosahedral symmetry, while information about nucleocapsid (NC) structural organization is lacking. DENV NC is composed of the viral genome, a positive-sense single-stranded RNA, packaged by the capsid (C) protein. Here, we established the conditions for a reproducible in vitro assembly of DENV nucleocapsid-like particles (NCLPs) using recombinant DENVC. We analyzed NCLP formation in the absence or presence of oligonucleotides in solution using small angle X-ray scattering, Rayleigh light scattering as well as fluorescence anisotropy, and characterized particle structural properties using atomic force and transmission electron microscopy imaging. The experiments in solution comparing 2-, 5- and 25-mer oligonucleotides established that 2-mer is too small and 5-mer is sufficient for the formation of NCLPs. The assembly process was concentration-dependent and showed a saturation profile, with a stoichiometry of 1:1 (DENVC:oligonucleotide) molar ratio, suggesting an equilibrium involving DENVC dimer and an organized structure compatible with NCLPs. Imaging methods proved that the decrease in concentration to sub-nanomolar concentrations of DENVC allows the formation of regular spherical NCLPs after protein deposition on mica or carbon surfaces, in the presence as well as in the absence of oligonucleotides, in this latter case being surface driven. Altogether, the results suggest that in vitro assembly of DENV NCLPs depends on DENVC charge neutralization, which must be a very coordinated process to avoid unspecific aggregation. Our hypothesis is that a specific highly positive spot in DENVC α4-α4’ is the main DENVC-RNA binding site, which is required to be firstly neutralized to allow NC formation.

Diabetes and COVID-19; A Bidirectional Interplay.

There seems to be a bidirectional interplay between Diabetes mellitus (DM) and coronavirus disease 2019 (COVID-19). On the one hand, people with diabetes are at higher risk of fatal or critical care unit-treated COVID-19 as well as COVID-19 related health complications compared to individuals without diabetes. On the other hand, clinical data so far suggest that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may result in metabolic dysregulation and in impaired glucose homeostasis. In addition, emerging data on new onset DM in previously infected with SARS-CoV-2 patients, reinforce the hypothesis of a direct effect of SARS-CoV-2 on glucose metabolism. Attempting to find the culprit, we currently know that the pancreas and the endothelium have been found to express Angiotensin-converting enzyme 2 (ACE2) receptors, the main binding site of the virus. To move from bench to bedside, understanding the effects of COVID-19 on metabolism and glucose homeostasis is crucial to prevent and manage complications related to COVID-19 and support recovering patients. In this article we review the potential underlying pathophysiological mechanisms between COVID-19 and glucose dysregulation as well as the effects of antidiabetic treatment in patients with diabetes and COVID-19.

Cholesterol Significantly Affects the Interactions between Pirfenidone and DPPC Liposomes: Spectroscopic Studies

In this work, we studied the effect of as on the interaction of membrane DPPC with the key antifibrotic drug pirfenidone. Liposomal forms of pirfenidone were obtained using passive loading. The addition of cholesterol reduces the loading efficiency of pirfenidone by 10%. The main binding site of pirfenidone in DPPC liposomes is the carbonyl group: the interaction with PF significantly increases the proportion of low-hydrated carbonyl groups as revealed by ATR-FTIR spectroscopy. The phosphate group acts as an additional binding site; however, due to shielding by the choline group, this interaction is weak. The hydrophobic part of the bilayer is not involved in PF binding at room temperature. Cholesterol changes the way of interaction between carbonyl groups and pirfenidone probably because of the formation of two subpopulations of DPPC and causes a dramatic redistribution of carbonyl groups onto the degrees of hydration. The proportion of moderately hydrated carbonyl groups increases, apparently due to the deepening of pirfenidone into the circumpolar region of the bilayer. For the first time, a change in the microenvironment of pirfenidone upon binding to liposomes was shown: aromatic moiety interacts with the bilayer.

A novel experimental approach for the selective isolation and characterization of human RNase MRP

ABSTRACT RNase MRP is a ribonucleoprotein complex involved in the endoribonucleolytic cleavage of different RNAs. Mutations in the RNA component of the RNP are the cause of cartilage hair hypoplasia. Patients with cartilage hair hypoplasia are characterized by skeletal dysplasia. Biochemical purification of RNase MRP is desired to be able to study its biochemical function, composition and activity in both healthy and disease situations. Due to the high similarity with RNase P, a method to specifically isolate the RNase MRP complex is currently lacking. By fusing a streptavidin-binding RNA aptamer, the S1m-aptamer, to the RNase MRP RNA we have been able to compare the relative expression levels of wildtype and mutant MRP RNAs. Moreover, we were able to isolate active RNase MRP complexes. We observed that mutant MRP RNAs are expressed at lower levels and have lower catalytic activity compared to the wildtype RNA. The observation that a single nucleotide substitution at position 40 in the P3 domain but not in other domains of RNase MRP RNA severely reduced the binding of the Rpp25 protein subunit confirmed that the P3 region harbours the main binding site for this protein. Altogether, this study shows that the RNA aptamer tagging approach can be used to identify RNase MRP substrates, but also to study the effect of mutations on MRP RNA expression levels and RNase MRP composition and endoribonuclease activity.

Food-Borne Nanocarriers for Calcium Delivery: A New Choice for Nutrient Supplements.

Calcium is considered as an important nutrient element for the maintenance of human health, and food-borne nanoparticles (FNs) produced during food processing may have potential as nanocarriers for calcium ion delivery. Beef is an important source of animal protein that has high protein and low fat content and is rich in a variety of amino acids; thus, beef may be a suitable material for the development of calcium nanocarriers. In this paper, FNs were synthesized from beef by one-step hydrothermal synthesis. The FNs had a spherical shape with a size of about 3.0 nm and emitted a bright blue fluorescence under 365 nm ultraviolet irradiation. The amino nitrogen atom and carboxyl oxygen atom of the functional groups on the surface of the FNs were the main binding sites for the chelation of Ca(II). The size of the FNs-Ca(II) complex was about 4.75 nm, and the specific signal peak of calcium at 3.7 keV was observed in its energy dispersive X-ray spectroscopy spectrum. The viability of cells treated with FNs-Ca(II) was more than 65%, while viability was only 60% after treatment with CaCl2. The results showed that the FNs from beef have great potential in calcium delivery for the development of a calcium supplement.

Structure-based virtual screening of plant-derived natural compounds as potential PPARα agonists for the treatment of dyslipidemia

Nowadays, metabolic disorders such as dyslipidemia have become serious health problems in the modern world. PPARs are regulators of numberous metabolic pathways, hence there has been a huge increase in the development and use of the PPARs agonists, especially PPARα agonists as main therapeutic of dyslipidemia. The study aimed to explore potential plant-derived natural compounds as PPARα agonist agent for drug discovery of dyslipidemia. Structure-based virtual screening through molecular docking was conducted for 142 bioactive compounds from 29 medicinal plants on the main binding site of PPARα (PDB ID: 5HYK). Binding affinities and binding interactions between the ligands and PPARα were investigated. Screening results showed that 34 compounds had strong binding affinities into the PPARα (binding affinities of less than -8.0 kcal.mol-1), including 20 flavonoid, 4 terpenoid and 10 alkaloid compounds. Flavonoid was found as the best group which fitted well in the binding site of the PPARα. Top compounds were identified, including formononetin from Thermopsis alterniflora (-10.2 kcal.mol-1), diosmetin from Musa spp. (-10.1 kcal.mol-1), luteolin from Elsholtzia ciliate (-9.9 kcal.mol-1); steviol from Stevia rebaudiana (-9.4 kcal.mol-1); and tuberocrooline from Stemona tuberosa (-10.5 kcal.mol-1), respectively. These compounds showed the potential agonistic activities due to forming the hydrogen bonds as well as hydrophobic interactions with four key residues of the receptor such as Ser280, Tyr314, His440 and Tyr464. These potential natural compounds may provide useful information in the drug design and discovery for anti-dyslipidemia agents.